cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5844777
title: The non-monotypic status of the neotropical fish genus <i>Hemiodontichthys</i> (Siluriformes, Loricariidae) evidenced by genetic approaches

description: The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus <i>Hemiodontichthys</i> Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. <i>Hemiodontichthys</i> samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between <i>Hemiodontichthys</i> sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.
DOI: 10.6084/m9.figshare.5844777.v2
title: The non-monotypic status of the neotropical fish genus <i>Hemiodontichthys</i> (Siluriformes, Loricariidae) evidenced by genetic approaches

description: The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus <i>Hemiodontichthys</i> Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. <i>Hemiodontichthys</i> samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between <i>Hemiodontichthys</i> sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.
DOI: 10.6084/m9.figshare.5844768
title: Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

description: The geographical centre of domestication and species diversity for sheep (<i>Ovis aries</i>) lies around the Kurdistan region of Northern Iraq, within the ‘Fertile Crescent’. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (<i>Capra</i>) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (<i>numts</i>). <i>In situ</i> hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of <i>numts</i>, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, <i>numts</i> and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.
DOI: 10.6084/m9.figshare.5844768.v2
title: Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

description: The geographical centre of domestication and species diversity for sheep (<i>Ovis aries</i>) lies around the Kurdistan region of Northern Iraq, within the ‘Fertile Crescent’. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (<i>Capra</i>) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (<i>numts</i>). <i>In situ</i> hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of <i>numts</i>, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, <i>numts</i> and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.
DOI: 10.6084/m9.figshare.5844765
title: dat.csv

description: minimal anonymized data set relating to rooting experiment in <i>Wrightia tinctoria.</i>
DOI: 10.6084/m9.figshare.5844765.v1
title: dat.csv

description: minimal anonymized data set relating to rooting experiment in <i>Wrightia tinctoria.</i>
DOI: 10.6084/m9.figshare.5844738
title: DATASET: Lipopolysaccharide-binding protein (LBP) can reverse the amyloid state of fibrin seen or induced in Parkinson’s Disease

description: Dataset for paper. ALSO see link to raw figure data files stored at the following link:<br><br>https://1drv.ms/f/s!AgoCOmY3bkKHmWY8VijKiQ-8_5RY
DOI: 10.6084/m9.figshare.5844738.v1
title: DATASET: Lipopolysaccharide-binding protein (LBP) can reverse the amyloid state of fibrin seen or induced in Parkinson’s Disease

description: Dataset for paper. ALSO see link to raw figure data files stored at the following link:<br><br>https://1drv.ms/f/s!AgoCOmY3bkKHmWY8VijKiQ-8_5RY
DOI: 10.6084/m9.figshare.5844720
title: Baseline Data

description: Baseline Data
DOI: 10.6084/m9.figshare.5844720.v1
title: Baseline Data.sav

description: The KAGUYA Baseline Data
DOI: 10.6084/m9.figshare.5844708
title: Baseline Data

description: The KAGUYA Baseline Data
DOI: 10.6084/m9.figshare.5844708.v1
title: Baseline Data

description: The KAGUYA Baseline Data
DOI: 10.6084/m9.figshare.5844663
title: Additional file 2: Table S1. of Whole exome sequencing of benign pulmonary metastasizing leiomyoma reveals mutation in the BMP8B gene

description: Summary of somatic variants identified in pulmonary metastasis of the BML patient by whole exome sequencing. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.5844663.v1
title: Additional file 2: Table S1. of Whole exome sequencing of benign pulmonary metastasizing leiomyoma reveals mutation in the BMP8B gene

description: Summary of somatic variants identified in pulmonary metastasis of the BML patient by whole exome sequencing. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.5844645
title: Additional file 1: of Influence of new societal factors on neovascular age-related macular degeneration outcomes

description: Raw data: categories and frequencies of each different variable and model parameter values showing the coefficients of the different categories of each variable. (ODT 6 kb)
DOI: 10.6084/m9.figshare.5844645.v1
title: Additional file 1: of Influence of new societal factors on neovascular age-related macular degeneration outcomes

description: Raw data: categories and frequencies of each different variable and model parameter values showing the coefficients of the different categories of each variable. (ODT 6 kb)
DOI: 10.6084/m9.figshare.5844609
title: Additional file 2: Table S2. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection

description: Contains the following information for every challenge submission: tumour, submission ID, precision, recall, F1-score, the number of germline variants leaked and whether it was a Challenge administrator submission. (XLS 39Â kb)
DOI: 10.6084/m9.figshare.5844609.v1
title: Additional file 2: Table S2. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection

description: Contains the following information for every challenge submission: tumour, submission ID, precision, recall, F1-score, the number of germline variants leaked and whether it was a Challenge administrator submission. (XLS 39Â kb)
DOI: 10.5281/zenodo.3993032
title: Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one

description: Datasets for 'Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one' by Zaninotto et al. (2020) in Ecology and Evolution.
DOI: 10.5281/zenodo.3993031
title: Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one

description: Datasets for 'Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one' by Zaninotto et al. (2020) in Ecology and Evolution.
DOI: 10.6084/m9.figshare.5844588
title: Additional file 1: Table S1. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection

description: Tumour information from each tumour challenge (IS1, IS2, IS3). This includes information on in silico tumour construction, composition, and a summary of participating teams and their challenge submissions. (XLS 12Â kb)
DOI: 10.6084/m9.figshare.5844588.v1
title: Additional file 1: Table S1. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection

description: Tumour information from each tumour challenge (IS1, IS2, IS3). This includes information on in silico tumour construction, composition, and a summary of participating teams and their challenge submissions. (XLS 12Â kb)
DOI: 10.6084/m9.figshare.5844570
title: Additional file 1: of Variation of poorly ventilated lung units (silent spaces) measured by electrical impedance tomography to dynamically assess recruitment

description: Variation of poorly ventilated lung units (silent spaces) measured by electrical impedance tomography to dynamically assess recruitment. Additional information about the manuscript methods and additional data analysis are provided. Figure S1. Study protocol. Study protocol consisted of five consecutive phases. Figure S2. Hyperinflation (%) and nondependent lung compliance (ml/cmH2O) during the decremental step of the protocol. Hyperinflation (%) and nondependent lung compliance (ml/cmH2O) during the decremental step of the protocol. The hyperinflation value is expressed as a percentage of the total pixels and is relative to the last step of the PEEP titration trial (in this case, PEEPâ =â 5 cmH2O). (ZIP 178 kb)
DOI: 10.6084/m9.figshare.5844570.v1
title: Additional file 1: of Variation of poorly ventilated lung units (silent spaces) measured by electrical impedance tomography to dynamically assess recruitment

description: Variation of poorly ventilated lung units (silent spaces) measured by electrical impedance tomography to dynamically assess recruitment. Additional information about the manuscript methods and additional data analysis are provided. Figure S1. Study protocol. Study protocol consisted of five consecutive phases. Figure S2. Hyperinflation (%) and nondependent lung compliance (ml/cmH2O) during the decremental step of the protocol. Hyperinflation (%) and nondependent lung compliance (ml/cmH2O) during the decremental step of the protocol. The hyperinflation value is expressed as a percentage of the total pixels and is relative to the last step of the PEEP titration trial (in this case, PEEPâ =â 5 cmH2O). (ZIP 178 kb)
DOI: 10.6084/m9.figshare.5844507
title: Additional file 2 of Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

description: Detailed information and statistics of read and base trimming per sample read file. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5844507.v1
title: Additional file 2 of Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

description: Detailed information and statistics of read and base trimming per sample read file. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5844486
title: Additional file 1 of Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

description: Trimmed Mean of M-values (TMM) of the estimated expression of selected defence-related genes in lentil–A. lentis transcriptome. Treatment – Mock (M) for H2O control, Treatment (T) for ALP2 A. lentis inoculation. HPI – Hours post inoculation. Norm_TMM_count – Trimmed Mean of M-values of the raw estimated counts, as calculated by edgeR. Count_SE – Standard error values per gene at each genotype/time point, calculated from TMM counts of subgroup replicates (n =3). (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5844486.v1
title: Additional file 1 of Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

description: Trimmed Mean of M-values (TMM) of the estimated expression of selected defence-related genes in lentil–A. lentis transcriptome. Treatment – Mock (M) for H2O control, Treatment (T) for ALP2 A. lentis inoculation. HPI – Hours post inoculation. Norm_TMM_count – Trimmed Mean of M-values of the raw estimated counts, as calculated by edgeR. Count_SE – Standard error values per gene at each genotype/time point, calculated from TMM counts of subgroup replicates (n =3). (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5844423
title: DFO. Lobster Landings (1995-present), Newfoundland and Labrador

description: Lobster Landings (1995-present), Newfoundland and Labrador
DOI: 10.6084/m9.figshare.5844423.v2
title: DFO. Lobster Landings (1995-present), Newfoundland and Labrador

description: Lobster Landings (1995-present), Newfoundland and Labrador
DOI: 10.6084/m9.figshare.5844423.v1
title: Lobster Landings (1995-present), Newfoundland and Labrador

description: Lobster Landings (1995-present), Newfoundland and Labrador
DOI: 10.6084/m9.figshare.5844408
title: Conservation genomics of an endangered subspecies of Southern Emu-Wren, <i>Stipiturus malachurus</i> (Passeriformes: Maluridae)

description: The endangered subspecies of Southern Emu-Wren (<i>Stipiturus malachurus intermedius</i>) in the Mount Lofty Ranges (MLR), South Australia has a fragmented distribution and poor dispersal capability. These factors make it susceptible to local population extinction, as evidenced by declining distribution and abundance since 1993. We documented genetic diversity by genotyping thousands of nuclear markers from samples collected in the 1990s to inform genetic management. We found that Southern Emu-Wrens from south-eastern South Australia and the MLR, which are separate subspecies that share mitochondrial haplotypes, are genetically distinct based on nuclear DNA, albeit at a low level (<i>F<sub>ST</sub></i> = 0.21). Within the MLR, differentiation between southern and northern sites is consistent with the presence of two populations, with the boundary reflecting a disjunction in the distribution of historical records. Although Southern Emu-Wrens are now absent from our MLR sample sites, nearby occupied sites within each of the populations require continued management, and our results suggest these may warrant treatment as separate management units. At one site where birds had disappeared over an 8-year period, our retrospective genotyping found low levels of inbreeding, reinforcing the need to distinguish factors impacting on population viability to mitigate extinction likelihood.
DOI: 10.6084/m9.figshare.5844408.v1
title: Conservation genomics of an endangered subspecies of Southern Emu-Wren, <i>Stipiturus malachurus</i> (Passeriformes: Maluridae)

description: The endangered subspecies of Southern Emu-Wren (<i>Stipiturus malachurus intermedius</i>) in the Mount Lofty Ranges (MLR), South Australia has a fragmented distribution and poor dispersal capability. These factors make it susceptible to local population extinction, as evidenced by declining distribution and abundance since 1993. We documented genetic diversity by genotyping thousands of nuclear markers from samples collected in the 1990s to inform genetic management. We found that Southern Emu-Wrens from south-eastern South Australia and the MLR, which are separate subspecies that share mitochondrial haplotypes, are genetically distinct based on nuclear DNA, albeit at a low level (<i>F<sub>ST</sub></i> = 0.21). Within the MLR, differentiation between southern and northern sites is consistent with the presence of two populations, with the boundary reflecting a disjunction in the distribution of historical records. Although Southern Emu-Wrens are now absent from our MLR sample sites, nearby occupied sites within each of the populations require continued management, and our results suggest these may warrant treatment as separate management units. At one site where birds had disappeared over an 8-year period, our retrospective genotyping found low levels of inbreeding, reinforcing the need to distinguish factors impacting on population viability to mitigate extinction likelihood.
DOI: 10.6084/m9.figshare.5844402
title: Phylogenetic relationships of the Eastern Polynesian swiftlets (<i>Aerodramus</i>, Apodidae) and considerations on other Western Pacific swiftlets

description: The patterns of colonisation and phylogenetic relationships of the swiftlets from Oceania, and in particular from the remotest archipelagos of Polynesia, remain a puzzle. In this study we used mitochondrial and nuclear DNA sequence data to infer the colonisation patterns of swiftlets endemic to Eastern Polynesia. The three endemic taxa did not form a monophyletic group. The Tahiti Swiftlet (<i>Aerodramus leucophaeus</i>) and the Marquesan Swiftlet (<i>A. ocistus</i>) were closely related to the group formed by the Himalayan Swiftlet (<i>A. brevirostris</i>) and the two Indian Ocean species, Seychelles Swiftlet (<i>A. elaphrus</i>) and Mascarene Swiftlet (<i>A. francicus</i>). The third taxon from Eastern Polynesia, the Atiu Swiftlet (<i>A. sawtelli</i>) from the Cook Islands, forms a group with the Mariana Swiftlet (<i>A. bartschi</i>), and the Uniform Swiftlet (<i>A. vanikorensis</i>), a widely distributed species, from the Philippines to Melanesia. Thus the colonisation of the remotest areas of Oceania by swiftlets occurred through long-distance events, as opposed to a regular, stepping-stone pattern from the west to the east. These results add to the body of evidence suggesting that Eastern Polynesia constituted a ‘sink’, from which birds did not come back to recolonise western islands.
DOI: 10.6084/m9.figshare.5844402.v1
title: Phylogenetic relationships of the Eastern Polynesian swiftlets (<i>Aerodramus</i>, Apodidae) and considerations on other Western Pacific swiftlets

description: The patterns of colonisation and phylogenetic relationships of the swiftlets from Oceania, and in particular from the remotest archipelagos of Polynesia, remain a puzzle. In this study we used mitochondrial and nuclear DNA sequence data to infer the colonisation patterns of swiftlets endemic to Eastern Polynesia. The three endemic taxa did not form a monophyletic group. The Tahiti Swiftlet (<i>Aerodramus leucophaeus</i>) and the Marquesan Swiftlet (<i>A. ocistus</i>) were closely related to the group formed by the Himalayan Swiftlet (<i>A. brevirostris</i>) and the two Indian Ocean species, Seychelles Swiftlet (<i>A. elaphrus</i>) and Mascarene Swiftlet (<i>A. francicus</i>). The third taxon from Eastern Polynesia, the Atiu Swiftlet (<i>A. sawtelli</i>) from the Cook Islands, forms a group with the Mariana Swiftlet (<i>A. bartschi</i>), and the Uniform Swiftlet (<i>A. vanikorensis</i>), a widely distributed species, from the Philippines to Melanesia. Thus the colonisation of the remotest areas of Oceania by swiftlets occurred through long-distance events, as opposed to a regular, stepping-stone pattern from the west to the east. These results add to the body of evidence suggesting that Eastern Polynesia constituted a ‘sink’, from which birds did not come back to recolonise western islands.
DOI: 10.6084/m9.figshare.5844375
title: Theoretical ribosomal protein mass fingerprint of Synechocystis sp. PCC 6803

description: This is a dataset containing the molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Synechocystis</i> sp. PCC 6803<br><br>
DOI: 10.6084/m9.figshare.5844375.v1
title: Theoretical ribosomal protein mass fingerprint of Synechocystis sp. PCC 6803

description: This is a dataset containing the molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Synechocystis</i> sp. PCC 6803<br><br>
DOI: 10.6084/m9.figshare.5844372
title: S. mutans biofilm

description: S. mutans biofilm
DOI: 10.6084/m9.figshare.5844366
title: Raw_data.ods

description: City dust of Antofagasta, northern Chile.Rocks and soil geochemistry, northern Chile.
DOI: 10.6084/m9.figshare.5844366.v1
title: Raw_data.ods

description: City dust of Antofagasta, northern Chile.Rocks and soil geochemistry, northern Chile.
DOI: 10.6084/m9.figshare.5844363
title: PTSD

description: Included ptsd data.
DOI: 10.6084/m9.figshare.5844264
title: Effects of cable sway, electrode surface area, and electrode mass on Electroencephalography signal quality during motion

description: The data was saved in .bdf format and was collected using the BioSemi ActiveTwo system with for 4 electrodes, 2 placed on the top of the head, 2 placed on the back of the head. Sampling rate was 512 Hz.<br>There are three datasets:a) Electrode Mass Recordings b) Electrode Surface Area Recordings c) Cable Sway Recordings <br>Each dataset was recorded in 4 blocks, so each folder contains the 4 recording blocks with the motion frequency conditions tested. The electrode mass experiment also contains the different mass conditions tested.<br>Mass Conditions:1 x Electrode Mass2 x Electrode Mass3 x Electrode Mass<br>Motion Frequency Conditions:0 = Motors Off0p0 = 0 Hz 1p0 = 1 Hz 1p2 = 1.25 Hz 1p5 = 1.5 Hz 1p75 = 1.75 Hz 2p0 = 2 Hz<br>-nosignal = with no signal from the head-signal = with signal from the head