cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16807579.v1
title: Additional file 6 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 6. Statistical analysis for ARGs. The first column indicates the ARGs to be compared among samples, while the second column indicates the ARG class they belongs to. Next columns (until the column titled Kruskal p-value, not included) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and each processing room on the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each processing room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807576.v1
title: Additional file 5 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 5. Statistical analysis for ARG and taxonomical assignments. Columns from C to H indicate average values for ARG classes and taxonomic assignments per sampling time and food contact status (NFCS: non food contact surfaces; FCS: food contact surfaces). Columns I and J indicate p-values obtained from Kruskal-Wallis analyses within FCS and within NFCS samples, respectively, to analyze significant differences across time. Columns from K to P indicate p-values from Wilcoxon pair-wise tests performed for each pair of Time samples within NFCS and within FCS samples. Columns from Q to S indicate p-values from Wilcoxon pair-wise tests performed for NFCS versus FCS samples for each Time group. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807573.v1
title: Additional file 4 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 4. Statistical analysis for ARG classes. The first column indicates the ARG class to be compared among samples. Next columns (until the column titled Kruskal p-value) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and processing room on the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807570.v1
title: Additional file 3 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 3. Statistical analysis for taxonomy. The first column indicates the genus to be compared among samples. Next columns (until the column titled Kruskal p-value) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and processing room in the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each processing room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807717
title: Additional file 9 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 9: Table S8. DEGs related to plant hormone signal transduction.
DOI: 10.6084/m9.figshare.16807714
title: Additional file 8 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 8: Table S7. Potential transcription factors involved in Pi signaling.
DOI: 10.6084/m9.figshare.16807711
title: Additional file 7 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 7: Table S6. DEGs related to root growth.
DOI: 10.6084/m9.figshare.16807708
title: Additional file 6 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 6: Table S5. DEGs encoding putative phosphatases.
DOI: 10.6084/m9.figshare.16807705
title: Additional file 5 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 5: Table S4. DEGs related to transporters.
DOI: 10.6084/m9.figshare.16807699
title: Additional file 3 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 3: Table S3. DEGs identified in stylo roots under 0 (LP) and 250 (HP) μM KH2PO4 supply treatments.
DOI: 10.6084/m9.figshare.16807696
title: Additional file 2 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 2: Table S2. Summary of stylo roots transcriptomes in 0 (LP) and 250 (HP) μM KH2PO4 supply treatments.
DOI: 10.6084/m9.figshare.16807693
title: Additional file 1 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 1: Table S1. The decrease rate of growth parameters of stylo under 0 (LP) and 100 μM KH2PO4 relative to that in 250 (HP) μM KH2PO4 treatment.
DOI: 10.6084/m9.figshare.16807690
title: Additional file 12 of Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

description: Additional file 12: Table S9. Primers used for qRT-PCR analysis of the selected genes.
DOI: 10.6084/m9.figshare.16807667
title: Additional file 1 of T lymphocyte senescence is attenuated in Parkinson’s disease

description: Additional file 1: Table S1. List of qPCR primers.
DOI: 10.6084/m9.figshare.16807640
title: Additional file 3 of Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping

description: Additional file 3: Table S1 All genomic annotations for iHS. Table S2 Gene enrichment results for TD, iHS, and ROH.
DOI: 10.6084/m9.figshare.16807637
title: Additional file 2 of Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping

description: Additional file 2: Data S1 TD output. Data S2 iHS output. Data S3 ROH output.
DOI: 10.5517/ccdc.csd.cc28m7cj
title: CCDC 2103857: Experimental Crystal Structure Determination

description: Related Article: Yong Xu, Zhen Wang, Jiangtao Sun|2021|Org.Lett.|23|7613|doi:10.1021/acs.orglett.1c02825
DOI: 10.5517/ccdc.csd.cc286yp4
title: CCDC 2092056: Experimental Crystal Structure Determination

description: Related Article: Xiyue Yuan, Yunli Zhao, Tao Zhan, Jiyeon Oh, Jiadong Zhou, Junyu Li, Xiaojing Wang, Zhiqiang Wang, Shuting Pang, Ping Cai, Changduk Yang, Zhicai He, Zengqi Xie, Chunhui Duan, Fei Huang, Yong Cao|2021|Energy Environ.Sci.|14|5530|doi:10.1039/D1EE01957K
DOI: 10.6084/m9.figshare.16807591
title: Additional file 9 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 9. Phenotypes table. Document phenotypes.txt downloaded from the ResFinder repository ( https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/ ) and manually curated in order to modify the class variable, grouping those genes that confer resistance to macrolides, lincosamides, streptogramins and pleuromutilins into the MLSP class, and those that confer resistance to oxazolidinones into the oxazolidinone class. This last group included cfr genes, which confer resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogramins, the optrA gene, which confers resistance to phenicols and oxazolidinones, and the poxtA gene, which confers resistance to phenicols, oxazolidinones and tetracyclines.
DOI: 10.6084/m9.figshare.16807588
title: Additional file 8 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 8. Samples Metadata, DNA quantity and quality, reads and information on the culture-dependent approach. Columns from A to G indicate sample names together with their temporal and spatial location. Columns from H to N correspond to parameters related to the DNA extraction process and the total and filtered reads obtained after shotgun sequencing. Columns from O to Z detail the occurrence of different microorganisms in the culture dependent analyses, their phenotypic resistance to specific antibiotics, as revealed through their growth on selective agar plates, and the detection of ARGs. Resistant Pseudomonas spp. isolates harboring ARGs for β-lactams and carbapenems were not detected.
DOI: 10.6084/m9.figshare.16807582
title: Additional file 7 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 7. LGTs-Integrons. Blastn results for those LGT and integron regions associated with ARGs. The first column indicates the contig name, while columns B to E indicate the origin of the sample where the contig was occurring (surface type, processing room, day of visit, sampling time). Column F indicates the best match obtained by blastn versus the ResFinder database, while columns G to P indicate the parameters of the alignment obtained by blastn. Columns Q to T show the hierarchical classification of the gene obtained as the best match hit, according to Supp. File 4. Column U indicates the genomic location obtained for the contig by the Plasflow pipeline. Columns V and W show the CladeA (host) and CladeB (source) for the lateral gene transfer (LGT) events detected. Rows highlighted in orange or yellow indicate contigs that contain more than one ARG within their integron region.
DOI: 10.6084/m9.figshare.16807579
title: Additional file 6 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 6. Statistical analysis for ARGs. The first column indicates the ARGs to be compared among samples, while the second column indicates the ARG class they belongs to. Next columns (until the column titled Kruskal p-value, not included) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and each processing room on the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each processing room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807576
title: Additional file 5 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 5. Statistical analysis for ARG and taxonomical assignments. Columns from C to H indicate average values for ARG classes and taxonomic assignments per sampling time and food contact status (NFCS: non food contact surfaces; FCS: food contact surfaces). Columns I and J indicate p-values obtained from Kruskal-Wallis analyses within FCS and within NFCS samples, respectively, to analyze significant differences across time. Columns from K to P indicate p-values from Wilcoxon pair-wise tests performed for each pair of Time samples within NFCS and within FCS samples. Columns from Q to S indicate p-values from Wilcoxon pair-wise tests performed for NFCS versus FCS samples for each Time group. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807573
title: Additional file 4 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 4. Statistical analysis for ARG classes. The first column indicates the ARG class to be compared among samples. Next columns (until the column titled Kruskal p-value) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and processing room on the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807570
title: Additional file 3 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

description: Additional file 3. Statistical analysis for taxonomy. The first column indicates the genus to be compared among samples. Next columns (until the column titled Kruskal p-value) indicate average values for each sample group being compared. Kruskal p-value columns indicate the p-values for the comparison between sample groups, which are presented for each surface type and processing room in the sheets surface_time and room_time respectively. The subsequent columns indicate p-values from the Wilcoxon pair-wise test for each pair of sample groups, which are also indicated on the column head. Statistical analyses performed by sampling time are presented on the time sheet, by sampling time for each surface type on the surface_time sheet, by surface type for each of the three time groups on the TX_surface sheets, by sampling time for each processing room on the room_time sheet, and by processing room for each of the three time groups on the TX_room sheets. NaN means not a number, and indicates those cases where statistical analyses could not be performed due to zero values on each sample to be compared.
DOI: 10.6084/m9.figshare.16807909.v1
title: BIOL 3250 LAB Metadata.docx

description: BIOL 3250 Bioblitz Data and Meta-Data
DOI: 10.6084/m9.figshare.16807918
title: BIOL 3250 Birds datasheet.xlsx

description: Dataset for Biol3250
DOI: 10.6084/m9.figshare.16807918.v1
title: BIOL 3250 Birds datasheet.xlsx

description: Dataset for Biol3250
DOI: 10.6084/m9.figshare.16807909.v2
title: BIOL 3250 Data and Meta-data

description: BIOL 3250 Bioblitz Data and Meta-Data
DOI: 10.6084/m9.figshare.16808443
title: Ab-CoV_identity_antibodies_VH-VL.csv

description: (VH+VL) sequence identity between SARS-CoV-2 neutralizing antibody and therapeutic antibody
DOI: 10.6084/m9.figshare.16808443.v1
title: Ab-CoV_identity_antibodies_VH-VL.csv

description: (VH+VL) sequence identity between SARS-CoV-2 neutralizing antibody and therapeutic antibody
DOI: 10.6084/m9.figshare.16802545
title: Ab-CoV_viral_protein_calculations.zip

description: Calculated features for SARS-CoV-2 viral proteins
DOI: 10.6084/m9.figshare.16802545.v2
title: Ab-CoV_viral_protein_calculations.zip

description: Calculated features for SARS-CoV-2 viral proteins
DOI: 10.6084/m9.figshare.16802545.v1
title: Ab-CoV_viral_protein_calculations.zip

description: Calculated features for SARS-CoV-2 viral proteins
DOI: 10.6084/m9.figshare.16802518
title: Ab-CoV_interface_detail.csv

description: Antibody information for detailed mutational analysis of the interface
DOI: 10.6084/m9.figshare.16802524
title: Ab-CoV_identity_nanobodies_VH.csv

description: nanobodies similarity with therapeutic antibody VH chain
DOI: 10.6084/m9.figshare.16802524.v1
title: Ab-CoV_identity_nanobodies_VH.csv

description: nanobodies similarity with therapeutic antibody VH chain
DOI: 10.6084/m9.figshare.16802527.v1
title: Ab-CoV_interface_mutation.csv

description: Detailed mutational analysis of the antibody interface (epitope and paratope). Change in stability and affinity predicted using FoldX, mCSM, ProAffiMuSeq, CUPSAT webservers/tools.
DOI: 10.6084/m9.figshare.16802527
title: Ab-CoV_interface_mutation.csv

description: Detailed mutational analysis of the antibody interface (epitope and paratope). Change in stability and affinity predicted using FoldX, mCSM, ProAffiMuSeq, CUPSAT webservers/tools.
DOI: 10.5517/ccdc.csd.ccsq02k
title: CCDC 736128: Experimental Crystal Structure Determination

description: Related Article: N.T. Pokhodylo, Y. Slyvka, V. Pavlyuk|2021|Acta Crystallogr.,Sect.E:Cryst.Commun.|77|1043|doi:10.1107/S2056989021009774
DOI: 10.5517/ccdc.csd.cc28vjym
title: CCDC 2110881: Experimental Crystal Structure Determination

description: Related Article: S.T. Frey, J.G. Ballot, A. Hands, H.A. Cirka, K.C. Rinaolo, N.N. Phalkun, M. Kaur, J.P. Jasinski|2021|Acta Crystallogr.,Sect.E:Cryst.Commun.|77|982|doi:10.1107/S2056989021009786
DOI: 10.5517/ccdc.csd.cc28vn71
title: CCDC 2110983: Experimental Crystal Structure Determination

description: Related Article: I. Korona-Głowniak, W. Nitek, W. Tejchman, E. Żesławska|2021|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|77|649|doi:10.1107/S205322962100975X
DOI: 10.5517/ccdc.csd.cc28vn82
title: CCDC 2110984: Experimental Crystal Structure Determination

description: Related Article: I. Korona-Głowniak, W. Nitek, W. Tejchman, E. Żesławska|2021|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|77|649|doi:10.1107/S205322962100975X
DOI: 10.5517/ccdc.csd.cc28vn93
title: CCDC 2110985: Experimental Crystal Structure Determination

description: Related Article: I. Korona-Głowniak, W. Nitek, W. Tejchman, E. Żesławska|2021|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|77|649|doi:10.1107/S205322962100975X
DOI: 10.5517/ccdc.csd.cc28vnb4
title: CCDC 2110986: Experimental Crystal Structure Determination

description: Related Article: I. Korona-Głowniak, W. Nitek, W. Tejchman, E. Żesławska|2021|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|77|649|doi:10.1107/S205322962100975X
DOI: 10.5517/ccdc.csd.cc28w29k
title: CCDC 2111388: Experimental Crystal Structure Determination

description: Related Article: S. Kodama, K. Bunno, A. Nomoto, A. Ogawa|2021|IUCrData|6|x210992|doi:10.1107/S2414314621009925
DOI: 10.5517/ccdc.csd.cc28yzv2
title: CCDC 2114195: Experimental Crystal Structure Determination

description: Related Article: Nicolas Ripoche, Marie Betou, Clotilde Philippe, Yann Trolez, Olivier Mongin, Marta Dudek, Ziemowit Pokladek, Katarzyna Matczyszyn, Marek Samoc, Hiba Sahnoune, Jean-François Halet, Thierry Roisnel, Loic Toupet, Marie Cordier, Graeme Moxey, Mark G Humphrey, Frédéric Paul|2021|Phys.Chem.Chem.Phys.(PCCP)|23|22283|doi:10.1039/D1CP03346H
DOI: 10.6084/m9.figshare.16802533
title: Ab-CoV_epitope_data.csv

description: Experimental and computationally predicted epitopes collected from literature for coronavirus related proteins.
DOI: 10.6084/m9.figshare.16802533.v1
title: Ab-CoV_epitope_data.csv

description: Experimental and computationally predicted epitopes collected from literature for coronavirus related proteins.
DOI: 10.6084/m9.figshare.16802512.v1
title: Ab-CoV_viral_protein.csv

description: Details of SARS-CoV-2 related protein.
DOI: 10.6084/m9.figshare.16802512
title: Ab-CoV_viral_protein.csv

description: Details of SARS-CoV-2 related protein.
DOI: 10.6084/m9.figshare.16802599
title: antibody_PDBs_with_neutralization_profile.zip

description: PDB structures of the antibodies known to neutralize coronaviruses.
DOI: 10.6084/m9.figshare.16802608.v1
title: IMGT-Collier-de-Perles_light_chain.zip

description: Supplementary information: 2D antibody structure information (Collier-de-Perles representation) of coronavirus related neutralizing antibodies. (for light chains)
DOI: 10.6084/m9.figshare.16802608
title: IMGT-Collier-de-Perles_light_chain.zip

description: Supplementary information: 2D antibody structure information (Collier-de-Perles representation) of coronavirus related neutralizing antibodies. (for light chains)
DOI: 10.6084/m9.figshare.16802665
title: IMGT-Collier-de-Perles_heavy_chain.zip

description: Supplementary information: 2D antibody structure information (Collier-de-Perles representation) of coronavirus related neutralizing antibodies. (for heavy chain)<br>
DOI: 10.6084/m9.figshare.16802665.v1
title: IMGT-Collier-de-Perles_heavy_chain.zip

description: Supplementary information: 2D antibody structure information (Collier-de-Perles representation) of coronavirus related neutralizing antibodies. (for heavy chain)<br>