cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5505088.v4
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505088.v5
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505037
title: Results Data from An empirical measure of nonlinear strain for soft tissue indentation

description: Data used to construct graphs and figures presented in results
DOI: 10.6084/m9.figshare.5505022
title: Reassessment of the late Campanian (Late Cretaceous) heteromorph ammonite fauna from Hornby Island, British Columbia, with implications for the taxonomy of the Diplomoceratidae and Nostoceratidae

description: Three heteromorph ammonite families are represented within upper Campanian (Upper Cretaceous) strata of the Northumberland Formation exposed on Hornby Island, British Columbia: Baculitidae, Diplomoceratidae and Nostoceratidae. A variety of species are distinguished within these families, of which only three taxa – <i>Baculites occidentalis</i> Meek, 1862, <i>Diplomoceras</i> (<i>Diplomoceras</i>) <i>cylindraceum</i> (Defrance, 1816) and <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> (Whiteaves, 1895) – have been reported previously. Over the last decade, large new collections and the further preparation of existing collections has provided new taxonomic and morphometric data for the Hornby Island ammonite fauna, from which new descriptions of heteromorph taxa are formulated. Eleven taxa are recognized, including the new species <i>Exiteloceras</i> (<i>Exiteloceras</i>) <i>densicostatum</i> sp. nov., <i>Nostoceras</i> (<i>Didymoceras</i>?) <i>adrotans</i> sp. nov. and <i>Solenoceras exornatus</i> sp. nov. Morphometric analyses of over 700 specimens demonstrate the considerable phenotypic plasticity of these ammonites, which exhibit a broad spectrum of variability in their ornamentation and shell dimensions. A large population sample of <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> provides an excellent case study of a member of the Nostoceratidae; the recovery of nearly complete, well-preserved specimens enables the re-evaluation of diagnostic traits within the genus <i>Nostoceras</i>. The north-east Pacific <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> Zone and the global <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hyatti</i> Assemblage Zone are here regarded as correlative, reinforcing a late Campanian age for the Northumberland Formation. http://zoobank.org/urn:lsid:zoobank.org:pub:EEF7416A-3AC7-47CC-8667-806F6A7FE567
DOI: 10.6084/m9.figshare.5505088.v6
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5505022.v1
title: Reassessment of the late Campanian (Late Cretaceous) heteromorph ammonite fauna from Hornby Island, British Columbia, with implications for the taxonomy of the Diplomoceratidae and Nostoceratidae

description: Three heteromorph ammonite families are represented within upper Campanian (Upper Cretaceous) strata of the Northumberland Formation exposed on Hornby Island, British Columbia: Baculitidae, Diplomoceratidae and Nostoceratidae. A variety of species are distinguished within these families, of which only three taxa – <i>Baculites occidentalis</i> Meek, 1862, <i>Diplomoceras</i> (<i>Diplomoceras</i>) <i>cylindraceum</i> (Defrance, 1816) and <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> (Whiteaves, 1895) – have been reported previously. Over the last decade, large new collections and the further preparation of existing collections has provided new taxonomic and morphometric data for the Hornby Island ammonite fauna, from which new descriptions of heteromorph taxa are formulated. Eleven taxa are recognized, including the new species <i>Exiteloceras</i> (<i>Exiteloceras</i>) <i>densicostatum</i> sp. nov., <i>Nostoceras</i> (<i>Didymoceras</i>?) <i>adrotans</i> sp. nov. and <i>Solenoceras exornatus</i> sp. nov. Morphometric analyses of over 700 specimens demonstrate the considerable phenotypic plasticity of these ammonites, which exhibit a broad spectrum of variability in their ornamentation and shell dimensions. A large population sample of <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> provides an excellent case study of a member of the Nostoceratidae; the recovery of nearly complete, well-preserved specimens enables the re-evaluation of diagnostic traits within the genus <i>Nostoceras</i>. The north-east Pacific <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hornbyense</i> Zone and the global <i>Nostoceras</i> (<i>Nostoceras</i>) <i>hyatti</i> Assemblage Zone are here regarded as correlative, reinforcing a late Campanian age for the Northumberland Formation. http://zoobank.org/urn:lsid:zoobank.org:pub:EEF7416A-3AC7-47CC-8667-806F6A7FE567
DOI: 10.6084/m9.figshare.5505088.v7
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5504989
title: Supplementary Material for: Improvement and Aggravation of Spontaneous Unruptured Vertebral Artery Dissection

description: <b><i>Background:</i></b> Intracranial vertebral artery dissection (VAD) is a well-recognized cause of stroke in young and middle-aged individuals, especially in Asian populations. However, a long-term natural course remains unclear. We investigated the long-term time course of VAD using imaging findings to examine the rate and predisposing factors for improvement. <b><i>Methods:</i></b> We registered 56 consecutive patients (40 males; mean age, 51.8 ± 10.7 years) with acute spontaneous VAD and retrospectively investigated neuroimaging and clinical course within 1 month and at 3 months ± 2 weeks, 6 months ± 2 weeks, and 12 months ± 2 weeks after onset to ascertain predisposing factors and time course for improvement. <b><i>Results:</i></b> The most common presenting symptoms were headache and/or posterior neck pain, seen in 41 patients (73%). Magnetic resonance imaging showed brainstem and/or cerebellum infarction in only 32 patients (57%). Of the 56 VADs, 16 (28%) presented with pearl and string sign, 5 (9%) with pearl sign, 15 (27%) with string sign, and 20 (36%) with occlusion sign. VAD occurred on the dominant side in 20 patients and on the nondominant side in the other 36 patients. The pearl and string sign was more frequently noted on the dominant side than on the nondominant side (50 vs. 17%, <i>p</i> = 0.008). On the other hand, occlusion occurred more often on the nondominant side than on the dominant side (47 vs. 15%, <i>p</i> = 0.016). Furthermore, the pearl and string sign was more frequently seen in the improvement group (41 vs. 15%, <i>p</i> = 0.028), whereas the occlusion sign was evident more frequently in the nonimprovement group (21 vs. 52%, <i>p</i> = 0.015). Follow-up neuroimaging evaluation was performed at 1 and 3 months in 91% each, and at 6 and 12 months in 82% each. VAD aggravation was identified within 1 month after onset in 14%, while VAD improvement was seen in 14, 38, 50, and 52% at each period, mainly within 6 months after onset. Older patients and current smoking were negatively associated with VAD improvement. <b><i>Conclusions:</i></b> VAD improvement primarily occurs within 6 months after onset, and VAD aggravation within 1 month. It seems that older patients and current smoking are negative predictors of VAD improvement as risk factors, and as image findings, the pearl and string sign is a positive predictor and occlusion a negative predictor.
DOI: 10.6084/m9.figshare.5504995
title: DiaCurv: a value-based curvature analysis application in diatom taxonomy

description: DiaCurv is a software application that uses a simple approach to calculating curvature by identifying the chord (length) and the sagitta (length) from a mid-point of an object or part of an object. This software application and associated R scripts provide the users with the possibilities to identify and apply curvature analysis in diatom taxonomy. Different taxa from the genera <i>Cymbella</i> and <i>Luticola</i>, with good size diminution series, were selected to validate curvature metrics for shape evaluations in taxonomy. The dorsal ventral curvature of <i>Cymbella</i> makes species within this genus a natural choice for comparison. In contrast, the lanceolate, elliptic-lanceolate to rhombic forms of species within <i>Luticola</i> are more problematic. Machine-learning techniques (principal component analysis and linear discriminant analysis (LDA)) were used to evaluate the curvature metrics for distinguishing diatom taxa. Selected taxa (<i>C. aspera</i>, <i>C. cymbiformis</i>, <i>C. diversa</i>, <i>C. excisa</i>, <i>C. japonica</i>, <i>C. neogena</i>, <i>C. neuquina</i>, <i>C. parva</i>, <i>C. saxoicola</i>, <i>C. tumidula</i>) were identified by valve curvature, except when valve shape was not a distinguishing character for the species. With the lanceolate, elliptic-lanceolate shapes of <i>Luticola</i>, curvature was effective in separating the linear-lanceolate forms (e.g., <i>L. australomutica</i>, <i>L. goeppertiana</i>, <i>L. murrayi</i>, <i>L. saprophila</i>), and some broadly lanceolate forms (<i>L. crozetensis</i>, <i>L. subcrozetensis</i>) but not elliptic-lanceolate forms within the same size range (e.g., <i>L. katkae</i>, <i>L. pseudocharcotii</i>, <i>L. yellowstonensis</i>). The experimental results indicated that LDA was more suitable for distinguishing taxa. Valve shapes which are circular, or centrally constricted or with polar differentiation or 3D in complexity may not be appropriate for curvature analysis unless specific parts of the valve are selected. The merits of this approach, or any other type of shape analysis, are that the subjective interpretation of shape differences between taxa is removed or reduced.
DOI: 10.6084/m9.figshare.5505088.v8
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This data includes the use of a novel internal control, CTCF binding, to normalise.
DOI: 10.6084/m9.figshare.5504995.v1
title: DiaCurv: a value-based curvature analysis application in diatom taxonomy

description: DiaCurv is a software application that uses a simple approach to calculating curvature by identifying the chord (length) and the sagitta (length) from a mid-point of an object or part of an object. This software application and associated R scripts provide the users with the possibilities to identify and apply curvature analysis in diatom taxonomy. Different taxa from the genera <i>Cymbella</i> and <i>Luticola</i>, with good size diminution series, were selected to validate curvature metrics for shape evaluations in taxonomy. The dorsal ventral curvature of <i>Cymbella</i> makes species within this genus a natural choice for comparison. In contrast, the lanceolate, elliptic-lanceolate to rhombic forms of species within <i>Luticola</i> are more problematic. Machine-learning techniques (principal component analysis and linear discriminant analysis (LDA)) were used to evaluate the curvature metrics for distinguishing diatom taxa. Selected taxa (<i>C. aspera</i>, <i>C. cymbiformis</i>, <i>C. diversa</i>, <i>C. excisa</i>, <i>C. japonica</i>, <i>C. neogena</i>, <i>C. neuquina</i>, <i>C. parva</i>, <i>C. saxoicola</i>, <i>C. tumidula</i>) were identified by valve curvature, except when valve shape was not a distinguishing character for the species. With the lanceolate, elliptic-lanceolate shapes of <i>Luticola</i>, curvature was effective in separating the linear-lanceolate forms (e.g., <i>L. australomutica</i>, <i>L. goeppertiana</i>, <i>L. murrayi</i>, <i>L. saprophila</i>), and some broadly lanceolate forms (<i>L. crozetensis</i>, <i>L. subcrozetensis</i>) but not elliptic-lanceolate forms within the same size range (e.g., <i>L. katkae</i>, <i>L. pseudocharcotii</i>, <i>L. yellowstonensis</i>). The experimental results indicated that LDA was more suitable for distinguishing taxa. Valve shapes which are circular, or centrally constricted or with polar differentiation or 3D in complexity may not be appropriate for curvature analysis unless specific parts of the valve are selected. The merits of this approach, or any other type of shape analysis, are that the subjective interpretation of shape differences between taxa is removed or reduced.
DOI: 10.6084/m9.figshare.5505088.v9
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This repository provides data generated using a novel internal control as well as data generated using a xenogenic spike-in method.
DOI: 10.6084/m9.figshare.5505088.v10
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This repository provides data generated using a novel internal control as well as data generated using a xenogenic spike-in method.
DOI: 10.6084/m9.figshare.5505088.v12
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This repository provides data generated using a novel internal control as well as data generated using a xenogenic spike-in method.
DOI: 10.6084/m9.figshare.5505088.v11
title: ER ChIP-seq on Treatment of Fulvestrant with CTCF Control

description: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated ChIP-seq data measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. This repository provides data generated using a novel internal control as well as data generated using a xenogenic spike-in method.
DOI: 10.6084/m9.figshare.5504947
title: Dataset for: Comparative effects of intraduodenal amino acid infusions on food intake and gut hormone release in healthy males

description: Background: In contrast to the many studies of the effects of individual amino acids (AAs) on eating, no studies have compared the effects of different AAs on eating and underlying preabsorptive gastrointestinal mechanisms. Objective: To compare the effects of intraduodenal infusions of L-tryptophan (TRP), L-leucine (LEU), L-phenylalanine (PHE) and L-glutamine (GLN) on appetite, gastrointestinal hormone responses (including ghrelin, cholecystokinin (CCK), peptide YY (PYY) and glucagon-like peptide-1 (GLP-1)), glycemia (glucagon, insulin and glucose) and test meal size in healthy males. Design: We retrospectively analyzed data from four published independent, randomized, double-blind, placebo-controlled studies of 90-min intraduodenal infusions of the individual AAs. The designs of the studies were identical, except the dose of TRP (0.15 kcal/min) was lower than that of the other AAs (0.45 kcal/min) because higher doses of this AA were not well tolerated. Results: TRP and LEU decreased intake more than PHE (reductions relative to control, ~219±68, ~170±48 and ~12±57 kcal, respectively), and TRP decreased intake more than GLN (~31±82 kcal). These effects of TRP and LEU vs. GLN, but not vs. PHE, were paralleled by greater decreases in plasma ghrelin, and increases in CCK, concentrations. TRP increased PYY more than GLN or LEU, but not PHE. LEU increased PYY less than PHE. No significant differences were detected for GLP-1. PHE increased glucagon more than TRP or LEU, and increased insulin more than TRP. Conclusion: Under our experimental conditions, intraduodenal TRP and LEU were more satiating than PHE and GLN. The greater satiating efficacy of LEU vs. PHE was significantly dissociated from the effects of these AAs on PYY, while the greater satiating potency of TRP vs. PHE was significantly dissociated from the effects of these AAs on insulin and glucagon. In contrast, ghrelin and CCK, and potentially other mechanisms, including central sensing of individual AAs, appear to be stronger candidate mechanisms for the relative satiating effects obtained.
DOI: 10.6084/m9.figshare.5504947.v1
title: Dataset for: Comparative effects of intraduodenal amino acid infusions on food intake and gut hormone release in healthy males

description: Background: In contrast to the many studies of the effects of individual amino acids (AAs) on eating, no studies have compared the effects of different AAs on eating and underlying preabsorptive gastrointestinal mechanisms. Objective: To compare the effects of intraduodenal infusions of L-tryptophan (TRP), L-leucine (LEU), L-phenylalanine (PHE) and L-glutamine (GLN) on appetite, gastrointestinal hormone responses (including ghrelin, cholecystokinin (CCK), peptide YY (PYY) and glucagon-like peptide-1 (GLP-1)), glycemia (glucagon, insulin and glucose) and test meal size in healthy males. Design: We retrospectively analyzed data from four published independent, randomized, double-blind, placebo-controlled studies of 90-min intraduodenal infusions of the individual AAs. The designs of the studies were identical, except the dose of TRP (0.15 kcal/min) was lower than that of the other AAs (0.45 kcal/min) because higher doses of this AA were not well tolerated. Results: TRP and LEU decreased intake more than PHE (reductions relative to control, ~219±68, ~170±48 and ~12±57 kcal, respectively), and TRP decreased intake more than GLN (~31±82 kcal). These effects of TRP and LEU vs. GLN, but not vs. PHE, were paralleled by greater decreases in plasma ghrelin, and increases in CCK, concentrations. TRP increased PYY more than GLN or LEU, but not PHE. LEU increased PYY less than PHE. No significant differences were detected for GLP-1. PHE increased glucagon more than TRP or LEU, and increased insulin more than TRP. Conclusion: Under our experimental conditions, intraduodenal TRP and LEU were more satiating than PHE and GLN. The greater satiating efficacy of LEU vs. PHE was significantly dissociated from the effects of these AAs on PYY, while the greater satiating potency of TRP vs. PHE was significantly dissociated from the effects of these AAs on insulin and glucagon. In contrast, ghrelin and CCK, and potentially other mechanisms, including central sensing of individual AAs, appear to be stronger candidate mechanisms for the relative satiating effects obtained.
DOI: 10.6084/m9.figshare.12901334.v1
title: Aesculus hippocastanum 2020

description: Unique genotypes of individuals from various <i>Aesculus </i>species, identified with using twelve new SSR markers designed for <i>A. hippocastanum</i>. Stands for <i>A. hippocastanum</i>: 1 – Ondria, 2 – Kalampaka, 3 – Dasos Nanitsa, 4 – Vaeni, 5 – Mariolata, 6 – Karitsa, 7 – Perivoli. Stands for others species: P - AMU Botanical Garden in Poznań, K – Kórnik Arboretum.
DOI: 10.6084/m9.figshare.5504851
title: Collection of 791 Traditional Chinese Medicine books

description: A collection of 791 ancient Traditional Chinese Medicine books in txt format. These files are based on the Medical Collection of Dai Zhi Ge www.daizhige.org/医藏/<br>
DOI: 10.6084/m9.figshare.12901334
title: Aesculus hippocastanum 2020

description: Unique genotypes of individuals from various <i>Aesculus </i>species, identified with using twelve new SSR markers designed for <i>A. hippocastanum</i>. Stands for <i>A. hippocastanum</i>: 1 – Ondria, 2 – Kalampaka, 3 – Dasos Nanitsa, 4 – Vaeni, 5 – Mariolata, 6 – Karitsa, 7 – Perivoli. Stands for others species: P - AMU Botanical Garden in Poznań, K – Kórnik Arboretum.