cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14371976.v1
title: BNTI matrix used in analyses

description: BNTI matrix generated using code from Stegen et al. (2013) - https://github.com/stegen/Stegen_etal_ISME_2013
DOI: 10.5281/zenodo.5495586
title: The impact of individual variation on abrupt collapses in mutualistic networks

description: R Data and R scripts for the paper in Ecology Letters "The impact of individual variation on abrupt collapses in mutualistic networks" Contact: gbaruahecoevo@gmail.com
DOI: 10.5281/zenodo.5495585
title: The impact of individual variation on abrupt collapses in mutualistic networks

description: R Data and R scripts for the paper in Ecology Letters "The impact of individual variation on abrupt collapses in mutualistic networks" Contact: gbaruahecoevo@gmail.com
DOI: 10.6084/m9.figshare.14371970
title: Results file needed for Contaminant Filtering Script

description: Binary results file to subset taxa in R after manually screened higher abundance contaminants. Used in line 282 of "CROMO_Contaminant_Filtering_Script.R" file.
DOI: 10.6084/m9.figshare.14371970.v1
title: Results file needed for Contaminant Filtering Script

description: Binary results file to subset taxa in R after manually screened higher abundance contaminants. Used in line 282 of "CROMO_Contaminant_Filtering_Script.R" file.
DOI: 10.6084/m9.figshare.14371964
title: Count Table and Taxonomy for OTUs removed in Contaminant Filtering

description: Excel file displaying OTU IDs, relative abundance of OTU in all samples, and assigned taxonomy of OTUs removed during contaminant filtering process.
DOI: 10.6084/m9.figshare.14371961
title: Phylogenetic tree used for ecological modeling

description: Phylogenetic tree generated using Fasttree used for ecological modeling work to calculate beta-Nearest Taxon Index (BNTI).
DOI: 10.6084/m9.figshare.14371961.v1
title: Phylogenetic tree used for ecological modeling

description: Phylogenetic tree generated using Fasttree used for ecological modeling work to calculate beta-Nearest Taxon Index (BNTI).
DOI: 10.6084/m9.figshare.14371955
title: Calculated RCbray matrix used in analyses

description: Abundance weight Raup Crick (RCbray) matrix generated using code from Stegen et al. (2013) - https://github.com/stegen/Stegen_etal_ISME_2013
DOI: 10.6084/m9.figshare.14371955.v1
title: Calculated RCbray matrix used in analyses

description: Abundance weight Raup Crick (RCbray) matrix generated using code from Stegen et al. (2013) - https://github.com/stegen/Stegen_etal_ISME_2013
DOI: 10.6084/m9.figshare.14371949
title: Final OTU IDs

description: Text file with generic OTU IDs for OTUs in final count table. Used for row names to create phyloseq object. Uploaded in line 29 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371946.v1
title: NTI Results

description: Nearest Taxon Index (NTI) results for individual samples. Calculated based on mean nearest taxon distance (MNTD) data. Assesses phylogenetic relationships within individual samples between closest relatives. Uploaded in line 107 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371946
title: NTI Results

description: Nearest Taxon Index (NTI) results for individual samples. Calculated based on mean nearest taxon distance (MNTD) data. Assesses phylogenetic relationships within individual samples between closest relatives. Uploaded in line 107 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371943
title: Metadata file for R

description: Metadata file used in R for data analyses
DOI: 10.6084/m9.figshare.14371943.v1
title: Metadata file for R

description: Metadata file used in R for data analyses
DOI: 10.6084/m9.figshare.14371940
title: R code to calculate MNTD and NTI

description: Code to generate within sample mean nearest taxon distance (MNTD) and nearest taxon index (NTI) values
DOI: 10.6084/m9.figshare.14371937
title: Final Taxonomy Table for R

description: Final taxonomy information for OTUs in final dataset. Species IDs were obtained using BLAST and percent similarity to the closest known relative is included in the file.
DOI: 10.6084/m9.figshare.14371937.v2
title: Final Taxonomy Table for R

description: Final taxonomy information for OTUs in final dataset. Species IDs were obtained using BLAST and percent similarity to the closest known relative is included in the file.
DOI: 10.6084/m9.figshare.14371937.v1
title: Taxonomy information for R

description: Final taxonomy information for OTUs in final dataset. Species IDs were obtained using BLAST and percent similarity to the closest known relative is included in the file.
DOI: 10.6084/m9.figshare.14371934
title: Final count table used for all analyses

description: Final count table used for all ecological modeling work and analyses
DOI: 10.6084/m9.figshare.14371925
title: Contaminant Filtering R Script

description: R script used to perform contaminant filtering of sequence data based on results from Shiek et al. (2018 ). Portions of code within were written by Katherine M. Fullerton (KMF) and utilized in work by Fullerton et al. (2021). Code comments indicate code written by KMF.<br>Sheik et al. 2018 doi:10.3389/fmicb.2018.00840<br>Fullerton et al. 2021 doi:10.1038/s41561-021-00725-0<br>
DOI: 10.6084/m9.figshare.14371925.v1
title: Contaminant Filtering R Script

description: R script used to perform contaminant filtering of sequence data based on results from Shiek et al. (2018 ). Portions of code within were written by Katherine M. Fullerton (KMF) and utilized in work by Fullerton et al. (2021). Code comments indicate code written by KMF.<br>Sheik et al. 2018 doi:10.3389/fmicb.2018.00840<br>Fullerton et al. 2021 doi:10.1038/s41561-021-00725-0<br>
DOI: 10.6084/m9.figshare.14371922
title: R Script to analyze and plot BNTI and RCbray data

description: R script used to analyze and visualize ecological modeling output (NTI, BNTI, and RCbray matrices and values), and create figures and SI figures within the manuscript.
DOI: 10.6084/m9.figshare.14371922.v1
title: R Script to analyze and plot BNTI and RCbray data

description: R script used to analyze and visualize ecological modeling output (NTI, BNTI, and RCbray matrices and values), and create figures and SI figures within the manuscript.
DOI: 10.6084/m9.figshare.14371919
title: Zipped raw Fasta file for Contaminant Filtering

description: Zipped raw fasta file used in initial input for "CROMO_Contaminant_Filtering_Script.R" file.
DOI: 10.6084/m9.figshare.14371919.v1
title: Zipped raw Fasta file for Contaminant Filtering

description: Zipped raw fasta file used in initial input for "CROMO_Contaminant_Filtering_Script.R" file.
DOI: 10.6084/m9.figshare.14371910
title: BNTI - Between well comparisons only

description: Manually curated pairwise comparisons of BNTI metric between each well and other wells only. Values were manually subset and reorganized. Uploaded in line 193 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371910.v1
title: BNTI - Between well comparisons only

description: Manually curated pairwise comparisons of BNTI metric between each well and other wells only. Values were manually subset and reorganized. Uploaded in line 193 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371907
title: Averaged Well data for Figure 1

description: Averaged well data to make average well geochemistry plots vs. depth. Uploaded in line 989 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371907.v2
title: Averaged Well data for Figure 1

description: Averaged well data to make average well geochemistry plots vs. depth. Uploaded in line 989 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.14371907.v1
title: Averaged Well data for Figure S1

description: Averaged well data to make average well geochemistry plots vs. depth. Uploaded in line 894 of "CROMO_Comm_Assemb_Analyses_Script.R" file.
DOI: 10.6084/m9.figshare.12620480
title: Chapter3_supplementary_tables

description: Supplementary data from Chapter 3, “Comparative genomics of <i>Bordetella pertussis </i>isolates from New Zealand, a country with uncommonly high incidence of whooping cough"<br>
DOI: 10.6084/m9.figshare.12620480.v1
title: Chapter3_supplementary_tables

description: Supplementary data from Chapter 3, “Comparative genomics of <i>Bordetella pertussis </i>isolates from New Zealand, a country with uncommonly high incidence of whooping cough"<br>
DOI: 10.6084/m9.figshare.14483040.v1
title: Myopia, Melatonin and Conjunctival Ultraviolet Autofluorescence: A Comparative Cross-sectional Study in Indian Myopes

description: <b>Purpose</b>: To explore the role of outdoor light exposure by estimating ocular sun exposure measured by Conjunctival Ultraviolet Autofluorescence (CUVAF) imaging and serum melatonin levels in myopes and non-myopes. <b>Materials & Methods</b>: Age and sex matched emmetropes and myopes (60 each) aged 10–25 years participated. Those with a history of ocular surgery or any ocular or systemic co-morbidity were excluded. Socio-demographic parameters, sun exposure questionnaires, indoor and outdoor activity profile, morning serum melatonin levels, sleep pattern, degree of myopia, ocular biometry and area of CUVAF on ultraviolet photography were noted and analyzed. <b>Results</b>: Mean age of myopes (18 ± 4.5 years) and emmetropes (18.5 ± 4 years) was similar (<i>P</i> = .523). Serum melatonin levels were significantly higher (<i>P</i> = .001) among myopes (89.45 pg/ml) as compared to emmetropes (52.83 pg/ml). Lifetime sun exposure was significantly lower in myopes than emmetropes (<i>P</i> = .0003). Area of CUVAF was inversely related to degree of myopia (<i>P</i> P P = .03). Age and gender had no association with serum melatonin levels. <b>Conclusion</b>: This study demonstrates an inverse relationship between serum melatonin levels and degree of CUVAF in myopes. A novel link between serum melatonin, axial length and outdoor sun exposure is highlighted in the current study.
DOI: 10.6084/m9.figshare.14406613.v1
title: Repeatability of Macular and Optic Nerve Head Measurements by Optical Coherence Tomography Angiography in Healthy Children

description: <b>Aims</b>: To evaluate the repeatability of the peripapillary and macular vascular parameters using optical coherence tomography angiography (OCT-A) in healthy children. <b>Materials and methods</b>: Cross-sectional study including 34 eyes of 34 healthy children. After a complete medical examination, two consecutive OCT-A exams were done using AngioPlex Cirrus 5000 (Carl Zeiss Meditec, Dublin, CA, USA) in the same session. The scan area used was 6 × 6 mm for the analysis of the superficial vascular plexus (SVP) in the macula, and 4.5 × 4.5 mm for the peripapillary plexus. To study the repeatability of the measurements, the intraclass correlation coefficient (ICC) and the coefficient of variation (CV) of each pair of exams were calculated. <b>Results</b>: The mean age of the children included was 10.77 ± 2.49 years (range 6 to 15 years). Good and excellent ICCs were obtained for all the parameters considered. Peripapillary vascular parameters showed greater reproducibility than macular ones (global peripapillary perfusion density (pPD): ICC = 0.834 CV = 0.89% vs. whole macular area PD (w-mPD): ICC = 0.697 CV = 3.49%; global peripapillary flux index (FI): ICC = 0.858 CV = 1.28%; whole macular area vascular density (VD): ICC = 0.699 CV = 3.30%). Amongst the macular parameters, the characteristics of the foveal avascular zone (FAZ) were the ones showing higher rates of repeatability (FAZ circularity: ICC = 0.858 CV = 8.83%). <b>Conclusion</b>: OCT-A is a non-invasive, time-efficient technology that may be useful in the evaluation of the retinal and peripapillary vascular network in healthy children. The repeatability of the measures will allow the follow-up and evaluation of any change occurring in the macular or optic nerve perfusion.
DOI: 10.5281/zenodo.5420001
title: Parkinson-HMR

description: The database includes the raw data of the article “Neuroprotective effects of lignan 7-hydroxymatairesinol (HMR/lignan) in a rodent model of Parkinson’s disease” (doi.org/10.1016/j.nut.2019.04.006). The aim of this study was to evaluate the effects of chronic treatment with lignan 7-hydroxymatairesinol (HMR/lignan) on Parkinson’s disease-associated neurodegenerative and neuroinflammatory processes, and motor deficits in the 6-hydroxydopamine (6-OHDA) model. The database contains the data obtained by the following evaluations: a) immunohistochemical analysis of the extent of nigrostriatal lesion, b) motor performance assessment by cylinder test (at baseline and after 28days), apomorphine-induced rotation test, c) immunohistochemical analysis of neuroinflammatory response - involving microglia and astrocytes - in the substantia nigra pars compacta, investigating both cell activation and polarization. chronic treatment with HMR/lignan was able to slow down the progression of degeneration of striatal dopaminergic terminals in a rat model of PD, with a consequent improvement in motor performance. Nevertheless, the anti-inflammatory effect of HMR/lignan observed in SNc was not sufficient to protect dopaminergic cells bodies. These results suggest intriguing properties of HMR/lignan at neuroprotective and symptomatic levels in the context of PD.
description: This research was funded by Linnea SA
DOI: 10.5281/zenodo.5420000
title: Parkinson-HMR

description: The database includes the raw data of the article “Neuroprotective effects of lignan 7-hydroxymatairesinol (HMR/lignan) in a rodent model of Parkinson’s disease” (doi.org/10.1016/j.nut.2019.04.006). The aim of this study was to evaluate the effects of chronic treatment with lignan 7-hydroxymatairesinol (HMR/lignan) on Parkinson’s disease-associated neurodegenerative and neuroinflammatory processes, and motor deficits in the 6-hydroxydopamine (6-OHDA) model. The database contains the data obtained by the following evaluations: a) immunohistochemical analysis of the extent of nigrostriatal lesion, b) motor performance assessment by cylinder test (at baseline and after 28days), apomorphine-induced rotation test, c) immunohistochemical analysis of neuroinflammatory response - involving microglia and astrocytes - in the substantia nigra pars compacta, investigating both cell activation and polarization. chronic treatment with HMR/lignan was able to slow down the progression of degeneration of striatal dopaminergic terminals in a rat model of PD, with a consequent improvement in motor performance. Nevertheless, the anti-inflammatory effect of HMR/lignan observed in SNc was not sufficient to protect dopaminergic cells bodies. These results suggest intriguing properties of HMR/lignan at neuroprotective and symptomatic levels in the context of PD.
description: This research was funded by Linnea SA
DOI: 10.18112/openneuro.ds003011.v1.2.3
title: Social Processes Initiative in Neurobiology of the Schizophrenia(s) Traveling Human Phantoms
DOI: 10.5281/zenodo.5495667
title: Cross-Register Projection for Headline Part of Speech Tagging

description: POSH: The POS-tagged HeadlIne corpus was created for the paper “Cross-Register Projection for Headline Part of Speech Tagging” published in EMNLP 2021. This dataset contains headlines with gold annotated POS tags. The <em>GSCh</em> evaluation set is here: GSCh/gsc-headline-gold.test.conllu The smaller evaluation set of GSC headlines sampled uniformly at random (described in section 2.3) is here: gold_unconstrained_headlines/unifrand_gsc.test.conllu The POS-tagged NYT headlines described in section 2.3 are not shared directly as this text was drawn from the New York Times Annotated Corpus (LDC2008T19), and subject to license constraints. However, if you have access to and have untarred LDC2008T19, you can recover this evaluation set with: TAG_PATH="./unifrand_onlynyt.tags.json" # mapping from NYT headline span to gold POS tag python build_gold_nyt_headlines.py --nyt_dir /PATH/TO/ANNOTATED/NYT/CORPUS/ --tag_path ${TAG_PATH} --num_proc 4 Increase the argument to --num_procs to process more shards from the NYT corpus in parallel and reduce build time. Under GSCproj we also share the <em>GSCproj</em> folds which we used to train and validate our models. These are not gold POS tags, and are shared purely for reproducibility sake.
DOI: 10.6084/m9.figshare.16587320
title: Table1.pdf

description: Error along 8 directions
DOI: 10.6084/m9.figshare.16587320.v1
title: Table1.pdf

description: Error along 8 directions
DOI: 10.6084/m9.figshare.16587314
title: Table3-4.pdf

description: a and b along 90 degree
DOI: 10.6084/m9.figshare.16587314.v1
title: Table3-4.pdf

description: a and b along 90 degree
DOI: 10.6084/m9.figshare.16587317
title: Table2.pdf

description: alpha and beta along 90 degrees
DOI: 10.6084/m9.figshare.16587317.v1
title: Table2.pdf

description: alpha and beta along 90 degrees
DOI: 10.25625/dffz9r/nldktw
title: Table S3 Kilianstollen_Hydrochemie_Hoppert.tab

description: Hydrochemical Analysis
DOI: 10.25625/dffz9r/ustr5w
title: Abundance graphs.tab

description: Class and Phylum levels
DOI: 10.25625/dffz9r
title: Composition and Niche-Specific Characteristics of Microbial Consortia Colonizing Marsberg Copper Mine in the Rhenish Massif

description: Hydrochemical Analysis
DOI: 10.5281/zenodo.5495684
title: Blood Pressure and Body Weight Have Different Effects on Pulse Wave Velocity and Cardiac Mass in Children.

description: <strong>Background: </strong>High blood pressure (BP) and excess weight can lead to early cardiovascular organ damage already in children. Carotid-femoral pulse wave velocity (cf-PWV) is the non-invasive gold standard method for assessing aortic stiffness, while carotid-radial PWV (cr-PWV) provides information on the distensibility of the upper limb arteries. The aim of this study was to evaluate the relationship of BP and BMI z-scores with arterial stiffness and left ventricular mass index (LVMI) in a pediatric population. <strong>Methods: </strong>In 343 children (57.7% males; age ± SD 11.7 ± 2.9 years), systolic (SBP) and diastolic (DBP) BP, BMI, cf-PWV, cr-PWV and LVMI were measured. A multiple linear regression model was used to assess the impact of BMI and SBP (or DBP) z-scores on cf-PWV, cr-PWV and LVMI. <strong>Results: </strong>About 21% of children were normal weight, 34% were overweight and 45% obese. Adjusted for possible confounders, SBP and DBP z-scores were significantly associated with cf-PWV (<em>p</em> &lt; 0.001), while only DBP z-scores were related to cr-PWV (<em>p</em> &lt; 0.01). BMI was neither associated with cf-PWV nor with cr-PWV values but was a strong predictor of LVMI (&lt;0.001), whereas cardiac mass and BP z-scores were not related. <strong>Conclusions: </strong>Our study suggests that, in children, elevated BP values and excess weight may have different effects on the heart and the vessels in causing early cardiovascular alterations.
DOI: 10.5281/zenodo.5495683
title: Blood Pressure and Body Weight Have Different Effects on Pulse Wave Velocity and Cardiac Mass in Children.

description: <strong>Background: </strong>High blood pressure (BP) and excess weight can lead to early cardiovascular organ damage already in children. Carotid-femoral pulse wave velocity (cf-PWV) is the non-invasive gold standard method for assessing aortic stiffness, while carotid-radial PWV (cr-PWV) provides information on the distensibility of the upper limb arteries. The aim of this study was to evaluate the relationship of BP and BMI z-scores with arterial stiffness and left ventricular mass index (LVMI) in a pediatric population. <strong>Methods: </strong>In 343 children (57.7% males; age ± SD 11.7 ± 2.9 years), systolic (SBP) and diastolic (DBP) BP, BMI, cf-PWV, cr-PWV and LVMI were measured. A multiple linear regression model was used to assess the impact of BMI and SBP (or DBP) z-scores on cf-PWV, cr-PWV and LVMI. <strong>Results: </strong>About 21% of children were normal weight, 34% were overweight and 45% obese. Adjusted for possible confounders, SBP and DBP z-scores were significantly associated with cf-PWV (<em>p</em> &lt; 0.001), while only DBP z-scores were related to cr-PWV (<em>p</em> &lt; 0.01). BMI was neither associated with cf-PWV nor with cr-PWV values but was a strong predictor of LVMI (&lt;0.001), whereas cardiac mass and BP z-scores were not related. <strong>Conclusions: </strong>Our study suggests that, in children, elevated BP values and excess weight may have different effects on the heart and the vessels in causing early cardiovascular alterations.
DOI: 10.5287/bodleian:koykbrbvb
title: Orielton field course student natural history knowledge data 2013 & 2014
DOI: 10.5281/zenodo.5495694
title: Dataset related to article" Hypomyelinating leukodystrophies in adults: Clinical and genetic features."

description: Dataset contains genetic data (including NGS, Sanger and Multiplex ligation-dependent probe amplification analysis) of a cohort of patients with hypomyelinating leukodystrophies
description: Study supported by Italian ministry of Health (Grant: RF-2018-12367768 and Progetto Rete IDEA "BIaNCA" to F.T. GR-2016-02363337 to S.M. RF-2016-02361285 to C.G.) anf Fondazione Regionale Ricerca Biomedica (grant Care4NeuroRare CP_20/2018 to F.T.)
DOI: 10.5281/zenodo.5495693
title: Dataset related to article" Hypomyelinating leukodystrophies in adults: Clinical and genetic features."

description: Dataset contains genetic data (including NGS, Sanger and Multiplex ligation-dependent probe amplification analysis) of a cohort of patients with hypomyelinating leukodystrophies
description: Study supported by Italian ministry of Health (Grant: RF-2018-12367768 and Progetto Rete IDEA "BIaNCA" to F.T. GR-2016-02363337 to S.M. RF-2016-02361285 to C.G.) anf Fondazione Regionale Ricerca Biomedica (grant Care4NeuroRare CP_20/2018 to F.T.)