cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh072677.07fu
title: SH072677.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh072678.07fu
title: SH072678.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.34664/1601150
title: 27 TeV pp collisions, Exotics type, PYTHIA8 generator: tev27pp_pythia8_darkpion_scan

description: The dark pions (emerging jets) model with the settings as those similar to the CMS paper in JHEP 02 (2019) 179 (https://arxiv.org/abs/1810.10069). The files use the A14 ATLAS tune with NNPDF23_lo_as_0130_qed. The luminosity was estimated from the first file and is not accurate for the entire dataset. All parameter settings and cross sections are included in the logfiles inside separate ProMC files. The files are designed for a detector scans. The emerging jet model is described in: Y. Bai and P. Schwaller, “Scale of dark QCD”,Phys. Rev. D89(2014) 063522,doi:10.1103/PhysRevD.89.063522,arXiv:1306.4676; P. Schwaller, D.Stolarski, and A. Weiler, “Emerging jets”,JHEP05(2015) 59,doi:10.1007/JHEP05(2015)059,arXiv:1502.05409. Evens are created using a fixed mediator mass of 10 TeV. The dark pion mass, m(DP), changes in the range 5 GeV - 2500 GeV. Together with the pion mass, Rho mass is m(DP)*4. pTminFSR changes as m(DP)*2+20 GeV. The decay length (ctau) changes in the range 1 -1500 mm. One file per a combination m(DP) - ctau is produced. How to use: Each file has the substring "_mXX_ctYY" where XX and YY indicate the dark pion mass and the decay length (in mm).
DOI: 10.34664/1601154
title: 13 TeV pp collisions, Exotics type, PYTHIA8 generator: tev13pp_pythia8_darkqcd

description: The Dark pions (emerging jets) model with the settings as for the CMS publication JHEP 02 (2019) 179 (https://arxiv.org/abs/1810.10069). The files use the A14 ATLAS tune with NNPDF23_lo_as_0130_qed. The luminosity was estimated from the first file and is not accurate for the entire dataset. All parameter settings and cross sections are included in the logfiles inside separate ProMC files. The emerging jet model is described in: Y. Bai and P. Schwaller, “Scale of dark QCD”,Phys. Rev. D89(2014) 063522,doi:10.1103/PhysRevD.89.063522,arXiv:1306.4676; P. Schwaller, D.Stolarski, and A. Weiler, “Emerging jets”,JHEP05(2015) 59,doi:10.1007/JHEP05(2015)059,arXiv:1502.05409. Evens are created using a fixed dark pion mass of 5 GeV and different decay length (ctau). Each file has the substring "_mXX_ctYY" where XX and YY indicate the mediator mass and the decay length (in mm) of dark pion with the mass 5 GeV (fixed).
DOI: 10.34664/1601158
title: 13 TeV pp collisions, Exotics type, MADGRAPH/PY8 generator: tev13pp_mg5_chaH4FNS_sys

description: Production of charged H+ (or H-) using MG5_aMC_v2_6_1 at LO QCD. Four flavor number scheme (4FNS) is used, i.e. tbH. H+ mass is 2 TeV. Each file has 20,000 events, and has different settings. The samples are created for studies of systematic uncertainties to understand PDF and polarization effects. Showering was done in Pyhia8 A14 with ATLAS tuning.
DOI: 10.6084/m9.figshare.11895573
title: Additional file 2 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 2. The iDU1756 model presented as a spreadsheet.
DOI: 10.6084/m9.figshare.11895573.v1
title: Additional file 2 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 2. The iDU1756 model presented as a spreadsheet.
DOI: 10.11577/1601281
title: Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

description: Please check the README file for more information about the dataset.
DOI: 10.6084/m9.figshare.11895579
title: Additional file 3 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 3. The iDU1756 model in SBML format.
DOI: 10.6084/m9.figshare.11895579.v1
title: Additional file 3 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 3. The iDU1756 model in SBML format.
DOI: 10.6084/m9.figshare.11895582
title: Additional file 4 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 4. A detailed complete comparison of the models iDU1756 and iJB1325.
DOI: 10.6084/m9.figshare.11895582.v1
title: Additional file 4 of In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output

description: Additional file 4. A detailed complete comparison of the models iDU1756 and iJB1325.
DOI: 10.6084/m9.figshare.11895678
title: Additional file 2 of MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

description: Additional file 2 Table S1: Flux distribution at each Pareto point. Table S2: All deletion candidates enumerated by Momo.
DOI: 10.6084/m9.figshare.11895678.v1
title: Additional file 2 of MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

description: Additional file 2 Table S1: Flux distribution at each Pareto point. Table S2: All deletion candidates enumerated by Momo.
DOI: 10.6084/m9.figshare.11895681
title: Additional file 10 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 10. MAGs having KEGG modules. Number of MAGs having each KEGG module are reported. Only MAGs having complete and 1 block missing KEGG modules are considered. In column B is reported the total number of MAGs per each phylum (considering only high quality and medium-high quality MAGs). KEGG modules are reported in columns.
DOI: 10.6084/m9.figshare.11895684
title: Additional file 11 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 11. KEGG pathways abundance in different microbial samples. Abundance of all HQ and MHQ MAGs having a complete or "one block missing" KEGG module were summed and the value is reported here as an estimate of the abundance of this pathway in each sample.
DOI: 10.6084/m9.figshare.11895681.v1
title: Additional file 10 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 10. MAGs having KEGG modules. Number of MAGs having each KEGG module are reported. Only MAGs having complete and 1 block missing KEGG modules are considered. In column B is reported the total number of MAGs per each phylum (considering only high quality and medium-high quality MAGs). KEGG modules are reported in columns.
DOI: 10.6084/m9.figshare.11895684.v1
title: Additional file 11 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 11. KEGG pathways abundance in different microbial samples. Abundance of all HQ and MHQ MAGs having a complete or "one block missing" KEGG module were summed and the value is reported here as an estimate of the abundance of this pathway in each sample.
DOI: 10.6084/m9.figshare.11895693.v1
title: Additional file 12 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 12. Enrichment of CAZymes classes in MAGs. Number of proteins assigned to different classes and determined using dbCAN software. Only HQ and MHQ MAGs have been considered.
DOI: 10.6084/m9.figshare.11895699
title: Additional file 13 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 13. Index of replication. iRep values were calculated for each MAG in all the samples considered. Average values were calculated for replicate samples. All samples are reported in column 2, while MAGs IDs and names are reported in columns A and B.
DOI: 10.6084/m9.figshare.11895693
title: Additional file 12 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 12. Enrichment of CAZymes classes in MAGs. Number of proteins assigned to different classes and determined using dbCAN software. Only HQ and MHQ MAGs have been considered.
DOI: 10.6084/m9.figshare.11895705
title: Additional file 14 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 14. Results obtained using RAST (Rapid Annotation using Subsystem Technology). MAGs genes were assigned to the function using RAST and the number of genes identified per each functional category (FL = first level; SL = second level) are reported. Functional categories are reported in column B, while MAGs are reported in rows (2 is MAG ID and 3 is MAG name assigned considering taxonomy).
DOI: 10.6084/m9.figshare.11895705.v1
title: Additional file 14 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 14. Results obtained using RAST (Rapid Annotation using Subsystem Technology). MAGs genes were assigned to the function using RAST and the number of genes identified per each functional category (FL = first level; SL = second level) are reported. Functional categories are reported in column B, while MAGs are reported in rows (2 is MAG ID and 3 is MAG name assigned considering taxonomy).
DOI: 10.6084/m9.figshare.11895699.v1
title: Additional file 13 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 13. Index of replication. iRep values were calculated for each MAG in all the samples considered. Average values were calculated for replicate samples. All samples are reported in column 2, while MAGs IDs and names are reported in columns A and B.
DOI: 10.6084/m9.figshare.11895711
title: Additional file 1 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 1. Metadata of the samples included in the present study. The composition of the feedstocks used in the different reactors was approximated using substrate information from various sources. When available, such data was taken from the publicly accessible description of the respective experiments or full-scale plant operation datasets. Otherwise, reactor feedstocks were estimated by a proportionality-based mixing technique: taking the characteristics of their individual constituents from available literature and combining them according to their fresh matter (FM) or volatile solid (VS) ratio in the feed.
DOI: 10.6084/m9.figshare.11895711.v1
title: Additional file 1 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 1. Metadata of the samples included in the present study. The composition of the feedstocks used in the different reactors was approximated using substrate information from various sources. When available, such data was taken from the publicly accessible description of the respective experiments or full-scale plant operation datasets. Otherwise, reactor feedstocks were estimated by a proportionality-based mixing technique: taking the characteristics of their individual constituents from available literature and combining them according to their fresh matter (FM) or volatile solid (VS) ratio in the feed.
DOI: 10.3886/e117904
title: Utah Air Quality Risk and Behavioral Action Survey

description: Our interdisciplinary team developed a Utah state-wide survey based on census demographics to assess the role of environmental attitudes and behavior on public health and public policy issues caused by poor air quality in Utah. To accomplish this task, we surveyed Utahns from across the state to assess seven hypothesized drivers of human values, beliefs and preferences that interact with perceptions of risk to promote specific environmental behaviors related to air pollution. By assessing these interacting processes, we can better understand the perceived range of acceptable public health and policy related outcomes within our state, fill in behavioral gaps in the research, and to identify what legislative or regulatory actions have the greatest potential for addressing this serious issue.
description: web-based survey~~Five stage, online quota sample through Qualtrics
description: Smallest Geographic Unit: County
description: Stratified sampling approach
DOI: 10.6084/m9.figshare.11895729
title: Additional file 3 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 3. Global statistics of the assemblies and binning.
DOI: 10.6084/m9.figshare.11895729.v1
title: Additional file 3 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 3. Global statistics of the assemblies and binning.
DOI: 10.6084/m9.figshare.11895735
title: Additional file 4 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 4. MAGs taxonomy. MAGs obtained after redundancy removal (based on ANI calculation) were assigned to the taxonomy using three different methods and results were subsequently combined.
DOI: 10.6084/m9.figshare.11895957
title: Additional file 1 of Optimization of PET protocol and interrater reliability of 18F-PSMA-11 imaging of prostate cancer

description: Additional file 1. Dataset representing detailed results of the Phase 2 clinical trial study on 18F-PSMA-11.
DOI: 10.6084/m9.figshare.11895957.v1
title: Additional file 1 of Optimization of PET protocol and interrater reliability of 18F-PSMA-11 imaging of prostate cancer

description: Additional file 1. Dataset representing detailed results of the Phase 2 clinical trial study on 18F-PSMA-11.
DOI: 10.6084/m9.figshare.11895735.v1
title: Additional file 4 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 4. MAGs taxonomy. MAGs obtained after redundancy removal (based on ANI calculation) were assigned to the taxonomy using three different methods and results were subsequently combined.
DOI: 10.6084/m9.figshare.11895744
title: Additional file 5 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 5. Comparison of MAGs with those reported in previous projects.
DOI: 10.6084/m9.figshare.11895744.v1
title: Additional file 5 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 5. Comparison of MAGs with those reported in previous projects.
DOI: 10.21227/a6yg-dz65
title: ChoCT2Vec: A Deep Learning Approach to Generate Diagnostic and Therapeutic Reports from Cholelithiasis CT Images

description: Dataset
DOI: 10.6084/m9.figshare.11895747
title: Additional file 6 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 6. Relative abundance of each taxa in the samples examined. Relative abundance of all the MAG having the same taxonomic assignment were combined in order to determine the relative abundance of each taxon as reported in columns D-CP. All the taxonomic levels from kingdom to genus were considered.
DOI: 10.6084/m9.figshare.11895747.v1
title: Additional file 6 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 6. Relative abundance of each taxa in the samples examined. Relative abundance of all the MAG having the same taxonomic assignment were combined in order to determine the relative abundance of each taxon as reported in columns D-CP. All the taxonomic levels from kingdom to genus were considered.
DOI: 10.21227/bszq-2089
title: ChoCT2Vec: A Deep Learning Approach to Generate Diagnostic and Therapeutic Reports from Cholelithiasis CT Images

description: Dataset
DOI: 10.6084/m9.figshare.11895753
title: Additional file 8 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 8. MAGs coverage per sample. MAGs coverage was calculated on all the samples (average values were considered for samples collected in replicates).
DOI: 10.6084/m9.figshare.11895750.v1
title: Additional file 7 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 7. Diversity indexes. Indexes were calculated for each sample in order to estimate the characteristics of the microbiome. Results were obtained starting from the files reporting the number of reads assigned to each MAG on each sample (subsampling all the samples to 1 million reads) and subsequently elaborated using PAST software. Colors reported in line 2 refer to the projects from which reads have been collected. Remaining colors were assigned in order to discriminate low and high values in a heatmap scale.
DOI: 10.6084/m9.figshare.11895750
title: Additional file 7 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 7. Diversity indexes. Indexes were calculated for each sample in order to estimate the characteristics of the microbiome. Results were obtained starting from the files reporting the number of reads assigned to each MAG on each sample (subsampling all the samples to 1 million reads) and subsequently elaborated using PAST software. Colors reported in line 2 refer to the projects from which reads have been collected. Remaining colors were assigned in order to discriminate low and high values in a heatmap scale.
DOI: 10.6084/m9.figshare.11895753.v1
title: Additional file 8 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 8. MAGs coverage per sample. MAGs coverage was calculated on all the samples (average values were considered for samples collected in replicates).
DOI: 10.6084/m9.figshare.11895756
title: Additional file 9 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 9. KEGG modules. Completeness of each KEGG module was reported for the high and medium-high quality MAGs.
DOI: 10.6084/m9.figshare.11895756.v1
title: Additional file 9 of New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

description: Additional file 9. KEGG modules. Completeness of each KEGG module was reported for the high and medium-high quality MAGs.
DOI: 10.6084/m9.figshare.11896521
title: Additional file 2 of Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus

description: Additional file 2. Amino acid alignments of the translated protein candidates for phosphoketolase and acetyl kinase enzymes.
DOI: 10.6084/m9.figshare.11896515
title: Additional file 1 of Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus

description: Additional file 1: Table S1. Atmosphere measurements of cultivation ‘Spruce + board Anaerobic’ and ‘Spruce + board aerobic’ at cultivation days 7, 14, 21 and 49. Table S2. Mfuzz center C-values of each cluster on each cultivation. Mfuzz classification of individual genes can be found in Additional file 1: Table S2 and Table S3. Table S3. Complete list of gene models, raw reads and DESeq 2-analysis of all 14 transcriptomes. Mfuzz cluster information of all 12,017 differentially expressed genes. Table S4. List and annotations of analysed 330 genes of primary metabolism and CAZy genes. Log2 fold change between ‘Spruce + board Anaerobic’ and ‘Spruce + board aerobic’—cultivations and promoter region analysis data of 11 different binding motif of common transcription factors. Mfuzz clusters and target/signal peptides of all studied core metabolism and CAZy genes. Annotation based on BlastP homology.