cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11550600.v1
title: Impact of stress on zebrafish behaviour

description: Impact of acute and chronic stress on swimming speed (sheet 1); time spent at the bottom of the tank (sheet) and fractal dimension (FD, sheet 3) where fish had no stress, acute or chronic stress and subject to no disturbance (control), anaesthesia and handling (Sham) and anaesthesia and fin clip. Acutely stressed controls and fin clip fish were subject to naloxone administration.Published in Journal of Experimental Biology (2020) 223, jeb224527. doi:10.1242/jeb.224527<br>
DOI: 10.6084/m9.figshare.11550774.v1
title: ukredlinks_pairs_final.pkl

description: Dataset of Wikipedia red links ffrom Ukrainian Wikipedia edition. Table 'ukredlinks_final.pkl' is a dataset of the most frequent 3 171 Ukrainian red links. They occur in 20 or more articles which have corresponding articles in English Wikipedia. The second table consists of 2 957 927 pairs which are red links and their candidate pages from English Wikipedia. The pairs are created as a dictionary for Named Entity Linking task.<br>
DOI: 10.6084/m9.figshare.11550774.v2
title: Red links from Ukrainian Wikipedia, dump September 2018

description: Dataset of Wikipedia red links ffrom Ukrainian Wikipedia edition (dump from 20th of September, 2018). Table 'ukredlinks_final.pkl' is a dataset of the most frequent 3 171 Ukrainian red links. They occur in 20 or more articles which have corresponding articles in English Wikipedia.Table 'ukredlinks_pairs_final.pkl' consists of 2 957 927 pairs which are red links and their candidate pages from English Wikipedia. The pairs are created as a dictionary for Named Entity Linking task. Tables 'redlinks_train_set.csv' and 'redlinks_test_set.csv' are sets of red link & English candidate page pairs for modelling.<br>
DOI: 10.6084/m9.figshare.11550774.v3
title: Red links from Ukrainian Wikipedia, dump September 2018

description: Dataset of Wikipedia red links from Ukrainian Wikipedia edition (dump from 20th of September, 2018). Table 'ukredlinks_final.csv' is a dataset of the most frequent 3 171 Ukrainian red links. They occur in 20 or more articles which have corresponding articles in English Wikipedia.Table 'ukredlinks_pairs_final.csv' consists of 2 957 927 pairs which are red links and their candidate pages from English Wikipedia. The pairs are created as a dictionary for Named Entity Linking task. Tables 'redlinks_train_set.csv' and 'redlinks_test_set.csv' are sets of red link & English candidate page pairs for modelling.
DOI: 10.6084/m9.figshare.11550774.v4
title: Red links from Ukrainian Wikipedia, dump September 2018

description: Dataset of Wikipedia red links from Ukrainian Wikipedia edition (dump from 20th of September, 2018). Table 'ukredlinks_final.csv' is a dataset of the most frequent 3 171 Ukrainian red links. They occur in 20 or more articles which have corresponding articles in English Wikipedia.Table 'ukredlinks_pairs_final.csv' consists of 2 957 927 pairs which are red links and their candidate pages from English Wikipedia. The pairs are created as a dictionary for Named Entity Linking task. Tables 'redlinks_train_set_indexes.csv' and 'redlinks_test_set_indexes.csv' are indexes for train and test sets of red link & English candidate page pairs.
DOI: 10.6084/m9.figshare.11550774.v5
title: Red links from Ukrainian Wikipedia, dump September 2018

description: Dataset of Wikipedia red links from Ukrainian Wikipedia edition (dump from 20th of September, 2018). Table 'ukredlinks_final.csv' is a dataset of the most frequent 3 171 Ukrainian red links. They occur in 20 or more articles which have corresponding articles in English Wikipedia.Table 'ukredlinks_pairs_final.csv' consists of 2 957 927 pairs which are red links and their candidate pages from English Wikipedia. The pairs are created as a dictionary for Named Entity Linking task. Tables 'redlinks_train_set_indexes.csv' and 'redlinks_test_set_indexes.csv' are indexes for train and test sets of red link & English candidate page pairs.
DOI: 10.6084/m9.figshare.11550336
title: Journal of soil and sediment contamination

description: Analysis
DOI: 10.6084/m9.figshare.11550336.v1
title: Journal of soil and sediment contamination

description: Analysis
DOI: 10.6084/m9.figshare.11550126
title: Supplementary Material for: Duodenal Neuroendocrine Tumour Resection with a New Duodenal Full-Thickness Resection Device

description: Medicine
DOI: 10.6084/m9.figshare.11550051
title: Supplementary Material for: Central Congenital Hypothyroidism Caused by a Novel Mutation, C47W, in the Cysteine Knot Region of TSHβ

description: <b><i>Background:</i></b> Isolated central congenital hypothyroidism (ICCH) is a rare form (1:50,000 newborns) of congenital hypothyroidism, which can present with growth and neuropsychological retardation. Unlike the more common primary CH (1:1,500–1:4,000), which presents on newborn screening with elevated serum thyroid-stimulating hormone (TSH) and low thyroxine (T<sub>4</sub>) and triiodothyronine (T<sub>3</sub>), ICCH presents with low TSH and low thyroid hormone levels. ICCH, therefore, may be missed in most newborn screens that are based only on elevated TSH. Most cases of ICCH have been associated with mutations in the <i>TSHβ</i> gene. <b><i>Patient:</i></b> We present a consanguineous Sudanese family where the proband was diagnosed with “atypical” CH (serum TSH was low, not high). <b><i>Intervention and Outcome:</i></b> The propositus underwent whole-exome sequencing, and the C47W TSHβ mutation was identified. Sanger sequencing confirmed the proband to be homozygous for C47W, and both parents were heterozygous for the same mutation. The mutation was predicted by several in silico methods to have a deleterious effect (SIFT 0.0, Damaging; Polyphen2_HDIV 0.973, probably damaging; MutationTaster 1, disease causing; and CADD 3.17, 16.62). C47W affects the first cysteine of the cysteine knot of the TSHβ subunit. The cysteine knot region of TSHβ is highly conserved across species and is critical for binding to the TSH receptor. Only two other mutations were previously reported along the cysteine knot and showed consistently low or undetectable serum TSH and low T<sub>4</sub> and T<sub>3</sub> levels. Other <i>TSHβ</i> gene mutations causing ICCH have been reported in the “seatbelt” region, necessary for TSHβ dimerization with the alpha subunit. <b><i>Conclusions:</i></b> Identification of a mutation in the <i>TSHβ</i> gene reinforces the importance of identifying ICCH that can occur in the absence of elevated serum TSH and demonstrates the functional significance of the TSHβ cysteine knot.
DOI: 10.6084/m9.figshare.11550051.v1
title: Supplementary Material for: Central Congenital Hypothyroidism Caused by a Novel Mutation, C47W, in the Cysteine Knot Region of TSHβ

description: <b><i>Background:</i></b> Isolated central congenital hypothyroidism (ICCH) is a rare form (1:50,000 newborns) of congenital hypothyroidism, which can present with growth and neuropsychological retardation. Unlike the more common primary CH (1:1,500–1:4,000), which presents on newborn screening with elevated serum thyroid-stimulating hormone (TSH) and low thyroxine (T<sub>4</sub>) and triiodothyronine (T<sub>3</sub>), ICCH presents with low TSH and low thyroid hormone levels. ICCH, therefore, may be missed in most newborn screens that are based only on elevated TSH. Most cases of ICCH have been associated with mutations in the <i>TSHβ</i> gene. <b><i>Patient:</i></b> We present a consanguineous Sudanese family where the proband was diagnosed with “atypical” CH (serum TSH was low, not high). <b><i>Intervention and Outcome:</i></b> The propositus underwent whole-exome sequencing, and the C47W TSHβ mutation was identified. Sanger sequencing confirmed the proband to be homozygous for C47W, and both parents were heterozygous for the same mutation. The mutation was predicted by several in silico methods to have a deleterious effect (SIFT 0.0, Damaging; Polyphen2_HDIV 0.973, probably damaging; MutationTaster 1, disease causing; and CADD 3.17, 16.62). C47W affects the first cysteine of the cysteine knot of the TSHβ subunit. The cysteine knot region of TSHβ is highly conserved across species and is critical for binding to the TSH receptor. Only two other mutations were previously reported along the cysteine knot and showed consistently low or undetectable serum TSH and low T<sub>4</sub> and T<sub>3</sub> levels. Other <i>TSHβ</i> gene mutations causing ICCH have been reported in the “seatbelt” region, necessary for TSHβ dimerization with the alpha subunit. <b><i>Conclusions:</i></b> Identification of a mutation in the <i>TSHβ</i> gene reinforces the importance of identifying ICCH that can occur in the absence of elevated serum TSH and demonstrates the functional significance of the TSHβ cysteine knot.
DOI: 10.6084/m9.figshare.11549715
title: Middle Eocene magmatism in the Khur region (Lut Block, Eastern Iran): implications for petrogenesis and tectonic setting

description: The Khur region is located in the Late Mesozoic-Cenozoic volcanic-plutonic rocks of the Lut Block, eastern Iran. There are several outcrops of subvolcanic rocks in the region which occur mainly as dike (granitoid and mafic dikes) and stock (monzonite porphyry). Volcanic rocks (basaltic andesites, andesites, trachyandesites, dacites and rhyodacites) are also abundant and cover pyroclastic rocks. U–Pb zircon ages indicate that granitic-dioritic dikes and monzonite porphyries were emplaced at 44.97 to 40.86 Ma and 41.11 Ma, respectively. Granitoid dikes are high-K calc-alkaline and metaluminous and geochemically belong to the I-type granitoids. Monzonite porphyries show I-type (and rarely A-type) signatures, with typical enrichments in alkalis, Zr and Ce, high FeO<sub>t</sub>/(FeO<sub>t</sub>+MgO) ratio and depletion in Sr and Nb. Primitive magmas of dikes, stocks and acidic volcanic rocks have formed in the lower crust and have undergone different degrees of AFC, while primitive magmas of mafic volcanic rocks have formed in the mantle and have presumably been modified by melts/fluids. Moreover, a syn to post-collision-related zone is responsible for the high magmatic rate during the Middle Eocene in the Lut Block.
DOI: 10.6084/m9.figshare.11549715.v1
title: Middle Eocene magmatism in the Khur region (Lut Block, Eastern Iran): implications for petrogenesis and tectonic setting

description: The Khur region is located in the Late Mesozoic-Cenozoic volcanic-plutonic rocks of the Lut Block, eastern Iran. There are several outcrops of subvolcanic rocks in the region which occur mainly as dike (granitoid and mafic dikes) and stock (monzonite porphyry). Volcanic rocks (basaltic andesites, andesites, trachyandesites, dacites and rhyodacites) are also abundant and cover pyroclastic rocks. U–Pb zircon ages indicate that granitic-dioritic dikes and monzonite porphyries were emplaced at 44.97 to 40.86 Ma and 41.11 Ma, respectively. Granitoid dikes are high-K calc-alkaline and metaluminous and geochemically belong to the I-type granitoids. Monzonite porphyries show I-type (and rarely A-type) signatures, with typical enrichments in alkalis, Zr and Ce, high FeO<sub>t</sub>/(FeO<sub>t</sub>+MgO) ratio and depletion in Sr and Nb. Primitive magmas of dikes, stocks and acidic volcanic rocks have formed in the lower crust and have undergone different degrees of AFC, while primitive magmas of mafic volcanic rocks have formed in the mantle and have presumably been modified by melts/fluids. Moreover, a syn to post-collision-related zone is responsible for the high magmatic rate during the Middle Eocene in the Lut Block.
DOI: 10.6084/m9.figshare.11548779
title: Habitat Suitability Model for Pied-Billed Grebe

description: Raster model of breeding habitat suitability for Pied-Billed Grebes within the contiguous U.S. Model development described by Stevens and Conway (2020).<br> These data are supplemental materials for the following manuscript: <br> Stevens, B.S., and C.J. Conway. 2020. Mapping habitat suitability at range-wide scales: spatially-explicit distribution models to inform conservation and research for marsh birds. Conservation Science and Practice 2:in press.
DOI: 10.6084/m9.figshare.11548917
title: data_20200108_He_and_Wang_HaiBei.csv

description: Hourly soil respiration data measured for 6 years in Tibetan alpine grassland.
DOI: 10.6084/m9.figshare.11548917.v1
title: data_20200108_He_and_Wang_HaiBei.csv

description: Hourly soil respiration data measured for 6 years in Tibetan alpine grassland.
DOI: 10.6084/m9.figshare.11548287
title: OA price and service transparency project - Data

description: This record contains the data from the OA price and service transparency project, an independent report done by Information Power.
DOI: 10.6084/m9.figshare.11548287.v1
title: OA price and service transparency project - Data

description: This record contains the data from the OA price and service transparency project, an independent report done by Information Power.
DOI: 10.6084/m9.figshare.11547273
title: Supplementary Code from Prediction of polyproline II secondary structure propensity in proteins

description: Downloadable code to allow local linux installation of the software
DOI: 10.6084/m9.figshare.11547273.v1
title: Supplementary Code from Prediction of polyproline II secondary structure propensity in proteins

description: Downloadable code to allow local linux installation of the software
DOI: 10.6084/m9.figshare.11547141
title: Supplementary Material for: Biological Sex and IgE Sensitization Influence Severity of Depression and Cortisol Levels in Atopic Dermatitis

description: <b><i>Background:</i></b> Depression is a common comorbid condition with atopic dermatitis (AD), particularly during the active disease cycle. Controversial results regarding the contribution of biological sex, immunoglobulin E (IgE) sensitization, and cortisol on AD severity and comorbid depression justify further investigation. <b><i>Objective and Methods:</i></b> To explore the influence of sex and IgE sensitization on biochemical and psychological parameters, and severity of AD, a case-control study of 105 volunteers (56 AD, 49 healthy controls (HC); 50 males, 55 females) was conducted over 10 weeks, starting at dermatological symptom onset. Disease severity, serum IgE, cortisol and testosterone levels, and depression scores were assessed at study baseline and after 10 weeks of conventional treatment. <b><i>Results:</i></b> Dermatological severity differed among AD males by IgE sensitization and was elevated in males with extrinsic atopic dermatitis (EAD). Hamilton Depression Rating Scale (HAMD) scores were elevated in all patients at study baseline and improved with symptom reduction to HC levels, except female EAD. Severity of depression and dermatitis were correlated in EAD males at baseline and at week 10. Serum cortisol was elevated in male EAD at baseline, in contrast to males with intrinsic atopic dermatitis (IAD) at week 10. In addition, cortisol levels were found negatively correlated with SCORAD and HAMD scores in EAD males at week 10. <b><i>Conclusion:</i></b> Pathophysiological features of AD and depression are likely related to different inflammation-based effects and appear to be biological sex-dependent. Cortisol levels depend on biological sex and IgE sensitization in AD and increase in males with EAD at exacerbation and IAD males at resolution. Biological sex-related disease triggers, IgE sensitization, and cortisol levels are important for the understanding of the mechanisms underlying AD and comorbid depression.
DOI: 10.6084/m9.figshare.11547141.v1
title: Supplementary Material for: Biological Sex and IgE Sensitization Influence Severity of Depression and Cortisol Levels in Atopic Dermatitis

description: <b><i>Background:</i></b> Depression is a common comorbid condition with atopic dermatitis (AD), particularly during the active disease cycle. Controversial results regarding the contribution of biological sex, immunoglobulin E (IgE) sensitization, and cortisol on AD severity and comorbid depression justify further investigation. <b><i>Objective and Methods:</i></b> To explore the influence of sex and IgE sensitization on biochemical and psychological parameters, and severity of AD, a case-control study of 105 volunteers (56 AD, 49 healthy controls (HC); 50 males, 55 females) was conducted over 10 weeks, starting at dermatological symptom onset. Disease severity, serum IgE, cortisol and testosterone levels, and depression scores were assessed at study baseline and after 10 weeks of conventional treatment. <b><i>Results:</i></b> Dermatological severity differed among AD males by IgE sensitization and was elevated in males with extrinsic atopic dermatitis (EAD). Hamilton Depression Rating Scale (HAMD) scores were elevated in all patients at study baseline and improved with symptom reduction to HC levels, except female EAD. Severity of depression and dermatitis were correlated in EAD males at baseline and at week 10. Serum cortisol was elevated in male EAD at baseline, in contrast to males with intrinsic atopic dermatitis (IAD) at week 10. In addition, cortisol levels were found negatively correlated with SCORAD and HAMD scores in EAD males at week 10. <b><i>Conclusion:</i></b> Pathophysiological features of AD and depression are likely related to different inflammation-based effects and appear to be biological sex-dependent. Cortisol levels depend on biological sex and IgE sensitization in AD and increase in males with EAD at exacerbation and IAD males at resolution. Biological sex-related disease triggers, IgE sensitization, and cortisol levels are important for the understanding of the mechanisms underlying AD and comorbid depression.
DOI: 10.6084/m9.figshare.11546730
title: Supplementary Data from The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee <i>Bombus terrestris</i>

description: Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee <i>Bombus terrestris</i> workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
DOI: 10.6084/m9.figshare.11546730.v1
title: Supplementary Data from The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee <i>Bombus terrestris</i>

description: Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee <i>Bombus terrestris</i> workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
DOI: 10.6084/m9.figshare.11546322
title: Data, Manuscript, Quantification of proteins in exhaled particles,2020

description: Data used for manuscript Quantification of proteins in exhaled particles using Luminex technology - considerations for analysis of samples from the small airways
DOI: 10.6084/m9.figshare.11545581
title: Antinociceptive effects of sinomenine combined with ligustrazine or paracetamol in animal models of incisional and inflammatory pain

description: The management of post-operative and inflammatory pain has been a pressing challenge in clinical settings. The present strategy involving opioid treatments is not satisfactory, which often associated with tolerance and addiction. Sinomenine (SN) is a morphinan derived alkaloid with remarkable analgesic properties in various kinds of pain models. The aim of the current study is to evaluate if SN can be used to enhance the effect of ligustrazine hydrochloride (LGZ) or paracetamol (PCM) in animal models of post-operative and inflammatory pain. And if therapeutic efficacies can be correlated to pharmacokinetics change due to drug combinations. Pharmacological studies were performed in rat model of incisional pain, or mouse model of carrageenan induced inflammatory pain, 24 hours after incision or carrageenan injection. Pharmacokenetic studies were performed using a sensitive HPLC-QQQ-MS method to quantify SN, LGZ and PCM levels in blood and extracellular fluids of brain. We found that SN and LGZ or SN and PCM produced marked synergistic analgesic effects. However, such synergy was subjected to pain modalities, and drug’s effects were differed in incisional and inflammatory pain. The pharmacological discoveries could be partially explained by pharmacokinetic alterations in SN combinations. Though further clinical evaluation is needed, our findings advocate the potential usages of SN with LGZ or SN with PCM respectively for post-operative pain or acute inflammatory pain as opioid-substitutional analgesics. This study also provided insights into the drug induced neuroimmune interactions reflecting the perplexing physiology of the nociceptive system.
DOI: 10.6084/m9.figshare.11545581.v1
title: Antinociceptive effects of sinomenine combined with ligustrazine or paracetamol in animal models of incisional and inflammatory pain

description: The management of post-operative and inflammatory pain has been a pressing challenge in clinical settings. The present strategy involving opioid treatments is not satisfactory, which often associated with tolerance and addiction. Sinomenine (SN) is a morphinan derived alkaloid with remarkable analgesic properties in various kinds of pain models. The aim of the current study is to evaluate if SN can be used to enhance the effect of ligustrazine hydrochloride (LGZ) or paracetamol (PCM) in animal models of post-operative and inflammatory pain. And if therapeutic efficacies can be correlated to pharmacokinetics change due to drug combinations. Pharmacological studies were performed in rat model of incisional pain, or mouse model of carrageenan induced inflammatory pain, 24 hours after incision or carrageenan injection. Pharmacokenetic studies were performed using a sensitive HPLC-QQQ-MS method to quantify SN, LGZ and PCM levels in blood and extracellular fluids of brain. We found that SN and LGZ or SN and PCM produced marked synergistic analgesic effects. However, such synergy was subjected to pain modalities, and drug’s effects were differed in incisional and inflammatory pain. The pharmacological discoveries could be partially explained by pharmacokinetic alterations in SN combinations. Though further clinical evaluation is needed, our findings advocate the potential usages of SN with LGZ or SN with PCM respectively for post-operative pain or acute inflammatory pain as opioid-substitutional analgesics. This study also provided insights into the drug induced neuroimmune interactions reflecting the perplexing physiology of the nociceptive system.