cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14748137.v2
title: How many sabertooths? Reevaluating the number of carnivoran sabretooth lineages with total-evidence Bayesian techniques and a novel origin of the Miocene Nimravidae

description: Sabertooth craniodental adaptations have evolved numerous times amongst carnivorous mammals. Some of the most extreme sabertooth adaptations are found within the carnivoran subfamily Barbourofelinae. However, the evolutionary origins of this group have been uncertain for more than 170 years, with variable placement as an independent case of sabertooth acquisition, as a clade within the Nimravidae (Eocene to Oligocene ‘false sabertooth cats’), or as a member of the Machairodontinae (true sabertooth cats such as <i>Smilodon</i>). Here we present a novel approach to assessing the validity of three independent sabertooth clades within Carnivora. We performed a total-evidence Bayesian analysis in Beast2 across all major carnivoran families, using the fossilized birth-death (FBD) model and incorporating 223 morphological characters, nuclear and mitochondrial gene sequences, and stratigraphic occurrence data. Our results place barbourofelines as terminal members of the Nimravidae, sister to the Nimravini (0.91 posterior probability), a relationship not found in prior cladistic studies. Ancestral area estimation performed in the R package BioGeoBEARS best supports a primarily European paleobiogeographic center for the barbourofelines with multiple dispersal events to other continents, a finding in direct opposition to past hypotheses for this group. Furthermore, new patterns in convergence between nimravids and machairodontines were revealed via Bayesian ancestral state estimation in BayesTraits. Results support a hypothesis of cats copying nimravids, and nimravids cats in certain aspects of sabertooth morphology, and not total evolutionary independence of these features as typically envisioned.
DOI: 10.6084/m9.figshare.14484526.v1
title: First record of a giant bird (Ornithuromorpha) from the uppermost Maastrichtian of the Southern Pyrenees, northeast Spain

description: Throughout the evolutionary history of Avialae, several members of this clade have evolved into giant forms, in different time periods and ecological contexts. In Europe, the first birds that show this condition, the Gargantuaviidae, occur during the Late Cretaceous (late Campanian–early Maastrichtian), but it is during the Paleogene when more groups evolve large forms. However, until now, there was no record of any giant bird during the late Maastrichtian of Europe, close to the K/Pg boundary. Here we describe a cervical vertebra (MPZ 2019/264) from Beranuy (Huesca, NE Spain), which is the first fossil evidence of a giant bird from the late Maastrichtian of Europe, within Chron C29r. The vertebra displays some features, such as a well-marked heterocoelous articulation, lateral pneumatic foramina, ventral carotid processes, and a low neural spine, that support its inclusion within the clade Ornithuromorpha. This phylogenetic assignment is supported by two cladistic analyses. The vertebra is clearly different from the one assigned to <i>Gargantuavis</i>, meaning that it belonged to a distinct taxon. Although the kinship between these two taxa of giant birds is still unclear, this finding demonstrates that large-sized birds were part of the ecological communities of the Ibero-Armorican island from the late Campanian to the Late Maastrichtian, being present during the last hundreds of thousands of years prior to the K/Pg extinction event.
DOI: 10.6084/m9.figshare.14709784.v2
title: A new plastomenid trionychid turtle,<i> Plastomenus joycei</i> , sp. nov., from the earliest Paleocene (Danian) Denver Formation of south-central Colorado, U.S.A.

description: North American soft-shelled turtles, including trionychines and plastomenids, are incredibly abundant in latest Cretaceous through earliest Paleocene sediments. Here we describe a new species of plastomenid turtle, <i>Plastomenus joycei</i>, based on a nearly complete early Danian skeleton from the Denver Formation in the Denver Basin, Colorado. <i>Plastomenus joycei</i> is differentiated from all other plastomenid turtles based on the presence of large eighth costals that are much longer than wide, sinusoidal raised ridges on the carapace, flat posterior edge of the carapace, spike-like epiplastra that lack callosities, a broad entoplastron that lacks a callosity, hyoplastra with two lateral processes, presence of metaplastically ossified hyoplastral shoulders (i.e., anteriorly protruding lappets), and a broad midline contact between the hypo- and xiphiplastra. <i>Plastomenus joycei</i> broadly resembles the Cretaceous <i>Gilmoremys</i> spp. and the Eocene <i>Plastomenus thomasii</i> and exhibits intermediate morphology between the two, most notably in the degree of ossification of the plastron. The increase in plastral ossification, as well as a decrease in overall size and an increase in the doming of the shell, co-occurs with the Cretaceous–Paleogene mass extinction and these morphological changes may be in response to an increase in mammalian predators during the early Paleogene. <i>Plastomenus joycei</i> is most commonly found in riverine sandstone sediments and is hypothesized to be a riverine turtle. http://zoobank.org/urn:lsid:zoobank.org:pub:F4FE56A9-3E63-4BF0-A5CB-0CF0F9B6B045
DOI: 10.6084/m9.figshare.14376212.v1
title: An Upper Triassic Terrestrial Vertebrate Assemblage from the Forgotten Kocury Locality (Poland) with a New Aetosaur Taxon

description: Since 1990, several localities within the Keuper (upper Middle to Upper Triassic) strata in southern Poland have yielded remains of numerous terrestrial vertebrate species. Here we report a new Upper Triassic vertebrate assemblage from the rediscovered Kocury locality. An incomplete theropod dinosaur fibula named <i>Velocipes guerichi</i> described in 1932 was found there. The site was then forgotten and not explored until our excavations began in 2012, that yielded material of a lungfish, a proterochersid turtle, and a new typothoracin aetosaur <i>Kocurypelta silvestris</i> gen. et sp. nov. The new taxon is characterized by autapomorphies of the maxilla: an elongated edentulous posterior portion longer than 80% of the posterior maxillary process, a short medial shelf restricted to the posterior portion of the bone, an anteriorly unroofed maxillary accessory cavity, and lack of a distinct groove for choanal recess on the anteromedial surface of the bone. These new finds improve our knowledge on the vertebrate diversity of the Germanic Basin in the Late Triassic, evidencing the presence of yet unrecognized taxa. Additionally, the partial cranial aetosaur material emphasizes the issues with the aetosaurian taxonomy that is focused mostly on the osteoderm morphology.
DOI: 10.6084/m9.figshare.14748137.v1
title: How many sabertooths? Reevaluating the number of carnivoran sabertooth lineages with total-evidence Bayesian techniques and a novel origin of the Miocene Nimravidae

description: Sabertooth craniodental adaptations have evolved numerous times amongst carnivorous mammals. Some of the most extreme sabertooth adaptations are found within the carnivoran subfamily Barbourofelinae. However, the evolutionary origins of this group have been uncertain for more than 170 years, with variable placement as an independent case of sabertooth acquisition, as a clade within the Nimravidae (Eocene to Oligocene ‘false sabertooth cats’), or as a member of the Machairodontinae (true sabertooth cats such as <i>Smilodon</i>). Here we present a novel approach to assessing the validity of three independent sabertooth clades within Carnivora. We performed a total-evidence Bayesian analysis in Beast2 across all major carnivoran families, using the fossilized birth-death (FBD) model and incorporating 223 morphological characters, nuclear and mitochondrial gene sequences, and stratigraphic occurrence data. Our results place barbourofelines as terminal members of the Nimravidae, sister to the Nimravini (0.91 posterior probability), a relationship not found in prior cladistic studies. Ancestral area estimation performed in the R package BioGeoBEARS best supports a primarily European paleobiogeographic center for the barbourofelines with multiple dispersal events to other continents, a finding in direct opposition to past hypotheses for this group. Furthermore, new patterns in convergence between nimravids and machairodontines were revealed via Bayesian ancestral state estimation in BayesTraits. Results support a hypothesis of cats copying nimravids, and nimravids cats in certain aspects of sabertooth morphology, and not total evolutionary independence of these features as typically envisioned.
DOI: 10.6084/m9.figshare.14709784.v1
title: A new plastomenid trionychid turtle, <i>Plastomenus joycei</i>, sp. nov., from the earliest Paleocene (Danian) Denver Formation of south-central Colorado, U.S.A.

description: North American soft-shelled turtles, including trionychines and plastomenids, are incredibly abundant in latest Cretaceous through earliest Paleocene sediments. Here we describe a new species of plastomenid turtle, <i>Plastomenus joycei</i>, based on a nearly complete early Danian skeleton from the Denver Formation in the Denver Basin, Colorado. <i>Plastomenus joycei</i> is differentiated from all other plastomenid turtles based on the presence of large eighth costals that are much longer than wide, sinusoidal raised ridges on the carapace, flat posterior edge of the carapace, spike-like epiplastra that lack callosities, a broad entoplastron that lacks a callosity, hyoplastra with two lateral processes, presence of metaplastically ossified hyoplastral shoulders (i.e., anteriorly protruding lappets), and a broad midline contact between the hypo- and xiphiplastra. <i>Plastomenus joycei</i> broadly resembles the Cretaceous <i>Gilmoremys</i> spp. and the Eocene <i>Plastomenus thomasii</i> and exhibits intermediate morphology between the two, most notably in the degree of ossification of the plastron. The increase in plastral ossification, as well as a decrease in overall size and an increase in the doming of the shell, co-occurs with the Cretaceous–Paleogene mass extinction and these morphological changes may be in response to an increase in mammalian predators during the early Paleogene. <i>Plastomenus joycei</i> is most commonly found in riverine sandstone sediments and is hypothesized to be a riverine turtle. http://zoobank.org/urn:lsid:zoobank.org:pub:F4FE56A9-3E63-4BF0-A5CB-0CF0F9B6B045
DOI: 10.5281/zenodo.5506613
title: Dataset related to article: "Exercise capacity and comorbidities in patients with obstructive sleep apnea"

description: We provide the raw data used for the following article: Vitacca M, Paneroni M, Braghiroli A, Balbi B, Aliani M, Guido P, Fanfulla F, Pertosa M, Ceriana P, Zampogna E, Raccanelli R, Sarno N, Spanevello A, Maniscalco M, Malovini A, Ambrosino N.<br> <em>Exercise capacity and comorbidities in patients with obstructive sleep apnea</em>.<br> "J Clin Sleep Med". 2020 Apr 15;16(4):531-538. doi: 10.5664/jcsm.8258. PMID: 32003743; PMCID: PMC7161454. <strong>Abstract</strong> <strong>Study objectives: </strong> There are few studies evaluating (1) exercise capacity as assessed by the 6-minute walking distance (6MWD) test in large populations with obstructive sleep apnea (OSA); and (2) correlations with patients' comorbidities.<br> <strong>Methods: </strong> This study presents a cluster analysis performed on the data of 1,228 patients. Severity of exercise limitation was defined on the basis of 6MWD.<br> <strong>Results: </strong> Sixty-one percent showed exercise limitation (29.2% and 31.9% mild and severe exercise limitation, respectively). About 60% and 40% of patients were included in cluster 1 (CL1) and 2 (CL2), respectively. CL1 included younger patients with high prevalence of apneas, desaturations, and hypertension with better exercise tolerance. CL2 included older patients, all with chronic obstructive pulmonary disease (COPD), high prevalence of chronic respiratory failure (CRF), fewer apneas but severe mean desaturation, daytime hypoxemia, more severe exercise limitation, and exercise-induced desaturations. Only CRF and COPD significantly (P &lt; .001) correlated with 6MWD &lt; 85% of predicted value. 6MWD correlated positively with apnea-hypopnea index, oxygen desaturation index, nocturnal pulse oxygen saturation (SpO₂), resting arterial oxygen tension, mean SpO₂ on exercise, and negatively with age, body mass index, time spent during night with SpO₂ &lt; 90%, mean nocturnal desaturation, arterial carbon dioxide tension, and number of comorbidities. Patients without severe comorbidities had higher exercise capacity than those with severe comorbidities, (P &lt; .001). Exercise limitation was significantly worse in OSA severity class I when compared to other classes (P &lt; .001).<br> <strong>Conclusions: </strong> A large number of patients with OSA experience exercise limitation. Older age, comorbidities such as COPD and CRF, OSA severity class I, severe mean nocturnal desaturation, and daytime hypoxemia are associated with worse exercise tolerance.
DOI: 10.5281/zenodo.5506612
title: Dataset related to article: "Exercise capacity and comorbidities in patients with obstructive sleep apnea"

description: We provide the raw data used for the following article: Vitacca M, Paneroni M, Braghiroli A, Balbi B, Aliani M, Guido P, Fanfulla F, Pertosa M, Ceriana P, Zampogna E, Raccanelli R, Sarno N, Spanevello A, Maniscalco M, Malovini A, Ambrosino N.<br> <em>Exercise capacity and comorbidities in patients with obstructive sleep apnea</em>.<br> "J Clin Sleep Med". 2020 Apr 15;16(4):531-538. doi: 10.5664/jcsm.8258. PMID: 32003743; PMCID: PMC7161454. <strong>Abstract</strong> <strong>Study objectives: </strong> There are few studies evaluating (1) exercise capacity as assessed by the 6-minute walking distance (6MWD) test in large populations with obstructive sleep apnea (OSA); and (2) correlations with patients' comorbidities.<br> <strong>Methods: </strong> This study presents a cluster analysis performed on the data of 1,228 patients. Severity of exercise limitation was defined on the basis of 6MWD.<br> <strong>Results: </strong> Sixty-one percent showed exercise limitation (29.2% and 31.9% mild and severe exercise limitation, respectively). About 60% and 40% of patients were included in cluster 1 (CL1) and 2 (CL2), respectively. CL1 included younger patients with high prevalence of apneas, desaturations, and hypertension with better exercise tolerance. CL2 included older patients, all with chronic obstructive pulmonary disease (COPD), high prevalence of chronic respiratory failure (CRF), fewer apneas but severe mean desaturation, daytime hypoxemia, more severe exercise limitation, and exercise-induced desaturations. Only CRF and COPD significantly (P &lt; .001) correlated with 6MWD &lt; 85% of predicted value. 6MWD correlated positively with apnea-hypopnea index, oxygen desaturation index, nocturnal pulse oxygen saturation (SpO₂), resting arterial oxygen tension, mean SpO₂ on exercise, and negatively with age, body mass index, time spent during night with SpO₂ &lt; 90%, mean nocturnal desaturation, arterial carbon dioxide tension, and number of comorbidities. Patients without severe comorbidities had higher exercise capacity than those with severe comorbidities, (P &lt; .001). Exercise limitation was significantly worse in OSA severity class I when compared to other classes (P &lt; .001).<br> <strong>Conclusions: </strong> A large number of patients with OSA experience exercise limitation. Older age, comorbidities such as COPD and CRF, OSA severity class I, severe mean nocturnal desaturation, and daytime hypoxemia are associated with worse exercise tolerance.
DOI: 10.5281/zenodo.5497524
title: Dataset related to article: "Nocturnal Hypoxemia Impacts Right Ventricle Diastolic Function in Obstructive Sleep Apnea: A Retrospective Observational Study"

description: We provide the raw data used for the following article: Scotti C, Porta R, Olivares A, Comini L, Cinelli A, Scalvini S, Vitacca M.<br> <em>Nocturnal Hypoxemia Impacts Right Ventricle Diastolic Function in Obstructive Sleep Apnea: A Retrospective Observational Study.</em><br> "J Clin Med." 2020 Jan 7;9(1):162. doi: 10.3390/jcm9010162. PMID: 31936097; PMCID: PMC7019852. <strong>Abstract</strong><br> Obstructive sleep apnea (OSA), although a growing healthcare problem and documented risk factor for cardiovascular diseases, is still under-diagnosed in cardiac patients. To investigate the correlation between OSA and echocardiographic parameters of right ventricle diastolic (RVD) dysfunction, in particular trans-tricuspid E-wave deceleration time (EDT), we retrospectively analyzed data of 103 pure (comorbidity-free) OSA patients with comprehensive echocardiographic examination (ETT). Apnea/hypopnea index (AHI), oxygen desaturation index (ODI), mean nighttime oxyhemoglobin saturation (SpO2), time elapsed with SpO2 &lt; 90% (T90) and mean peak desaturation of nocturnal events (Mdes, graded as mild, medium or severe) were compared with echocardiographic parameters. We found RVD dysfunction present in 58.3% of patients. Altered EDT correlated significantly with mean SpO2, T90, and Mdes (p &lt; 0.01, all). Nocturnal desaturators had a significantly worse EDT than non-desaturators (p = 0.027) and a higher risk of prolonged EDT (odds ratio, OR = 2.86). EDT differed significantly according to Mdes severity (p = 0.005) with a higher risk of prolonged EDT in medium/severe vs. mild Mdes (OR = 3.44). EDT detected the presence of RVD dysfunction in 58.3% of our pure OSA patients. It correlated poorly with AHI severity but strongly with nocturnal desaturation severity, independently of age. This ETT marker may be useful for deciding appropriate diagnostic and therapeutic strategies.
DOI: 10.5281/zenodo.5497523
title: Dataset related to article: "Nocturnal Hypoxemia Impacts Right Ventricle Diastolic Function in Obstructive Sleep Apnea: A Retrospective Observational Study"

description: We provide the raw data used for the following article: Scotti C, Porta R, Olivares A, Comini L, Cinelli A, Scalvini S, Vitacca M.<br> <em>Nocturnal Hypoxemia Impacts Right Ventricle Diastolic Function in Obstructive Sleep Apnea: A Retrospective Observational Study.</em><br> "J Clin Med." 2020 Jan 7;9(1):162. doi: 10.3390/jcm9010162. PMID: 31936097; PMCID: PMC7019852. <strong>Abstract</strong><br> Obstructive sleep apnea (OSA), although a growing healthcare problem and documented risk factor for cardiovascular diseases, is still under-diagnosed in cardiac patients. To investigate the correlation between OSA and echocardiographic parameters of right ventricle diastolic (RVD) dysfunction, in particular trans-tricuspid E-wave deceleration time (EDT), we retrospectively analyzed data of 103 pure (comorbidity-free) OSA patients with comprehensive echocardiographic examination (ETT). Apnea/hypopnea index (AHI), oxygen desaturation index (ODI), mean nighttime oxyhemoglobin saturation (SpO2), time elapsed with SpO2 &lt; 90% (T90) and mean peak desaturation of nocturnal events (Mdes, graded as mild, medium or severe) were compared with echocardiographic parameters. We found RVD dysfunction present in 58.3% of patients. Altered EDT correlated significantly with mean SpO2, T90, and Mdes (p &lt; 0.01, all). Nocturnal desaturators had a significantly worse EDT than non-desaturators (p = 0.027) and a higher risk of prolonged EDT (odds ratio, OR = 2.86). EDT differed significantly according to Mdes severity (p = 0.005) with a higher risk of prolonged EDT in medium/severe vs. mild Mdes (OR = 3.44). EDT detected the presence of RVD dysfunction in 58.3% of our pure OSA patients. It correlated poorly with AHI severity but strongly with nocturnal desaturation severity, independently of age. This ETT marker may be useful for deciding appropriate diagnostic and therapeutic strategies.
DOI: 10.5281/zenodo.5156585
title: Epigenome-wide DNA Methylation and Pesticide Use in the Agricultural Lung Health Study

description: An epigenome-wide association study of blood DNA methylation and pesticide use was conducted in adults in the Agricultural Lung Health Study. Sixteen specific pesticides were analyzed: dicamba, picloram, mesotrione, acetochlor, metolachlor, glyphosate, 2,4-Dichlorophenoxyacetic acid (2,4-D), atrazine, malathion, aldrin, chlordane, DDT, dieldrin, heptachlor, lindane, and toxaphene. 162 differentially methylated CpGs across 9 specific pesticides (acetochlor, atrazine, dicamba, glyphosate, malathion, metolachlor, mesotrione, picloram, and heptachlor.
DOI: 10.5281/zenodo.5156584
title: Epigenome-wide DNA Methylation and Pesticide Use in the Agricultural Lung Health Study

description: An epigenome-wide association study of blood DNA methylation and pesticide use was conducted in adults in the Agricultural Lung Health Study. Sixteen specific pesticides were analyzed: dicamba, picloram, mesotrione, acetochlor, metolachlor, glyphosate, 2,4-Dichlorophenoxyacetic acid (2,4-D), atrazine, malathion, aldrin, chlordane, DDT, dieldrin, heptachlor, lindane, and toxaphene. 162 differentially methylated CpGs across 9 specific pesticides (acetochlor, atrazine, dicamba, glyphosate, malathion, metolachlor, mesotrione, picloram, and heptachlor.
DOI: 10.25345/c5ss0k
title: MassIVE MSV000088093 - Microbiota-derived acetate enables the metabolic fitness of the CNS innate immune system during health and disease
title: As tissue macrophages of the central nervous system (CNS) microglia constitute the pivotal immune cells of this organ. Microglial maturation and function are strongly dependent on environmental cues such as commensal microbiota. Gut bacteria are known to continuously modulate microglia features by the production of short-chain fatty acids (SCFA). However, the precise mechanism of this crosstalk is unknown. Here we determined that the immature phenotype of microglia from germ-free (GF) mice is epigenetically imprinted by H3K4me3 and H3K9ac on metabolic genes associated with substantial functional alterations including increased mitochondrial mass and specific respiratory chain dysfunctions. We identified acetate as the essential microbiome-derived SCFA driving microglia maturation and regulating the homeostatic metabolic state, and further showed that it is able to modulate microglial phagocytosis and disease progression during neurodegeneration. These findings indicate that acetate is an essential bacteria-derived molecule driving metabolic pathways and functions of microglia during health and perturbation.
DOI: 10.6084/m9.figshare.15082263
title: Supplementary Material for: Role of epigenetic therapy in the modulation of tumor growth and migration in human castration resistance prostate cancer cells with neuroendocrine differentiation.

description: Medicine
DOI: 10.6084/m9.figshare.15082263.v1
title: Supplementary Material for: Role of epigenetic therapy in the modulation of tumor growth and migration in human castration resistance prostate cancer cells with neuroendocrine differentiation.

description: Medicine
DOI: 10.34740/kaggle/dsv/2614155
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.5498096
title: CCG Starter Data Kit: Indonesia

description: A starter data kit for Indonesia
DOI: 10.5281/zenodo.5498095
title: CCG Starter Data Kit: Indonesia

description: A starter data kit for Indonesia
DOI: 10.6084/m9.figshare.14781903.v1
title: 2021_Sa_et_al_Marine-mammalsMHC.zip

description: Datasets and R scripts used for the "Novel insights on aquatic mammal’s MHC evolution: evidence from manatees' DQB diversity" manuscript.