cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24885216
title: Supplementary Material for: Association of Root Biofilm Bacteriome with Root Caries Lesion Severity and Activity

description: Introduction: This research aimed to assess the association of root biofilm bacteriome with root caries lesion severity and activity in institutionalised Colombian elderlies and was conducted to gather data on the root caries bacteriome in this population. Methods: A bacteriome evaluation of biofilm samples from sound, and carious root surfaces was performed. Root caries was categorised (ICDAS Root criteria) based on severity (Sound surfaces, Initial: non-cavitated, Moderate/Extensive combined: cavitated) and activity status (Active and Inactive). DNA was extracted and the V4 region of the 16S rRNA gene was sequenced, after the classification of features employing amplicon sequence variants (ASVs) and taxonomic assignment via the Human Oral Microbiome Database (HOMD). Bacterial richness, diversity (Simpson's and Shannon's indices), and relative abundance estimation were assessed and compared based on root caries severity and activity status (including Sound surfaces). Results: A total of 130 biofilm samples were examined: Sound (n=45) and with root caries lesions (n=85; Initial: n=41; Moderate/Extensive: n=44; Active: n=60; Inactive: n=25). Species richness was significantly lower in biofilms from Moderate/Extensive and Active groups compared to Sound sites. There was a higher relative abundance of species like Lechtotricia wadei, Capnocytophaga granulosa, Cardiobacterium valvarum, Porphyromonas pasteri -in Sound sites; Dialister invisus, Streptococcus mutans, Pseudoramibacter alactolyticus and Bacteroidetes (G-5) bacterium 511 -in Moderate/Extensive lesions, and Fusobacterium nucleatum subsp. animalis, Prevotella denticola, Lactobacillus fermentum, Saccharibacteria (TM7) [G-5] bacterium HMT 356 -in active lesions. Conclusion: Root caries bacteriome exhibited differences in species proportions between the compared groups. Specifically, cavitated lesions and active lesions showed higher relative abundance of acidogenic bacteria.
DOI: 10.6084/m9.figshare.24885216.v1
title: Supplementary Material for: Association of Root Biofilm Bacteriome with Root Caries Lesion Severity and Activity

description: Introduction: This research aimed to assess the association of root biofilm bacteriome with root caries lesion severity and activity in institutionalised Colombian elderlies and was conducted to gather data on the root caries bacteriome in this population. Methods: A bacteriome evaluation of biofilm samples from sound, and carious root surfaces was performed. Root caries was categorised (ICDAS Root criteria) based on severity (Sound surfaces, Initial: non-cavitated, Moderate/Extensive combined: cavitated) and activity status (Active and Inactive). DNA was extracted and the V4 region of the 16S rRNA gene was sequenced, after the classification of features employing amplicon sequence variants (ASVs) and taxonomic assignment via the Human Oral Microbiome Database (HOMD). Bacterial richness, diversity (Simpson's and Shannon's indices), and relative abundance estimation were assessed and compared based on root caries severity and activity status (including Sound surfaces). Results: A total of 130 biofilm samples were examined: Sound (n=45) and with root caries lesions (n=85; Initial: n=41; Moderate/Extensive: n=44; Active: n=60; Inactive: n=25). Species richness was significantly lower in biofilms from Moderate/Extensive and Active groups compared to Sound sites. There was a higher relative abundance of species like Lechtotricia wadei, Capnocytophaga granulosa, Cardiobacterium valvarum, Porphyromonas pasteri -in Sound sites; Dialister invisus, Streptococcus mutans, Pseudoramibacter alactolyticus and Bacteroidetes (G-5) bacterium 511 -in Moderate/Extensive lesions, and Fusobacterium nucleatum subsp. animalis, Prevotella denticola, Lactobacillus fermentum, Saccharibacteria (TM7) [G-5] bacterium HMT 356 -in active lesions. Conclusion: Root caries bacteriome exhibited differences in species proportions between the compared groups. Specifically, cavitated lesions and active lesions showed higher relative abundance of acidogenic bacteria.
DOI: 10.6084/m9.figshare.20330280
title: Lactic acid bacteria viability in different refrigerated food matrices: a systematic review and Meta‑analysis

description: The aim of this systematic review and meta-analysis was to determine which variables affect the viability of lactic acid bacteria (LAB) added to different types of refrigerated foods during the first 28 days. Scopus, ScienceDirect, PubMed and Cochrane Central Register of Reviews databases were searched from 1997 to April 2022. A total of 278 studies, which showed randomized and controlled experiments published in peer reviewed journals, were included. The viability of LAB in different moments during the storage process was synthesized as mean point estimate (MPE) via random-effects meta-analyses and the effect of multiple factors on the LAB´s viability was evaluated by multiple meta-regression. The meta-analysis showed that the decrease in LAB viability will be more abrupt the greater the initial dose. The physical structure of food may influence bacterial viability. Fruit was the type of product that most quickly lost viability. Co-culture of two or more species did not affect viability. Preservation methods had an unfavorable effect and prebiotics had a beneficial effect on bacterial viability. Viability was genus dependent. The data obtained in this study provide an overview of the factors to be taken into account for the design of new foods.
DOI: 10.6084/m9.figshare.20310018
title: Effect of chicory-derived inulin-type fructans on abundance of <i>Bifidobacterium</i> and on bowel function: a systematic review with meta-analyses

description: Inulin-type fructans are considered to stimulate the growth of beneficial microorganisms, like <i>Bifidobacterium</i> in the gut and support health. However, both the fructan source and chemical structure may modify these effects. A systematic review was conducted to assess the effects of chicory-derived inulin-type fructans consumed either in specific foods or as dietary supplements on abundance of <i>Bifidobacterium</i> in the gut and on health-related outcomes. Three electronic databases and two clinical trial registries were systematically searched until January 2021. Two authors independently selected randomized controlled trials that investigated with a protocol of minimum seven days supplementation the effect of chicory-derived inulin-type fructans on <i>Bifidobacterium</i> abundance in any population. Meta-analyses with random-effects model were conducted on <i>Bifidobacterium</i> abundance and bowel function parameters. We evaluated risk of bias using Cochrane RoB tool. Chicory-derived inulin-type fructans at a dose of 3–20 g/day significantly increased <i>Bifidobacterium</i> abundance in participants with an age range from 0 to 83 years (standardized mean difference: 0.83, 95% CI: 0.58–1.08; <i>p</i> &lt; 0.01; 50 studies; 2525 participants). Significant bifidogenic effects were observed in healthy individuals and in populations with health impairments, except gastrointestinal disorders. Significant beneficial effects on bowel function parameters were observed in healthy subjects. Chicory-derived inulin-type fructans may have significant bifidogenic effects and may beneficially influence bowel function in healthy individuals. PROSPERO registration number CRD42020162892.
DOI: 10.6084/m9.figshare.20310018.v1
title: Effect of chicory-derived inulin-type fructans on abundance of <i>Bifidobacterium</i> and on bowel function: a systematic review with meta-analyses

description: Inulin-type fructans are considered to stimulate the growth of beneficial microorganisms, like <i>Bifidobacterium</i> in the gut and support health. However, both the fructan source and chemical structure may modify these effects. A systematic review was conducted to assess the effects of chicory-derived inulin-type fructans consumed either in specific foods or as dietary supplements on abundance of <i>Bifidobacterium</i> in the gut and on health-related outcomes. Three electronic databases and two clinical trial registries were systematically searched until January 2021. Two authors independently selected randomized controlled trials that investigated with a protocol of minimum seven days supplementation the effect of chicory-derived inulin-type fructans on <i>Bifidobacterium</i> abundance in any population. Meta-analyses with random-effects model were conducted on <i>Bifidobacterium</i> abundance and bowel function parameters. We evaluated risk of bias using Cochrane RoB tool. Chicory-derived inulin-type fructans at a dose of 3–20 g/day significantly increased <i>Bifidobacterium</i> abundance in participants with an age range from 0 to 83 years (standardized mean difference: 0.83, 95% CI: 0.58–1.08; <i>p</i> &lt; 0.01; 50 studies; 2525 participants). Significant bifidogenic effects were observed in healthy individuals and in populations with health impairments, except gastrointestinal disorders. Significant beneficial effects on bowel function parameters were observed in healthy subjects. Chicory-derived inulin-type fructans may have significant bifidogenic effects and may beneficially influence bowel function in healthy individuals. PROSPERO registration number CRD42020162892.
DOI: 10.6084/m9.figshare.20286600
title: The effect of vitamin D supplementation on depressive symptoms in adults: A systematic review and meta‐analysis of randomized controlled trials

description: Neurosteroid and immunological actions of vitamin D may regulate depression-linked physiology. Meta‐analyses investigating the effect of vitamin D on depression have been inconsistent. This meta-analysis investigated the efficacy of vitamin D in reducing depressive symptoms among adults in randomized placebo-controlled trials (RCT). General and clinical populations, and studies of ill individuals with systemic diseases were included. Light therapy, co-supplementation (except calcium) and bipolar disorder were exclusionary. Databases Medline, PsycINFO, CINAHL and The Cochrane Library were searched to identify relevant articles in English published before April 2022. Cochrane risk-of-bias tool (RoB 2) and GRADE were used to appraise studies. Forty-one RCTs (<i>n</i> = 53,235) were included. Analyses based on random-effects models were performed with the Comprehensive Meta-analysis Software. Results for main outcome (<i>n</i> = 53,235) revealed a positive effect of vitamin D on depressive symptoms (Hedges’ <i>g</i> = −0.317, 95% CI [−0.405, −0.230], <i>p</i> &lt; 0.001, I<sup>2</sup> = 88.16%; GRADE: very low certainty). RoB assessment was concerning in most studies. Notwithstanding high heterogeneity, vitamin D supplementation ≥ 2,000 IU/day appears to reduce depressive symptoms. Future research should investigate possible benefits of augmenting standard treatments with vitamin D in clinical depression. PROSPERO registration number: CRD42020149760. Funding: Finnish Medical Foundation, grant 4120 and Juho Vainio Foundation, grant 202100353.
DOI: 10.6084/m9.figshare.20286600.v1
title: The effect of vitamin D supplementation on depressive symptoms in adults: A systematic review and meta‐analysis of randomized controlled trials

description: Neurosteroid and immunological actions of vitamin D may regulate depression-linked physiology. Meta‐analyses investigating the effect of vitamin D on depression have been inconsistent. This meta-analysis investigated the efficacy of vitamin D in reducing depressive symptoms among adults in randomized placebo-controlled trials (RCT). General and clinical populations, and studies of ill individuals with systemic diseases were included. Light therapy, co-supplementation (except calcium) and bipolar disorder were exclusionary. Databases Medline, PsycINFO, CINAHL and The Cochrane Library were searched to identify relevant articles in English published before April 2022. Cochrane risk-of-bias tool (RoB 2) and GRADE were used to appraise studies. Forty-one RCTs (<i>n</i> = 53,235) were included. Analyses based on random-effects models were performed with the Comprehensive Meta-analysis Software. Results for main outcome (<i>n</i> = 53,235) revealed a positive effect of vitamin D on depressive symptoms (Hedges’ <i>g</i> = −0.317, 95% CI [−0.405, −0.230], <i>p</i> &lt; 0.001, I<sup>2</sup> = 88.16%; GRADE: very low certainty). RoB assessment was concerning in most studies. Notwithstanding high heterogeneity, vitamin D supplementation ≥ 2,000 IU/day appears to reduce depressive symptoms. Future research should investigate possible benefits of augmenting standard treatments with vitamin D in clinical depression. PROSPERO registration number: CRD42020149760. Funding: Finnish Medical Foundation, grant 4120 and Juho Vainio Foundation, grant 202100353.
DOI: 10.6084/m9.figshare.20330280.v1
title: Lactic acid bacteria viability in different refrigerated food matrices: a systematic review and Meta‑analysis

description: The aim of this systematic review and meta-analysis was to determine which variables affect the viability of lactic acid bacteria (LAB) added to different types of refrigerated foods during the first 28 days. Scopus, ScienceDirect, PubMed and Cochrane Central Register of Reviews databases were searched from 1997 to April 2022. A total of 278 studies, which showed randomized and controlled experiments published in peer reviewed journals, were included. The viability of LAB in different moments during the storage process was synthesized as mean point estimate (MPE) via random-effects meta-analyses and the effect of multiple factors on the LAB´s viability was evaluated by multiple meta-regression. The meta-analysis showed that the decrease in LAB viability will be more abrupt the greater the initial dose. The physical structure of food may influence bacterial viability. Fruit was the type of product that most quickly lost viability. Co-culture of two or more species did not affect viability. Preservation methods had an unfavorable effect and prebiotics had a beneficial effect on bacterial viability. Viability was genus dependent. The data obtained in this study provide an overview of the factors to be taken into account for the design of new foods.
DOI: 10.5281/zenodo.10417840
title: THE "SOFT POWER" FACTOR IN THE FOREIGN POLICY OF THE REPUBLIC OF KOREA IN ASIAN COUNTRIES.
DOI: 10.5281/zenodo.10417841
title: THE "SOFT POWER" FACTOR IN THE FOREIGN POLICY OF THE REPUBLIC OF KOREA IN ASIAN COUNTRIES.
DOI: 10.2907/eusilc2004-2022v1
title: EU Statistics on Income and Living Conditions microdata, release 2 in 2023, data 2004-2022 version 1
DOI: 10.25573/serc.23960784
title: Coastal Blue Carbon Assessment of Mangroves, Salt Marshes, and Salt Barrens in Tampa Bay, Florida, USA

description: Compared to other terrestrial environments, coastal “blue carbon” habitats such as salt marshes and mangrove forests sequester disproportionately large amounts of carbon as standing plant biomass and peat deposits. This study quantified organic carbon stocks in 16 salt marshes, salt barrens, and mangrove forests in Tampa Bay, Florida, USA. The sites included natural, restored, and created wetlands of varying ages and degrees of anthropogenic impacts. Peat deposits were generally less than 30-cm deep and organic content rapidly decreased with depth in all habitats. The top 15 cm of mangrove soil contained an average of 11.0% organic carbon by weight, salt marshes contained 6.6%, and salt barrens contained 1.0%. Total organic carbon stock in mangroves was 133.6 ± 12.8 Mg ha<sup>−1</sup>, with 69.5% of that carbon stored belowground. Salt marshes contained 66.4 ± 25.0 Mg ha<sup>−1</sup> (93.5% belowground carbon), and salt barrens contained 26.6 ± 8.3 Mg ha<sup>−1</sup> (96.1% belowground carbon). These values were much lower than global averages for carbon stocks in mangroves and salt marshes, likely due to Tampa Bay’s location near the northern limit of mangrove habitat, sandy soil, young age of the restored wetlands, presence of mosquito ditches, and recent habitat conversion from salt marshes to mangroves. In the late 1800s, Tampa Bay’s coastal wetlands were dominated by salt marshes, but today they are dominated by mangroves. Based on the blue carbon values from the natural sites in this study, this habitat switching has led to the additional sequestration of 141,000 Mg of carbon in remaining wetlands in the Tampa Bay watershed.
DOI: 10.25573/serc.23960784.v1
title: Coastal Blue Carbon Assessment of Mangroves, Salt Marshes, and Salt Barrens in Tampa Bay, Florida, USA

description: Compared to other terrestrial environments, coastal “blue carbon” habitats such as salt marshes and mangrove forests sequester disproportionately large amounts of carbon as standing plant biomass and peat deposits. This study quantified organic carbon stocks in 16 salt marshes, salt barrens, and mangrove forests in Tampa Bay, Florida, USA. The sites included natural, restored, and created wetlands of varying ages and degrees of anthropogenic impacts. Peat deposits were generally less than 30-cm deep and organic content rapidly decreased with depth in all habitats. The top 15 cm of mangrove soil contained an average of 11.0% organic carbon by weight, salt marshes contained 6.6%, and salt barrens contained 1.0%. Total organic carbon stock in mangroves was 133.6 ± 12.8 Mg ha<sup>−1</sup>, with 69.5% of that carbon stored belowground. Salt marshes contained 66.4 ± 25.0 Mg ha<sup>−1</sup> (93.5% belowground carbon), and salt barrens contained 26.6 ± 8.3 Mg ha<sup>−1</sup> (96.1% belowground carbon). These values were much lower than global averages for carbon stocks in mangroves and salt marshes, likely due to Tampa Bay’s location near the northern limit of mangrove habitat, sandy soil, young age of the restored wetlands, presence of mosquito ditches, and recent habitat conversion from salt marshes to mangroves. In the late 1800s, Tampa Bay’s coastal wetlands were dominated by salt marshes, but today they are dominated by mangroves. Based on the blue carbon values from the natural sites in this study, this habitat switching has led to the additional sequestration of 141,000 Mg of carbon in remaining wetlands in the Tampa Bay watershed.
DOI: 10.5281/zenodo.10417809
title: Image dataset for quantification of virus-infected cells

description: The dataset contains microscopy images of hantavirus-infected cells stained with antibodies against the viral nucleocapsid protein.
DOI: 10.5281/zenodo.10417810
title: Image dataset for quantification of virus-infected cells

description: The dataset contains microscopy images of hantavirus-infected cells stained with antibodies against the viral nucleocapsid protein.
DOI: 10.5281/zenodo.10417826
title: Data for evaluation of modelled versus observed NMVOC compounds at EMEP sites in Europe

description: Data (model outputs, emission files, python scripts) for the publication of "Evaluation of modelled versus observed NMVOC compounds at EMEP sites in Europe".
DOI: 10.5281/zenodo.10417827
title: Data for evaluation of modelled versus observed NMVOC compounds at EMEP sites in Europe

description: Data (model outputs, emission files, python scripts) for the publication of "Evaluation of modelled versus observed NMVOC compounds at EMEP sites in Europe".
DOI: 10.25573/serc.23960811
title: Early indicators of stress in mangrove forests with altered hydrology in Tampa Bay, Florida, USA

description: Mangroves experience stress or mortality when gas exchange by aerial root structures is hindered by sediment burial or constant inundation. The resulting loss of belowground roots and increased decomposition can lead to a loss of surface elevation through peat collapse, furthering the degree of inundation. This study identified ten live mangrove forests across Tampa Bay (Florida, USA) with stagnant water and/or abundant adventitious root growth (a sign of stress) and compared vegetative, water, and soil characteristics of stressed and reference mangrove forests to identify early indicators of stress and potential peat collapse. Two stressed sites were characterized by sandy, high-density soils and were hypothesized to have been stressed by a burial event. The remaining eight stressed locations had stagnant pools of discolored water with low dissolved oxygen (1.1 ± 1.3 mg L<sup>−1</sup>). Soil from the hydrologic stress sites had significantly lower dry bulk density than reference mangrove sites (0.24 ± 0.14 g cm<sup>−3</sup> vs. 0.40 ± 0.11 g cm<sup>−3</sup>), greater organic matter composition (49.3 ± 17.2% vs. 26.1 ± 9.0%), and a higher proportion of root material. Salinity and porewater dissolved organic carbon varied widely but were not significantly different between reference and hydrologic stress sites. Altered hydrology due to anthropogenic alteration can often be improved; thus, proactive restoration is recommended to prevent mortality and peat collapse in affected mangrove forests.
DOI: 10.25573/serc.23960811.v1
title: Early indicators of stress in mangrove forests with altered hydrology in Tampa Bay, Florida, USA

description: Mangroves experience stress or mortality when gas exchange by aerial root structures is hindered by sediment burial or constant inundation. The resulting loss of belowground roots and increased decomposition can lead to a loss of surface elevation through peat collapse, furthering the degree of inundation. This study identified ten live mangrove forests across Tampa Bay (Florida, USA) with stagnant water and/or abundant adventitious root growth (a sign of stress) and compared vegetative, water, and soil characteristics of stressed and reference mangrove forests to identify early indicators of stress and potential peat collapse. Two stressed sites were characterized by sandy, high-density soils and were hypothesized to have been stressed by a burial event. The remaining eight stressed locations had stagnant pools of discolored water with low dissolved oxygen (1.1 ± 1.3 mg L<sup>−1</sup>). Soil from the hydrologic stress sites had significantly lower dry bulk density than reference mangrove sites (0.24 ± 0.14 g cm<sup>−3</sup> vs. 0.40 ± 0.11 g cm<sup>−3</sup>), greater organic matter composition (49.3 ± 17.2% vs. 26.1 ± 9.0%), and a higher proportion of root material. Salinity and porewater dissolved organic carbon varied widely but were not significantly different between reference and hydrologic stress sites. Altered hydrology due to anthropogenic alteration can often be improved; thus, proactive restoration is recommended to prevent mortality and peat collapse in affected mangrove forests.