cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14237150
title: Supplementary Material for: Novel Data about Association of the Functionally Significant Polymorphisms of the <b><i>MMP9</i></b> Gene with Exfoliation Glaucoma in the Caucasian Population of Central Russia

description: <b><i>Aim:</i></b> This study aimed to investigate the role of functionally significant polymorphisms of the <i>MMP1, MMP3,</i> and <i>MMP9</i> genes in the development of exfoliation glaucoma (XFG) in the Caucasian population of Central Russia. <b><i>Methods:</i></b> The study sample consisted of 724 participants, including 328 patients with XFG and 396 individuals in the control group. The participants were of Russian ethnicity (self-reported) born in Central Russia. The participants were genotyped at 8 functionally significant polymorphisms of the <i>MMP</i> genes (rs3918242, rs3918249, rs17576, rs3787268, rs2250889, rs17577 <i>MMP9,</i> rs679620 <i>MMP3</i>, and rs1799750 <i>MMP1</i>). The association analysis was performed using logistic regression. Two polymorphisms, which were associated with XFG, and 12 polymorphisms linked to them (<i>r</i><sup>2</sup> ≥ 0.8) were analyzed for their functional significance in silico. <b><i>Results:</i></b> Allele C of rs3918249 <i>MMP9</i> was associated with XFG according to the additive model (OR = 0.75, 95% CI: 0.56–0.93, <i>p</i><sub>perm</sub> = 0.015), and allele G of the rs2250889 <i>MMP9</i> locus was associated with XFG according to the additive (OR = 1.59, 95% CI: 1.10–2.29, <i>p</i><sub>perm</sub> = 0.013) and dominant (OR = 1.68, 95% CI: 1.11–2.56, <i>p</i><sub>perm</sub> = 0.016) models. Two XFG-associated loci of the <i>MMP9</i> gene and 12 SNPs linked to them had a significant regulatory potential (they are located in the evolutionarily conserved regions, promoter and enhancer histone marks, the DNAase-hypersensitivity regions, a region binding to regulatory protein, and a region of regulatory motifs) and may influence the expression of 13 genes and alternative splicing of 4 genes in various tissues and organs related to the pathogenesis of XFG. <b><i>Conclusion:</i></b> Allele C rs3918249 <i>MMP9</i> decreased risk for XFG (OR = 0.75), and allele G of the rs2250889 <i>MMP9</i> locus increased risk for XFG (OR = 1.59–1.68) in the Caucasian population of Central Russia.
DOI: 10.6084/m9.figshare.14237156
title: Supplementary Material for: Microfluidic Assays for Probing Neutrophil-<b><i>Borrelia</i></b> Interactions in Blood During Lyme Disease

description: Human neutrophils are highly sensitive to the presence of <i>Borrelia burgdorferi</i> (Bb), the agent of Lyme disease (LD), in tissues. Although Bb is also found in the blood of LD patients, far less is known about how neutrophils respond to Bb in the presence of blood. In this study, we employed microfluidic tools to probe the interaction between human neutrophils and Bb and measured the activation of human neutrophils in blood samples from patients. We found that neutrophils migrate vigorously toward Bb in the presence of serum, and this process was complement-dependent. Preventing complement factor 5 cleavage or blocking complement receptors decreased neutrophil’s ability to interact with Bb. We also found that spiking Bb directly into the blood from healthy donors induced spontaneous neutrophil motility. This response to Bb was also complement-dependent. Preventing complement factor 5 cleavage decreased spontaneous neutrophil motility in Bb-spiked blood. Moreover, we found that neutrophils in blood samples from acute LD patients displayed spontaneous motility patterns similar to those observed in Bb-spiked samples. Neutrophil motility was more robust in blood samples from LD patients than that measured in healthy and ill controls, validating the utility of the microfluidic assay for the study of neutrophil-Bb interactions in the presence of blood.
DOI: 10.6084/m9.figshare.14237156.v1
title: Supplementary Material for: Microfluidic Assays for Probing Neutrophil-<b><i>Borrelia</i></b> Interactions in Blood During Lyme Disease

description: Human neutrophils are highly sensitive to the presence of <i>Borrelia burgdorferi</i> (Bb), the agent of Lyme disease (LD), in tissues. Although Bb is also found in the blood of LD patients, far less is known about how neutrophils respond to Bb in the presence of blood. In this study, we employed microfluidic tools to probe the interaction between human neutrophils and Bb and measured the activation of human neutrophils in blood samples from patients. We found that neutrophils migrate vigorously toward Bb in the presence of serum, and this process was complement-dependent. Preventing complement factor 5 cleavage or blocking complement receptors decreased neutrophil’s ability to interact with Bb. We also found that spiking Bb directly into the blood from healthy donors induced spontaneous neutrophil motility. This response to Bb was also complement-dependent. Preventing complement factor 5 cleavage decreased spontaneous neutrophil motility in Bb-spiked blood. Moreover, we found that neutrophils in blood samples from acute LD patients displayed spontaneous motility patterns similar to those observed in Bb-spiked samples. Neutrophil motility was more robust in blood samples from LD patients than that measured in healthy and ill controls, validating the utility of the microfluidic assay for the study of neutrophil-Bb interactions in the presence of blood.
DOI: 10.48370/ofd/qtrkms
title: Wierzba trójpręcikowa (Salix triandra L.), 8164

description: Herbarium
DOI: 10.6084/m9.figshare.14237175.v1
title: Table 5: Apatite Trace elements. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 5: Apatite Trace elements
DOI: 10.6084/m9.figshare.14237175
title: Table 5: Apatite Trace elements. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 5: Apatite Trace elements
DOI: 10.6084/m9.figshare.14237178
title: Table 1: Grain Population. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 1: Grain Population
DOI: 10.6084/m9.figshare.14237181
title: Table 7: Sample list of all sample locations, depths and types. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 7: Sample list of all sample locations, depths and types
DOI: 10.6084/m9.figshare.14237178.v1
title: Table 1: Grain Population. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 1: Grain Population
DOI: 10.6084/m9.figshare.14237181.v1
title: Table 7: Sample list of all sample locations, depths and types. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 7: Sample list of all sample locations, depths and types
DOI: 10.6084/m9.figshare.14237184
title: Table 3: Zircon U–Pb Geochronology. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 3: Zircon U–Pb Geochronology
DOI: 10.6084/m9.figshare.14237184.v1
title: Table 3: Zircon U–Pb Geochronology. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 3: Zircon U–Pb Geochronology
DOI: 10.6084/m9.figshare.14237187.v1
title: Table 6: White Mica. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 6: White Mica
DOI: 10.6084/m9.figshare.14237187
title: Table 6: White Mica. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 6: White Mica
DOI: 10.6084/m9.figshare.14237190.v1
title: Table 2: Heavy Minerals. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 2: Heavy Minerals
DOI: 10.6084/m9.figshare.14237193
title: Table 4: Apatite U–Pb Geochronology. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 4: Apatite U–Pb Geochronology
DOI: 10.6084/m9.figshare.14237193.v1
title: Table 4: Apatite U–Pb Geochronology. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 4: Apatite U–Pb Geochronology
DOI: 10.6084/m9.figshare.14237150.v1
title: Supplementary Material for: Novel Data about Association of the Functionally Significant Polymorphisms of the <b><i>MMP9</i></b> Gene with Exfoliation Glaucoma in the Caucasian Population of Central Russia

description: <b><i>Aim:</i></b> This study aimed to investigate the role of functionally significant polymorphisms of the <i>MMP1, MMP3,</i> and <i>MMP9</i> genes in the development of exfoliation glaucoma (XFG) in the Caucasian population of Central Russia. <b><i>Methods:</i></b> The study sample consisted of 724 participants, including 328 patients with XFG and 396 individuals in the control group. The participants were of Russian ethnicity (self-reported) born in Central Russia. The participants were genotyped at 8 functionally significant polymorphisms of the <i>MMP</i> genes (rs3918242, rs3918249, rs17576, rs3787268, rs2250889, rs17577 <i>MMP9,</i> rs679620 <i>MMP3</i>, and rs1799750 <i>MMP1</i>). The association analysis was performed using logistic regression. Two polymorphisms, which were associated with XFG, and 12 polymorphisms linked to them (<i>r</i><sup>2</sup> ≥ 0.8) were analyzed for their functional significance in silico. <b><i>Results:</i></b> Allele C of rs3918249 <i>MMP9</i> was associated with XFG according to the additive model (OR = 0.75, 95% CI: 0.56–0.93, <i>p</i><sub>perm</sub> = 0.015), and allele G of the rs2250889 <i>MMP9</i> locus was associated with XFG according to the additive (OR = 1.59, 95% CI: 1.10–2.29, <i>p</i><sub>perm</sub> = 0.013) and dominant (OR = 1.68, 95% CI: 1.11–2.56, <i>p</i><sub>perm</sub> = 0.016) models. Two XFG-associated loci of the <i>MMP9</i> gene and 12 SNPs linked to them had a significant regulatory potential (they are located in the evolutionarily conserved regions, promoter and enhancer histone marks, the DNAase-hypersensitivity regions, a region binding to regulatory protein, and a region of regulatory motifs) and may influence the expression of 13 genes and alternative splicing of 4 genes in various tissues and organs related to the pathogenesis of XFG. <b><i>Conclusion:</i></b> Allele C rs3918249 <i>MMP9</i> decreased risk for XFG (OR = 0.75), and allele G of the rs2250889 <i>MMP9</i> locus increased risk for XFG (OR = 1.59–1.68) in the Caucasian population of Central Russia.
DOI: 10.6084/m9.figshare.14237190
title: Table 2: Heavy Minerals. The Provenance of Middle Jurassic to Cretaceous sediments in the Irish and Celtic Sea Basins: Tectonic and Environmental controls on sediment sourcing

description: Table 2: Heavy Minerals
DOI: 10.6084/m9.figshare.14237207
title: Old_Female_CG_MethRatio.bw

description: File to be uploaded to UCSC genome browser
DOI: 10.6084/m9.figshare.14237207.v1
title: Old_Female_CG_MethRatio.bw

description: File to be uploaded to UCSC genome browser
DOI: 10.6084/m9.figshare.14237222
title: Supplementary Material for: Evolution of Sex Chromosome Heteromorphy in Geographic Populations of the Japanese Tago’s Brown Frog Complex

description: The sex chromosomes of most anuran amphibians are characterized by homomorphy in both sexes, and evolution to heteromorphy rarely occurs at the species or geographic population level. Here, we report sex chromosome heteromorphy in geographic populations of the Japanese Tago’s brown frog complex (2<i>n</i> = 26), comprising <i>Rana sakuraii</i> and <i>R. tagoi</i>. The sex chromosomes of <i>R. sakuraii</i> from the populations in western Japan were homomorphic in both sexes, whereas chromosome 7 from the populations in eastern Japan were heteromorphic in males. Chromosome 7 of <i>R. tagoi</i>, which is distributed close to <i>R. sakuraii</i> in eastern Japan, was highly similar in morphology to the Y chromosome of <i>R. sakuraii</i>. Based on this and on mitochondrial gene sequence analysis, we hypothesize that in the <i>R. sakuraii</i> populations from eastern Japan the XY heteromorphic sex chromosome system was established by the introduction of chromosome 7 from <i>R. tagoi</i> via interspecies hybridization. In contrast, chromosome 13 of <i>R. tagoi</i> from the 2 large islands in western Japan, Shikoku and Kyushu, showed a heteromorphic pattern of constitutive heterochromatin distribution in males, while this pattern was homomorphic in females. Our study reveals that sex chromosome heteromorphy evolved independently at the geographic lineage level in this species complex.
DOI: 10.5281/zenodo.4616689
title: CoPro - example input data

description: This data set contains example data to build and run a simple machine learning model to project conflict risk. It contains hydro-meteorological input sample data set as well as observed conflict data as target variable. Together with the CoPro model, a classifier can be trained and tested as well as used to project conflict risk. A README.md file is provided. It must be noted that the data provided here is only meant for showcasing the model functionality. For developing an actual machine learning model with sufficient accuracy, additional input data set may need to be used.
DOI: 10.3886/e117644
title: Transmission of Monetary Policy with Heterogeneity in Household Portfolios

description: This paper assesses the importance of heterogeneity in household portfolios for the transmission of monetary policy in a New Keyne- sian business cycle model with uninsurable income risk and assets with different liquidity. In this environment, monetary transmis- sion works through investment, but redistribution lowers the elas- ticity of investment via two channels: 1) heterogeneity in marginal propensities to invest, 2) time variation in the liquidity premium. Monetary contractions redistribute to wealthy households who have high propensities to invest and a low marginal value of liquidity, thereby stabilizing investment. I provide empirical evidence for counter-cyclical liquidity premia and heterogeneity in household portfolio responses.
DOI: 10.3886/e117644v1
title: Transmission of Monetary Policy with Heterogeneity in Household Portfolios

description: This paper assesses the importance of heterogeneity in household portfolios for the transmission of monetary policy in a New Keyne- sian business cycle model with uninsurable income risk and assets with different liquidity. In this environment, monetary transmis- sion works through investment, but redistribution lowers the elas- ticity of investment via two channels: 1) heterogeneity in marginal propensities to invest, 2) time variation in the liquidity premium. Monetary contractions redistribute to wealthy households who have high propensities to invest and a low marginal value of liquidity, thereby stabilizing investment. I provide empirical evidence for counter-cyclical liquidity premia and heterogeneity in household portfolio responses.
DOI: 10.7910/dvn/w3ipnt
title: A discussion on Geometry and General Relativity

description: There have been numerous introductory papers that describe the geometric nature of Space-time in General Relativity. This paper is a dialogue between a Physics student in High school and a researcher in 2017. Vaibhav is a High school student who is interested in understanding more of General Relativity, and his father, Donnie is a researcher who works in General Relativity. The following is one of the many conversations that could be heard over coffee in Donnie’s office in a major Canadian University.
DOI: 10.6084/m9.figshare.13193600
title: Data for the manuscript Predicting microbial growth dynamics in response to nutrient availability

description: Data for the manuscript Predicting microbial growth dynamics in response to nutrient availability
DOI: 10.6084/m9.figshare.13193600.v2
title: Data for the manuscript Predicting microbial growth dynamics in response to nutrient availability

description: Data for the manuscript Predicting microbial growth dynamics in response to nutrient availability
DOI: 10.5281/zenodo.4597088
title: A Dataset of Breaking Waves Remotly Sensed at La Jument Lighthouse During the 2019-2020 Winter Storm Season

description: This dataset was used in the paper "Remote Sensing Observations of Dominant Breaking Waves in Intermediate to Deep Water from a Lighthouse During Storm Conditions" (title may change during peer-review) which has been submitted to Remote Sensing. Both processed data and identified breaking waves are available here. This dataset is closely related to this Github repository.
description: This work benefited from France Energies Marines and State financing managed by the National Research Agency under the Investments for the Future program bearing the reference numbers ANR-10-IED-0006-14, ANR-10-IEED-0006-26, ANR-10-IEED-0006-20 for the projects DiME, CARAVELE and DIMPACT.
DOI: 10.5281/zenodo.4597087
title: A Dataset of Breaking Waves Remotly Sensed at La Jument Lighthouse During the 2019-2020 Winter Storm Season

description: This dataset was used in the paper "Remote Sensing Observations of Dominant Breaking Waves in Intermediate to Deep Water from a Lighthouse During Storm Conditions" (title may change during peer-review) which has been submitted to Remote Sensing. Both processed data and identified breaking waves are available here. This dataset is closely related to this Github repository.
description: This work benefited from France Energies Marines and State financing managed by the National Research Agency under the Investments for the Future program bearing the reference numbers ANR-10-IED-0006-14, ANR-10-IEED-0006-26, ANR-10-IEED-0006-20 for the projects DiME, CARAVELE and DIMPACT.
DOI: 10.15468/9kp5ku
title: A new species of the genus Girardia (Tricladida: Dugesiidae) from China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Chen, Xiao-Min, Chen, Yu-Hui, Wu, Cheng-Chen, Wang, An-Tai (2015): A new species of the genus Girardia (Tricladida: Dugesiidae) from China. Zoological Systematics 40 (2): 166-178, DOI: 10.11865/zs.20150202, URL: http://zoobank.org/5520163b-0355-4362-9b98-8aa0ae049e4a
DOI: 10.6084/m9.figshare.14237279.v1
title: Supplementary files

description: Three tables (Circadian_Sequences_Table.tsv, Vision_Sequences_Table.tsv, Pigmentation_Table.tsv) with every sequences and their genomic position used in this study.<br>Three tables summarizing found LoF mutations (LoF_Table_Pigmentation.tsv, LoF_Table_Circadian.tsv, LoF_Table_Vision.tsv)<br>Two tables that are from Policarpo et al. 2020 (Astyanax_Table.tsv, Dentata_Table.tsv) with vision gene sequences from A. mexicanus and L. dentata<br>Exonerate_raw_results.zip contains every exonerate raw files from which sequences were inferred. <br><br>Orthology_Confirmation.zip contains every gene alignments and IQ-Tree results. It also contain a folder called "PDF" with every phylogenies rooted and visualized with iTOL<br>
DOI: 10.5281/zenodo.4439509
title: A Dataset of State-Censored Tweets

description: This is the dataset associated with the paper of the same name. You can find it here: https://arxiv.org/abs/2101.05919 <br> <strong>Files:</strong> tweets.csv : All 583k censored tweets tweets_debiased.csv : Debiased sample of tweets (Section 6.1) all_users.csv : All users who are censored once at least once users.csv : All 4301 users whose entire profile is censored users_inferred.csv : 1931 extra users inferred to be the censored by the procedure described in Section 3.3 supplement.csv : The supplementary tweet data. (Section 3.5) Please refer to this Github repo for the detailed documentation and the code for reproduction. https://github.com/tugrulz/CensoredTweets
DOI: 10.5281/zenodo.4435113
title: A Dataset of State-Censored Tweets

description: This is the dataset associated with the paper of the same name. You can find it here: https://arxiv.org/abs/2101.05919 <br> <strong>Files:</strong> tweets.csv : All 583k censored tweets tweets_debiased.csv : Debiased sample of tweets (Section 6.1) all_users.csv : All users who are censored once at least once users.csv : All 4301 users whose entire profile is censored users_inferred.csv : 1931 extra users inferred to be the censored by the procedure described in Section 3.3 supplement.csv : The supplementary tweet data. (Section 3.5) Please refer to this Github repo for the detailed documentation and the code for reproduction. https://github.com/tugrulz/CensoredTweets
DOI: 10.6084/m9.figshare.14207327
title: Economic costs of accessing TB diagnostic services in Malawi: questionnaires

description: This contains the questionnaire used to conduct a study on the Economic costs of accessing TB diagnostic services in Malawi. <br><br>
DOI: 10.6084/m9.figshare.14207327.v2
title: Economic costs of accessing TB diagnostic services in Malawi: questionnaires

description: This contains the questionnaire used to conduct a study on the Economic costs of accessing TB diagnostic services in Malawi. <br><br>
DOI: 10.6084/m9.figshare.14207327.v1
title: Economic costs of accessing TB diagnostic services in Malawi: questionnaires

description: This contains the questionnaire used to conduct a study on the Economic costs of accessing TB diagnostic services in Malawi. <br><br>Both the english and translated version (in Chichewa) are provided. <br>
DOI: 10.5519/qd.2dohz5o4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (19054 records)
DOI: 10.5281/zenodo.4617642
title: Dataset for lake stratification manuscript

description: Dataset for in-situ lake stratification phenology of Lake Tahoe, Geneva, Vattern, and Washington
DOI: 10.6084/m9.figshare.14237279
title: Supplementary files

description: Three tables (Circadian_Sequences_Table.tsv, Vision_Sequences_Table.tsv, Pigmentation_Table.tsv) with every sequences and their genomic position used in this study.<br>Three tables summarizing found LoF mutations (LoF_Table_Pigmentation.tsv, LoF_Table_Circadian.tsv, LoF_Table_Vision.tsv)<br>Two tables that are from Policarpo et al. 2020 (Astyanax_Table.tsv, Dentata_Table.tsv) with vision gene sequences from A. mexicanus and L. dentata<br>Exonerate_raw_results.zip contains every exonerate raw files from which sequences were inferred. <br><br>Orthology_Confirmation.zip contains every gene alignments and IQ-Tree results. It also contain a folder called "PDF" with every phylogenies rooted and visualized with iTOL<br>
DOI: 10.6084/m9.figshare.14237279.v3
title: Supplementary files

description: Three tables (Circadian_Sequences_Table.tsv, Vision_Sequences_Table.tsv, Pigmentation_Table.tsv) with every sequences and their genomic position used in this study.<br>Three tables summarizing found LoF mutations (LoF_Table_Pigmentation.tsv, LoF_Table_Circadian.tsv, LoF_Table_Vision.tsv)<br>Two tables that are from Policarpo et al. 2020 (Astyanax_Table.tsv, Dentata_Table.tsv) with vision gene sequences from A. mexicanus and L. dentata<br>Exonerate_raw_results.zip contains every exonerate raw files from which sequences were inferred. <br><br>Orthology_Confirmation.zip contains every gene alignments and IQ-Tree results. It also contain a folder called "PDF" with every phylogenies rooted and visualized with iTOL<br>