cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6011408.v1
title: Supplementary Material for: Resting Heart Rate Is Not Associated with Cognitive Function

description: <b><i>Aims:</i></b> In order to examine the hypothesis that elevated resting heart rate (RHR) is associated with impaired cognitive score, we investigated the relationship between RHR and cognitive score in middle-aged, elderly and old Danish subjects from the general population. <b><i>Methods:</i></b> Composite cognitive scores derived from the result of 5 age-sensitive cognitive tests for a total of 7,002 individuals (Middle-aged Danish twin: <i>n</i> = 4,132, elderly Danish twins: <i>n</i> = 2,104 and Danish nonagenarian: <i>n</i> = 766) divided according to RHR and compared using linear regression models adjusted for sex, age, previous heart conditions and hypertension. RHR was assessed by palpating radial pulse. Genetic and shared environmental confounding was addressed in intrapair analyses of 2,049 twin pairs. <b><i>Results:</i></b><i></i> In unadjusted multivariate models and in multivariable models adjusting for age, sex, heart conditions and hypertension, RHR was not associated with cognitive function. Furthermore, the intrapair analyses showed that RHR was not associated with cognitive score testing within twin pairs, as measured by the proportion of twin pairs in which the twin with higher RHR also was the twin with the lowest composite cognitive score (1,049 pairs of 2,049 pairs [51% (95% CI 49–53), <i>p</i> &lt; 0.289]). <b><i>Conclusion:</i></b> While elevated RHR has been shown to be associated with adverse health events and poor fitness level, RHR has no relation to cognitive function in the general population.
DOI: 10.6084/m9.figshare.6011381
title: Phylogenetic relationships in <i>Bulbostylis</i> (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

description: Previous molecular phylogenetic analyses of the family Cyperaceae based on <i>rbc</i>L sequences showed <i>Bulbostylis</i> as paraphyletic, with <i>B. atrosanguinea</i> and <i>B. hispidula</i> forming a clade with <i>Nemum spadiceum</i>. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (<i>trn</i>L-F region) showed <i>Bulbostylis</i> as monophyletic, although they only incorporated four species of <i>Bulbostylis</i> and none of <i>Nemum</i>. In this work, we presented a phylogenetic hypothesis of <i>Bulbostylis</i> based on a comprehensive sampling, including species from different continents for the first time. New sequences of <i>Abildgaardia</i>, <i>Crosslandia</i>, <i>Fimbristylis</i>, and <i>Nemum</i> were included to test the monophyly of <i>Bulbostylis</i>. In total, 84 sequences of both ITS and <i>trn</i>L regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, <i>Bulbostylis</i> resulted paraphyletic as <i>Nemum atracuminatum</i> is nested within it. Most American species of <i>Bulbostylis</i> grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of <i>Bulbostylis</i>, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the <i>Bulbostylis</i>.
DOI: 10.6084/m9.figshare.6011381.v1
title: Phylogenetic relationships in <i>Bulbostylis</i> (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

description: Previous molecular phylogenetic analyses of the family Cyperaceae based on <i>rbc</i>L sequences showed <i>Bulbostylis</i> as paraphyletic, with <i>B. atrosanguinea</i> and <i>B. hispidula</i> forming a clade with <i>Nemum spadiceum</i>. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (<i>trn</i>L-F region) showed <i>Bulbostylis</i> as monophyletic, although they only incorporated four species of <i>Bulbostylis</i> and none of <i>Nemum</i>. In this work, we presented a phylogenetic hypothesis of <i>Bulbostylis</i> based on a comprehensive sampling, including species from different continents for the first time. New sequences of <i>Abildgaardia</i>, <i>Crosslandia</i>, <i>Fimbristylis</i>, and <i>Nemum</i> were included to test the monophyly of <i>Bulbostylis</i>. In total, 84 sequences of both ITS and <i>trn</i>L regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, <i>Bulbostylis</i> resulted paraphyletic as <i>Nemum atracuminatum</i> is nested within it. Most American species of <i>Bulbostylis</i> grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of <i>Bulbostylis</i>, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the <i>Bulbostylis</i>.
DOI: 10.6084/m9.figshare.6011375
title: A stable tRNA-like molecule is generated from the long noncoding RNA <i>GUT15</i> in <i>Arabidopsis</i>

description: The <i>Arabidopsis GUT15</i> RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed <i>GUT15</i> transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and <i>GUT15</i>-tRF-F5, which are both encoded by the final intron in the <i>GUT15</i> gene. The <i>GUT15</i>-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The <i>GUT15</i>-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.
DOI: 10.6084/m9.figshare.6011375.v1
title: A stable tRNA-like molecule is generated from the long noncoding RNA <i>GUT15</i> in <i>Arabidopsis</i>

description: The <i>Arabidopsis GUT15</i> RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed <i>GUT15</i> transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and <i>GUT15</i>-tRF-F5, which are both encoded by the final intron in the <i>GUT15</i> gene. The <i>GUT15</i>-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The <i>GUT15</i>-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.
DOI: 10.6084/m9.figshare.6011318
title: Optimization and production of curdlan gum using <i>Bacillus cereus</i> PR3 isolated from rhizosphere of leguminous plant

description: Curdlan gum is a neutral water-insoluble bacterial exopolysaccharide composed primarily of linear β-(1,3) glycosidic linkages. Recently, there has been increasing interest in the applications of curdlan and its derivatives. Curdlan is found to inhibit tumors and its sulfated derivative possess anti-HIV activity. Curdlan is biodegradable, non-toxic towards human, environment and edible which makes it suitable as drug-delivery vehicles for sustained drug release. The increasing demand for the growing applications of curdlan requires an efficient high yield fermentation production process so as to satisfy the industrial needs. In this perspective, the present work is aimed to screen and isolate an efficient curdlan gum producing bacteria from rhizosphere of ground nut plant using aniline-blue agar. High yielding isolate was selected based on curdlan yield and identified as <i>Bacillus cereus</i> using gas-chromatography fatty acid methyl ester analysis. <i>B. cereus</i> PR3 curdlan gum was characterized using FT-IR spectroscopy, SEM, XRD and TGA. Fermentation time for curdlan production using <i>B. cereus</i> PR3 was optimized. Media constituents like carbon, nitrogen and mineral sources were screened using Plackett–Burman design. Subsequent statistical analysis revealed that Starch, NH<sub>4</sub>NO<sub>3</sub>, K<sub>2</sub>HPO<sub>4</sub>, Na<sub>2</sub>SO<sub>4</sub>, KH<sub>2</sub>SO<sub>4</sub> and CaCl<sub>2</sub> were significant media constituents and these concentrations were optimized for enhancement of curdlan production up to 20.88 g/l.
DOI: 10.6084/m9.figshare.6011318.v2
title: Optimization and production of curdlan gum using <i>Bacillus cereus</i> PR3 isolated from rhizosphere of leguminous plant

description: Curdlan gum is a neutral water-insoluble bacterial exopolysaccharide composed primarily of linear β-(1,3) glycosidic linkages. Recently, there has been increasing interest in the applications of curdlan and its derivatives. Curdlan is found to inhibit tumors and its sulfated derivative possess anti-HIV activity. Curdlan is biodegradable, non-toxic towards human, environment and edible which makes it suitable as drug-delivery vehicles for sustained drug release. The increasing demand for the growing applications of curdlan requires an efficient high yield fermentation production process so as to satisfy the industrial needs. In this perspective, the present work is aimed to screen and isolate an efficient curdlan gum producing bacteria from rhizosphere of ground nut plant using aniline-blue agar. High yielding isolate was selected based on curdlan yield and identified as <i>Bacillus cereus</i> using gas-chromatography fatty acid methyl ester analysis. <i>B. cereus</i> PR3 curdlan gum was characterized using FT-IR spectroscopy, SEM, XRD and TGA. Fermentation time for curdlan production using <i>B. cereus</i> PR3 was optimized. Media constituents like carbon, nitrogen and mineral sources were screened using Plackett–Burman design. Subsequent statistical analysis revealed that Starch, NH<sub>4</sub>NO<sub>3</sub>, K<sub>2</sub>HPO<sub>4</sub>, Na<sub>2</sub>SO<sub>4</sub>, KH<sub>2</sub>SO<sub>4</sub> and CaCl<sub>2</sub> were significant media constituents and these concentrations were optimized for enhancement of curdlan production up to 20.88 g/l.
DOI: 10.6084/m9.figshare.6011318.v1
title: Optimization and production of curdlan gum using <i>Bacillus cereus</i> pr3 isolated from rhizosphere of leguminous plant

description: Curdlan gum is a neutral water-insoluble bacterial exopolysaccharide composed primarily of linear β-(1,3) glycosidic linkages. Recently, there has been increasing interest in the applications of curdlan and its derivatives. Curdlan is found to inhibit tumors and its sulfated derivative possess anti- HIV activity. Curdlan is biodegradable, non-toxic towards human, environment and edible which makes it suitable as drug-delivery vehicles for sustained drug release. The increasing demand for the growing applications of curdlan requires an efficient high yield fermentation production process so as to satisfy the industrial needs. In this perspective, the present work is aimed to screen and isolate an efficient curdlan gum producing bacteria from rhizosphere of ground nut plant using aniline-blue agar. High yielding isolate was selected based on curdlan yield and identified as <i>Bacillus cereus</i> using GC-FAME analysis. <i>B. cereus</i> PR3 curdlan gum was characterized using FT-IR spectroscopy, SEM and XRD. Fermentation time for curdlan production using <i>B. cereus</i> PR3 was optimized. Media constituents like carbon, nitrogen and mineral sources were screened using Plackett- Burman design. Subsequent statistical analysis revealed that Starch, NH<sub>4</sub>NO<sub>3</sub>, K<sub>2</sub>HPO<sub>4</sub>, Na<sub>2</sub>SO<sub>4</sub>, KH<sub>2</sub>SO<sub>4</sub> and CaCl<sub>2</sub> were significant media constituents and these concentrations were optimized for enhancement of curdlan production up to 20.88 g/L.
DOI: 10.6084/m9.figshare.6011237
title: Supplementary Material for: The Influence of Cognitive Bias on Caries Lesion Detection in Preschool Children

description: We aimed to evaluate whether children’s caries experience exerts an influence on the performance of visual and radiographic methods in detecting nonevident proximal caries lesions in primary molars. Eighty children (3–6 years old) were selected and classified as having a lower (≤3 decayed, missing, or filled surfaces; dmf-s) or higher (&gt; 3 dmf-s) caries experience. Two calibrated examiners then assessed 526 proximal surfaces for caries lesions using visual and radiographic methods. As a reference standard, 2 other examiners checked the surfaces after temporary separation. Noncavitated and cavitated lesion thresholds were considered and Poisson multilevel regression analyses were conducted to evaluate the influence of caries experience on the performance of diagnostic strategies. Accuracy parameters stratified by caries experience were also derived. A statistically significant influence of caries experience was observed only for visual inspection, with more false-positive results in children with a higher caries experience at the noncavitated lesion threshold, and more false results at the cavitated threshold. The detection of noncavitated caries lesions in children with a higher caries experience was overestimated (specificity = 0.696), compared to children with a lower caries experience (specificity = 0.918), probably due to confirmation bias. However, the examiners underestimated the detection of cavitated lesions in children with a higher caries experience (sensitivity = 0.143) compared to lower-caries-experience children (sensitivity = 0.222), possibly because of representativeness bias. The radiographic method was not influenced by children’s caries experience. In conclusion, children’s caries experience influences the performance of visual inspection in detecting proximal caries lesions in primary teeth, evidencing the occurrence of cognitive biases.
DOI: 10.6084/m9.figshare.6011237.v1
title: Supplementary Material for: The Influence of Cognitive Bias on Caries Lesion Detection in Preschool Children

description: We aimed to evaluate whether children’s caries experience exerts an influence on the performance of visual and radiographic methods in detecting nonevident proximal caries lesions in primary molars. Eighty children (3–6 years old) were selected and classified as having a lower (≤3 decayed, missing, or filled surfaces; dmf-s) or higher (&gt; 3 dmf-s) caries experience. Two calibrated examiners then assessed 526 proximal surfaces for caries lesions using visual and radiographic methods. As a reference standard, 2 other examiners checked the surfaces after temporary separation. Noncavitated and cavitated lesion thresholds were considered and Poisson multilevel regression analyses were conducted to evaluate the influence of caries experience on the performance of diagnostic strategies. Accuracy parameters stratified by caries experience were also derived. A statistically significant influence of caries experience was observed only for visual inspection, with more false-positive results in children with a higher caries experience at the noncavitated lesion threshold, and more false results at the cavitated threshold. The detection of noncavitated caries lesions in children with a higher caries experience was overestimated (specificity = 0.696), compared to children with a lower caries experience (specificity = 0.918), probably due to confirmation bias. However, the examiners underestimated the detection of cavitated lesions in children with a higher caries experience (sensitivity = 0.143) compared to lower-caries-experience children (sensitivity = 0.222), possibly because of representativeness bias. The radiographic method was not influenced by children’s caries experience. In conclusion, children’s caries experience influences the performance of visual inspection in detecting proximal caries lesions in primary teeth, evidencing the occurrence of cognitive biases.
DOI: 10.6084/m9.figshare.6011129
title: Wave data during two severe storms in a Dutch Wadden Sea marsh

description: This dataset (netCDF file) includes wave data (e.g. significant wave height, wave period, etc.) during two winter storms (Jan.11, 2015, and Jan. 13, 2017) observed in a Dutch Wadden Sea marsh using wave sensors deployed at multiple locations in the marsh or in the bare mudflat.
DOI: 10.6084/m9.figshare.6011129.v1
title: Wave data during two severe storms in a Dutch Wadden Seamarsh

description: This dataset (netCDF file) includes wave data (e.g. significant wave height, wave period, etc.) during two winter storms (Jan.11, 2015, and Jan. 13, 2017) observed in a Dutch Wadden Sea marsh using wave sensors deployed at multiple locations in the marsh or in the bare mudflat.
DOI: 10.6084/m9.figshare.6011018
title: Search System Survey Report

description: We examined the practices that data repositories employ in helping users search their holdings and demonstrate the value of looking across disciplines at the common data discovery issues, such as relevancy, that all data repositories face.
DOI: 10.6084/m9.figshare.6010958
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge_v5.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth6.m', with the rest as supporting functions.<br>
DOI: 10.6084/m9.figshare.6010958.v2
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth4.m', with the rest as supporting functions.<br>
DOI: 10.6084/m9.figshare.6010958.v3
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth4.m', with the rest as supporting functions.<br>
DOI: 10.6084/m9.figshare.6010958.v4
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth4.m', with the rest as supporting functions.<br>
DOI: 10.6084/m9.figshare.6010958.v6
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge_v5.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth6.m', with the rest as supporting functions.<br>
DOI: 10.6084/m9.figshare.6010958.v5
title: Matlab codes for computing 1) breach discharge when a dike fails and 2) the resultant fatality 3) the impacts of sea level rise, for two different scenarios: with and without a saltmarsh foreshore.

description: These codes are made to compare: 1) water discharge through a dike breache behind a saltmarsh foreshore vs. behind a bare mudflat. The main script is 'breachDischarge.m', with the rest as supporting functions.<br>2) the resultant flooding behind the dike breach and the expected fatality, as well as the impacts of sea level rise. The main script for this purpose is 'Motality_SLR_breachwidth5.m', with the rest as supporting functions.<br>