cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11902542
title: Reassessment of the Order Trinucleida (Trilobita)

description: Trinucleoids have been considered as a superfamily of the Order Asaphida, based on: a pre-occipital glabellar tubercle, a cephalic median suture in most ancestral forms, and the presence of broadly similar globular protaspid larvae in the life cycle. Recent discoveries cast doubts on the monophyly of the two last characters. This study provides a phylogenetic analysis whose main purpose is to test the affiliation of trinucleoids. The topology of the strict consensus tree obtained indicates that trinucleoids share a more recent common ancestor with members of the Order Ptychopariida than they do with any asaphid. The stratigraphically higher and most derived trinucleoids are well defined and easy to recognize. Their basal representatives can also be identified with confidence, in spite of substantial variation in the diagnostic characters of the group. These early trinucleoids are similar enough to the typical basal ‘ptychopariid’ bauplan to suggest ancestry within that diffuse and poorly defined trilobite order. Indeed, Ptychopariida is presently regarded as being paraphyletic. We consider that raising trinucleids to ordinal status, by proposing the Order Trinucleida, will make it easier to decipher higher level relationships among trilobites. This action, sustained by improved morphological and ontogenetic information of Cambro-Ordovician trilobites, reveals convergences of the three characters that have been used to support the inclusion of trinucleids within Asaphida. Based on this new information, we propose six distinct morphotypes of commutavi protaspis and, as a probable sensorial organ, that the cephalic axial tubercle migration might be caused by an increase in the height of the glabella and thus may not bear an important systematic signal. Moreover, the tree topology provided herein offers a preliminary overview of evolution within the order. Alsataspididae and Raphiophoridae are paraphyletic, suggesting that more investigation is needed to define them clearly. Dionidae appears to be more closely related to Raphiophoridae than to Trinucleidae, suggesting that the character state of ‘a perforated fringe’ evolved more than once.
DOI: 10.6084/m9.figshare.11902542.v1
title: Reassessment of the Order Trinucleida (Trilobita)

description: Trinucleoids have been considered as a superfamily of the Order Asaphida, based on: a pre-occipital glabellar tubercle, a cephalic median suture in most ancestral forms, and the presence of broadly similar globular protaspid larvae in the life cycle. Recent discoveries cast doubts on the monophyly of the two last characters. This study provides a phylogenetic analysis whose main purpose is to test the affiliation of trinucleoids. The topology of the strict consensus tree obtained indicates that trinucleoids share a more recent common ancestor with members of the Order Ptychopariida than they do with any asaphid. The stratigraphically higher and most derived trinucleoids are well defined and easy to recognize. Their basal representatives can also be identified with confidence, in spite of substantial variation in the diagnostic characters of the group. These early trinucleoids are similar enough to the typical basal ‘ptychopariid’ bauplan to suggest ancestry within that diffuse and poorly defined trilobite order. Indeed, Ptychopariida is presently regarded as being paraphyletic. We consider that raising trinucleids to ordinal status, by proposing the Order Trinucleida, will make it easier to decipher higher level relationships among trilobites. This action, sustained by improved morphological and ontogenetic information of Cambro-Ordovician trilobites, reveals convergences of the three characters that have been used to support the inclusion of trinucleids within Asaphida. Based on this new information, we propose six distinct morphotypes of commutavi protaspis and, as a probable sensorial organ, that the cephalic axial tubercle migration might be caused by an increase in the height of the glabella and thus may not bear an important systematic signal. Moreover, the tree topology provided herein offers a preliminary overview of evolution within the order. Alsataspididae and Raphiophoridae are paraphyletic, suggesting that more investigation is needed to define them clearly. Dionidae appears to be more closely related to Raphiophoridae than to Trinucleidae, suggesting that the character state of ‘a perforated fringe’ evolved more than once.
DOI: 10.6084/m9.figshare.11902548
title: Dataset

description: Coded data of a systematic review.<br>
DOI: 10.6084/m9.figshare.11902548.v1
title: Dataset

description: Coded data of a systematic review.<br>
DOI: 10.6084/m9.figshare.11902311
title: Nanotoxicology data for <i>in silico</i> tools: a literature review

description: The exercise of non-testing approaches in nanoparticles (NPs) hazard assessment is necessary for the risk assessment, considering cost and time efficiency, to identify, assess, and classify potential risks. One strategy for investigating the toxicological properties of a variety of NPs is by means of computational tools that decode how nano-specific features relate to toxicity and enable its prediction. This literature review records systematically the data used in published studies that predict nano (eco)-toxicological endpoints using machine learning models. Instead of seeking mechanistic interpretations this review maps the pathways followed, involving biological features in relation to NPs exposure, their physico-chemical characteristics and the most commonly predicted outcomes. The results, derived from published research of the last decade, are summarized visually, providing prior-based data mining paradigms to be readily used by the nanotoxicology community in computational studies.
DOI: 10.6084/m9.figshare.11902314
title: Supplementary Material for: High-Phosphate Diet Improved the Skeletal Development of <b><i>Fam20c</i></b>-Deficient Mice

description: FAM20C (family with sequence similarity 20 – member C) is a protein kinase that phosphorylates secretory proteins, including the proteins that are essential to the formation and mineralization of calcified tissues. Previously, we reported that inactivation of <i>Fam20c</i> in mice led to hypophosphatemic rickets/osteomalacia along with increased circulating fibroblast growth factor 23 (FGF23) levels and dental defects. In this study, we examined whether a high-phosphate (hPi) diet could rescue the skeletal defects in <i>Fam20c</i>-deficient mice. <i>Fam20c</i> conditional knockout (cKO) mice were generated by crossing female <i>Fam20c</i>-floxed mice (<i>Fam20cfl/fl</i>) with male <i>Sox2-Cre;Fam20cfl/+</i> mice. The pregnant female <i>Fam20cfi/fl</i> mice were fed either a normal or hPi diet until the litters were weaned. The cKO and control offspring were continuously given a normal or hPi diet for 4 weeks after weaning. Plain X-ray radiography, micro-CT, histology, immunohistochemistry (FGF23, DMP1, OPN, and SOX9), and in situ hybridization (type II and type X collagen) analyses were performed to evaluate the effects of an hPi diet on the mouse skeleton. Plain X-ray radiography and micro-CT radiography analyses showed that the hPi diet improved the shape and mineral density of the <i>Fam20c</i>-deficient femurs/tibiae, and rescued the growth plate defects in the long bone. Histology analyses further demonstrated that an hPi diet nearly completely rescued the growth plate-widening defects in the long bone and restored the expanded hypertrophic zone to nearly normal width. These results suggested that the hPi diet significantly improved the skeletal development of the <i>Fam20c</i>-deficient mice, implying that hypophosphatemia partially contributed to the skeletal defects in <i>Fam20c</i>-deficient subjects.
DOI: 10.6084/m9.figshare.11902311.v1
title: Nanotoxicology data for <i>in silico</i> tools: a literature review

description: The exercise of non-testing approaches in nanoparticles (NPs) hazard assessment is necessary for the risk assessment, considering cost and time efficiency, to identify, assess, and classify potential risks. One strategy for investigating the toxicological properties of a variety of NPs is by means of computational tools that decode how nano-specific features relate to toxicity and enable its prediction. This literature review records systematically the data used in published studies that predict nano (eco)-toxicological endpoints using machine learning models. Instead of seeking mechanistic interpretations this review maps the pathways followed, involving biological features in relation to NPs exposure, their physico-chemical characteristics and the most commonly predicted outcomes. The results, derived from published research of the last decade, are summarized visually, providing prior-based data mining paradigms to be readily used by the nanotoxicology community in computational studies.
DOI: 10.6084/m9.figshare.11902314.v1
title: Supplementary Material for: High-Phosphate Diet Improved the Skeletal Development of <b><i>Fam20c</i></b>-Deficient Mice

description: FAM20C (family with sequence similarity 20 – member C) is a protein kinase that phosphorylates secretory proteins, including the proteins that are essential to the formation and mineralization of calcified tissues. Previously, we reported that inactivation of <i>Fam20c</i> in mice led to hypophosphatemic rickets/osteomalacia along with increased circulating fibroblast growth factor 23 (FGF23) levels and dental defects. In this study, we examined whether a high-phosphate (hPi) diet could rescue the skeletal defects in <i>Fam20c</i>-deficient mice. <i>Fam20c</i> conditional knockout (cKO) mice were generated by crossing female <i>Fam20c</i>-floxed mice (<i>Fam20cfl/fl</i>) with male <i>Sox2-Cre;Fam20cfl/+</i> mice. The pregnant female <i>Fam20cfi/fl</i> mice were fed either a normal or hPi diet until the litters were weaned. The cKO and control offspring were continuously given a normal or hPi diet for 4 weeks after weaning. Plain X-ray radiography, micro-CT, histology, immunohistochemistry (FGF23, DMP1, OPN, and SOX9), and in situ hybridization (type II and type X collagen) analyses were performed to evaluate the effects of an hPi diet on the mouse skeleton. Plain X-ray radiography and micro-CT radiography analyses showed that the hPi diet improved the shape and mineral density of the <i>Fam20c</i>-deficient femurs/tibiae, and rescued the growth plate defects in the long bone. Histology analyses further demonstrated that an hPi diet nearly completely rescued the growth plate-widening defects in the long bone and restored the expanded hypertrophic zone to nearly normal width. These results suggested that the hPi diet significantly improved the skeletal development of the <i>Fam20c</i>-deficient mice, implying that hypophosphatemia partially contributed to the skeletal defects in <i>Fam20c</i>-deficient subjects.
DOI: 10.6084/m9.figshare.11902299
title: Supplementary Material for: Hemodynamic Response to Glucose-Insulin Infusion and Meals during Hemodialysis

description: <b><i>Introduction:</i></b> Intradialytic nutrition may improve nutritional status and reduce mortality in patients on maintenance hemodialysis (HD) but has been associated with adverse events, mainly hemodynamic instability. Some dialysis centers therefore restrict intradialytic meals. In 2 clinical studies, we investigated the effects of intradialytic glucose-insulin infusion (GII) and meal intake on blood pressure (BP), pulse wave velocity (PWV), pulse wave analysis (PWA), and cardiac output (CO). PWA yielded augmentation index standardized with heart rate 75 (AIx@HR75). <b><i>Methods:</i></b> In the GII study, 12 nondiabetic HD patients had BP, PWV, PWA, and CO measured during 3 HD sessions: standard HD, HD with glucose infusion, and HD with GII. In the Meal study, 12 nondiabetic patients had BP and PWA measured on 3 study days: meal alone (non-HD), meal and HD, 2 meals and HD. Twelve matched healthy controls completed the non-HD day. <b><i>Findings:</i></b> In the GII study, glucose or GII had no additional effects on hemodynamic parameters compared with standard HD. HD resulted in a decrease in systolic BP of 13%, in diastolic BP of 9%, in AIx@HR75 of 17%, and CO of 18%. PWV was reduced by only 5%. In the Meal study, a meal alone did not change BP, whereas the combined influence of HD and meal intake reduced systolic BP with 22% and diastolic BP with 19%. Furthermore, AIx@HR75 decreased by 37% on HD days and by 36% in controls, but was unaffected on non-HD days. <b><i>Discussion:</i></b> In the GII study, HD significantly reduced BP, AIx@75, and CO, whereas PWV remained almost constant. No additional effects were observed by concomitant GII during HD. BP reductions seemed larger in the Meal study compared with the GII study. Taken together, HD per se appears as the main discriminant for intradialytic hypotension but in hemodynamically unstable patients the timing and route of nutrition provision should be considered carefully.
DOI: 10.6084/m9.figshare.11902236
title: Metadata record for: Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

description: This dataset contains key characteristics about the data described in the Data Descriptor Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.11902299.v1
title: Supplementary Material for: Hemodynamic Response to Glucose-Insulin Infusion and Meals during Hemodialysis

description: <b><i>Introduction:</i></b> Intradialytic nutrition may improve nutritional status and reduce mortality in patients on maintenance hemodialysis (HD) but has been associated with adverse events, mainly hemodynamic instability. Some dialysis centers therefore restrict intradialytic meals. In 2 clinical studies, we investigated the effects of intradialytic glucose-insulin infusion (GII) and meal intake on blood pressure (BP), pulse wave velocity (PWV), pulse wave analysis (PWA), and cardiac output (CO). PWA yielded augmentation index standardized with heart rate 75 (AIx@HR75). <b><i>Methods:</i></b> In the GII study, 12 nondiabetic HD patients had BP, PWV, PWA, and CO measured during 3 HD sessions: standard HD, HD with glucose infusion, and HD with GII. In the Meal study, 12 nondiabetic patients had BP and PWA measured on 3 study days: meal alone (non-HD), meal and HD, 2 meals and HD. Twelve matched healthy controls completed the non-HD day. <b><i>Findings:</i></b> In the GII study, glucose or GII had no additional effects on hemodynamic parameters compared with standard HD. HD resulted in a decrease in systolic BP of 13%, in diastolic BP of 9%, in AIx@HR75 of 17%, and CO of 18%. PWV was reduced by only 5%. In the Meal study, a meal alone did not change BP, whereas the combined influence of HD and meal intake reduced systolic BP with 22% and diastolic BP with 19%. Furthermore, AIx@HR75 decreased by 37% on HD days and by 36% in controls, but was unaffected on non-HD days. <b><i>Discussion:</i></b> In the GII study, HD significantly reduced BP, AIx@75, and CO, whereas PWV remained almost constant. No additional effects were observed by concomitant GII during HD. BP reductions seemed larger in the Meal study compared with the GII study. Taken together, HD per se appears as the main discriminant for intradialytic hypotension but in hemodynamically unstable patients the timing and route of nutrition provision should be considered carefully.
DOI: 10.6084/m9.figshare.11902236.v1
title: Metadata record for: Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

description: This dataset contains key characteristics about the data described in the Data Descriptor Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.5522/04/11902230
title: Curling of epithelial monolayers reveals coupling between active bending and tissue tension

description: This repository contains data pertaining to the publication entitled "Curling of epithelial monolayers reveals coupling between active bending and tissue tension".<br>This publication can be found at:<br>https://www.biorxiv.org/content/10.1101/806455v1<br>
DOI: 10.5522/04/11902230.v1
title: Curling of epithelial monolayers reveals coupling between active bending and tissue tension

description: This repository contains data pertaining to the publication entitled "Curling of epithelial monolayers reveals coupling between active bending and tissue tension".<br>This publication can be found at:<br>https://www.biorxiv.org/content/10.1101/806455v1<br>
DOI: 10.6084/m9.figshare.11902104
title: BrainAGE and regional volumetric analysis of a Buddhist monk: a longitudinal MRI case study

description: Yongey Mingyur Rinpoche (YMR) is a Tibetan Buddhist monk, and renowned meditation practitioner and teacher who has spent an extraordinary number of hours of his life meditating. The brain-aging profile of this expert meditator in comparison to a control population was examined using a machine learning framework, which estimates “brain-age” from brain imaging. YMR’s brain-aging rate appeared slower than that of controls suggesting early maturation and delayed aging. At 41 years, his brain resembled that of a 33-year-old. Specific regional changes did not differentiate YMR from controls, suggesting that the brain-aging differences may arise from coordinated changes spread throughout the gray matter.
DOI: 10.6084/m9.figshare.11902104.v1
title: BrainAGE and regional volumetric analysis of a Buddhist monk: a longitudinal MRI case study

description: Yongey Mingyur Rinpoche (YMR) is a Tibetan Buddhist monk, and renowned meditation practitioner and teacher who has spent an extraordinary number of hours of his life meditating. The brain-aging profile of this expert meditator in comparison to a control population was examined using a machine learning framework, which estimates “brain-age” from brain imaging. YMR’s brain-aging rate appeared slower than that of controls suggesting early maturation and delayed aging. At 41 years, his brain resembled that of a 33-year-old. Specific regional changes did not differentiate YMR from controls, suggesting that the brain-aging differences may arise from coordinated changes spread throughout the gray matter.
DOI: 10.25375/uct.11902077
title: Dataset: Standard echocardiography versus handheld echocardiography for the detection of subclinical rheumatic heart disease: A systematic review and meta-analysis of diagnostic accuracy

description: Extracted data used for meta-analysis in the systematic review:<br><br>Standard echocardiography versus handheld echocardiography for the detection of subclinical rheumatic heart disease: A systematic review and meta-analysis of diagnostic accuracy<br><br>PROSPERO registration number: CRD42016051261<br><b></b>
DOI: 10.6084/m9.figshare.11902008
title: A novel method for observing proportional group awareness and consensus of items arising from list-generating questioning

description: <b>Background:</b> Current healthcare professional consensus-generating methodologies work by forcing consensus, which risks corrupting original opinions and often fails to assess prior expert knowledge awareness. Experience gained with a novel method in a progressive life-long rare disease, X-linked hypophosphataemia, which addresses these risks is presented here. <b>Methods:</b> Four case-studies are reported, presenting a novel methodology comprised of two survey rounds. Round 1 generated a list of items from healthcare professionals in response to an open-ended research question, alongside systematic literature reviews (when appropriate). These responses were thematically coded into mutually exclusive items then used to develop a structured questionnaire (Round 2), for which each participant identified their level of agreement using Likert scales; all responses were analyzed anonymously. Item awareness, observed agreement, consensus and prompted agreement were objectively measured. <b>Results:</b> The free-text responses to Round 1 tested the awareness of specific items regarding establishing a European registry for X-linked Hypophosphatemia (XLH), limitations of empirical treatment for XLH (adults and paediatrics), and triggers for treatment of XLH in adults. The four cases showed different levels of item awareness, observed consensus and degrees of prompted agreement. All participants agreed or strongly agreed with statements based on the most frequent items listed in Round 1. Less frequent Round 1 items had various degrees of prompted agreement consensus; some did not reach the consensus threshold of &gt;50% participant agreement. <b>Conclusions:</b> Observed proportional group awareness and consensus is quicker than the Delphi technique and its variants, providing objective assessments of expert knowledge and standardized categorization of items regarding awareness, consensus and prompting. Further, it offers tailored management of each item in terms of educational need and further investigation.
DOI: 10.6084/m9.figshare.11902008.v1
title: A novel method for observing proportional group awareness and consensus of items arising from list-generating questioning

description: <b>Background:</b> Current healthcare professional consensus-generating methodologies work by forcing consensus, which risks corrupting original opinions and often fails to assess prior expert knowledge awareness. Experience gained with a novel method in a progressive life-long rare disease, X-linked hypophosphataemia, which addresses these risks is presented here. <b>Methods:</b> Four case-studies are reported, presenting a novel methodology comprised of two survey rounds. Round 1 generated a list of items from healthcare professionals in response to an open-ended research question, alongside systematic literature reviews (when appropriate). These responses were thematically coded into mutually exclusive items then used to develop a structured questionnaire (Round 2), for which each participant identified their level of agreement using Likert scales; all responses were analyzed anonymously. Item awareness, observed agreement, consensus and prompted agreement were objectively measured. <b>Results:</b> The free-text responses to Round 1 tested the awareness of specific items regarding establishing a European registry for X-linked Hypophosphatemia (XLH), limitations of empirical treatment for XLH (adults and paediatrics), and triggers for treatment of XLH in adults. The four cases showed different levels of item awareness, observed consensus and degrees of prompted agreement. All participants agreed or strongly agreed with statements based on the most frequent items listed in Round 1. Less frequent Round 1 items had various degrees of prompted agreement consensus; some did not reach the consensus threshold of &gt;50% participant agreement. <b>Conclusions:</b> Observed proportional group awareness and consensus is quicker than the Delphi technique and its variants, providing objective assessments of expert knowledge and standardized categorization of items regarding awareness, consensus and prompting. Further, it offers tailored management of each item in terms of educational need and further investigation.
DOI: 10.6084/m9.figshare.11901933
title: Isotopic niche differs between seal and fish-eating killer whales (Orcinus orca) in northern Norway

description: This dataset includes the nitrogen and carbon isotopic values from killer whale skin samples (Orcinus orca, n=38), and from herring (Clupea harengus, n=4), lumpfish (Cyclopterus lumpus, n=5) and harbor seal (Phoca vitulina, n=1) muscle samples collected in 2017-2018 in northern Norway. Nitrogen values (d15N) are non-lipid extracted and (d13C) are lipid-extracted. <br>