cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7215554.v1
title: Influence of head and linear growth on the development of malocclusion at six years of age: a cohort study

description: Abstract The aim of this article was to evaluate the influence of biological and sociobehavioral factors on the development of malocclusions in children. This is a cross-sectional study nested in a cohort of 350 children who participated in a community intervention study. After six years, an active search identified 290 children with occlusal abnormalities. Socioeconomic status, linear growth, and nutritional status of the child at birth and at the time of measurement, as well as dietary and sucking habits, were investigated. Malocclusions were evaluated across three spatial planes - anteroposterior, vertical, and transverse. The prevalence of these anomalies was 64.5%, primarily in the anteroposterior plane. The logistic regression analysis revealed that pacifier use for 60 months or more, stunting as measured at age six, and reduced gain in head circumference from birth to six years of age, were significantly associated with the development of malocclusion in childhood. Head circumference and linear growth are associated with occlusal anomalies in infants, independent of pacifier sucking.
DOI: 10.6084/m9.figshare.14924905.v1
title: Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of <i>Agaricus bisporus</i> by SSR Markers

description: <i>Agaricus bisporus</i> is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated <i>A. bisporus</i> strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected <i>A</i>. <i>bisporus</i> strains using simple sequence repeat (SSR) markers. <i>Agaricus bisporus</i> strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance <i>A</i>. <i>bisporus</i> breeding programs and support the protection of genetic resources.
DOI: 10.6084/m9.figshare.15138098
title: Fungal Community Analyses of Endophytic Fungi from Two Oak Species, <i>Quercus mongolica</i> and <i>Quercus serrata</i>, in Korea

description: Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (<i>Quercus mongolica</i> and <i>Q. serrata</i>) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of <i>Q. serrata</i> were higher than that of <i>Q. mongolica</i> with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that <i>Q. serrata</i> had a significantly higher level of fungal diversity than <i>Q. mongolica</i>. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. <i>Leptosillia, Aureobasidium</i> and <i>Acanthostigma</i> were the most abundant genera detected in <i>Q. serrata</i> with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, <i>Peltaster</i>, <i>Cladosporium</i> and <i>Monochaetia</i> were the most common genera detected in <i>Q. mongolica</i> with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by <i>Raffaelea quercus-mongolicae</i>.
DOI: 10.6084/m9.figshare.15138098.v1
title: Fungal Community Analyses of Endophytic Fungi from Two Oak Species, <i>Quercus mongolica</i> and <i>Quercus serrata</i>, in Korea

description: Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (<i>Quercus mongolica</i> and <i>Q. serrata</i>) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of <i>Q. serrata</i> were higher than that of <i>Q. mongolica</i> with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that <i>Q. serrata</i> had a significantly higher level of fungal diversity than <i>Q. mongolica</i>. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. <i>Leptosillia, Aureobasidium</i> and <i>Acanthostigma</i> were the most abundant genera detected in <i>Q. serrata</i> with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, <i>Peltaster</i>, <i>Cladosporium</i> and <i>Monochaetia</i> were the most common genera detected in <i>Q. mongolica</i> with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by <i>Raffaelea quercus-mongolicae</i>.
DOI: 10.6084/m9.figshare.14924905
title: Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of <i>Agaricus bisporus</i> by SSR Markers

description: <i>Agaricus bisporus</i> is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated <i>A. bisporus</i> strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected <i>A</i>. <i>bisporus</i> strains using simple sequence repeat (SSR) markers. <i>Agaricus bisporus</i> strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance <i>A</i>. <i>bisporus</i> breeding programs and support the protection of genetic resources.
DOI: 10.6084/m9.figshare.14945724.v1
title: Transcriptome Analysis and Expression Profiling of Molecular Responses to Cd Toxicity in <i>Morchella spongiola</i>

description: <i>Morchella</i> is a genus of fungi with the ability to concentrate Cd both in the fruit-body and mycelium. However, the molecular mechanisms conferring resistance to Cd stress in <i>Morchella</i> are unknown. Here, RNA-based transcriptomic sequencing was used to identify the genes and pathways involved in Cd tolerance in <i>Morchella spongiola</i>. 7444 differentially expressed genes (DEGs) were identified by cultivating <i>M. spongiola</i> in media containing 0.15, 0.90, or 1.50 mg/L Cd<sup>2+</sup>. The DEGs were divided into six sub-clusters based on their global expression profiles. GO enrichment analysis indicated that numerous DEGs were associated with catalytic activity, cell cycle control, and the ribosome. KEGG enrichment analysis showed that the main pathways under Cd stress were MAPK signaling, oxidative phosphorylation, pyruvate metabolism, and propanoate metabolism. In addition, several DEGs encoding ion transporters, enzymatic/non-enzymatic antioxidants, and transcription factors were identified. Based on these results, a preliminary gene regulatory network was firstly proposed to illustrate the molecular mechanisms of Cd detoxification in <i>M. spongiola</i>. These results provide valuable insights into the Cd tolerance mechanism of <i>M. spongiola</i> and constitute a robust foundation for further studies on detoxification mechanisms in macrofungi that could potentially lead to the development of new and improved fungal bioremediation strategies.
DOI: 10.6084/m9.figshare.14945724
title: Transcriptome Analysis and Expression Profiling of Molecular Responses to Cd Toxicity in <i>Morchella spongiola</i>

description: <i>Morchella</i> is a genus of fungi with the ability to concentrate Cd both in the fruit-body and mycelium. However, the molecular mechanisms conferring resistance to Cd stress in <i>Morchella</i> are unknown. Here, RNA-based transcriptomic sequencing was used to identify the genes and pathways involved in Cd tolerance in <i>Morchella spongiola</i>. 7444 differentially expressed genes (DEGs) were identified by cultivating <i>M. spongiola</i> in media containing 0.15, 0.90, or 1.50 mg/L Cd<sup>2+</sup>. The DEGs were divided into six sub-clusters based on their global expression profiles. GO enrichment analysis indicated that numerous DEGs were associated with catalytic activity, cell cycle control, and the ribosome. KEGG enrichment analysis showed that the main pathways under Cd stress were MAPK signaling, oxidative phosphorylation, pyruvate metabolism, and propanoate metabolism. In addition, several DEGs encoding ion transporters, enzymatic/non-enzymatic antioxidants, and transcription factors were identified. Based on these results, a preliminary gene regulatory network was firstly proposed to illustrate the molecular mechanisms of Cd detoxification in <i>M. spongiola</i>. These results provide valuable insights into the Cd tolerance mechanism of <i>M. spongiola</i> and constitute a robust foundation for further studies on detoxification mechanisms in macrofungi that could potentially lead to the development of new and improved fungal bioremediation strategies.
DOI: 10.6084/m9.figshare.7710947
title: The effect of colchicine on alveolar bone loss in ligature-induced periodontitis

description: Abstract Colchicine is widely used in the treatment of several inflammatory diseases due to its anti-inflammatory effect, but effects on bone metabolism are unclear. The aim of this study was to evaluate the effects of systemically-administered colchicine on healthy periodontium and experimentally-induced periodontitis. In total, 42 male Wistar rats were included in this study. A non-ligated group constituting the negative control group (Control, C, n = 6) and a ligature-only group forming the positive control group (LO, n = 12) were created separately. Twelve rats were treated with 0.4 mg/kg colchicine and another 12 with 1 mg/kg colchicine. In the colchicine-administered groups, right mandibles constituted the ligated groups (1 mgC-L or 0.4 mgC-L) and left mandibles formed the corresponding non-ligated controls (1mgC or 0.4mgC). Silk ligatures were placed at the gingival margin of the lower first molars. The animals were euthanized at different time-points of healing (11 or 30 days). Alveolar bone loss was clinically measured and TRAP+ osteoclasts, osteoblastic activity, and MMP-1 expression were examined histologically. There was no increase in alveolar bone loss with either colchicine dose in healthy periodontium (p &gt; 0.05) and the highest level of alveolar bone loss, TRAP+ osteoclast number, and MMP-1 expression were measured in the LO group (p &lt; 0.05). The 0.4 mgC-L group showed less alveolar bone loss at 11 days (p &lt; 0.05), but greater loss at 30 days. The 1 mgC-L group showed higher osteoblast number than the other ligated groups (p &lt; 0.05) at both time-points. In summary, colchicine did not increase alveolar bone loss in healthy periodontium and also may tend to reduce periodontitis progression. However, further extensive study is necessary to understand the mechanism of colchicine action on alveolar bone loss in periodontitis.
DOI: 10.6084/m9.figshare.7710947.v1
title: The effect of colchicine on alveolar bone loss in ligature-induced periodontitis

description: Abstract Colchicine is widely used in the treatment of several inflammatory diseases due to its anti-inflammatory effect, but effects on bone metabolism are unclear. The aim of this study was to evaluate the effects of systemically-administered colchicine on healthy periodontium and experimentally-induced periodontitis. In total, 42 male Wistar rats were included in this study. A non-ligated group constituting the negative control group (Control, C, n = 6) and a ligature-only group forming the positive control group (LO, n = 12) were created separately. Twelve rats were treated with 0.4 mg/kg colchicine and another 12 with 1 mg/kg colchicine. In the colchicine-administered groups, right mandibles constituted the ligated groups (1 mgC-L or 0.4 mgC-L) and left mandibles formed the corresponding non-ligated controls (1mgC or 0.4mgC). Silk ligatures were placed at the gingival margin of the lower first molars. The animals were euthanized at different time-points of healing (11 or 30 days). Alveolar bone loss was clinically measured and TRAP+ osteoclasts, osteoblastic activity, and MMP-1 expression were examined histologically. There was no increase in alveolar bone loss with either colchicine dose in healthy periodontium (p &gt; 0.05) and the highest level of alveolar bone loss, TRAP+ osteoclast number, and MMP-1 expression were measured in the LO group (p &lt; 0.05). The 0.4 mgC-L group showed less alveolar bone loss at 11 days (p &lt; 0.05), but greater loss at 30 days. The 1 mgC-L group showed higher osteoblast number than the other ligated groups (p &lt; 0.05) at both time-points. In summary, colchicine did not increase alveolar bone loss in healthy periodontium and also may tend to reduce periodontitis progression. However, further extensive study is necessary to understand the mechanism of colchicine action on alveolar bone loss in periodontitis.
DOI: 10.6084/m9.figshare.7710938
title: Iodoform Vs Calcium Hydroxide/Zinc Oxide based pastes: 12-month findings of a Randomized Controlled Trial

description: Abstract This study evaluated clinical and radiographic twelve-month outcomes of root canal treatments (CT) with smear layer removal, performed in primary teeth, using two different root canal filling materials. Pulpectomy was performed on 27 primary teeth with necrosis or irreversible pulpitis, caused by dental caries or trauma, in 23 children (2-7 years old). A single trained operator performed the CT in a single visit in cases without periapical or interradicular radiolucency (PIR) or in multiple visits in cases with PIR. Participants were selected based on specific inclusion and exclusion criteria, and randomly allocated into two groups: Group 1 (G1) – iodoform paste (iodoform + camphorated parachlorophenol + ointment comprising prednisolone acetate 5.0 mg and rifamycin 1.5 mg); Group 2 (G2) – Calen®/ZO paste. Treated teeth were restored with composite resin immediately after the root canal filling. The outcomes were evaluated clinically and radiographically according to specific criteria. Two blinded and standardized evaluators assessed the radiographic outcomes. We used descriptive analyses due to the small sample size. CTs were performed due to caries lesions in 70.4% of the cases and due to trauma in 29.6%. Only one tooth of G1 was unsuccessful; hence, pulpectomy performance in both groups was not influenced by the filling material, nor by any other analyzed variable. The level of the root canal filling was better in the Calen®/ZO group. The clinical and radiographic twelve-month outcomes indicated successful treatment, independently of the root filling material used.
DOI: 10.6084/m9.figshare.7710938.v1
title: Iodoform Vs Calcium Hydroxide/Zinc Oxide based pastes: 12-month findings of a Randomized Controlled Trial

description: Abstract This study evaluated clinical and radiographic twelve-month outcomes of root canal treatments (CT) with smear layer removal, performed in primary teeth, using two different root canal filling materials. Pulpectomy was performed on 27 primary teeth with necrosis or irreversible pulpitis, caused by dental caries or trauma, in 23 children (2-7 years old). A single trained operator performed the CT in a single visit in cases without periapical or interradicular radiolucency (PIR) or in multiple visits in cases with PIR. Participants were selected based on specific inclusion and exclusion criteria, and randomly allocated into two groups: Group 1 (G1) – iodoform paste (iodoform + camphorated parachlorophenol + ointment comprising prednisolone acetate 5.0 mg and rifamycin 1.5 mg); Group 2 (G2) – Calen®/ZO paste. Treated teeth were restored with composite resin immediately after the root canal filling. The outcomes were evaluated clinically and radiographically according to specific criteria. Two blinded and standardized evaluators assessed the radiographic outcomes. We used descriptive analyses due to the small sample size. CTs were performed due to caries lesions in 70.4% of the cases and due to trauma in 29.6%. Only one tooth of G1 was unsuccessful; hence, pulpectomy performance in both groups was not influenced by the filling material, nor by any other analyzed variable. The level of the root canal filling was better in the Calen®/ZO group. The clinical and radiographic twelve-month outcomes indicated successful treatment, independently of the root filling material used.
DOI: 10.6084/m9.figshare.7710635
title: Influence of chlorhexidine and zinc oxide in calcium hydroxide pastes on pH changes in external root surface

description: Abstract The objective of this study was to assess the influence of chlorhexidine (liquid and gel) and zinc oxide in calcium hydroxide (CH) pastes on root pH in simulated external resorption. One hundred human anterior teeth with a single root canal were selected. After decoronation and root canal instrumentation, the specimens were divided into 4 experimental groups and 1 control group (without intracanal paste): CH + saline (CH+S), CH + 2% chlorhexidine liquid (CH+ CHX), CH + 2% chlorhexidine gel (CH+ CHXg), and CH + 2% chlorhexidine gel + zinc oxide (CH+ CHXg+ZnO). pH was measured using a microelectrode at 3 and 24 h, and 1, 2, 3, and 4 weeks after inserting intracanal pastes. Data were analyzed statistically using an ANOVA and Tukey’s test (p &lt; 0.05). The CH+CHXg+ZnO group had the highest pH values throughout (p&lt;0.05). The CH+S and CH+ CHX groups had the highest pH values after 1 week and the CH+ CHXg group after 2 weeks. CH+ CHXg maintained the highest pH until the fourth week compared with CH+ CHX (p &lt; 0.05). The control group remained at a neutral pH at all evaluated times. It can be concluded that chlorhexidine solution or gel maintained the alkaline pH of CH, and chlorhexidine gel allowed a slower decrease in pH over time. CH+ CHXg+ZnO showed the highest pH values and was an effective intracanal medication for maintaining alkaline root pH in the area of resorption.
DOI: 10.6084/m9.figshare.7710635.v1
title: Influence of chlorhexidine and zinc oxide in calcium hydroxide pastes on pH changes in external root surface

description: Abstract The objective of this study was to assess the influence of chlorhexidine (liquid and gel) and zinc oxide in calcium hydroxide (CH) pastes on root pH in simulated external resorption. One hundred human anterior teeth with a single root canal were selected. After decoronation and root canal instrumentation, the specimens were divided into 4 experimental groups and 1 control group (without intracanal paste): CH + saline (CH+S), CH + 2% chlorhexidine liquid (CH+ CHX), CH + 2% chlorhexidine gel (CH+ CHXg), and CH + 2% chlorhexidine gel + zinc oxide (CH+ CHXg+ZnO). pH was measured using a microelectrode at 3 and 24 h, and 1, 2, 3, and 4 weeks after inserting intracanal pastes. Data were analyzed statistically using an ANOVA and Tukey’s test (p &lt; 0.05). The CH+CHXg+ZnO group had the highest pH values throughout (p&lt;0.05). The CH+S and CH+ CHX groups had the highest pH values after 1 week and the CH+ CHXg group after 2 weeks. CH+ CHXg maintained the highest pH until the fourth week compared with CH+ CHX (p &lt; 0.05). The control group remained at a neutral pH at all evaluated times. It can be concluded that chlorhexidine solution or gel maintained the alkaline pH of CH, and chlorhexidine gel allowed a slower decrease in pH over time. CH+ CHXg+ZnO showed the highest pH values and was an effective intracanal medication for maintaining alkaline root pH in the area of resorption.
DOI: 10.6084/m9.figshare.7710935
title: The effect of enamel matrix derivatives on root coverage: a 12-month follow-up of a randomized clinical trial

description: Abstract Subepithelial connective tissue grafts (SCTGs) with a coronally advanced flap (CAF) are accepted as the gold standard for covering denuded root surfaces. In recent years, enamel matrix derivatives (EMDs) have been used for their regenerative potential in periodontics. The aim of this split-mouth and randomized controlled study was to assess the clinical and aesthetical impacts of EMD application in combination with SCTG+CAF in patients with Miller’s Class I and II gingival recessions in contralateral canines of the maxilla. Participants who underwent SCTG+CAF+EMD application were identified as the test group (n = 19) and those who underwent SCTG+CAF as control group (n = 19). The outcome parameters were recession depth/width, root coverage percentage, and root coverage aesthetic score (RES). RES was evaluated by two calibrated blind periodontists one year after the treatment. Statistically significant root coverage percentage was observed at one year post-treatment for both groups (p &lt; 0.05). However, significant differences between the groups were not observed in terms of total RES and complete root coverage rate (p &gt; 0.05). The test group had significantly better results than the control according to the soft tissue texture and mucogingival junction alignment results (p &lt; 0.05). These results indicate that EMDs contribute to the healing of soft tissue without scarring. As a result of better wound healing, the EMD-added group exhibited better results in terms of the harmony of the mucogingival junction between adjacent teeth. This paper is the first split-mouth study in which SCTG+CAF and SCTG+CAF+EMD were compared using RES in bilateral canines.