cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7751780.v4
title: Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (Oreochromis niloticus)

description: Dataset to GWAS, genomic prediction and imputation analysis for the paper "<b>Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (<i>Oreochromis niloticus</i>)". </b>Furthermore, supplemental tables and figures are avaliable <b>(</b><b>https://doi.org/10.1534/g3.119.400116).</b><b><br></b><b><br></b><br><b></b>
DOI: 10.7284/113627
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1314 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751780.v3
title: Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (Oreochromis niloticus)

description: Dataset to GWAS, genomic prediction and imputation analysis for the paper "<b>Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (<i>Oreochromis niloticus</i>)". </b>Furthermore, supplemental figures are avaliable <b>(</b><b>https://doi.org/10.1534/g3.119.400116).</b><b><br></b><b><br></b><b>Figure S1.</b> Correlations between observed and imputed genotypes for each SNP for imputation from low-density (LD3K) to high-density (HD) panel in Nile tilapia using parents (n = 108) and 20% of offspring (n = 226) genotyped with the HD panel as the reference set and 80% of offspring (n = 904) as the validation set. The black line indicates the mean imputation accuracy. <b>Figure S2.</b> Correlations between observed and imputed genotypes for each SNP for imputation from low-density (LD1K) to high-density (HD) in Nile tilapia using parents (n = 108) and 20% of the offspring (n = 226) genotyped with the HD panel as the reference set and 80% of the offspring (n = 904) as the validation set. The black line indicates the mean imputation accuracy. <b>Figure S3.</b> Correlations between observed and imputed genotypes for each SNP for imputation from low-density (LD0.5K) to high-density (HD) in Nile tilapia using parents (n = 108) and 20% of offspring (n = 226) genotyped with the HD panel as the reference set and 80% of the offspring (n = 904) as the validation set. The black line indicates the mean imputation accuracy. <b>Figure S4.</b> Genotyping cost reduction (%) compared to scenario A, where all animals are genotyped using a HD panel.<b></b>
DOI: 10.7284/113625
title: Winch data collected during research cruise AE1314 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113633
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1315 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113634
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1315 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113631
title: Fluorometer data collected during research cruise AE1315 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113632
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1315 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113630
title: Winch data collected during research cruise AE1315 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113638
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1316 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113639
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1316 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113636
title: Fluorometer data collected during research cruise AE1316 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113637
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1316 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113635
title: Winch data collected during research cruise AE1316 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113643
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1317 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113644
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1317 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113641
title: Fluorometer data collected during research cruise AE1317 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113642
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1317 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113640
title: Winch data collected during research cruise AE1317 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113650
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1319 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751432
title: FSE 2019: Bias in the Wild

description: Coding Scheme<br>
DOI: 10.7284/113651
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1319 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751432.v1
title: FSE 2019: Bias in the Wild

description: Coding Scheme<br>
DOI: 10.7284/113648
title: Fluorometer data collected during research cruise AE1319 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113649
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1319 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113647
title: Singlebeam Echosounder data collected during research cruise AE1319 using a Knudsen 3260 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751294
title: phil-trans-data from On the limits of observing motion in time-resolved X-ray scattering

description: raw data for the processed Legendre decomposition of the x-ray scattering images
DOI: 10.6084/m9.figshare.7751297
title: Supplementary Material for: Association between Trimetazidine and Parkinsonism: A Population-Based Study

description: <b><i>Background:</i></b> The prevalence of drug-induced parkinsonism (DIP) has been reported with the use of trimetazidine (TMZ), an antianginal medication available in Asian and European countries. Very few studies have evaluated the association between DIP and TMZ use, and studies using population-based data from national databases are lacking. <b><i>Objectives:</i></b> To investigate the association between DIP and use of TMZ in patients with angina using data from a national healthcare claims database and to determine the predictive factors of DIP in TMZ use. <b><i>Methods:</i></b> A cross-sectional study was conducted on patients aged 40 years or more diagnosed with angina, using the Korean National Healthcare claims 2014 database. The association between TMZ use and DIP was evaluated using multivariate logistic regression analysis, adjusting for confounders, including age; sex; insurance type; comorbidities; and concurrent medications known to be commonly associated with DIP, such as typical and atypical antipsychotics. <b><i>Results:</i></b> Of the patients included in the study, 19% were prescribed TMZ. In addition, 2.5% of TMZ users had preexisting extrapyramidal and movement disorders. TMZ use was found to be a significant predictor of a new diagnosis of parkinsonism (adjusted OR [aOR] 1.39; 95% CI 1.06–1.81; <i>p</i> = 0.016). Age ≥65 years (aOR 2.07; 95% CI 1.13– 3.74; <i>p</i> = 0.017) and stroke as comorbid disease (aOR 3.23; 95% CI 1.87–5.61; <i>p</i> &lt; 0.001) were also significantly associated with a new diagnosis of parkinsonism in TMZ users. <b><i>Conclusions:</i></b> Treatment with TMZ was a statistically significant predictor of a new diagnosis of parkinsonism. Efforts should focus on close monitoring of, and education on, TMZ use in relation to DIP in all patients who are prescribed TMZ, including those with preexisting extrapyramidal and movement disorders.
DOI: 10.6084/m9.figshare.7751294.v1
title: phil-trans-data from On the limits of observing motion in time-resolved X-ray scattering

description: raw data for the processed Legendre decomposition of the x-ray scattering images
DOI: 10.6084/m9.figshare.7751297.v1
title: Supplementary Material for: Association between Trimetazidine and Parkinsonism: A Population-Based Study

description: <b><i>Background:</i></b> The prevalence of drug-induced parkinsonism (DIP) has been reported with the use of trimetazidine (TMZ), an antianginal medication available in Asian and European countries. Very few studies have evaluated the association between DIP and TMZ use, and studies using population-based data from national databases are lacking. <b><i>Objectives:</i></b> To investigate the association between DIP and use of TMZ in patients with angina using data from a national healthcare claims database and to determine the predictive factors of DIP in TMZ use. <b><i>Methods:</i></b> A cross-sectional study was conducted on patients aged 40 years or more diagnosed with angina, using the Korean National Healthcare claims 2014 database. The association between TMZ use and DIP was evaluated using multivariate logistic regression analysis, adjusting for confounders, including age; sex; insurance type; comorbidities; and concurrent medications known to be commonly associated with DIP, such as typical and atypical antipsychotics. <b><i>Results:</i></b> Of the patients included in the study, 19% were prescribed TMZ. In addition, 2.5% of TMZ users had preexisting extrapyramidal and movement disorders. TMZ use was found to be a significant predictor of a new diagnosis of parkinsonism (adjusted OR [aOR] 1.39; 95% CI 1.06–1.81; <i>p</i> = 0.016). Age ≥65 years (aOR 2.07; 95% CI 1.13– 3.74; <i>p</i> = 0.017) and stroke as comorbid disease (aOR 3.23; 95% CI 1.87–5.61; <i>p</i> &lt; 0.001) were also significantly associated with a new diagnosis of parkinsonism in TMZ users. <b><i>Conclusions:</i></b> Treatment with TMZ was a statistically significant predictor of a new diagnosis of parkinsonism. Efforts should focus on close monitoring of, and education on, TMZ use in relation to DIP in all patients who are prescribed TMZ, including those with preexisting extrapyramidal and movement disorders.
DOI: 10.6084/m9.figshare.7751309
title: New approach to investigate Common Variable Immunodeficiency Disorder using Spectrochemical analysis of blood

description: ATR-FTIR spectroscopy was used for the analysis of blood serum and blood plasma to investigate samples from patients with common variable immune deficiency. The uploaded files contain raw data (classed) and pre-processed data from the recruited cohort of patients and healthy controls. For each study subject, blood spots of both serum and plasma were produced in duplicate; 10 spectra were collected per 50 µL dried blood spot (total of 20 spectra per biofluid). The spectra files were pre-processed using the IRootLab toolbox (trevisanj.github.io/irootlab/), within MATLAB R2017a software (MathWorks). Initially, the 20 replica spectra per sample were averaged in order to work with a sample-based classification. Two pre-processing techniques were independently tested: 1) rubber-band baseline correction followed by vector normalisation and 2) by Savitzky-Golay (SG) smoothing (second-order polynomial and nine filter coefficients). Once the spectra had been pre-processed, two regions of interest were extracted from the spectra; the Fingerprint region, which covers the area between wavenumbers 1800-900 cm<sup>-1</sup>; and the High region, which covers wavenumbers 3700-2800 cm<sup>-1</sup>.<br>
DOI: 10.7284/113646
title: Winch data collected during research cruise AE1319 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751255
title: Auxosporulation in <i>Chaetoceros acadianus</i> sp. nov. (Bacillariophyceae), a new member of the Section Compressa

description: We document the fine structure of auxospores in a <i>Chaetoceros</i> species isolated from the Acadian coast of New Brunswick, Canada. Auxospore development in this species occurs in a terminal rather than lateral position, a characteristic never before observed in this genus. Our observations suggest that auxosporulation was uniparental, probably an extreme form of autogamy with sister nuclei fusing following meiosis II. Mature auxospores were adze-shaped to sub-globular and contained both scales and transverse perizonia in their walls. The transverse perizonial band structure was similar to longitudinal perizonial bands found in other species of <i>Chaetoceros</i> and differed from the pinnate bands of pennate transverse perizonia, which consisted of a central rib and bilateral fimbria. Instead, the band structure in <i>C. acadianus</i> was more similar to unilateral fimbriate bands in cymatosiroids. We also propose that our diatom represents a species new to science and is a member of the <i>Chaetoceros</i> Section Compressa. We provide its morphological, molecular and reproductive characterization.
DOI: 10.6084/m9.figshare.7751255.v1
title: Auxosporulation in <i>Chaetoceros acadianus</i> sp. nov. (Bacillariophyceae), a new member of the Section Compressa

description: We document the fine structure of auxospores in a <i>Chaetoceros</i> species isolated from the Acadian coast of New Brunswick, Canada. Auxospore development in this species occurs in a terminal rather than lateral position, a characteristic never before observed in this genus. Our observations suggest that auxosporulation was uniparental, probably an extreme form of autogamy with sister nuclei fusing following meiosis II. Mature auxospores were adze-shaped to sub-globular and contained both scales and transverse perizonia in their walls. The transverse perizonial band structure was similar to longitudinal perizonial bands found in other species of <i>Chaetoceros</i> and differed from the pinnate bands of pennate transverse perizonia, which consisted of a central rib and bilateral fimbria. Instead, the band structure in <i>C. acadianus</i> was more similar to unilateral fimbriate bands in cymatosiroids. We also propose that our diatom represents a species new to science and is a member of the <i>Chaetoceros</i> Section Compressa. We provide its morphological, molecular and reproductive characterization.
DOI: 10.7284/113655
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1320 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751237
title: Supplementary Material for: Risk Factors for Low Bone Density in Inflammatory Bowel Disease: Use of Glucocorticoids, Low Body Mass Index, and Smoking

description: <b><i>Background:</i></b> Inflammatory bowel disease (IBD) patients are reported to have lower bone density compared to healthy controls. There is limited consensus regarding factors affecting bone density among these patients. Our aim, therefore, was to determine clinical and genetic variables that contribute to lower bone mineral density (BMD) in IBD patients. <b><i>Methods:</i></b> A cross-sectional study of IBD patients treated in a tertiary referral center was performed. Epidemiological and clinical data were collected, and genetic testing for the common mutations in Nucleotide-binding Oligomerization Domain-containing protein (NOD)2 was performed. We examined correlations between the different variables and BMD in the total hip, femoral neck, and lumbar spine. <b><i>Results:</i></b> Eighty-nine patients (49% males, 67 Crohn’s disease [CD]) participated in the study. 42Forty-two (63%) of the CD and 13 (59%) of the ulcerative colitis patients met the criteria for osteoporosis/osteopenia. Factors associated with lower Z scores were low body mass index (BMI; <i>r</i> = –0.307, <i>p</i> = 0.005), use of glucocorticoids (likelihood ratio [LR] 5.1, <i>p</i> = 0.028), and a trend for male gender (LR = 3.4, <i>p</i> = 0.079). Among CD patients, low bone density showed borderline significance for association with gastrointestinal surgery (LR = 4.1, <i>p</i> = 0.07) and smoking (LR = 3.58, <i>p</i> = 0.06). Low levels of 25OHD were not associated with low BMD, nor were mutations in NOD2. No increased rate of fractures was seen among patients with osteopenia or osteoporosis. <b><i>Conclusion:</i></b> In addition to the generally accepted risk factors for osteoporosis (glucocorticoids, low BMI, smoking), male IBD patients had a trend toward lower BMD. Carrying a mutaticon in NOD2 did not confer a risk for bone loss.
DOI: 10.7284/113656
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1320 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113653
title: Fluorometer data collected during research cruise AE1320 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113654
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1320 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751189
title: Evaluating the structure of commensalistic epiphyte–phorophyte networks. A comparative perspective of biotic interactions

description: Dataset To compare epiphyte–phorophyte networks with mutualistic networks we compiled a dataset of 122 interaction networks (See Table S1). We restricted data to tropical and subtropical areas to minimize potential biases in topological metrics due to heterogeneous environmental conditions. Twelve published datasets that measured quantitatively interactions between vascular epiphyte and host species in tropical and subtropical areas were included in the study. Epiphyte species vary across studies, but they are distributed mainly among the families Orchidaceae and Bromeliaceae (Table S1). The dataset also included 86 pollination, 13 seed dispersal and 11 ant-mymercophyte (plant-ant) networks from published studies considering only studies carried out in tropical and subtropical areas, available in Web of life (http://www.web-of-life.es) and additional works (Table S1). The main characteristics of the analysed networks are described in the electronic supplementary material, Table S1; detailed description of datasets and field sampling procedures can be found in the attached references. Data analysis For each of the 122 networks, data were completely reanalysed to compute the following network metrics: <i>i</i>) nestedness, <i>ii</i>) complementary specialisation and <i>iii</i>) modularity. Nestedness quantifies the degree to which species with few interactions are connected to highly connected species. Nestedness was evaluated with the NODF index. As NODF metric is dependent on network size and sampling intensity. To characterize, network specialization at the community level, we used the index of complementary specialisation <i>H</i>’2, which quantifies the degree of niche divergence of elements within an entire bipartite network, that is, whether species in a network tend to partition or share their interaction partners. Modularity was estimated using the <i>QuaBiMo</i> algorithm (<i>Q</i>), which is based on a hierarchical random graph approach, adapted for quantitative bipartite networks. As the algorithm is a stochastic process, results may vary among computations. For each network, we therefore ran the <i>QuaBiMo</i> algorithm 10 times and retained the optimal modular configuration, <i>i.e.</i> the iteration with highest <i>Q</i> value. To characterize specialization at the species level, we quantified the roles of species within networks with two species‐level metrics: complementary specialization (<i>d</i>’) and between‐module connector values (<i>c</i>‐values). <br>
DOI: 10.7284/113652
title: Winch data collected during research cruise AE1320 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113660
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1321 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751114
title: PALINDROMIC WORD PUZZLES

description: We show that it is NP-complete to determine if a given set of strings can be arranged to form a palindrome.
DOI: 10.7284/113661
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1321 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7751114.v2
title: PALINDROMIC WORD PUZZLES

description: We show that it is NP-complete to determine if a given set of strings can be arranged to form a palindrome.
DOI: 10.7284/113658
title: Fluorometer data collected during research cruise AE1321 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition