cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3699808_d1.v1
title: MOESM3 of The discovery of novel LPMO families with a new Hidden Markov model

description: Additional file 3. The Hidden Markov model constructed in this study. This Hidden Markov model, can be used in combination with the HMMER tool version 3 [19]. When searching with the hmmsearch program, using a trusted e-value (-E option in hmmsearch) of 1.2eâ  15 (lowest scoring true positive) will limit the results to mainly AA9, AA10, AA11 and AA13 LPMOs. To also allow the detection of the LPMO14 family, a lower trusted e-value of 0.001 is necessary. However, it should be noted that a lower e-value will also increase the theoretical chance of finding false positives (an e-value of 0.001, has a 1 in a 1000 chance to find a false positive). However, in our search using this e-value no false positives were identified in the 8 genomes searched.
DOI: 10.34760/5f5b7df3e9879
title: Predictive value of the microlesion effect on motor and cognitive outcome after Deep Brain Stimulation in Parkinson&rsquo;s Disease

description: Study to investigate the motor and cognitive effects of inserting a Deep Brain Stimulation electrode into the brain of a Parkinson’s disease patient.
description: 
Data categories: Imaging data, Medical records, Other
Material collected: Not available
Experimental data: Not available
Sex: Female, Male
Diseases studied: Parkinson's disease
DOI: 10.6084/m9.figshare.c.3699808_d1
title: MOESM3 of The discovery of novel LPMO families with a new Hidden Markov model

description: Additional file 3. The Hidden Markov model constructed in this study. This Hidden Markov model, can be used in combination with the HMMER tool version 3 [19]. When searching with the hmmsearch program, using a trusted e-value (-E option in hmmsearch) of 1.2eâ  15 (lowest scoring true positive) will limit the results to mainly AA9, AA10, AA11 and AA13 LPMOs. To also allow the detection of the LPMO14 family, a lower trusted e-value of 0.001 is necessary. However, it should be noted that a lower e-value will also increase the theoretical chance of finding false positives (an e-value of 0.001, has a 1 in a 1000 chance to find a false positive). However, in our search using this e-value no false positives were identified in the 8 genomes searched.
DOI: 10.15468/dl.vv6sx3
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puccinia polysora Underw."
 ]
}

 The dataset includes 625 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038825-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.75zpcc
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Saxifraga taygetea Boiss. & Heldr., Saxifraga geum Sm., Saxifraga taygetea subsp. chelmea Voliotis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038826-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vtck2h
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apogon phenax Böhlke & Randall, 1968",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 47 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038827-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2cxam
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puccinia polysora Underw."
 ]
}

 The dataset includes 625 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038828-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34760/5f5b811381b1e
title: PREHAB
title: Prehabilitation in Amputees

description: Sex: Female, Male
Diseases studied: Care involving use of other rehabilitation procedures
DOI: 10.15468/dl.2zpbzd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Scabiosa hladnikiana Host, Scabiosa columbaria subsp. hladnikiana (Host) Jasiewicz, Asterocephalus lucidus var. hladnikianus (Host) Rchb., Scabiosa cinerea subsp. hladnikiana (Host) Zangh.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038830-241126133413365/datasets/export for details.
DOI: 10.15468/dl.tb232j
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apogon pillionatus Böhlke & Randall, 1968",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038829-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/nyz4wy
title: Results of the study "Analysis of stress indicators caused by the presence of selected by-products of pre-treatment of lignocellulosic biomass in S. cerevisiae."

description: The results of the study "Analysis of stress indicators caused by the presence of selected by-products of pre-treatment of lignocellulosic biomass in S. cerevisiae." containing the growth of yeast biomass, the level of malondialdehyde and the activity of superoxide dismutase, catalase and glutathione peroxidase, the expression profile of the following heat shock proteins: HSP70 and HSP104. This research was funded by National Science Centre, Poland, grant number 2023/07/X/NZ9/00756.
DOI: 10.6084/m9.figshare.c.3700000_d1.v1
title: Additional file 1: of Reproducibility of thoracic kyphosis measurements in patients with adolescent idiopathic scoliosis

description: Original primary data. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3700000_d1
title: Additional file 1: of Reproducibility of thoracic kyphosis measurements in patients with adolescent idiopathic scoliosis

description: Original primary data. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3701884_d1.v1
title: Additional file 6: Table S1. of Vocal exchanges during pair formation and maintenance in the zebra finch (Taeniopygia guttata)

description: Total and proportion of different call type by bird. Total number and proportion (in brackets) of each call type for each individual. The total number of calls is the mean of the four days of recording and the proportion is calculated from this mean. Misp. Intr. is the abbreviation of misplaced introductory syllables (those which were not followed by the song). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3701884_d1
title: Additional file 6: Table S1. of Vocal exchanges during pair formation and maintenance in the zebra finch (Taeniopygia guttata)

description: Total and proportion of different call type by bird. Total number and proportion (in brackets) of each call type for each individual. The total number of calls is the mean of the four days of recording and the proportion is calculated from this mean. Misp. Intr. is the abbreviation of misplaced introductory syllables (those which were not followed by the song). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3701884_d2.v1
title: Additional file 7: Table S2. of Vocal exchanges during pair formation and maintenance in the zebra finch (Taeniopygia guttata)

description: Response strength for each pair each day each combination. Within a time window of interest of 4 s before and 4 s after call onset for our cross-correlation histograms we counted the number of calls. We divided the time window with a binwidth of 50 ms (i.e. 160 bins in total). The number of calls in the bins in the first 0.5-s (Nbase, i.e. the calls between 4 and 3.5 seconds before the focal calls) was used as baseline and those in the 0.5-s bins after call onset (Nresponse) as the response. We calculated the response strength index for each call combination for each pair for each day as follows: Rresponse = (Nresponse –Nbase) / (Nresponse + Nbase). The index range between -1 and +1, positive values correspond to an increase of calling after the stimuli (partner calls) compared to the baseline, negative value to an inhibition of calling, values close to 0 to maintenance of baseline calling (all the values are multiplied by 100 to aid readability). We set a threshold to avoid weak correlations to bias the results: if the number of calls within the time window considered did not reach 160 (i.e. one call for each bin) the index was not computed (reported as 0). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3701884_d2
title: Additional file 7: Table S2. of Vocal exchanges during pair formation and maintenance in the zebra finch (Taeniopygia guttata)

description: Response strength for each pair each day each combination. Within a time window of interest of 4 s before and 4 s after call onset for our cross-correlation histograms we counted the number of calls. We divided the time window with a binwidth of 50 ms (i.e. 160 bins in total). The number of calls in the bins in the first 0.5-s (Nbase, i.e. the calls between 4 and 3.5 seconds before the focal calls) was used as baseline and those in the 0.5-s bins after call onset (Nresponse) as the response. We calculated the response strength index for each call combination for each pair for each day as follows: Rresponse = (Nresponse –Nbase) / (Nresponse + Nbase). The index range between -1 and +1, positive values correspond to an increase of calling after the stimuli (partner calls) compared to the baseline, negative value to an inhibition of calling, values close to 0 to maintenance of baseline calling (all the values are multiplied by 100 to aid readability). We set a threshold to avoid weak correlations to bias the results: if the number of calls within the time window considered did not reach 160 (i.e. one call for each bin) the index was not computed (reported as 0). (XLSX 31 kb)
DOI: 10.17637/rh.28043204
title: Llangorse 14C date table

description: <b>Summer warmth between 15.5 and 15 ka BP enabled human repopulation of the Northwest European Margin.</b>High-magnitude decadal to centennial-scale abrupt changes in climate had a transformative effect on many past human populations. However, understanding these human/climate relationships is limited because robust tests of these linkages require region-specific quantified palaeoclimatic data with sufficient chronological precision to permit comparisons to the archaeological record. Here we present new high-resolution palaeoclimatic data and combine these with radiocarbon inventories of archaeological and faunal material, to test the relationship between abrupt warming and the ability of humans to rapidly re-populate the NW margins of Europe (&gt;50°N and encompassing the area of the current British Isles and North Sea basin) after regional abandonment during the Last Glacial Maximum. We address the timing of this process, and the relevance of the abrupt climate changes recorded in the Greenland ice cores. We use the IntCal20 radiocarbon calibration curve to show that the earliest human re-population in this region occurred up to 500 years before the climate of Greenland warmed. However, our analyses show that parts of the NW European margin had already experienced substantial summer warming by this time, likely driven by changes of sea-ice area in the eastern North Atlantic. The associated warming influenced the distribution of key hunter-gatherer prey species e.g. reindeer, which were a key resource for humans. Accordingly, this study highlights asynchrony in seasonal warming across the North Atlantic region during the last deglaciation and that this asynchrony permitted human exploitation of Northwest European margin paraglacial landscapes by ~15.2 ka BP.
DOI: 10.17637/rh.28043204.v1
title: Llangorse 14C date table

description: <b>Summer warmth between 15.5 and 15 ka BP enabled human repopulation of the Northwest European Margin.</b>High-magnitude decadal to centennial-scale abrupt changes in climate had a transformative effect on many past human populations. However, understanding these human/climate relationships is limited because robust tests of these linkages require region-specific quantified palaeoclimatic data with sufficient chronological precision to permit comparisons to the archaeological record. Here we present new high-resolution palaeoclimatic data and combine these with radiocarbon inventories of archaeological and faunal material, to test the relationship between abrupt warming and the ability of humans to rapidly re-populate the NW margins of Europe (&gt;50°N and encompassing the area of the current British Isles and North Sea basin) after regional abandonment during the Last Glacial Maximum. We address the timing of this process, and the relevance of the abrupt climate changes recorded in the Greenland ice cores. We use the IntCal20 radiocarbon calibration curve to show that the earliest human re-population in this region occurred up to 500 years before the climate of Greenland warmed. However, our analyses show that parts of the NW European margin had already experienced substantial summer warming by this time, likely driven by changes of sea-ice area in the eastern North Atlantic. The associated warming influenced the distribution of key hunter-gatherer prey species e.g. reindeer, which were a key resource for humans. Accordingly, this study highlights asynchrony in seasonal warming across the North Atlantic region during the last deglaciation and that this asynchrony permitted human exploitation of Northwest European margin paraglacial landscapes by ~15.2 ka BP.
DOI: 10.34760/61fb8f5fe6a96
title: Amanita intoxications
title: Clinical data from 18 patients that have experienced a amanita intoxicatoin

description: Data categories: Physiological/Biochemical measurements, Biological samples
Sex	: Female, Male
Age: 3-72 Year
Diseases studied: 
Accidental poisoning by and exposure to noxious substances; 
Poisoning by and exposure to other and unspecified chemicals and noxious substances, undetermined intent;
Intentional self-poisoning by and exposure to other and unspecified chemicals and noxious substances;
Ingested mushrooms
DOI: 10.15468/dl.dpkecw
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apogon planifrons Longley & Hildebrand, 1940",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 42 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038831-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3701968_d3.v1
title: Additional file 2: of ITIH5 mediates epigenetic reprogramming of breast cancer cells

description: Overlap of hypo-and hypermethylated CpG sites with published gene sets (GSEA). This table summarizes an overlap of significantly hyper- and hypomethylated CpG sites between ΔpBK-ITIH5 and ΔpBK-mock clones with gene set data bases. (XLS 72 kb)
DOI: 10.6084/m9.figshare.c.3701962_d5
title: Additional file 3: Table S3. of Landscape of genomic diversity and host adaptation in Fusarium graminearum

description: Information and annotations for all genetic variants detected in this analysis. (XLSX 32569 kb)
DOI: 10.6084/m9.figshare.c.3701968_d3
title: Additional file 2: of ITIH5 mediates epigenetic reprogramming of breast cancer cells

description: Overlap of hypo-and hypermethylated CpG sites with published gene sets (GSEA). This table summarizes an overlap of significantly hyper- and hypomethylated CpG sites between ΔpBK-ITIH5 and ΔpBK-mock clones with gene set data bases. (XLS 72 kb)
DOI: 10.6084/m9.figshare.c.3701977_d1.v1
title: Additional file 1: of Exploratory bioinformatics investigation reveals importance of â  junkâ   DNA in early embryo development

description: Table S1. Stage-specific expression level of 36882 genes, calculated using the formula log2 (FPKM + 1). Table S2. Gene lists of 10 gene clusters defined in Figure 1B. Table S3. Expression levels of transposable elements in mouse embryos at different stages. Table S4. List of all repetitive elements (REs) in the mouse genome with repeat name, repeat family, and repeat class. Table S5. Frequencies of REs in the promoters of different gene clusters. Table S6. List of 117 genes that contain ERVL elements in promoters and show an expression pattern similar to these LTRs. (XLSX 4556 kb)
DOI: 10.6084/m9.figshare.c.3701953_d5
title: Additional file 4: of Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

description: Plant compartment effect on the individual bacterial phyla. Values represent average number of reads (±standard error) and relative read abundances (%) based on 15 biological replicates (rhizosphere soil and root samples) and 11 replicates (stem and leaf samples) after normalization to 2000 sequences. Normal distributions of the data were checked with the Shapiro–Wilk test and homoscedasticity of variances was analyzed using either Bartlett’s or the Fligner–Killeens test. The ANOVA model was [OTU] ~ compartment and included all four plant compartments followed by Tukey’s honest significant differences post hoc tests. Plant compartment effects show the overall ANOVA results: F(DFn, DFd) and P value. Significant differences at the 95% confidence interval (P
DOI: 10.6084/m9.figshare.c.3701956_d6.v1
title: Additional file 9: Table S6. of Epigenetic modifications and glucocorticoid sensitivity in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

description: Differentially methylated sites unique to ME/CFS GC-Typical. Epigenetic loci that are specifically differentially methylated in the ME/CFS GC-Typical subgroup (p ≤ 0.05, Beta-difference ≥ 5%, after 10 000 permutations). (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3701956_d6
title: Additional file 9: Table S6. of Epigenetic modifications and glucocorticoid sensitivity in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

description: Differentially methylated sites unique to ME/CFS GC-Typical. Epigenetic loci that are specifically differentially methylated in the ME/CFS GC-Typical subgroup (p ≤ 0.05, Beta-difference ≥ 5%, after 10 000 permutations). (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3701971_d1
title: Additional file 1: of Cluster analysis of sputum cytokine-high profiles reveals diversity in T(h)2-high asthma patients

description: Cluster analysis of sputum cytokine-high profiles reveals diversity in T(h)2-high asthma patients. (ZIP 247Â kb)
DOI: 10.6084/m9.figshare.c.3701977_d1
title: Additional file 1: of Exploratory bioinformatics investigation reveals importance of â  junkâ   DNA in early embryo development

description: Table S1. Stage-specific expression level of 36882 genes, calculated using the formula log2 (FPKM + 1). Table S2. Gene lists of 10 gene clusters defined in Figure 1B. Table S3. Expression levels of transposable elements in mouse embryos at different stages. Table S4. List of all repetitive elements (REs) in the mouse genome with repeat name, repeat family, and repeat class. Table S5. Frequencies of REs in the promoters of different gene clusters. Table S6. List of 117 genes that contain ERVL elements in promoters and show an expression pattern similar to these LTRs. (XLSX 4556 kb)
DOI: 10.6084/m9.figshare.c.3701968_d4.v1
title: Additional file 7: of ITIH5 mediates epigenetic reprogramming of breast cancer cells

description: Primer sequences for pyrosequencing. This table shows sequences of DAPK1 pyrosequencing. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3701968_d4
title: Additional file 7: of ITIH5 mediates epigenetic reprogramming of breast cancer cells

description: Primer sequences for pyrosequencing. This table shows sequences of DAPK1 pyrosequencing. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3701980_d1.v1
title: MOESM4 of Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution

description: Additional file 4 R-Markdown file including script and results of MeSH and GO analysis on maize genes under selection for an increase in ear number per plant.
DOI: 10.6084/m9.figshare.c.3701962_d6.v1
title: Additional file 2: Table S2. of Landscape of genomic diversity and host adaptation in Fusarium graminearum

description: Genes described the reference genome (RRES v4.0) not covered by reads in any isolate genomes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3701980_d1
title: MOESM4 of Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution

description: Additional file 4 R-Markdown file including script and results of MeSH and GO analysis on maize genes under selection for an increase in ear number per plant.
DOI: 10.6084/m9.figshare.c.3701956_d7.v1
title: Additional file 2: Table S1. of Epigenetic modifications and glucocorticoid sensitivity in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

description: Differentially methylated sites in ME/CFS. Sites that were significantly differentially methylated between ME/CFS and controls (FDR ≤ 0.05, Beta-difference ≥ 5% ). (XLSX 1.58 mb)
DOI: 10.6084/m9.figshare.c.3701962_d6
title: Additional file 2: Table S2. of Landscape of genomic diversity and host adaptation in Fusarium graminearum

description: Genes described the reference genome (RRES v4.0) not covered by reads in any isolate genomes. (XLSX 16 kb)
DOI: 10.15468/dl.rwz3eu
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Scabiosa silenifolia Waldst. & Kit.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038833-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.224c7w
title: Occurrence Download

description: A dataset containing 465 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-10.04881 34.28717,-3.21323 34.28717,-3.21323 40.98632,-10.04881 40.98632,-10.04881 34.28717))",
 "HasCoordinate is true",
 "TaxonKey is Paeonia broteroi Boiss. & Reut."
 ]
}

 The dataset includes 465 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038832-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.