cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12462893.v1
title: Additional file 17 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 17: Table S16. Number of Caudovirales genomes and genomic fragments identified per quality estimation category, exact rules used to estimate genome quality and the interpretation of quality estimations.
DOI: 10.6084/m9.figshare.12462884.v1
title: Additional file 15 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 15: Table S15. Complete VIBRANT-derived annotations of validated viral scaffolds that encode putative DAGs, respective of Table 2.
DOI: 10.6084/m9.figshare.12462872
title: Additional file 13 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 13: Table S13. Lists of KEGG, Pfam and VOG annotations used to generate annotation metrics for neural network classification. Designated by asterisks are the lists of all VOG annotations determined as nucleotide replication-associated or viral hallmark-associated, which are used during prediction and quality estimation.
DOI: 10.6084/m9.figshare.12462875
title: Additional file 14 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 14: Table S14. Results from DESeq2 analysis for 8,789 non-redundant viruses from the Crohn’s Disease discovery dataset.
DOI: 10.6084/m9.figshare.12462863
title: Additional file 11 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 11: Table S11. Calculations and results of benchmarking analyses for VIBRANT, VirSorter, VirFinder and MARVEL.
DOI: 10.6084/m9.figshare.12462869
title: Additional file 12 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 12: Table S12. List of all KEGG annotations determined as AMGs.
DOI: 10.6084/m9.figshare.12462863.v1
title: Additional file 11 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 11: Table S11. Calculations and results of benchmarking analyses for VIBRANT, VirSorter, VirFinder and MARVEL.
DOI: 10.6084/m9.figshare.12462875.v1
title: Additional file 14 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 14: Table S14. Results from DESeq2 analysis for 8,789 non-redundant viruses from the Crohn’s Disease discovery dataset.
DOI: 10.6084/m9.figshare.12462854
title: Additional file 9 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 9: Spreadsheet S5. Relative contributions of different genera to multiple Dirichlet components (metacommunities).
DOI: 10.6084/m9.figshare.12462857
title: Additional file 10 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 10: Table S10. Equations used for benchmarking analyses.
DOI: 10.6084/m9.figshare.12462869.v1
title: Additional file 12 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 12: Table S12. List of all KEGG annotations determined as AMGs.
DOI: 10.6084/m9.figshare.12462872.v1
title: Additional file 13 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 13: Table S13. Lists of KEGG, Pfam and VOG annotations used to generate annotation metrics for neural network classification. Designated by asterisks are the lists of all VOG annotations determined as nucleotide replication-associated or viral hallmark-associated, which are used during prediction and quality estimation.
DOI: 10.6084/m9.figshare.12462851
title: Additional file 8 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 8: Spreadsheet S4. Analysis of similarities results from pairwise comparisons of different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462845
title: Additional file 6 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 6: Spreadsheet S2. Wilcoxon rank-sum test results comparing species richness (Chao1 index) between different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462848
title: Additional file 7 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 7: Spreadsheet S3. Wilcoxon rank-sum test results comparing diversity (Shannon diversity index) between different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462854.v1
title: Additional file 9 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 9: Spreadsheet S5. Relative contributions of different genera to multiple Dirichlet components (metacommunities).
DOI: 10.6084/m9.figshare.12462857.v1
title: Additional file 10 of VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

description: Additional File 10: Table S10. Equations used for benchmarking analyses.
DOI: 10.6084/m9.figshare.12462845.v1
title: Additional file 6 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 6: Spreadsheet S2. Wilcoxon rank-sum test results comparing species richness (Chao1 index) between different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462848.v1
title: Additional file 7 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 7: Spreadsheet S3. Wilcoxon rank-sum test results comparing diversity (Shannon diversity index) between different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462851.v1
title: Additional file 8 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 8: Spreadsheet S4. Analysis of similarities results from pairwise comparisons of different sampling location metagroups.
DOI: 10.6084/m9.figshare.12462830
title: Additional file 1 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 1: Spreadsheet S1. Raw abundance of sequence variants for negative and positive control samples.
DOI: 10.6084/m9.figshare.12462827
title: Additional file 16 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 16: Spreadsheet S8. Preliminary analysis of similarities results for pairwise comparisons of all sampling locations.
DOI: 10.6084/m9.figshare.12462830.v1
title: Additional file 1 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 1: Spreadsheet S1. Raw abundance of sequence variants for negative and positive control samples.
DOI: 10.6084/m9.figshare.12462827.v1
title: Additional file 16 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 16: Spreadsheet S8. Preliminary analysis of similarities results for pairwise comparisons of all sampling locations.
DOI: 10.6084/m9.figshare.12462809
title: Additional file 10 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 10: Spreadsheet S6. Relative contributions of different sequence variants to multiple Dirichlet components (metacommunities).
DOI: 10.6084/m9.figshare.12462809.v1
title: Additional file 10 of Topography of the respiratory tract bacterial microbiota in cattle

description: Additional file 10: Spreadsheet S6. Relative contributions of different sequence variants to multiple Dirichlet components (metacommunities).
DOI: 10.6084/m9.figshare.12462722
title: Additional file 3 of The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

description: Additional file 3 : Text S2. The detailed datasets in this work.
DOI: 10.6084/m9.figshare.12462719
title: Additional file 2 of The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

description: Additional file 2 : Text S1. The gene set used in this work.
DOI: 10.6084/m9.figshare.12462722.v1
title: Additional file 3 of The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

description: Additional file 3 : Text S2. The detailed datasets in this work.
DOI: 10.6084/m9.figshare.12462719.v1
title: Additional file 2 of The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease

description: Additional file 2 : Text S1. The gene set used in this work.
DOI: 10.6084/m9.figshare.12462689
title: Additional file 3 of Is it time to RE-AIM? A systematic review of economic empowerment as HIV prevention intervention for adolescent girls and young women in sub-Saharan Africa using the RE-AIM framework

description: Additional file 3. RE-AIM components extraction.
DOI: 10.6084/m9.figshare.12462689.v1
title: Additional file 3 of Is it time to RE-AIM? A systematic review of economic empowerment as HIV prevention intervention for adolescent girls and young women in sub-Saharan Africa using the RE-AIM framework

description: Additional file 3. RE-AIM components extraction.
DOI: 10.23641/asha.12462596
title: Semantic feature effects on SFA treatment outcomes (Evans et al., 2020)

description: <b>Purpose: </b>Semantic feature analysis (SFA) is a naming treatment found to improve naming performance for both treated and semantically related untreated words in aphasia. A crucial treatment component is the requirement that patients generate semantic features of treated items. This article examined the role feature generation plays in treatment response to SFA in several ways: It attempted to replicate preliminary findings from Gravier et al. (2018), which found feature generation predicted treatment-related gains for both trained and untrained words. It examined whether feature diversity or the number of features generated in specific categories differentially affected SFA treatment outcomes.<b>Method: </b>SFA was administered to 44 participants with chronic aphasia daily for 4 weeks. Treatment was administered to multiple lists sequentially in a multiple-baseline design. Participant-generated features were captured during treatment and coded in terms of feature category, total average number of features generated per trial, and total number of unique features generated per item. Item-level naming accuracy was analyzed using logistic mixed-effects regression models.<b>Results: </b>Producing more participant-generated features was found to improve treatment response for trained but not untrained items in SFA, in contrast to Gravier et al. (2018). There was no effect of participant-generated feature diversity or any differential effect of feature category on SFA treatment outcomes.<b>Conclusions: </b>Patient-generated features remain a key predictor of direct training effects and overall treatment response in SFA. Aphasia severity was also a significant predictor of treatment outcomes. Future work should focus on identifying potential nonresponders to therapy and explore treatment modifications to improve treatment outcomes for these individuals.<br><b>Supplemental Material S1. </b>Participant demographics.<br><b>Supplemental Material S2. </b>Language testing results.<br><b>Supplemental Material S3.</b> Performance variables (summarized across all treated items).<br>Evans, W. S., Cavanaugh, R., Gravier, M. L., Autenreith, A. M., Doyle, P. J., Hula, W. D., & Dickey, M. W. (2020). Effects of semantic feature type, diversity, and quantity on semantic feature analysis treatment outcomes in aphasia. <i>American Journal of Speech-Language Pathology.</i> Advance online publication. https://doi.org/10.1044/2020_AJSLP-19-00112<br><b>Publisher Note:</b> This article is part of the Special Issue: Select Papers From the 49th Clinical Aphasiology Conference.
DOI: 10.6084/m9.figshare.12462587
title: Review protocol for leaf extracts on EIMD

description: <b>Background</b> Strenuous activities can cause exercise-induced muscle damage (EIMD), particularly those that involve unfamiliar exercises. The typical signs and symptoms of EIMD include increased intra-muscular proteins, delayed onset muscle soreness and impaired muscular contractility. Thus, these signs and symptoms may compromise the quality of training and induce sub-optimal training adaptations. More recently, the antioxidant and anti-inflammatory agents of leaf extracts, such as tea leaves and herbs, has been reported to minimise the signs and symptoms of EIMD. However, several studies have also reported equivocal findings, possibly due to variation in study designs. A systematic exploration of the literature that addresses these methodological limitations may provide the overall benefit of ingesting leaf extracts for recovery, although a thorough investigation has yet to be determined. Thus, the purpose of this systematic review and meta-analysis will collate findings from various studies that have reported on the effects of BCAA supplementation on markers of EIMD.
DOI: 10.6084/m9.figshare.12462590
title: S1_Datasets.xlsx

description: PLOS ONE: submission PONE-D-20-06416
DOI: 10.6084/m9.figshare.12462590.v1
title: S1_Datasets.xlsx

description: PLOS ONE: submission PONE-D-20-06416
DOI: 10.6084/m9.figshare.12462587.v1
title: Untitled Item

description: <b>Background</b> Strenuous activities can cause exercise-induced muscle damage (EIMD), particularly those that involve unfamiliar exercises. The typical signs and symptoms of EIMD include increased intra-muscular proteins, delayed onset muscle soreness and impaired muscular contractility. Thus, these signs and symptoms may compromise the quality of training and induce sub-optimal training adaptations. More recently, the antioxidant and anti-inflammatory agents of leaf extracts, such as tea leaves and herbs, has been reported to minimise the signs and symptoms of EIMD. However, several studies have also reported equivocal findings, possibly due to variation in study designs. A systematic exploration of the literature that addresses these methodological limitations may provide the overall benefit of ingesting leaf extracts for recovery, although a thorough investigation has yet to be determined. Thus, the purpose of this systematic review and meta-analysis will collate findings from various studies that have reported on the effects of BCAA supplementation on markers of EIMD.
DOI: 10.6084/m9.figshare.12462605.v1
title: NGD constructing code.txt

description: Key code for NGD website constructing are described
DOI: 10.6084/m9.figshare.12462587.v3
title: Review protocol for leaf extracts on EIMD

description: <b>Background</b> Strenuous activities can cause exercise-induced muscle damage (EIMD), particularly those that involve unfamiliar exercises. The typical signs and symptoms of EIMD include increased intra-muscular proteins, delayed onset muscle soreness and impaired muscular contractility. Thus, these signs and symptoms may compromise the quality of training and induce sub-optimal training adaptations. More recently, the antioxidant and anti-inflammatory agents of leaf extracts, such as tea leaves and herbs, has been reported to minimise the signs and symptoms of EIMD. However, several studies have also reported equivocal findings, possibly due to variation in study designs. A systematic exploration of the literature that addresses these methodological limitations may provide the overall benefit of ingesting leaf extracts for recovery, although a thorough investigation has yet to be determined. Thus, the purpose of this systematic review and meta-analysis will collate findings from various studies that have reported on the effects of BCAA supplementation on markers of EIMD.
DOI: 10.6084/m9.figshare.12462587.v2
title: Leaf extracts on EIMD

description: <b>Background</b> Strenuous activities can cause exercise-induced muscle damage (EIMD), particularly those that involve unfamiliar exercises. The typical signs and symptoms of EIMD include increased intra-muscular proteins, delayed onset muscle soreness and impaired muscular contractility. Thus, these signs and symptoms may compromise the quality of training and induce sub-optimal training adaptations. More recently, the antioxidant and anti-inflammatory agents of leaf extracts, such as tea leaves and herbs, has been reported to minimise the signs and symptoms of EIMD. However, several studies have also reported equivocal findings, possibly due to variation in study designs. A systematic exploration of the literature that addresses these methodological limitations may provide the overall benefit of ingesting leaf extracts for recovery, although a thorough investigation has yet to be determined. Thus, the purpose of this systematic review and meta-analysis will collate findings from various studies that have reported on the effects of BCAA supplementation on markers of EIMD.
DOI: 10.6084/m9.figshare.12462509
title: JUPPId

description: <i>JUPPI</i> Dataset (<i>JUPPId</i>)
DOI: 10.6084/m9.figshare.12462509.v1
title: Untitled Item

description: <b>JUPPI Dataset</b> (<i>JUPPId</i>)
DOI: 10.6084/m9.figshare.12462479
title: Data from: Targeted sampling successfully detects the cryptic and declining arboreal marsupial (Phascogale pirata) in northern Australia

description: Contains all data necessary to duplicate the analyses described in Geyle et al<i>.</i> 2020. Includes a key to column headings and a description of variables.<br>The threatened northern brush-tailed phascogale (<i>Phascogale pirata</i>) is one of the most poorly known mammals in Australia. While the few available records indicate a decline in its distribution and abundance, it has not previously been subject to intensive targeted survey. Here, we trialled a specifically tailored methodology for detection of <i>P. pirata</i>, with the aim of informing ongoing survey and monitoring of this species. We deployed 50 motion-sensor cameras (spaced closely together in a grid 500 × 1000 m) on Melville Island (Northern Territory, Australia), between June 2018 and May 2019. Cameras were baited and secured to trees ~3 m above the ground on a bracket facing the trunk. We selected for large (&gt;30 cm diameter at breast height [DBH]) trunks of the dominant tree species (<i>Eucalyptus miniata</i>, <i>E. tetrodonta</i> and <i>Corymbia nesophila</i>). We detected <i>P. pirata</i> 16 times on eight cameras over the duration of the study, finding that detection was most likely on large (DBH &gt;41.5 cm) <i>E. tetrodonta</i> trees during the wet season. Our results indicate that survey effort for this species should be seasonally targeted and focussed on large trees. However, the efficacy of additional methods (nest boxes, Elliott traps) and a comparison between detections on arboreal versus ground-based cameras requires further investigation. We highlight the importance of conducting additional work on this species, as little is known about its ecology, population trends and threats, making it difficult to assess its conservation status. Without more targeted work, <i>P. pirata</i> is at risk of slipping into extinction unnoticed.
DOI: 10.6084/m9.figshare.12462509.v2
title: JUPPI: A Multi-level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment

description: <b>JUPPI Dataset</b> (<i>JUPPId</i>)
DOI: 10.6084/m9.figshare.12462413
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-68260 to JVASP-71053)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.12462416
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-71054 to JVASP-74989)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.12462509.v3
title: JUPPId

description: <b>JUPPI Dataset</b> (<i>JUPPId</i>)
DOI: 10.6084/m9.figshare.12462410
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-66035 to JVASP-68256)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.12462407
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-60610 to JVASP-66027)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.12462413.v1
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-68260 to JVASP-71053)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6073/pasta/6087f646f47402396d1d0b66bcbe8bfb
title: Soil nutrient availability from the 2007 Anaktuvuk River fire scar during the 2016 growing season

description: This file contains plant-available NO3, NH4, PO4 in the upper 5-10 cm of organic matter from a burned and unburned site in the southern section of the 2007 Anaktuvuk River fire in northern Alaska. Soil nutrients were assessed using ion-exchange resin membranes incubated in the soil during the growing season of 2016.
DOI: 10.6084/m9.figshare.12462245
title: NAIP before and after cold springs fire cropped data

description: This dataset contains NAIP data cropped to the cold springs fire study area in Colorado near Nederland. It was designed to be used for shorter teaching activities that use spatial and remote sensing data.
DOI: 10.6084/m9.figshare.12462245.v1
title: NAIP before and after cold springs fire cropped data

description: This dataset contains NAIP data cropped to the cold springs fire study area in Colorado near Nederland. It was designed to be used for shorter teaching activities that use spatial and remote sensing data.
DOI: 10.25377/sussex.12462152
title: Data for research article 'Multimodal influences on learning walks in desert ants (Cataglyphis fortis)'

description: <b>Data for paper published in the Journal of Comparative Physiology A (published June 2020).</b><br>Data contains paths from recorded ants during the experiments. Files can be opened with TextEdit (on a Macintosh) or WordPad (Windows).For details please see the README.txt and view the experiment methods in the published paper. <br><b>Abstract:</b>Ants are excellent navigators using multimodal information for navigation. To accurately localise the nest at the end of a foraging journey, visual cues, wind direction and also olfactory cues need to be learnt. Learning walks are performed at the start of an ant’s foraging career or when the appearance of the nest surrounding has changed. We investigated here whether the structure of such learning walks in the desert ant <i>Cataglyphis fortis</i> takes into account wind direction in conjunction with the learning of new visual information. Ants learnt to travel back and forth between their nest and a feeder, and we then introduced a black cylinder near their nest to induce learning walks in regular foragers. By doing this across days with different wind directions, we were able to probe how ants balance different sensory modalities. We found that (1) the ants’ outwards headings are influenced by the wind direction with their routes deflected such that they will arrive downwind of their target, (2) a novel object along the route induces learning walks in experienced ants and (3) the structure of learning walks is shaped by the wind direction rather than the position of the visual cue.