cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4598062.v1
title: Table S3. Early Andean tectonomagmatic stages in north Patagonia: insights from field and geochemical data

description: Table S3. Sr, Nd and Pb isotopic composition of Jurassic and Cretaceous volcanic rocks.
DOI: 10.6084/m9.figshare.4598029
title: Chlorocharis

description: Niche modeling results and data points used for Chlorocharis manuscript.
DOI: 10.6084/m9.figshare.4598047.v2
title: EFoldMine analysis data

description: The EFoldMine_analysisData contains three directories:<br><br>MS_analysis/ contains information about MS HDX data (as Python dictionary in infoDict_msProteins.py) in relation to EFoldMine predictions (.pred file in dynaMineResults/)<br><br>psicov/ contains information about residues with an evolutionary co-variation signal from the PSICOV dataset (as Python pickle in degree.pickle) in relation to EFoldMine predictions (.pred file in dynaMineResults/)<br><br>pisces/ contains protein structure-derived parameters from a PISCES subset (as Python dictionary in infoDict_pisces.py) in relation to EFoldMine predictions (.pred file in dynaMineResults/)<br><br>The prediction.tgz files contains the full features and cross-validation performed to develop EFoldMine.<br>
DOI: 10.6084/m9.figshare.4598029.v1
title: Chlorocharis

description: Niche modeling results and data points used for Chlorocharis manuscript.
DOI: 10.6084/m9.figshare.4598047.v1
title: EFoldMine analysis data

description: This is a dataset with three directories:<br><br>MS_analysis/ contains information about MS HDX data (as Python dictionary in infoDict_msProteins.py) in relation to EFoldMine predictions (.pred file in dynaMineResults/)<br><br>psicov/ contains information about residues with an evolutionary co-variation signal from the PSICOV dataset (as Python pickle in degree.pickle) in relation to EFoldMine predictions (.pred file in dynaMineResults/)<br><br>pisces/ contains protein structure-derived parameters from a PISCES subset (as Python dictionary in infoDict_pisces.py) in relation to EFoldMine predictions (.pred file in dynaMineResults/)
DOI: 10.6084/m9.figshare.4597993
title: Supplementary Material for: Perioperative Hemodynamic Instability and Fluid Overload are Associated with Increasing Acute Kidney Injury Severity and Worse Outcome after Cardiac Surgery

description: <b><i>Purpose:</i></b> The study aimed to investigate patients' characteristics, fluid and hemodynamic management, and outcomes according to the severity of cardiac surgery-associated acute kidney injury (CSA-AKI). <b><i>Methods:</i></b> In a single-center, prospective cohort study, we enrolled 282 adult cardiac surgical patients. In a secondary analysis, we assessed preoperative patients' characteristics, physiological variables, and medication for intra- and postoperative fluid and hemodynamic management and outcomes according to CSA-AKI stages by the Renal risk, Injury, Failure, Loss, End-stage renal disease (RIFLE) classification. Variables of fluid and hemodynamic management were further assessed with regard to the need for postoperative renal replacement therapy (RRT) and in-hospital mortality by the area under the curve for the receiver operating characteristic (AUC-ROC) and multivariate regression analysis. <b><i>Results:</i></b> Patients with worsening RIFLE stage, were significantly older, had lower estimated glomerular filtration rate and higher body mass index, more peripheral vascular and chronic obstructive pulmonary disease, atrial fibrillation, and prolonged duration of cardiopulmonary bypass (all <i>p</i> &lt; 0.01). Patients with more severe AKI stage stayed longer in the intensive care and hospital, had higher in-hospital mortality, and requirement for RRT (all <i>p</i> &lt; 0.001). Also, with worsening RIFLE stage, patients had lower intraoperative mean arterial pressure (MAP); <i>p</i> = 0.047, despite higher doses of norepinephrine (<i>p</i> &lt; 0.001). The intraoperative MAP showed the best discriminatory ability (AUC-ROC: &gt;0.8) for and was independently associated with RRT and in-hospital mortality. Moreover, with increasing AKI severity, patients received significantly more fluid infusion, and required higher dose of furosemide; nonetheless, they had increased postoperative fluid balance. <b><i>Conclusions:</i></b> In this cohort, reduced MAP and increased fluid balance were independently associated with increased mortality and need for RRT after cardiac surgery.
DOI: 10.6084/m9.figshare.4597918
title: Even Good Bots Fight: The Case of Wikipedia

description: Each file contains the history of all the articles in the WP. Articles are separated by their names within the file. Each line of the file below the name of an article, contains a delimiter "^^^" followed by the timestamp of each edit, a binary flag of 0/1 corresponding to a normal/revert edit, an accenting integer code, starting from 1, assigned to each new revision, whose text is not similar to any of the previous ones, otherwise the same code as the previous version with the similar text, and finally the editor of the version.
DOI: 10.6084/m9.figshare.4597903
title: Suppplementary data 3

description: Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases, and AIFs. Separate session files are available for calculations based on maximum likelihood estimation (MLE), neighbor-joining (NJ), and minimal evolution (ME).
DOI: 10.6084/m9.figshare.4597912
title: Light-Induced Retinopathy: Young Age Protects more than Ocular Pigmentation

description: <i>Purpose</i>: The purpose of this study was to compare the efficacy that ocular melanin confers in protecting the retina of juvenile and adult rats exposed to a bright luminous environment. <i>Methods</i>: Juvenile (JLE) and adult (ALE) Long–Evans pigmented rats were thus exposed to a bright cyclic light (10,000lux; white light) from postnatal day 14–28 or for 6 consecutive days, respectively. Flash electroretinograms (ERG) and retinal histology were performed at different predetermined ages, post-light exposure. <i>Results</i>: Despite a significant reduction in ERG responses immediately following light exposure, with time, retinal function fully recovered in JLE compared to a 54% recovery for the ALE. In ALE, we noted a region of the supero-temporal quadrant that was highly vulnerable to light damage. This region was also devoid of melanin granules prior to the light exposure. This melanin-free zone increased in size in the days that followed the end of exposure, a process that was accompanied by the gradual degeneration of the thus uncovered photoreceptors. In contrast, melanin and photoreceptor losses were minimal in JLE. <i>Conclusion</i>: Our results suggest that the light-induced photoreceptor degeneration in ALE would be secondary to the initial destruction of the RPE and ensuing loss of melanin protection. In contrast, the melanin granules of JLE appear to be significantly more resistant to light damage, a characteristic that would explain the higher resistance of JLE photoreceptors to light damage. Our results would thus suggest that the efficacy of ocular melanin protection against light damage declines with age.
DOI: 10.6084/m9.figshare.4597918.v1
title: Even Good Bots Fight: The Case of Wikipedia

description: Each file contains the history of all the articles in the WP. Articles are separated by their names within the file. Each line of the file below the name of an article, contains a delimiter "^^^" followed by the timestamp of each edit, a binary flag of 0/1 corresponding to a normal/revert edit, an accenting integer code, starting from 1, assigned to each new revision, whose text is not similar to any of the previous ones, otherwise the same code as the previous version with the similar text, and finally the editor of the version.
DOI: 10.6084/m9.figshare.4597912.v1
title: Light-Induced Retinopathy: Young Age Protects more than Ocular Pigmentation

description: <i>Purpose</i>: The purpose of this study was to compare the efficacy that ocular melanin confers in protecting the retina of juvenile and adult rats exposed to a bright luminous environment. <i>Methods</i>: Juvenile (JLE) and adult (ALE) Long–Evans pigmented rats were thus exposed to a bright cyclic light (10,000lux; white light) from postnatal day 14–28 or for 6 consecutive days, respectively. Flash electroretinograms (ERG) and retinal histology were performed at different predetermined ages, post-light exposure. <i>Results</i>: Despite a significant reduction in ERG responses immediately following light exposure, with time, retinal function fully recovered in JLE compared to a 54% recovery for the ALE. In ALE, we noted a region of the supero-temporal quadrant that was highly vulnerable to light damage. This region was also devoid of melanin granules prior to the light exposure. This melanin-free zone increased in size in the days that followed the end of exposure, a process that was accompanied by the gradual degeneration of the thus uncovered photoreceptors. In contrast, melanin and photoreceptor losses were minimal in JLE. <i>Conclusion</i>: Our results suggest that the light-induced photoreceptor degeneration in ALE would be secondary to the initial destruction of the RPE and ensuing loss of melanin protection. In contrast, the melanin granules of JLE appear to be significantly more resistant to light damage, a characteristic that would explain the higher resistance of JLE photoreceptors to light damage. Our results would thus suggest that the efficacy of ocular melanin protection against light damage declines with age.
DOI: 10.6084/m9.figshare.4597900
title: Supplementary data 2

description: Additional BLASTP results and taxonomy reports to confirm the key results in the case of the following three protein families: AIF, caspase/metacaspase, and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with the use of two strategies: selection of only a few eukaryotic proteomes (for the species from Table 2 in Materials and Methods) as a search database (see file eukaryotic_strategy.pdf) and extension of the selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details on the specific file indicated.
DOI: 10.6084/m9.figshare.4597903.v1
title: Suppplementary data 3

description: Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases, and AIFs. Separate session files are available for calculations based on maximum likelihood estimation (MLE), neighbor-joining (NJ), and minimal evolution (ME).
DOI: 10.6084/m9.figshare.4597900.v1
title: Supplementary data 2

description: Additional BLASTP results and taxonomy reports to confirm the key results in the case of the following three protein families: AIF, caspase/metacaspase, and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with the use of two strategies: selection of only a few eukaryotic proteomes (for the species from Table 2 in Materials and Methods) as a search database (see file eukaryotic_strategy.pdf) and extension of the selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details on the specific file indicated.
DOI: 10.6084/m9.figshare.4597894
title: Supplementary data 1

description: Final alignments (files with .aln and .fasta extensions) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. In the case of three protein families, AIF and caspase/metacaspase, OMI/HTRA proteases three subfolders were created, and these contained the key subtrees (files in nexml format generated with Dendroscope).
DOI: 10.6084/m9.figshare.4597888
title: An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples

description: Supplemental material and sequences obtained from the paper "An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples". <br>- Files "peerj-13885-Supplementary_table_1 and peerj-13885-Supplementary_table_2" are the supplemental material, and include the species used for cross amplification and extra sensitivity assays for the family specific primers designed.<br>- In the file "Sequences_16S_tissue" are the sequences obtained with universal primers from different fishes species used in the cross-amplification tests. The Genbank accession numbers are indicated in each sequence. <br>- In the file "Sequences_specific_primer_tissue" are the sequences obtained with the family specific primer for the five salmonids described in the paper. The Genbank accession numbers are indicated in each sequence.<br>- In the file "Sequences_specific_primer_eDNA" are the sequences obtained with the family specific primer for the environmental DNA samples of the positive controls: Nora River and El Arenero. The Genbank accession numbers are indicated in each sequence.<br><br>
DOI: 10.6084/m9.figshare.4597894.v1
title: Supplementary data 1

description: Final alignments (files with .aln and .fasta extensions) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. In the case of three protein families, AIF and caspase/metacaspase, OMI/HTRA proteases three subfolders were created, and these contained the key subtrees (files in nexml format generated with Dendroscope).
DOI: 10.6084/m9.figshare.4597879
title: Ethnobotany at a local scale: diversity of knowledge of medicinal plants and assessment of plant cultural importance in the Polokwane local municipality, South Africa

description: Unravelling the pattern of traditional plant usages in a society is necessary to inform interventions for biodiversity conservation. In the present study, we documented traditional knowledge of plant usages and analysed the pattern of culturally important plants along a phylogeny of South Africa’s medicinal plants. Data were collected through interviews, field visits and group discussions, and cultural importance was assessed using two metrics: use value (UV<sub><i>s</i></sub>) and quality use value of species (QUV<sub><i>s</i></sub>). K statistic was used to assess how UV<sub><i>s</i></sub> and QUV<sub><i>s</i></sub> values are distributed on a phylogeny. Overall, 50 medicinal plant species in 35 botanical families were reported. Fabaceae and Celastraceae contain more medicinal species than any other family, perhaps because of a wider distribution in the study area. Although there was no evidence that knowledge of medicinal uses varies significantly according to informant status, sex, ethnic group and age category, or residence time of the informant in the study area, traditional healers show a wider range of medicinal knowledge than any other informants. Culturally important plants are not significantly clustered on the phylogeny, suggesting <i>a priori</i> a limited value of phylogeny in identifying culturally valuable plants. However, this potential limitation could be driven by the local focus of the present study. We call for further investigations at a broader scale to establish potential phylogenetic signals in plant cultural importance.
DOI: 10.6084/m9.figshare.4597888.v1
title: An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples

description: Supplemental material and sequences obtained from the paper "An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples". <br>- Files "peerj-13885-Supplementary_table_1 and peerj-13885-Supplementary_table_2" are the supplemental material, and include the species used for cross amplification and extra sensitivity assays for the family specific primers designed.<br>- In the file "Sequences_16S_tissue" are the sequences obtained with universal primers from different fishes species used in the cross-amplification tests. The Genbank accession numbers are indicated in each sequence. <br>- In the file "Sequences_specific_primer_tissue" are the sequences obtained with the family specific primer for the five salmonids described in the paper. The Genbank accession numbers are indicated in each sequence.<br>- In the file "Sequences_specific_primer_eDNA" are the sequences obtained with the family specific primer for the environmental DNA samples of the positive controls: Nora River and El Arenero. The Genbank accession numbers are indicated in each sequence.<br><br>
DOI: 10.6084/m9.figshare.4597879.v1
title: Ethnobotany at a local scale: diversity of knowledge of medicinal plants and assessment of plant cultural importance in the Polokwane local municipality, South Africa

description: Unravelling the pattern of traditional plant usages in a society is necessary to inform interventions for biodiversity conservation. In the present study, we documented traditional knowledge of plant usages and analysed the pattern of culturally important plants along a phylogeny of South Africa’s medicinal plants. Data were collected through interviews, field visits and group discussions, and cultural importance was assessed using two metrics: use value (UV<sub><i>s</i></sub>) and quality use value of species (QUV<sub><i>s</i></sub>). K statistic was used to assess how UV<sub><i>s</i></sub> and QUV<sub><i>s</i></sub> values are distributed on a phylogeny. Overall, 50 medicinal plant species in 35 botanical families were reported. Fabaceae and Celastraceae contain more medicinal species than any other family, perhaps because of a wider distribution in the study area. Although there was no evidence that knowledge of medicinal uses varies significantly according to informant status, sex, ethnic group and age category, or residence time of the informant in the study area, traditional healers show a wider range of medicinal knowledge than any other informants. Culturally important plants are not significantly clustered on the phylogeny, suggesting <i>a priori</i> a limited value of phylogeny in identifying culturally valuable plants. However, this potential limitation could be driven by the local focus of the present study. We call for further investigations at a broader scale to establish potential phylogenetic signals in plant cultural importance.
DOI: 10.6084/m9.figshare.4597837
title: Soy peptide ingestion augments the synthesis and metabolism of noradrenaline in the mouse brain

description: To examine whether edible peptide intake affects neurotransmitter metabolism in the brain, we evaluated the effect of peptides derived from soy proteins or fish collagen on free amino acids and monoamines in the mouse brain. Ingestion of soy peptides led to markedly higher levels of tyrosine, a catecholamine precursor, in the serum, and cerebral cortex compared to those following ingestion of vehicle alone or collagen peptides. Soy peptide ingestion also effectively increased 3-methoxy-4-hydroxyphenylethyleneglycol and normetanephrine, the principal metabolites of noradrenaline, in the cerebral cortex, hippocampus, and brainstem, whereas collagen peptides did not exert such effects. Further, soy peptide ingestion led to a significant increase in noradrenaline itself in the brainstem, where noradrenergic neurons are present. Noradrenergic turnover was also markedly stimulated in these regions after soy peptide ingestion. These <i>in vivo</i> observations suggest that soy peptide ingestion can maintain and promote the synthesis and metabolism of noradrenaline in the brain. Soy peptide ingestion promotes the synthesis and metabolism of noradrenaline in the brain via increased Tyr availability.
DOI: 10.6084/m9.figshare.4597825
title: Counting on number: effects of number information on grammatical processing of mass and count nouns

description: Previous research has found an influence of semantic number (SINGLE, MULTIPLE) on grammatical processing of mass nouns in people with aphasia. This is the first study to investigate these effects in language-unimpaired individuals. In two experiments, participants had to decide which were the appropriate determiners (e.g. Experiment 1: a<sub>singularcount</sub> – some<sub>mass/plural count</sub>) for the name of mass and count noun pictures that were depicted either as single (one bulb of garlic<sub>mass</sub>, one cat<sub>count</sub>) or as multiple objects (three bulbs of garlic<sub>mass</sub>, three cats<sub>count</sub>). Semantic number congruency between depictions and determiners was manipulated for mass nouns. A semantic number congruency effect was found in both experiments with faster and more accurate determiner decisions in the number congruent (e.g. Experiment 1: MULTIPLE) compared to the number incongruent condition (e.g. Experiment 1: SINGLE). These results provide further evidence for an influence of semantic number information on lexical-syntactic processing of mass nouns.
DOI: 10.6084/m9.figshare.4597834
title: Sulforaphene attenuates multinucleation of pre-osteoclasts by suppressing expression of cell–cell fusion-associated genes <i>DC</i>-<i>STAMP</i>, <i>OC</i>-<i>STAMP,</i> and <i>Atp6v0d2</i>

description: We assessed the effect of sulforaphene (SFE) on osteoclast differentiation. SFE significantly decreased the number of RANKL-induced tartrate-resistant acid phosphatase-positive cells and suppressed pre-osteoclast multinucleation. Furthermore, SFE downregulated mRNA expression of <i>DC</i>-<i>STAMP</i>, <i>OC</i>-<i>STAMP,</i> and <i>Atp6v0d2</i>, which encode cell–cell fusion molecules. Our data suggest that SFE attenuates pre-osteoclast multinucleation via suppression of cell–cell fusion.
DOI: 10.6084/m9.figshare.4597837.v1
title: Soy peptide ingestion augments the synthesis and metabolism of noradrenaline in the mouse brain

description: To examine whether edible peptide intake affects neurotransmitter metabolism in the brain, we evaluated the effect of peptides derived from soy proteins or fish collagen on free amino acids and monoamines in the mouse brain. Ingestion of soy peptides led to markedly higher levels of tyrosine, a catecholamine precursor, in the serum, and cerebral cortex compared to those following ingestion of vehicle alone or collagen peptides. Soy peptide ingestion also effectively increased 3-methoxy-4-hydroxyphenylethyleneglycol and normetanephrine, the principal metabolites of noradrenaline, in the cerebral cortex, hippocampus, and brainstem, whereas collagen peptides did not exert such effects. Further, soy peptide ingestion led to a significant increase in noradrenaline itself in the brainstem, where noradrenergic neurons are present. Noradrenergic turnover was also markedly stimulated in these regions after soy peptide ingestion. These <i>in vivo</i> observations suggest that soy peptide ingestion can maintain and promote the synthesis and metabolism of noradrenaline in the brain. Soy peptide ingestion promotes the synthesis and metabolism of noradrenaline in the brain via increased Tyr availability.