cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10473806
title: Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome

description: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time. Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed. A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA <i>R</i><sup>2</sup> = 0.044, <i>p</i> = .002) but later courses did not (<i>R</i><sup>2</sup> = 0.023, <i>p</i> = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray–Curtis distance 0.29 vs. 0.63, Wilcoxon <i>p</i> = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (<i>p</i> &lt; .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome. Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in <i>Escherichia coli</i>. Further characterization of the infant mycobiome is still needed.
DOI: 10.6084/m9.figshare.10473806.v1
title: Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome

description: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time. Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed. A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA <i>R</i><sup>2</sup> = 0.044, <i>p</i> = .002) but later courses did not (<i>R</i><sup>2</sup> = 0.023, <i>p</i> = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray–Curtis distance 0.29 vs. 0.63, Wilcoxon <i>p</i> = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (<i>p</i> &lt; .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome. Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in <i>Escherichia coli</i>. Further characterization of the infant mycobiome is still needed.
DOI: 10.6084/m9.figshare.11522382
title: Identifying the differentially expressed microRNAs in autoimmunity: A systemic review and meta-analysis

description: The evidence indicates that microRNAs (miRNAs) can regulate gene expression and play an important role in the pathogenesis of autoimmune diseases, yet studies on expression profiles of miRNAs are still inconclusive. Our objective is to identify miRNAs that demonstrate enduring differential expression on autoimmune diseases. A systemic review and meta-analysis were performed by analysing the expression profile of miRNAs in several types of autoimmune disease, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type-1 diabetes (T1D). Several most significant differentially expressed miRNAs were identified and showed significant deregulation in autoimmune diseases. The most compelling results for SLE were with miR-21, miR-148a, miR-223, miR-125b in blood and miR-26a in kidney samples, for RA, miR-21, miR-24, miR-26a, miR-155 and miR-223 in blood, and for T1D, miR-148a, miR-181a in blood and miR-21, miR-155 in urine samples. Interestingly, some of miRNAs were differentially expressed in more than one autoimmune disease, such as miR-21, miR-26a, miR-155, miR-148a, miR-223. These miRNAs are commonly associated with the immune response and increases in the activity of the immune system and inflammation in specific organs such as skin, joint, lung, and kidney. These miRNAs can potentially be not only good biomarkers for the prediction, diagnosis, but also therapeutic targets in autoimmune diseases.
DOI: 10.6084/m9.figshare.11522382.v1
title: Identifying the differentially expressed microRNAs in autoimmunity: A systemic review and meta-analysis

description: The evidence indicates that microRNAs (miRNAs) can regulate gene expression and play an important role in the pathogenesis of autoimmune diseases, yet studies on expression profiles of miRNAs are still inconclusive. Our objective is to identify miRNAs that demonstrate enduring differential expression on autoimmune diseases. A systemic review and meta-analysis were performed by analysing the expression profile of miRNAs in several types of autoimmune disease, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type-1 diabetes (T1D). Several most significant differentially expressed miRNAs were identified and showed significant deregulation in autoimmune diseases. The most compelling results for SLE were with miR-21, miR-148a, miR-223, miR-125b in blood and miR-26a in kidney samples, for RA, miR-21, miR-24, miR-26a, miR-155 and miR-223 in blood, and for T1D, miR-148a, miR-181a in blood and miR-21, miR-155 in urine samples. Interestingly, some of miRNAs were differentially expressed in more than one autoimmune disease, such as miR-21, miR-26a, miR-155, miR-148a, miR-223. These miRNAs are commonly associated with the immune response and increases in the activity of the immune system and inflammation in specific organs such as skin, joint, lung, and kidney. These miRNAs can potentially be not only good biomarkers for the prediction, diagnosis, but also therapeutic targets in autoimmune diseases.
DOI: 10.6084/m9.figshare.19386804
title: Additional file 1 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 1: Supplemental Figure 1. Identification of total proteins and immunoprecipitated proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Supplemental Figure 2. Summary of chromatin immunoprecipitation sequencing (ChIP-seq). Supplemental Figure 3. Targets of GIF1 detected by chromatin immunoprecipitation sequencing (ChIP-seq). Supplemental Figure 4. Schematic diagram of the gif1 over-expression construct. The construct components include the T-DNA right border, RB; and left border, LB; CaMV35S promoter, CaMV35S; terminator of nopaline synthase gene, tnos; enhanced green fluorescent protein gene, eGFP; the phosphinothricin acetyltransferase cassette, bar. Supplemental Table 1. Conservation of identified proteins in Arabidopsis, maize leaf and maize ear. Supplemental. Table 2. Putative GIF1-bound targets identified by ChIP-seq and RNA-seq. Supplemental Table 3. Primer sequences used in this study.
DOI: 10.6084/m9.figshare.19386804.v1
title: Additional file 1 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 1: Supplemental Figure 1. Identification of total proteins and immunoprecipitated proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Supplemental Figure 2. Summary of chromatin immunoprecipitation sequencing (ChIP-seq). Supplemental Figure 3. Targets of GIF1 detected by chromatin immunoprecipitation sequencing (ChIP-seq). Supplemental Figure 4. Schematic diagram of the gif1 over-expression construct. The construct components include the T-DNA right border, RB; and left border, LB; CaMV35S promoter, CaMV35S; terminator of nopaline synthase gene, tnos; enhanced green fluorescent protein gene, eGFP; the phosphinothricin acetyltransferase cassette, bar. Supplemental Table 1. Conservation of identified proteins in Arabidopsis, maize leaf and maize ear. Supplemental. Table 2. Putative GIF1-bound targets identified by ChIP-seq and RNA-seq. Supplemental Table 3. Primer sequences used in this study.
DOI: 10.6084/m9.figshare.19386807
title: Additional file 2 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 2: Supplemental Data Set 1. A list of differentially expressed genes and their expression levels. Gene expression is calculated using the FPKM (Fragments per kilobase transcriptome per million mapped) method. Fold change: average FPKM of given gene in gif1 mutant / that in wild type. The differentially expression genes (DEGs) are identified using p&lt;10-5 and q &lt;10-4. Rep: biological replicate.
DOI: 10.6084/m9.figshare.19386807.v1
title: Additional file 2 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 2: Supplemental Data Set 1. A list of differentially expressed genes and their expression levels. Gene expression is calculated using the FPKM (Fragments per kilobase transcriptome per million mapped) method. Fold change: average FPKM of given gene in gif1 mutant / that in wild type. The differentially expression genes (DEGs) are identified using p&lt;10-5 and q &lt;10-4. Rep: biological replicate.
DOI: 10.6084/m9.figshare.19386810
title: Additional file 3 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 3: Supplemental Data Set 2. Gene ontology enrichment of down-regulated differentially expressed genes. GO_acc: GO accession; term_type includes molecular function (F), cellular component (C), biological process (P); queryitem: item number mapping the GO in the query list; querytotal: total number of query list; bgitem: item number mapping the GO in the background; bgtotal: total number of background; FDR: Yekutieli (FDR under dependency).
DOI: 10.6084/m9.figshare.19386810.v1
title: Additional file 3 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 3: Supplemental Data Set 2. Gene ontology enrichment of down-regulated differentially expressed genes. GO_acc: GO accession; term_type includes molecular function (F), cellular component (C), biological process (P); queryitem: item number mapping the GO in the query list; querytotal: total number of query list; bgitem: item number mapping the GO in the background; bgtotal: total number of background; FDR: Yekutieli (FDR under dependency).
DOI: 10.6084/m9.figshare.19386813
title: Additional file 4 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 4: Supplemental Data Set 3. Gene ontology enrichment of up-regulated differentially expressed genes. GO_acc: GO accession; term_type includes molecular function (F), cellular component (C), biological process (P); queryitem: item number mapping the GO in the query list; querytotal: total number of query list; bgitem: item number mapping the GO in the background; bgtotal: total number of background; FDR: Yekutieli (FDR under dependency).
DOI: 10.6084/m9.figshare.19386813.v1
title: Additional file 4 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 4: Supplemental Data Set 3. Gene ontology enrichment of up-regulated differentially expressed genes. GO_acc: GO accession; term_type includes molecular function (F), cellular component (C), biological process (P); queryitem: item number mapping the GO in the query list; querytotal: total number of query list; bgitem: item number mapping the GO in the background; bgtotal: total number of background; FDR: Yekutieli (FDR under dependency).
DOI: 10.6084/m9.figshare.19386816
title: Additional file 5 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 5: Supplemental Data Set 4. Representative GO terms of differentially expressed genes in the ~5 mm ears of the gif1-1 and the wild type.
DOI: 10.6084/m9.figshare.19386816.v1
title: Additional file 5 of GIF1 controls ear inflorescence architecture and floral development by regulating key genes in hormone biosynthesis and meristem determinacy in maize

description: Additional file 5: Supplemental Data Set 4. Representative GO terms of differentially expressed genes in the ~5 mm ears of the gif1-1 and the wild type.
DOI: 10.48597/n9mk-tm34
title: Measurement of Manganese at Vavihill

description: Measurement of Manganese at Vavihill
DOI: 10.48597/r9wh-xctd
title: Measurement of Chloride at Vavihill

description: Measurement of Chloride at Vavihill
DOI: 10.6084/m9.figshare.19386823
title: Additional file 2 of Relationship between gene expression patterns from nasopharyngeal swabs and serum biomarkers in patients hospitalized with COVID-19, following treatment with the neutralizing monoclonal antibody bamlanivimab

description: Additional file 2. Listing of inflammation-related and COVID-19 implicated genes in custom Ion AmpliSeq RNA panel.
DOI: 10.48597/tmh2-hchy
title: Measurement of Chromium at Vavihill

description: Measurement of Chromium at Vavihill
DOI: 10.6084/m9.figshare.19386823.v1
title: Additional file 2 of Relationship between gene expression patterns from nasopharyngeal swabs and serum biomarkers in patients hospitalized with COVID-19, following treatment with the neutralizing monoclonal antibody bamlanivimab

description: Additional file 2. Listing of inflammation-related and COVID-19 implicated genes in custom Ion AmpliSeq RNA panel.
DOI: 10.48597/ucdw-cppp
title: Measurement of Cobalt at Vavihill

description: Measurement of Cobalt at Vavihill
DOI: 10.48597/22wf-9zrz
title: Measurement of Aerosol_absorption_coefficient at Southern Great Plains E13

description: Measurement of Aerosol_absorption_coefficient at Southern Great Plains E13
DOI: 10.48597/2a7g-3e6n
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch
DOI: 10.48597/2bq6-ufbb
title: Measurement of Aerosol light scattering at Cape San Juan

description: Measurement of Aerosol light scattering at Cape San Juan
DOI: 10.48597/2pgn-bbzd
title: Measurement of Aerosol light scattering at K-puszta

description: Measurement of Aerosol light scattering at K-puszta
DOI: 10.48597/2z7f-qrbf
title: Measurement of Ozone at Cabauw Wielsekade

description: Measurement of Ozone at Cabauw Wielsekade
DOI: 10.48597/3epf-h9rz
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/3wd2-nzyg
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/4dje-5nb3
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/4gdk-cpqd
title: Measurement of Heavy metals and inorganics in air and particle phase at Cabauw Wielsekade

description: Measurement of Heavy metals and inorganics in air and particle phase at Cabauw Wielsekade
DOI: 10.48597/4x55-8ajp
title: Measurement of Sulphate_corrected at Birkenes

description: Measurement of Sulphate_corrected at Birkenes
DOI: 10.48597/53xw-8bmd
title: Measurement of Aerosol light scattering at Southern Great Plains E13

description: Measurement of Aerosol light scattering at Southern Great Plains E13
DOI: 10.48597/58ef-937u
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch
DOI: 10.48597/5d3q-e7fj
title: Measurement of Ozone at Vredepeel

description: Measurement of Ozone at Vredepeel
DOI: 10.48597/5n9r-b3pc
title: Measurement of Pm25_mass at Cabauw Wielsekade

description: Measurement of Pm25_mass at Cabauw Wielsekade
DOI: 10.48597/5uwy-hg23
title: Measurement of Aerosol light scattering at Southern Great Plains E13

description: Measurement of Aerosol light scattering at Southern Great Plains E13
DOI: 10.48597/5xet-bm3m
title: Measurement of Aerosol light scattering at Southern Great Plains E13

description: Measurement of Aerosol light scattering at Southern Great Plains E13
DOI: 10.48597/62rx-esuz
title: Measurement of Aerosol light scattering at K-puszta

description: Measurement of Aerosol light scattering at K-puszta
DOI: 10.48597/79fu-askr
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch
DOI: 10.48597/7b65-zvzx
title: Measurement of Sulphur_dioxide at Cabauw Wielsekade

description: Measurement of Sulphur_dioxide at Cabauw Wielsekade
DOI: 10.48597/7w2s-8eu7
title: Measurement of Pm10_mass at Vredepeel

description: Measurement of Pm10_mass at Vredepeel
DOI: 10.48597/7xkc-qtwa
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch
DOI: 10.48597/86kx-cj7w
title: Measurement of Aerosol light scattering at Southern Great Plains E13

description: Measurement of Aerosol light scattering at Southern Great Plains E13
DOI: 10.48597/8vvq-k7n9
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/8xvn-pdgs
title: Measurement of Inorganics in air and particle phase at Birkenes

description: Measurement of Inorganics in air and particle phase at Birkenes
DOI: 10.48597/8z8y-2vte
title: Measurement of Inorganics in air and particle phase at Birkenes

description: Measurement of Inorganics in air and particle phase at Birkenes
DOI: 10.48597/9a8g-6f53
title: Measurement of Heavy metals at Vredepeel

description: Measurement of Heavy metals at Vredepeel
DOI: 10.48597/9bbz-rerw
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch
DOI: 10.48597/9nwz-tpwf
title: Measurement of Carbon_monoxide at Cabauw Wielsekade

description: Measurement of Carbon_monoxide at Cabauw Wielsekade
DOI: 10.48597/ac42-jaj5
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/amys-cu2x
title: Measurement of Aerosol_absorption_coefficient at Steamboat Springs, Colorado (Storm Peak Laboratory)

description: Measurement of Aerosol_absorption_coefficient at Steamboat Springs, Colorado (Storm Peak Laboratory)
DOI: 10.48597/aq56-3hu4
title: Measurement of Aerosol light scattering at K-puszta

description: Measurement of Aerosol light scattering at K-puszta
DOI: 10.48597/asct-brfz
title: Measurement of Aerosol_absorption_coefficient at Steamboat Springs, Colorado (Storm Peak Laboratory)

description: Measurement of Aerosol_absorption_coefficient at Steamboat Springs, Colorado (Storm Peak Laboratory)
DOI: 10.48597/ate4-64ew
title: Measurement of Aerosol light scattering at Southern Great Plains E13

description: Measurement of Aerosol light scattering at Southern Great Plains E13
DOI: 10.48597/b36y-ucdg
title: Measurement of Pm10_mass at Eibergen

description: Measurement of Pm10_mass at Eibergen
DOI: 10.48597/b5be-2kh7
title: Measurement of Inorganics in air and particle phase at Birkenes

description: Measurement of Inorganics in air and particle phase at Birkenes
DOI: 10.48597/b6yn-bjkv
title: Measurement of Pm10_mass at De Zilk

description: Measurement of Pm10_mass at De Zilk
DOI: 10.48597/cf6h-8zaj
title: Measurement of Relative_humidity at Cape San Juan

description: Measurement of Relative_humidity at Cape San Juan
DOI: 10.48597/cp95-bcz2
title: Measurement of Temperature at Cape San Juan

description: Measurement of Temperature at Cape San Juan
DOI: 10.48597/cpw5-9pcx
title: Measurement of Temperature at Southern Great Plains E13

description: Measurement of Temperature at Southern Great Plains E13
DOI: 10.60521/331528
title: Processed Acoustic Backscatter, Sidescan and Swath Bathymetry Data acquired during R/V Thomas G. Thompson expedition TN319 (2015)

description: This data set was acquired with a Kongsberg Maritime EM302 Multibeam Sonar during R/V Thomas G. Thompson expedition TN319 conducted in 2015 (Chief Scientist: Dr. Craig Smith). These data files are of MBSystem-compatible format and include Acoustic Backscatter, Sidescan and Swath Bathymetry data that were processed after acquisition. This data was processed by Girl Talk Program @ LDEO and was included in the Global Multi-Resolution Topography (GMRT) Synthesis (version 4.2.1). Girl Talk 2024 participants who processed these data include: Mariapaola Ambrosone, Carol Calle, Jillary Castillo, Charlene Chung, Gabriella Garcia, JK Goongoon, Naeema Haque, Maria Henriquez, Albane Hoxha, May Lyle, Jarely Mendez, Fatima Nasyr, Emely Nunez, Diomaris Padilla, Juniagay Patterson, Valeria A. Pérez Rivera, Yuliya Selevich, Elena Shefsky, Otillia Steadman, Alan Vision.
DOI: 10.48597/d2d3-a47f
title: Measurement of Carbon_monoxide at Cabauw Wielsekade

description: Measurement of Carbon_monoxide at Cabauw Wielsekade
DOI: 10.48597/d82s-xa6z
title: Measurement of Particle_number_concentration at Jungfraujoch

description: Measurement of Particle_number_concentration at Jungfraujoch