cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12115170
title: Plasma creatinine and oxidative stress biomarkers in amyotrophic lateral sclerosis

description: <b>Objective:</b> To determine the associations between plasma creatinine (PCr), plasma uric acid (PUA), and urinary oxidative stress (OS) biomarkers with the ALSFRS-R at baseline and survival in a large epidemiological cohort study (ALS COSMOS) with a well-phenotyped patient population (<i>N</i> = 355). <b>Methods:</b> Fasting plasma and first void urine samples were obtained. PCr, PUA, urinary 8-oxo-deoxy guanosine (8-oxodG), and 15-F<sub>2t</sub>-isoprostane (IsoP) were analyzed at baseline, near the midpoint of follow-up, and at the final blood draw (before death or withdrawal from study). We estimated associations between these biomarkers and the ALSFRS-R at baseline and survival. <b>Results:</b> At baseline, PCr correlated with ALSFRS-R (Spearman <i>r</i> = 0.30), percent (%) FVC (<i>r</i> = 0.20), PUA (<i>r</i> = 0.37), and 8-oxodG (<i>r</i> = −0.13, all <i>p</i> p r = 0.29, midpoint: <i>r</i> = 0.23, final: <i>r</i> = 0.38, all <i>p</i> <b>Conclusions:</b> To date, PCr predicted survival the best, compared to PUA, 8-oxodG, and IsoP. Although PCr represents the degree of muscle mass, it may also represent complex biochemical changes in ALS. Because the field has no reliable prognostic biomarkers, the importance of PCr warrants further investigation through clinical studies in ALS.
DOI: 10.6084/m9.figshare.12115170.v1
title: Plasma creatinine and oxidative stress biomarkers in amyotrophic lateral sclerosis

description: <b>Objective:</b> To determine the associations between plasma creatinine (PCr), plasma uric acid (PUA), and urinary oxidative stress (OS) biomarkers with the ALSFRS-R at baseline and survival in a large epidemiological cohort study (ALS COSMOS) with a well-phenotyped patient population (<i>N</i> = 355). <b>Methods:</b> Fasting plasma and first void urine samples were obtained. PCr, PUA, urinary 8-oxo-deoxy guanosine (8-oxodG), and 15-F<sub>2t</sub>-isoprostane (IsoP) were analyzed at baseline, near the midpoint of follow-up, and at the final blood draw (before death or withdrawal from study). We estimated associations between these biomarkers and the ALSFRS-R at baseline and survival. <b>Results:</b> At baseline, PCr correlated with ALSFRS-R (Spearman <i>r</i> = 0.30), percent (%) FVC (<i>r</i> = 0.20), PUA (<i>r</i> = 0.37), and 8-oxodG (<i>r</i> = −0.13, all <i>p</i> p r = 0.29, midpoint: <i>r</i> = 0.23, final: <i>r</i> = 0.38, all <i>p</i> <b>Conclusions:</b> To date, PCr predicted survival the best, compared to PUA, 8-oxodG, and IsoP. Although PCr represents the degree of muscle mass, it may also represent complex biochemical changes in ALS. Because the field has no reliable prognostic biomarkers, the importance of PCr warrants further investigation through clinical studies in ALS.
DOI: 10.6084/m9.figshare.12115080
title: TCGA Tumor clinical annotations

description: Data frame containing the clinical annotations of all TCGA samples<br>
DOI: 10.6084/m9.figshare.12115086
title: SPSS_Dataset_Dalit adoloscents

description: This the data set on the study of unplanned pregnancy and risky behaviors among the dalit adolescents girls in Bangladesh.<br>
DOI: 10.6084/m9.figshare.12115086.v1
title: SPSS_Dataset_Dalit adoloscents

description: This the data set on the study of unplanned pregnancy and risky behaviors among the dalit adolescents girls in Bangladesh.<br>
DOI: 10.6084/m9.figshare.12114885
title: Additional file 2 of In vitro cell culture of patient derived malignant pleural and peritoneal effusions for personalised drug screening

description: Additional file 2: Table S1. List of antibodies used for immunohistochemistry (IHC) studies. Abbreviations: thyroid transcription factor 1 (TTF-1), estrogen receptor (ER). Table S2. Quantification results of markers for proliferation, diagnosis and representative cellular components. The ratio of positive pixels to the total number of pixels of each marker measured by digitalised image approach was presented as the percentage expression ± SD (n = 3). Table S3. Quantification result of CD3+ immune cells.
DOI: 10.6084/m9.figshare.12114885.v1
title: Additional file 2 of In vitro cell culture of patient derived malignant pleural and peritoneal effusions for personalised drug screening

description: Additional file 2: Table S1. List of antibodies used for immunohistochemistry (IHC) studies. Abbreviations: thyroid transcription factor 1 (TTF-1), estrogen receptor (ER). Table S2. Quantification results of markers for proliferation, diagnosis and representative cellular components. The ratio of positive pixels to the total number of pixels of each marker measured by digitalised image approach was presented as the percentage expression ± SD (n = 3). Table S3. Quantification result of CD3+ immune cells.
DOI: 10.6084/m9.figshare.12114864
title: Additional file 1 of Transcriptomic analysis of brain tissues identifies a role for CCAAT enhancer binding protein β in HIV-associated neurocognitive disorder

description: Additional file 1: Table S1. Related to Figure 2. Full differential gene expression (DEG) between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S2. Related to Figure 2. Enriched cellular components between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S3. Related to Figure 2. Enriched biological processes between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S4. Disease-gene associations for differentially regulated genes in Minor Neurocognitive Disorders (MND) compared to HIV+ cognitively normal subjects (CNHIV+). Table S5. List of differentially regulated transcription factors and along with targets also differentially expressed in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S6. Related to Figure 2. All enriched pathways for C/EBPβ targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S7. Related to Figure 3. List of astrocyte specific marker genes that are also C/EBPβ targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S8. Related to Figure 3. All enriched pathways for C/EBPβ regulated astrocyte marker genes targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+).
DOI: 10.6084/m9.figshare.12114861
title: Additional file 5 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 5: Table S4. Quantitative results of skin secondary metabolite analysis and MANOVA output.
DOI: 10.6084/m9.figshare.12114864.v1
title: Additional file 1 of Transcriptomic analysis of brain tissues identifies a role for CCAAT enhancer binding protein β in HIV-associated neurocognitive disorder

description: Additional file 1: Table S1. Related to Figure 2. Full differential gene expression (DEG) between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S2. Related to Figure 2. Enriched cellular components between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S3. Related to Figure 2. Enriched biological processes between Minor Neurocognitive Disorder and HIV+ cognitively normal subjects (CNHIV+). Table S4. Disease-gene associations for differentially regulated genes in Minor Neurocognitive Disorders (MND) compared to HIV+ cognitively normal subjects (CNHIV+). Table S5. List of differentially regulated transcription factors and along with targets also differentially expressed in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S6. Related to Figure 2. All enriched pathways for C/EBPβ targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S7. Related to Figure 3. List of astrocyte specific marker genes that are also C/EBPβ targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+). Table S8. Related to Figure 3. All enriched pathways for C/EBPβ regulated astrocyte marker genes targets in Minor Neurocognitive Disorder compared to HIV+ cognitively normal subjects (CNHIV+).
DOI: 10.6084/m9.figshare.12114855
title: Additional file 3 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 3: Table S3. Quantitative results of skin primary metabolite analysis and MANOVA output.
DOI: 10.6084/m9.figshare.12114849
title: Additional file 2 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 2: Table S2. Texture properties, main cracking of cultivars at harvest and MANOVA output.
DOI: 10.6084/m9.figshare.12114861.v1
title: Additional file 5 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 5: Table S4. Quantitative results of skin secondary metabolite analysis and MANOVA output.
DOI: 10.6084/m9.figshare.12114849.v1
title: Additional file 2 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 2: Table S2. Texture properties, main cracking of cultivars at harvest and MANOVA output.
DOI: 10.6084/m9.figshare.12114843
title: Additional file 1 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 1: Table S1. Physiological traits of seventeen cherry cultivars at harvest and MANOVA output.
DOI: 10.6084/m9.figshare.12114843.v1
title: Additional file 1 of Sweet cherry fruit cracking: follow-up testing methods and cultivar-metabolic screening

description: Additional file 1: Table S1. Physiological traits of seventeen cherry cultivars at harvest and MANOVA output.
DOI: 10.5281/zenodo.4000327
title: Data generated for the EDO chapter case study

description: This archive contains a ZIP archive, `data.zip`, that contains several directories and a `README`. Further details of this archive's contents are described in that file. The source code used to generate this data is available here.
DOI: 10.6084/m9.figshare.12114825
title: Additional file 2 of Disease prediction via Bayesian hyperparameter optimization and ensemble learning

description: Additional file 2. The dataset used in the manuscript.The .csv file contains a breast cancer diagnosis dataset and a cardiovasculardisease dataset.
DOI: 10.5281/zenodo.4000299
title: Data generated for the EDO chapter case study

description: This archive contains a ZIP archive, `data.zip`, that contains several directories and a `README`. Further details of this archive's contents are described in that file. The source code used to generate this data is available here.
DOI: 10.6084/m9.figshare.12114819
title: Additional file 9 of Aggravated brain injury after neonatal hypoxic ischemia in microglia-depleted mice

description: Additional file 9: Table S2. qPCR Primer.
DOI: 10.6084/m9.figshare.12114825.v1
title: Additional file 2 of Disease prediction via Bayesian hyperparameter optimization and ensemble learning

description: Additional file 2. The dataset used in the manuscript.The .csv file contains a breast cancer diagnosis dataset and a cardiovasculardisease dataset.
DOI: 10.6084/m9.figshare.12114816
title: Additional file 8 of Aggravated brain injury after neonatal hypoxic ischemia in microglia-depleted mice

description: Additional file 8: Table S1. Genotyping Primer.
DOI: 10.6084/m9.figshare.12114819.v1
title: Additional file 9 of Aggravated brain injury after neonatal hypoxic ischemia in microglia-depleted mice

description: Additional file 9: Table S2. qPCR Primer.
DOI: 10.6084/m9.figshare.12114816.v1
title: Additional file 8 of Aggravated brain injury after neonatal hypoxic ischemia in microglia-depleted mice

description: Additional file 8: Table S1. Genotyping Primer.
DOI: 10.6084/m9.figshare.12114762
title: Additional file 1 of SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides

description: Additional file 1. List of 1 million SMILES strings extracted from the V1B library.
DOI: 10.6084/m9.figshare.12114762.v1
title: Additional file 1 of SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides

description: Additional file 1. List of 1 million SMILES strings extracted from the V1B library.
DOI: 10.6084/m9.figshare.12114738
title: Additional file 3 of Effect of Gallic acid and Myricetin on ovarian cancer models: a possible alternative antitumoral treatment

description: Additional file 3.
DOI: 10.6084/m9.figshare.12114741
title: Additional file 4 of Effect of Gallic acid and Myricetin on ovarian cancer models: a possible alternative antitumoral treatment

description: Additional file 4.
DOI: 10.6084/m9.figshare.12114738.v1
title: Additional file 3 of Effect of Gallic acid and Myricetin on ovarian cancer models: a possible alternative antitumoral treatment

description: Additional file 3.
DOI: 10.6084/m9.figshare.12114741.v1
title: Additional file 4 of Effect of Gallic acid and Myricetin on ovarian cancer models: a possible alternative antitumoral treatment

description: Additional file 4.
DOI: 10.6084/m9.figshare.12114678
title: Additional file 2 of Enteral nutrition protects children undergoing allogeneic hematopoietic stem cell transplantation from blood stream infections

description: Additional file 2. Mean BMI Z-score during hospitalization by group.
DOI: 10.6084/m9.figshare.12114678.v1
title: Additional file 2 of Enteral nutrition protects children undergoing allogeneic hematopoietic stem cell transplantation from blood stream infections

description: Additional file 2. Mean BMI Z-score during hospitalization by group.
DOI: 10.6084/m9.figshare.12114540
title: Supplementary Table S3

description: <b>Supplementary Table S3:</b> Expression of the 84 genes on the RT2 Profiler PCR Array that were identified using the IMPRes analysis. The genes significantly upregulated compared to controls are shown in red font, and downregulated genes in green font with respective fold changes.
DOI: 10.6084/m9.figshare.12114540.v1
title: Supplementary Table S3

description: <b>Supplementary Table S3:</b> Expression of the 84 genes on the RT2 Profiler PCR Array that were identified using the IMPRes analysis. The genes significantly upregulated compared to controls are shown in red font, and downregulated genes in green font with respective fold changes.
DOI: 10.6084/m9.figshare.12114432
title: Supplementary Table S1

description: <b>Supplementary Table S1:</b> The list of 84 genes that were used to design a custom 96-well RT2 Profiler PCR Array to validate genes and pathways identified using the IMPRes analysis. The custom PCR array also included controls for genomic DNA contamination (GDC, well H6, H7, and H12), reverse transcription efficiency (RTC, well H8 and H9), real-time PCR efficiency (PPC, well H10 and H11) and housekeeping genes β-glucuronidase (Gusb, well H1), glyceraldehyde-3-phosphate dehydrogenase (Gapdh, well H2), β-actin (Actb, well H3), heat shock protein 90 alpha (cytosolic), class B member (Hsp90ab1, well H4) and β-2 microglobulin (B2m, well H5).
DOI: 10.6084/m9.figshare.12114444
title: Supplementary Table S2

description: <b>Supplementary Table S2:</b> The genes identified to be differentially expressed (p&lt;0.05) for significant pathways (p&lt;0.05) using the IMPRes analysis.
DOI: 10.6084/m9.figshare.12114411
title: BoB_July

description: Copernicus marine service<br>Global Observed Ocean Physics Temperature Salinity Heights MLD Geostrophic Currents Sea Surface Salinity and Sea Surface Density Reprocessing<br>Contains variables: mixed layer depth, salinity, temperature, geostrophic zonal velocity from thermal wind equation, geostrophic meridional velocity from thermal wind equation, absolute height.
DOI: 10.6084/m9.figshare.12114432.v1
title: Supplementary Table S1

description: <b>Supplementary Table S1:</b> The list of 84 genes that were used to design a custom 96-well RT2 Profiler PCR Array to validate genes and pathways identified using the IMPRes analysis. The custom PCR array also included controls for genomic DNA contamination (GDC, well H6, H7, and H12), reverse transcription efficiency (RTC, well H8 and H9), real-time PCR efficiency (PPC, well H10 and H11) and housekeeping genes β-glucuronidase (Gusb, well H1), glyceraldehyde-3-phosphate dehydrogenase (Gapdh, well H2), β-actin (Actb, well H3), heat shock protein 90 alpha (cytosolic), class B member (Hsp90ab1, well H4) and β-2 microglobulin (B2m, well H5).
DOI: 10.6084/m9.figshare.12114393
title: BoB_June

description: Copernicus marine service<br>Global Observed Ocean Physics Temperature Salinity Heights MLD Geostrophic Currents Sea Surface Salinity and Sea Surface Density Reprocessing<br>Contains variables: mixed layer depth, salinity, temperature, geostrophic zonal velocity from thermal wind equation, geostrophic meridional velocity from thermal wind equation, absolute height.<br>
DOI: 10.6084/m9.figshare.12114444.v1
title: Supplementary Table S2

description: <b>Supplementary Table S2:</b> The genes identified to be differentially expressed (p&lt;0.05) for significant pathways (p&lt;0.05) using the IMPRes analysis.
DOI: 10.6084/m9.figshare.12114393.v1
title: BoB_June

description: From Marine Copernicus<br>
DOI: 10.6084/m9.figshare.12114411.v1
title: BoB_July

description: Copernicus marine service<br>Global Observed Ocean Physics Temperature Salinity Heights MLD Geostrophic Currents Sea Surface Salinity and Sea Surface Density Reprocessing<br>Contains variables: mixed layer depth, salinity, temperature, geostrophic zonal velocity from thermal wind equation, geostrophic meridional velocity from thermal wind equation, absolute height.
DOI: 10.6084/m9.figshare.12114315
title: Data+for+Agent+Motivation+and+Principal+Anticipation (2).xlsx

description: Data for paper "Agent Motivation and Principal Intentions: Non-monotonicity, Intentions, and Other Factors
DOI: 10.6084/m9.figshare.12114315.v1
title: Data+for+Agent+Motivation+and+Principal+Anticipation (2).xlsx

description: Data for paper "Agent Motivation and Principal Intentions: Non-monotonicity, Intentions, and Other Factors
DOI: 10.6084/m9.figshare.12114279
title: ESM_Tunisian_EQ-5D-3L_valuation.zip

description: ESM_1 contains a regression model that wasn't included in the manuscript.ESM_2 contains the 243 utility values for the EQ-5D-3L health states for TunisiaESM_3 contains the Tunisian EQ-5D-5L crosswalk value set
DOI: 10.6084/m9.figshare.12114279.v1
title: ESM_Tunisian_EQ-5D-3L_valuation.zip

description: ESM_1 contains a regression model that wasn't included in the manuscript.ESM_2 contains the 243 utility values for the EQ-5D-3L health states for TunisiaESM_3 contains the Tunisian EQ-5D-5L crosswalk value set
DOI: 10.6084/m9.figshare.12114129
title: Culicidae evolutionary history focusing on the Culicinae subfamily

description: Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans and other mammals. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquitoes species. Here we sequenced the mitogenomes of mosquitoes species through low-coverage sequencing and data mining. A total of 37 draft mitogenomes were assembled representing 11 genera and 16 of those were sequenced for the first time. The recovered mitogenomes showed a coverage breadth average of 81.24%. Most of the species were clustered in monophyletic clades with other members of their own genus with exception of the Aedini tribe which was paraphyletic corroborating other findings. We established for the first time the monophyletic status of eight species from the tribe Mansoniini including both Coquillettidia and Mansonia genus and established the basal positioning of Aedeomyiini and Uranotaeniini tribes regarding the Culicinae subfamily. Molecular clock analysis dated the Culicidae family emergence around 273 MYA and the split between Anophelinae and Culicinae subfamily around 182 MYA in the Jurassic period. Low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge generating basic fundamental information to the understanding of the role of these species as pathogen vectors.
DOI: 10.6084/m9.figshare.12114129.v1
title: Time and mode of Culicidae evolutionary history

description: Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans and other mammals. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquitoes species. Here we sequenced the mitogenomes of mosquitoes species through low-coverage sequencing and data mining. A total of 37 draft mitogenomes were assembled representing 11 genera and 16 of those were sequenced for the first time. The recovered mitogenomes showed a coverage breadth average of 81.24%. Most of the species were clustered in monophyletic clades with other members of their own genus with exception of the Aedini tribe which was paraphyletic corroborating other findings. We established for the first time the monophyletic status of eight species from the tribe Mansoniini including both Coquillettidia and Mansonia genus and established the basal positioning of Aedeomyiini and Uranotaeniini tribes regarding the Culicinae subfamily. Molecular clock analysis dated the Culicidae family emergence around 273 MYA and the split between Anophelinae and Culicinae subfamily around 182 MYA in the Jurassic period. Low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge generating basic fundamental information to the understanding of the role of these species as pathogen vectors.
DOI: 10.6084/m9.figshare.12114129.v3
title: Culicidae evolutionary history focusing on the Culicinae subfamily

description: Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans and other mammals. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquitoes species. Here we sequenced the mitogenomes of mosquitoes species through low-coverage sequencing and data mining. A total of 37 draft mitogenomes were assembled representing 11 genera and 16 of those were sequenced for the first time. The recovered mitogenomes showed a coverage breadth average of 81.24%. Most of the species were clustered in monophyletic clades with other members of their own genus with exception of the Aedini tribe which was paraphyletic corroborating other findings. We established for the first time the monophyletic status of eight species from the tribe Mansoniini including both Coquillettidia and Mansonia genus and established the basal positioning of Aedeomyiini and Uranotaeniini tribes regarding the Culicinae subfamily. Molecular clock analysis dated the Culicidae family emergence around 273 MYA and the split between Anophelinae and Culicinae subfamily around 182 MYA in the Jurassic period. Low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge generating basic fundamental information to the understanding of the role of these species as pathogen vectors.