cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568456
title: Wildlife sequences of islet amyloid polypeptide (IAPP) identify critical species variants for fibrillization

description: Amyloid can be detected in the islets of Langerhans in a majority of type 2 diabetic patients. These deposits have been associated with β-cell death, thereby furthering diabetes progression. Islet amyloid polypeptide (IAPP) amyloidogenicity is quite variable among animal species, and studying this variability could further our understanding of the mechanisms involved in the aggregation process. Thus, the general aim of this study was to identify IAPP isoforms in different animal species and characterize their propensity to form fibrillar aggregates. A library of 23 peptides (fragment 8–32) was designed to study the amyloid formation using <i>in silico</i> analysis and <i>in vitro</i> assays. Amyloid formation was impeded when the NFLVH motif found in segment 8–20 was substituted by DFLGR or KFLIR segments. A 29P, 14K and 18R substitution were often present in non-amyloidogenic sequences. Non-amyloidogenic sequences were obtained from <i>Leontopithecus rosalia, Tursiops truncatus</i> and <i>Vicugna pacos</i>. Fragment peptides from 34 species were amyloidogenic. To conclude, this project advances our knowledge on the comparative pathogenesis of amyloidosis in type II diabetes. It is conceivable that the additional information gained may help point towards new therapeutic strategies for diabetes patients.
DOI: 10.6084/m9.figshare.1568459.v1
title: Hair Follicle and Interfollicular Epidermal Stem Cells Make Varying Contributions to Wound Regeneration

description: ABSTRACTUpon wounding, multiple stem cell populations in the hair follicle (HF) and interfollicular epidermis (IFE) converge at the site of injury. Although these cells can contribute permanently to the regenerating epithelium, it remains unclear whether these contributions vary among cells originating from diverse compartments in the skin. By comparing the fates of several keratinocyte lineages, we observed here an initial decrease in both HF- and IFE-derived cells within the transient acanthotic layers of the regenerating epithelium. At the same time, the relative abundance of early-arriving IFE-derived cells specifically in the wound basal layer declined as later-arriving HF-derived cells entered the site of injury. Although laggard bulge-derived cells were typically constrained at the regenerative periphery, these cells persisted in the wound basal layer. Finally, suppressing Notch enabled IFE-derived cells to out-compete HF-derived cells. Taken together, these findings indicate that IFE-, HF- and bulge-derived cells make varying contributions to regeneration. Furthermore, we speculate that extrinsic, non-genetic factors such as spatial constraint, distance from the wound, and basal versus suprabasal position may largely determine whether a cell ultimately persists.
DOI: 10.6084/m9.figshare.1568456.v2
title: Wildlife sequences of islet amyloid polypeptide (IAPP) identify critical species variants for fibrillization

description: Amyloid can be detected in the islets of Langerhans in a majority of type 2 diabetic patients. These deposits have been associated with β-cell death, thereby furthering diabetes progression. Islet amyloid polypeptide (IAPP) amyloidogenicity is quite variable among animal species, and studying this variability could further our understanding of the mechanisms involved in the aggregation process. Thus, the general aim of this study was to identify IAPP isoforms in different animal species and characterize their propensity to form fibrillar aggregates. A library of 23 peptides (fragment 8–32) was designed to study the amyloid formation using <i>in silico</i> analysis and <i>in vitro</i> assays. Amyloid formation was impeded when the NFLVH motif found in segment 8–20 was substituted by DFLGR or KFLIR segments. A 29P, 14K and 18R substitution were often present in non-amyloidogenic sequences. Non-amyloidogenic sequences were obtained from <i>Leontopithecus rosalia, Tursiops truncatus</i> and <i>Vicugna pacos</i>. Fragment peptides from 34 species were amyloidogenic. To conclude, this project advances our knowledge on the comparative pathogenesis of amyloidosis in type II diabetes. It is conceivable that the additional information gained may help point towards new therapeutic strategies for diabetes patients.
DOI: 10.6084/m9.figshare.1568456.v1
title: Wildlife sequences of islet amyloid polypeptide (IAPP) identify critical species variants for fibrillization

description: Amyloid can be detected in the islets of Langerhans in a majority of type 2 diabetic patients. These deposits have been associated with β-cell death, thereby furthering diabetes progression. Islet amyloid polypeptide (IAPP) amyloidogenicity is quite variable among animal species, and studying this variability could further our understanding of the mechanisms involved in the aggregation process. Thus, the general aim of this study was to identify IAPP isoforms in different animal species and characterize their propensity to form fibrillar aggregates. A library of 23 peptides (fragment 8–32) was designed to study the amyloid formation using <i>in silico</i> analysis and <i>in vitro</i> assays. Amyloid formation was impeded when the NFLVH motif found in segment 8–20 was substituted by DFLGR or KFLIR segments. A 29P, 14K and 18R substitution were often present in non-amyloidogenic sequences. Non-amyloidogenic sequences were obtained from <i>Leontopithecus rosalia, Tursiops truncatus</i> and <i>Vicugna pacos</i>. Fragment peptides from 34 species were amyloidogenic. To conclude, this project advances our knowledge on the comparative pathogenesis of amyloidosis in type II diabetes. It is conceivable that the additional information gained may help point towards new therapeutic strategies for diabetes patients.
DOI: 10.6084/m9.figshare.1568445
title: A new earliest Paleocene (Puercan) arctocyonid mammal from the Fort Union Formation, Great Divide Basin, Wyoming, and its phylogenetic position among early ‘condylarths’

description: A new arctocyonid ‘condylarth’, <i>Sigynorum magnadivisus</i> gen. et sp. nov., is described from a recently discovered earliest Paleocene (early Puercan) fauna from the China Butte Member of the Fort Union Formation in the Great Divide Basin, southern Wyoming. Based on a sample of 18 specimens (including 14 partial dentaries) whose combined dentitions represent the p2, p4 and m1–3, the new taxon appears most similar in size and molar morphology to the early Puercan arctocyonid <i>Oxyprimus erikseni</i>, but differs in its p4 morphology. To examine the relationship between <i>S. magnadivisus</i> and other Puercan ‘condylarths’ from the Western Interior of North America, a phylogenetic analysis was performed, utilizing 23 taxa (including 21 ‘condylarth’ species and the outgroup taxa <i>Cimolestes</i> and <i>Gypsonictops</i>) and 73 dental characters. The resulting strict consensus tree of 248 steps confirms the close relationship between <i>S. magnadivisus</i> and <i>O. erikseni</i>. Interestingly, our phylogenetic analysis also suggests that Puercan Periptychidae is paraphyletic; the early Puercan periptychids <i>Mimatuta morgoth, Mimatuta minuial, Maiorana noctiluca</i> and <i>Auraria urbana</i> appear more closely allied with arctocyonid and hyopsodontid taxa, while other Puercan periptychids <i>Conacodon</i> spp., <i>Ampliconus browni, Alticonus gazini, Oxyacodon</i> spp. and <i>Mithrandir gillianus</i> fall into a separate monophyletic clade. This analysis is among the first to focus on a large set of Puercan ‘condylarth’ taxa across geographically widespread localities, and, with the addition of the new species from the Great Divide Basin, suggests that diversity among early Puercan ‘condylarths’ is higher than previously recognized. http://zoobank.org/urn:lsid:zoobank.org:pub:4BF2E9D5-1803-43E9-82FF-EC4723203A87
DOI: 10.6084/m9.figshare.1568445.v1
title: A new earliest Paleocene (Puercan) arctocyonid mammal from the Fort Union Formation, Great Divide Basin, Wyoming, and its phylogenetic position among early ‘condylarths’

description: A new arctocyonid ‘condylarth’, <i>Sigynorum magnadivisus</i> gen. et sp. nov., is described from a recently discovered earliest Paleocene (early Puercan) fauna from the China Butte Member of the Fort Union Formation in the Great Divide Basin, southern Wyoming. Based on a sample of 18 specimens (including 14 partial dentaries) whose combined dentitions represent the p2, p4 and m1–3, the new taxon appears most similar in size and molar morphology to the early Puercan arctocyonid <i>Oxyprimus erikseni</i>, but differs in its p4 morphology. To examine the relationship between <i>S. magnadivisus</i> and other Puercan ‘condylarths’ from the Western Interior of North America, a phylogenetic analysis was performed, utilizing 23 taxa (including 21 ‘condylarth’ species and the outgroup taxa <i>Cimolestes</i> and <i>Gypsonictops</i>) and 73 dental characters. The resulting strict consensus tree of 248 steps confirms the close relationship between <i>S. magnadivisus</i> and <i>O. erikseni</i>. Interestingly, our phylogenetic analysis also suggests that Puercan Periptychidae is paraphyletic; the early Puercan periptychids <i>Mimatuta morgoth</i>, <i>Mimatuta minuial</i>, <i>Maiorana noctiluca</i> and <i>Auraria urbana</i> appear more closely allied with arctocyonid and hyopsodontid taxa, while other Puercan periptychids <i>Conacodon</i> spp., <i>Ampliconus browni</i>, <i>Alticonus gazini</i>, <i>Oxyacodon</i> spp. and <i>Mithrandir gillianus</i> fall into a separate monophyletic clade. This analysis is among the first to focus on a large set of Puercan ‘condylarth’ taxa across geographically widespread localities, and, with the addition of the new species from the Great Divide Basin, suggests that diversity among early Puercan ‘condylarths’ is higher than previously recognized.http://zoobank.org/urn:lsid:zoobank.org:pub:4BF2E9D5-1803-43E9-82FF-EC4723203A87
DOI: 10.6084/m9.figshare.1568441
title: Reef fishes recruited at midwater coral nurseries consume biofouling and reduce cleaning time in Seychelles, Indian Ocean

description: In coral reef restoration, coral gardening involves rearing coral fragments in underwater nurseries prior to transplantation. These nurseries become fish-aggregating devices and attract biofouling. We hypothesised that: (1) the presence of corals at a nursery is critical to recruit fish assemblages and (2) the recruited fish assemblages control biofouling, reducing person-hours invested in nursery cleaning. Three midwater coral nurseries were deployed at 8 m depth for 27 months within the marine protected area of Cousin Island Special Reserve, Seychelles, Indian Ocean. Each nursery consisted of a 6 m×6 m PVC pipe frame, layered with a recycled 5.5-cm-mesh tuna net. Human cleaning effort was calculated based on daily dive logs. Nursery-associated fish assemblages and behaviour were video-recorded prior to harvesting corals after a 20-month growth period and seven months post-coral harvesting. The density (ind. m–2) of blue-yellow damselfish <i>Pomacentrus caeruleus</i> was 12–16 times higher when corals were present than when corals were absent at the nurseries. Fish assemblages recruited into the nurseries included three trophic levels, from herbivores to omnivores, in six families: Ephippidae, Pomacentridae, Labridae (Scarinae), Gobiidae, Siganidae and Monacanthidae. Higher abundance of large fish (total number of individuals) resulted in 2.75 times less person-hours spent in nursery cleaning. These results have important implications for cost-effective coral reef restoration.
DOI: 10.6084/m9.figshare.1568445.v3
title: A new earliest Paleocene (Puercan) arctocyonid mammal from the Fort Union Formation, Great Divide Basin, Wyoming, and its phylogenetic position among early ‘condylarths’

description: A new arctocyonid ‘condylarth’, <i>Sigynorum magnadivisus</i> gen. et sp. nov., is described from a recently discovered earliest Paleocene (early Puercan) fauna from the China Butte Member of the Fort Union Formation in the Great Divide Basin, southern Wyoming. Based on a sample of 18 specimens (including 14 partial dentaries) whose combined dentitions represent the p2, p4 and m1–3, the new taxon appears most similar in size and molar morphology to the early Puercan arctocyonid <i>Oxyprimus erikseni</i>, but differs in its p4 morphology. To examine the relationship between <i>S. magnadivisus</i> and other Puercan ‘condylarths’ from the Western Interior of North America, a phylogenetic analysis was performed, utilizing 23 taxa (including 21 ‘condylarth’ species and the outgroup taxa <i>Cimolestes</i> and <i>Gypsonictops</i>) and 73 dental characters. The resulting strict consensus tree of 248 steps confirms the close relationship between <i>S. magnadivisus</i> and <i>O. erikseni</i>. Interestingly, our phylogenetic analysis also suggests that Puercan Periptychidae is paraphyletic; the early Puercan periptychids <i>Mimatuta morgoth, Mimatuta minuial, Maiorana noctiluca</i> and <i>Auraria urbana</i> appear more closely allied with arctocyonid and hyopsodontid taxa, while other Puercan periptychids <i>Conacodon</i> spp., <i>Ampliconus browni, Alticonus gazini, Oxyacodon</i> spp. and <i>Mithrandir gillianus</i> fall into a separate monophyletic clade. This analysis is among the first to focus on a large set of Puercan ‘condylarth’ taxa across geographically widespread localities, and, with the addition of the new species from the Great Divide Basin, suggests that diversity among early Puercan ‘condylarths’ is higher than previously recognized. http://zoobank.org/urn:lsid:zoobank.org:pub:4BF2E9D5-1803-43E9-82FF-EC4723203A87
DOI: 10.6084/m9.figshare.1568445.v2
title: A new earliest Paleocene (Puercan) arctocyonid mammal from the Fort Union Formation, Great Divide Basin, Wyoming, and its phylogenetic position among early ‘condylarths’

description: A new arctocyonid ‘condylarth’, <i>Sigynorum magnadivisus</i> gen. et sp. nov., is described from a recently discovered earliest Paleocene (early Puercan) fauna from the China Butte Member of the Fort Union Formation in the Great Divide Basin, southern Wyoming. Based on a sample of 18 specimens (including 14 partial dentaries) whose combined dentitions represent the p2, p4 and m1–3, the new taxon appears most similar in size and molar morphology to the early Puercan arctocyonid <i>Oxyprimus erikseni</i>, but differs in its p4 morphology. To examine the relationship between <i>S. magnadivisus</i> and other Puercan ‘condylarths’ from the Western Interior of North America, a phylogenetic analysis was performed, utilizing 23 taxa (including 21 ‘condylarth’ species and the outgroup taxa <i>Cimolestes</i> and <i>Gypsonictops</i>) and 73 dental characters. The resulting strict consensus tree of 248 steps confirms the close relationship between <i>S. magnadivisus</i> and <i>O. erikseni</i>. Interestingly, our phylogenetic analysis also suggests that Puercan Periptychidae is paraphyletic; the early Puercan periptychids <i>Mimatuta morgoth</i>, <i>Mimatuta minuial</i>, <i>Maiorana noctiluca</i> and <i>Auraria urbana</i> appear more closely allied with arctocyonid and hyopsodontid taxa, while other Puercan periptychids <i>Conacodon</i> spp., <i>Ampliconus browni</i>, <i>Alticonus gazini</i>, <i>Oxyacodon</i> spp. and <i>Mithrandir gillianus</i> fall into a separate monophyletic clade. This analysis is among the first to focus on a large set of Puercan ‘condylarth’ taxa across geographically widespread localities, and, with the addition of the new species from the Great Divide Basin, suggests that diversity among early Puercan ‘condylarths’ is higher than previously recognized.http://zoobank.org/urn:lsid:zoobank.org:pub:4BF2E9D5-1803-43E9-82FF-EC4723203A87
DOI: 10.6084/m9.figshare.1568441.v2
title: Reef fishes recruited at midwater coral nurseries consume biofouling and reduce cleaning time in Seychelles, Indian Ocean

description: In coral reef restoration, coral gardening involves rearing coral fragments in underwater nurseries prior to transplantation. These nurseries become fish-aggregating devices and attract biofouling. We hypothesised that: (1) the presence of corals at a nursery is critical to recruit fish assemblages and (2) the recruited fish assemblages control biofouling, reducing person-hours invested in nursery cleaning. Three midwater coral nurseries were deployed at 8 m depth for 27 months within the marine protected area of Cousin Island Special Reserve, Seychelles, Indian Ocean. Each nursery consisted of a 6 m×6 m PVC pipe frame, layered with a recycled 5.5-cm-mesh tuna net. Human cleaning effort was calculated based on daily dive logs. Nursery-associated fish assemblages and behaviour were video-recorded prior to harvesting corals after a 20-month growth period and seven months post-coral harvesting. The density (ind. m–2) of blue-yellow damselfish <i>Pomacentrus caeruleus</i> was 12–16 times higher when corals were present than when corals were absent at the nurseries. Fish assemblages recruited into the nurseries included three trophic levels, from herbivores to omnivores, in six families: Ephippidae, Pomacentridae, Labridae (Scarinae), Gobiidae, Siganidae and Monacanthidae. Higher abundance of large fish (total number of individuals) resulted in 2.75 times less person-hours spent in nursery cleaning. These results have important implications for cost-effective coral reef restoration.
DOI: 10.6084/m9.figshare.1568438
title: Dynamic Covariance Models

description: An important problem in contemporary statistics is to understand the relationship among a large number of variables based on a dataset, usually with <i>p</i>, the number of the variables, much larger than <i>n</i>, the sample size. Recent efforts have focused on modeling static covariance matrices where pairwise covariances are considered invariant. In many real systems, however, these pairwise relations often change. To characterize the changing correlations in a high-dimensional system, we study a class of dynamic covariance models (DCMs) assumed to be sparse, and investigate for the first time a unified theory for understanding their nonasymptotic error rates and model selection properties. In particular, in the challenging high-dimensional regime, we highlight a new uniform consistency theory in which the sample size can be seen as <i>n</i><sup>4/5</sup> when the bandwidth parameter is chosen as <i>h</i>∝<i>n</i><sup>− 1/5</sup> for accounting for the dynamics. We show that this result holds uniformly over a range of the variable used for modeling the dynamics. The convergence rate bears the mark of the familiar bias-variance trade-off in the kernel smoothing literature. We illustrate the results with simulations and the analysis of a neuroimaging dataset. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568441.v1
title: Reef fishes recruited at midwater coral nurseries consume biofouling and reduce cleaning time in Seychelles, Indian Ocean

description: In coral reef restoration, coral gardening involves rearing coral fragments in underwater nurseries prior to transplantation. These nurseries become fish-aggregating devices and attract biofouling. We hypothesised that: (1) the presence of corals at a nursery is critical to recruit fish assemblages and (2) the recruited fish assemblages control biofouling, reducing person-hours invested in nursery cleaning. Three midwater coral nurseries were deployed at 8 m depth for 27 months within the marine protected area of Cousin Island Special Reserve, Seychelles, Indian Ocean. Each nursery consisted of a 6 m×6 m PVC pipe frame, layered with a recycled 5.5-cm-mesh tuna net. Human cleaning effort was calculated based on daily dive logs. Nursery-associated fish assemblages and behaviour were video-recorded prior to harvesting corals after a 20-month growth period and seven months post-coral harvesting. The density (ind. m–2) of blue-yellow damselfish <i>Pomacentrus caeruleus</i> was 12–16 times higher when corals were present than when corals were absent at the nurseries. Fish assemblages recruited into the nurseries included three trophic levels, from herbivores to omnivores, in six families: Ephippidae, Pomacentridae, Labridae (Scarinae), Gobiidae, Siganidae and Monacanthidae. Higher abundance of large fish (total number of individuals) resulted in 2.75 times less person-hours spent in nursery cleaning. These results have important implications for cost-effective coral reef restoration.
DOI: 10.6084/m9.figshare.1568438.v2
title: Dynamic Covariance Models

description: An important problem in contemporary statistics is to understand the relationship among a large number of variables based on a dataset, usually with <i>p</i>, the number of the variables, much larger than <i>n</i>, the sample size. Recent efforts have focused on modeling static covariance matrices where pairwise covariances are considered invariant. In many real systems, however, these pairwise relations often change. To characterize the changing correlations in a high-dimensional system, we study a class of dynamic covariance models (DCMs) assumed to be sparse, and investigate for the first time a unified theory for understanding their nonasymptotic error rates and model selection properties. In particular, in the challenging high-dimensional regime, we highlight a new uniform consistency theory in which the sample size can be seen as <i>n</i><sup>4/5</sup> when the bandwidth parameter is chosen as <i>h</i>∝<i>n</i><sup>− 1/5</sup> for accounting for the dynamics. We show that this result holds uniformly over a range of the variable used for modeling the dynamics. The convergence rate bears the mark of the familiar bias-variance trade-off in the kernel smoothing literature. We illustrate the results with simulations and the analysis of a neuroimaging dataset. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568438.v1
title: Dynamic Covariance Models

description: An important problem in contemporary statistics is to understand the relationship among a large number of variables based on a dataset, usually with <i>p</i>, the number of the variables, much larger than <i>n</i>, the sample size. Recent efforts have focused on modeling static covariance matrices where pairwise covariances are considered invariant. In many real systems, however, these pairwise relations often change. To characterize the changing correlations in a high dimensional system, we study a class of dynamic covariance models (DCMs) assumed to be sparse, and investigate for the first time a unified theory for understanding their non-asymptotic error rates and model selection properties. In particular, in the challenging high dimension regime, we highlight a new uniform consistency theory in which the sample size can be seen as <i>n</i><sup>4/5</sup> when the bandwidth parameter is chosen as <i>h</i>∝<i>n</i><sup>−1/5</sup> for accounting for the dynamics. We show that this result holds uniformly over a range of the variable used for modeling the dynamics. The convergence rate bears the mark of the familiar bias-variance trade-off in the kernel smoothing literature. We illustrate the results with simulations and the analysis of a neuroimaging dataset.