cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6004325.v1
title: Regulation of the circadian rhythmic expression of <i>Sglt1</i> in the mouse small intestine through histone acetylation and the mRNA elongation factor, BRD4-P-TEFb

description: Jejunal sodium/glucose co-transporter (<i>Sglt1</i>) displays circadian expression. The jejunum was collected every 4 h from mice, and we examined histone acetylation and binding of bromodomain-containing protein-4 (BRD4) around of the gene. Histone acetylation increased in the transcribed region of <i>Sglt1</i> prior to induction of the gene. Furthermore, the binding of mRNA elongation factor around the gene showed circadian rhythm.
DOI: 10.6084/m9.figshare.6004316
title: Supplementary Material for: Amyloid Angiopathy in Brain Hemorrhage: A Postmortem Neuropathological-Magnetic Resonance Imaging Study

description: <b><i>Background:</i></b> Risk factors for intracerebral hemorrhage (ICH) include hypertension and cerebral amyloid angiopathy (CAA). The objective of this study was to determine the autopsy prevalence of CAA and the potential overlap with other risk factors among patients who died from ICH and also the correlation of CAA with cerebral microbleeds. <b><i>Methods:</i></b> We analyzed 81 consecutive autopsy brains from patients with ICH. Staining for CAA detection was performed. We used an age- and sex-matched control group of routine brain autopsies of nonneurological patients to determine the frequencies of CAA and hypertension. Postmortem 3D T2-weighted gradient-echo magnetic resonance imaging (MRI) with a 1.5-T magnet was performed in 11 brains with ICH (5 with CAA and 6 without) and histological correlation was performed when microbleeds were detected. <b><i>Results:</i></b> Hypertension and CAA were found in 69.1 and 24.7% of cases respectively. Among patients with CAA, 65.0% also had hypertension. The prevalence of CAA was similar among non-hypertensive cases and controls (33.3 and 23.1%; <i>p =</i> 0.54), whereas a significant difference was found between hypertensive cases vs. controls (28.9% vs. 0; <i>p =</i> 0.01). MRI documented 48 microbleeds and all 5 brains with CAA had ≥1 microbleed, compared to 3/6 brains without CAA. Among 48 microbleeds on MRI, 45 corresponded histologically to microbleeds surrounding microvessels (23 &lt;200 µm in diameter, 19 between 200 µm and 2 mm, 3 were hemosiderin granules). <b><i>Conclusions:</i></b> Both hypertension and CAA frequently coexist in patients with ICH. MRI-detected microbleeds, proven by histological analysis, were twice as common in patients with CAA as in those with hypertensive ICH.
DOI: 10.6084/m9.figshare.6004316.v1
title: Supplementary Material for: Amyloid Angiopathy in Brain Hemorrhage: A Postmortem Neuropathological-Magnetic Resonance Imaging Study

description: <b><i>Background:</i></b> Risk factors for intracerebral hemorrhage (ICH) include hypertension and cerebral amyloid angiopathy (CAA). The objective of this study was to determine the autopsy prevalence of CAA and the potential overlap with other risk factors among patients who died from ICH and also the correlation of CAA with cerebral microbleeds. <b><i>Methods:</i></b> We analyzed 81 consecutive autopsy brains from patients with ICH. Staining for CAA detection was performed. We used an age- and sex-matched control group of routine brain autopsies of nonneurological patients to determine the frequencies of CAA and hypertension. Postmortem 3D T2-weighted gradient-echo magnetic resonance imaging (MRI) with a 1.5-T magnet was performed in 11 brains with ICH (5 with CAA and 6 without) and histological correlation was performed when microbleeds were detected. <b><i>Results:</i></b> Hypertension and CAA were found in 69.1 and 24.7% of cases respectively. Among patients with CAA, 65.0% also had hypertension. The prevalence of CAA was similar among non-hypertensive cases and controls (33.3 and 23.1%; <i>p =</i> 0.54), whereas a significant difference was found between hypertensive cases vs. controls (28.9% vs. 0; <i>p =</i> 0.01). MRI documented 48 microbleeds and all 5 brains with CAA had ≥1 microbleed, compared to 3/6 brains without CAA. Among 48 microbleeds on MRI, 45 corresponded histologically to microbleeds surrounding microvessels (23 &lt;200 µm in diameter, 19 between 200 µm and 2 mm, 3 were hemosiderin granules). <b><i>Conclusions:</i></b> Both hypertension and CAA frequently coexist in patients with ICH. MRI-detected microbleeds, proven by histological analysis, were twice as common in patients with CAA as in those with hypertensive ICH.
DOI: 10.6084/m9.figshare.6004262
title: Identifying local and regional groundwater in basins: chemical and stable isotopic attributes of multivariate classification of hydrochemical data, the Lower Virgin River Basin, Nevada, Arizona and Utah, U.S.A

description: In the Basin and Range Province of the Southwestern U.S.A., deep carbonate groundwater has been suggested as a significant source to many overlying basin-fill alluvial aquifer systems. Notwithstanding, testing this hypothesis is limited by obtaining data from such considerable depths and complex geology. This study uses δ<sup>2</sup>H and δ<sup>18</sup>O data from springs, rivers, and wells tapping shallow basin-fill groundwater to test the hydrochemical interpretation of deep regional carbonate groundwater flow into the basin-fill aquifers. Stable isotopic and major ion attributes of hydrochemical facies suggest basin-fill alluvial groundwater of the Lower Virgin River Basin is a mixture of precipitation recharge within the Lower Virgin River Basin or the Clover and Escalante Desert Basin northwards, and the deep carbonate flow. The data support the conclusions that in the Lower Virgin River Basin, deep carbonate groundwater is an important source to the alluvial aquifer system and likely accounts for approximately 50% of the alluvial aquifer groundwater. Na<sup>+</sup>, K<sup>+</sup>, and SO<sub>4</sub><sup>2–</sup> increase in the basin-fill alluvial groundwaters outside the Virgin River floodplain appears to be related with upwelling of deep regional groundwater, and indicating that the chemical character of the basin-fill alluvial groundwaters are related to the deeper flow systems.
DOI: 10.6084/m9.figshare.6004262.v1
title: Identifying local and regional groundwater in basins: chemical and stable isotopic attributes of multivariate classification of hydrochemical data, the Lower Virgin River Basin, Nevada, Arizona and Utah, U.S.A

description: In the Basin and Range Province of the Southwestern U.S.A., deep carbonate groundwater has been suggested as a significant source to many overlying basin-fill alluvial aquifer systems. Notwithstanding, testing this hypothesis is limited by obtaining data from such considerable depths and complex geology. This study uses δ<sup>2</sup>H and δ<sup>18</sup>O data from springs, rivers, and wells tapping shallow basin-fill groundwater to test the hydrochemical interpretation of deep regional carbonate groundwater flow into the basin-fill aquifers. Stable isotopic and major ion attributes of hydrochemical facies suggest basin-fill alluvial groundwater of the Lower Virgin River Basin is a mixture of precipitation recharge within the Lower Virgin River Basin or the Clover and Escalante Desert Basin northwards, and the deep carbonate flow. The data support the conclusions that in the Lower Virgin River Basin, deep carbonate groundwater is an important source to the alluvial aquifer system and likely accounts for approximately 50% of the alluvial aquifer groundwater. Na<sup>+</sup>, K<sup>+</sup>, and SO<sub>4</sub><sup>2–</sup> increase in the basin-fill alluvial groundwaters outside the Virgin River floodplain appears to be related with upwelling of deep regional groundwater, and indicating that the chemical character of the basin-fill alluvial groundwaters are related to the deeper flow systems.
DOI: 10.6084/m9.figshare.6004250
title: data_HmmCleaner.tar.gz

description: associated Dataset to "Hmmcleaner, a tool to reduce the detrimental effect of errors in protein alignments on evolutionary inference"
DOI: 10.6084/m9.figshare.6004250.v1
title: data_HmmCleaner.tar.gz

description: associated Dataset to "Hmmcleaner, a tool to reduce the detrimental effect of errors in protein alignments on evolutionary inference"
DOI: 10.6084/m9.figshare.6004238
title: Visual communication and aggressive behaviour in a giant mute torrent-frog, Megaelosia apuana (Anura; Hylodidae): Supplementary Material

description: Advertisement call is the most common signal used by anurans for intraspecific communication. However, some species have lost the ability to emit these vocalizations and are denoted as mute. Alternatively, these species may communicate by visual, tactile and chemical signals. The lack of advertisement call could be explained by the high background noise of breeding microhabitats. A model group to study alternative communication tactics is the genus <i>Megaelosia</i>, which is composed by seven mute species that inhabit noisy streams, and for which no information on intraspecific communication is available. We monitored a population of <i>M. apuana</i> and described its visual signalling during aggressive interactions between males. This interaction included visual signalling, physical combat, and the retreat of the smaller individual. No audible sound was detected during the whole aggressive interaction, reinforcing the genus muteness. This is the first report of any communication behaviour for the genus <i>Megaelosia</i>.
DOI: 10.6084/m9.figshare.6004238.v1
title: Visual communication and aggressive behaviour in a giant mute torrent-frog, Megaelosia apuana (Anura; Hylodidae): Supplementary Material

description: Advertisement call is the most common signal used by anurans for intraspecific communication. However, some species have lost the ability to emit these vocalizations and are denoted as mute. Alternatively, these species may communicate by visual, tactile and chemical signals. The lack of advertisement call could be explained by the high background noise of breeding microhabitats. A model group to study alternative communication tactics is the genus <i>Megaelosia</i>, which is composed by seven mute species that inhabit noisy streams, and for which no information on intraspecific communication is available. We monitored a population of <i>M. apuana</i> and described its visual signalling during aggressive interactions between males. This interaction included visual signalling, physical combat, and the retreat of the smaller individual. No audible sound was detected during the whole aggressive interaction, reinforcing the genus muteness. This is the first report of any communication behaviour for the genus <i>Megaelosia</i>.
DOI: 10.6084/m9.figshare.6004130
title: Parity games

description: A set of parity games for benchmarking purposes. See https://github.com/jkeiren/paritygame-generator Model checking: Parity games encoding model checking problems.Equivalence checking: Parity games encoding equivalence checking problems.PGSolver: Parity games generated using PGSolver. These include: random games, and games that are hard for certain algorithms.MLSolver Parity games generated using MLSolver. These are games that encode satisfiability and validity problems for modal logics.Data (YAML) This is a file in YAML format that includes high-level information about <em>all</em> parity games described before. Detailed (structural) information about the games can be found as separate YAML files in the respectipe ZIP archives.Data (SQLite) This contains a database in SQLite format that was derived from the YAML files provided in the archives, and the previous data file. The sole purpose of this derived data is to enable efficient plotting of results. The plots in the paper have been based on this file.
DOI: 10.6084/m9.figshare.6004094
title: cache.rar

description: CS918
DOI: 10.6084/m9.figshare.6004067
title: Additional file 9: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Plant transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 8. Compressed .tar.gz text file. (GZ 8552 kb)
DOI: 10.6084/m9.figshare.6004067.v1
title: Additional file 9: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Plant transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 8. Compressed .tar.gz text file. (GZ 8552 kb)
DOI: 10.6084/m9.figshare.6004061
title: Additional file 8: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Plant-assigned transcripts, full results table, annotation and DESeq2 analysis. The table contains the following information for each expressed plant-assigned transcript: 1) The annotation of transcripts: this includes functional annotation (KOG class, KOG group, KOG definition) and best BLAST match against plant-refseq (match accession number, match description, percentage ID, BLAST score, length of alignment and percentage sequence coverage); 2) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype) in shoots and roots: Shoot Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Shoot Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Shoot Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Shoot La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype, Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype; 3) The count table; 4) Additional BLAST annotations showing the best BLAST match against Arabidopsis lyrata, Arabidopsis thaliana and Brachypodium distachyon databases (sequence length, match accession number, e-value, percentage ID, BLAST score and length of alignment). (XLSX 18037 kb)
DOI: 10.6084/m9.figshare.6004061.v1
title: Additional file 8: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Plant-assigned transcripts, full results table, annotation and DESeq2 analysis. The table contains the following information for each expressed plant-assigned transcript: 1) The annotation of transcripts: this includes functional annotation (KOG class, KOG group, KOG definition) and best BLAST match against plant-refseq (match accession number, match description, percentage ID, BLAST score, length of alignment and percentage sequence coverage); 2) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype) in shoots and roots: Shoot Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Shoot Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Shoot Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Shoot La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype, Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype; 3) The count table; 4) Additional BLAST annotations showing the best BLAST match against Arabidopsis lyrata, Arabidopsis thaliana and Brachypodium distachyon databases (sequence length, match accession number, e-value, percentage ID, BLAST score and length of alignment). (XLSX 18037 kb)
DOI: 10.6084/m9.figshare.6004046
title: Additional file 6: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Selected plant expressed gene results, for those genes discussed in the text. The table contains the following information for selected plant-assigned transcripts that are discussed in the text: 1) Plant root/shoot (for reported DESeq2 pairwise comparison); 2) Transcript ID; 3) gene description; 4) function; 5) possible role; 6) relevant reference (citations for relevant references are contained in Additional file 7); 7) DESeq2 result: Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype; 8) Two columns to indicate whether the transcript was significantly upregulated in acid or limestone soil and/or acid or limestone ecotype. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6004046.v1
title: Additional file 6: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Selected plant expressed gene results, for those genes discussed in the text. The table contains the following information for selected plant-assigned transcripts that are discussed in the text: 1) Plant root/shoot (for reported DESeq2 pairwise comparison); 2) Transcript ID; 3) gene description; 4) function; 5) possible role; 6) relevant reference (citations for relevant references are contained in Additional file 7); 7) DESeq2 result: Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype; 8) Two columns to indicate whether the transcript was significantly upregulated in acid or limestone soil and/or acid or limestone ecotype. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6004037
title: Additional file 5: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Extended REViGO results for the 16 up-regulated and down-regulated plant gene lists. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.6004037.v1
title: Additional file 5: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Extended REViGO results for the 16 up-regulated and down-regulated plant gene lists. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.6004028
title: Additional file 4: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Significant DAVID GO enrichment results obtained for the 16 up-regulated and down-regulated plant gene lists. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.6004028.v1
title: Additional file 4: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Significant DAVID GO enrichment results obtained for the 16 up-regulated and down-regulated plant gene lists. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.6003929
title: Additional file 11: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

description: Table S5. Statistical differences in the relative abundances of enzyme commission (EC) level-4 categories between HUMAnN2 and SUPER-FOCUS. (CSV 16Â kb)
DOI: 10.6084/m9.figshare.6003929.v1
title: Additional file 11: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

description: Table S5. Statistical differences in the relative abundances of enzyme commission (EC) level-4 categories between HUMAnN2 and SUPER-FOCUS. (CSV 16Â kb)
DOI: 10.6084/m9.figshare.6003923
title: Additional file 15: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Microbial transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 12. Compressed .tar.gz text file. (GZ 2398 kb)
DOI: 10.6084/m9.figshare.6003923.v1
title: Additional file 15: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Microbial transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 12. Compressed .tar.gz text file. (GZ 2398 kb)
DOI: 10.6084/m9.figshare.6003917
title: Additional file 10: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

description: Table S4. Statistical differences in alpha diversity at different sequencing depths. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6003917.v1
title: Additional file 10: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

description: Table S4. Statistical differences in alpha diversity at different sequencing depths. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6003884
title: Additional file 12: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Microbial-assigned transcripts, full results table, annotation and DESeq2 analysis. Description of File: The table includes information on expressed microbial transcripts. 1) Phylogenetic annotation of each transcript; 2) Whether significantly expressed in root acid bog soil (RA), root limestone soil (RL), shoot acid bog soil (SA) and/or shoot limestone soil (SL). Significantly expressed transcripts is defined as the number of microbial annotated transcripts that obtained ≥5 aligned reads in at least 3 samples in each of the treatments RA (total 8 samples), RL (total 9 samples), SA (total 10 samples), SL (total 9 samples); 3) two columns indicating whether the transcript is “upregulated in acid or limestone ecotype in acid bog soil” and/or “upregulated in acid or limestone ecotype in limestone soil” 4) KOG functional annotation (KOG ID, KOG definition, KOG class, KOG group) and best BLAST match (sequence length, database that contained the best match, accession number, gene description, best match organism, e-value, percentage ID, BLAST score, percentage sequence coverage); 5) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype), shoots and roots (Shoot, Root), see sheet “DESeq2 pairwise comparisons” for further explanation of the 8 pairwise comparisons; 6) The count table. (XLSX 6498 kb)