cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4547203
title: Supplementary Material for: Sociodemographic and Behavioural Determinants of a Healthy Diet in Switzerland

description: <strong><em>Background/Aims:</em></strong> The determinants of a healthy diet have not been studied in Switzerland. This study aimed at assessing the individual and behavioural factors associated with a healthy diet in a Swiss city. <b><i>Methods:</i></b> Cross-sectional, population-based study conducted between 2009 and 2013 (n = 4,439, 2,383 women, mean age 57.5 ± 10.3 years) in Lausanne. Food consumption was assessed using a validated food frequency questionnaire. Two Mediterranean diet scores (classic score and specific for Switzerland) and the Harvard School of Public Health alternate healthy eating index were computed. <b><i>Results:</i></b> For all three dietary scores considered, living in couple or having a high education were associated with a healthier diet. An unhealthy lifestyle (smoking, sedentary behaviour) or a high body mass index were associated with an unhealthier diet. Participants born in Italy, Portugal and Spain had healthier diets than participants born in France or Switzerland. Women and elderly participants had healthier diets than men and young participants according to 2 scores, while no differences were found for the Swiss-specific Mediterranean score. <b><i>Conclusions:</i></b> In Switzerland, healthy eating is associated with high education, a healthy lifestyle, marital status and country of origin. The associations with gender and age depend on the dietary score considered.
DOI: 10.6084/m9.figshare.4547218
title: Supplementary Material for: Impaired Regulation of ALDH2 Protein Expression Revealing a Yet Unknown Epigenetic Impact of rs886205 on Specific Methylation of a Negative Regulatory Promoter Region in Alcohol-Dependent Patients

description: Acetaldehyde, the carcinogenic metabolite of ethanol known to provoke aversive symptoms of alcohol consumption, is predominantly eliminated by aldehyde dehydrogenase 2 (ALDH2). Reduced ALDH2 activity correlates with low alcohol tolerance and low risk for alcohol dependence. The ALDH2 promoter polymorphism rs886205 (A&gt;G) is associated with decreased promoter activity, but a molecular mechanism and allele-dependent ALDH2 protein expression has not been described yet. On the basis of allele-dependent epigenetic effects, we analyzed the rs886205 genotype, methylation rates of cytosine-phosphatidyl-guanine (CpG)-sites within a regulatory promoter region and ALDH2 protein levels in 82 alcohol-dependent patients during a 2-week withdrawal and compared them to 34 matched controls. Patients without the G-allele of rs886205 showed higher methylation of the promoter region than controls and readily adapted epigenetically as well as on protein level during withdrawal, while patients with the G-allele displayed retarded methylation readjustment and no change in ALDH2 protein levels. Our data provide novel insights into an unknown genetic-epigenetic interaction, revealing impaired ALDH2 protein expression in patients with the G-allele of rs886205. Additionally, we checked for an association between rs886205 and protection against alcohol dependence and found a trend association between the G-allele and protection against alcohol dependence that needs replication in a larger Caucasian cohort.
DOI: 10.6084/m9.figshare.4547293.v2
title: Antioxidant molecular targets of wheat bran fermented by white rot fungi and its potential modulation of antioxidative status in broiler chickens

description: 1. The study focused on antioxidant molecular targets of wheat bran fermented by white rot fungi (WRF) in poultry. After solid-state fermentation of wheat bran by WRF for 12 d, scanning electron microscopy found that the lignocellulose structure showed degradation and fragmentation. 2. A total of 300 1-d-old broilers were evenly divided by gender and randomly allocated into the following treatments: (1) maize–soybean meal (control group), (2) 10% of wheat bran replacing maize (10% WB group) or (3) 10% of fermented wheat bran replacing maize (10% FWB group). 3. The results indicated that the antioxidant gene expression, such as haem oxygenase-1 and glutathione-S-transferase of chicken peripheral blood mononuclear cells, of the 10% FWB group was significantly higher than that of the control group at d 35. For genes of Nicotinamide adenine dinucleotide phosphate oxygenase 1 and reactive oxygen species modulator protein 1, the expression of the 10% FWB group was lower than that of the control group at d 21 and 35. 4. In conclusion, wheat bran fermented by WRF could increase lignocellulolytic enzyme activities and the levels of active components that further regulate the expression of antioxidant molecular targets in poultry.
DOI: 10.6084/m9.figshare.4547218.v1
title: Supplementary Material for: Impaired Regulation of ALDH2 Protein Expression Revealing a Yet Unknown Epigenetic Impact of rs886205 on Specific Methylation of a Negative Regulatory Promoter Region in Alcohol-Dependent Patients

description: Acetaldehyde, the carcinogenic metabolite of ethanol known to provoke aversive symptoms of alcohol consumption, is predominantly eliminated by aldehyde dehydrogenase 2 (ALDH2). Reduced ALDH2 activity correlates with low alcohol tolerance and low risk for alcohol dependence. The ALDH2 promoter polymorphism rs886205 (A&gt;G) is associated with decreased promoter activity, but a molecular mechanism and allele-dependent ALDH2 protein expression has not been described yet. On the basis of allele-dependent epigenetic effects, we analyzed the rs886205 genotype, methylation rates of cytosine-phosphatidyl-guanine (CpG)-sites within a regulatory promoter region and ALDH2 protein levels in 82 alcohol-dependent patients during a 2-week withdrawal and compared them to 34 matched controls. Patients without the G-allele of rs886205 showed higher methylation of the promoter region than controls and readily adapted epigenetically as well as on protein level during withdrawal, while patients with the G-allele displayed retarded methylation readjustment and no change in ALDH2 protein levels. Our data provide novel insights into an unknown genetic-epigenetic interaction, revealing impaired ALDH2 protein expression in patients with the G-allele of rs886205. Additionally, we checked for an association between rs886205 and protection against alcohol dependence and found a trend association between the G-allele and protection against alcohol dependence that needs replication in a larger Caucasian cohort.
DOI: 10.6084/m9.figshare.4547293.v1
title: Antioxidant molecular targets of wheat bran fermented by white rot fungi and its potential modulation of anti-oxidative status in broiler chickens

description: 1. The study focused on antioxidant molecular targets of wheat bran fermented by white rot fungi in poultry. After solid-state fermentation of wheat bran by white rot fungi for 12 d, scanning electron microscopy found that the lignocellulose structure showed degradation and fragmentation. 2. The fermented wheat bran had significantly increased laccase and manganese peroxidase activity, as well as twice as high concentration of total quercetin, phenolics and crude polysaccharides compared to the unfermented wheat bran. 3. A total of 300 1-d-old broilers were evenly divided by gender and randomly allocated into the following treatments: 1) maize-soybean meal (control group), 2) 10% of wheat bran replacing maize (10% WB group) or 3) 10% of fermented wheat bran replacing maize (10% FWB group). 4. The results indicated that the antioxidant gene expression, such as Haeme oxygenase-1 and Glutathione-S-transferase of chicken peripheral blood mononuclear cells, of the 10% FWB group were significantly higher than the control group at d 35. For genes of NADPH oxygenase 1 and Reactive oxygen species modulator protein 1, the expression of the 10% FWB group was lower than the control group at d 21 and 35. The malondialdehyde concentration in serum in the FWB group was significantly decreased compared to the control group at the age of 35 d. 5. In conclusion, wheat bran fermented by white rot fungi could increase lignocellulolytic enzyme activities and the levels of active components that further regulate the expression of antioxidant molecular targets in poultry.
DOI: 10.6084/m9.figshare.4547200
title: Genome size variation and evolution in Dipterocarpaceae

description: <b><i>Background</i></b>: Dipterocarpaceae is a pantropical tree family that plays an important role in our understanding of the ecology of Asian tropical rain forests. However, genome sizes for members of the Dipterocarpaceae are still poorly known. <b><i>Aims</i></b>: To report the genome size of 115 dipterocarp species and examine the variation and evolution of genome size in this family. <b><i>Methods</i></b>: Genome size was estimated using flow cytometry. Both the <i>rpoB</i> and <i>trn</i>L intron were sequenced to uncover the evolution of genome size within a phylogenetic framework. <b><i>Results</i></b>: The 1<i>C</i> genome size varied between 0.267 and 0.705 pg in <i>Shorea hemsleyana</i> and <i>Shorea ovalis</i>, respectively, a 2.64-fold variation across the family. Most dipterocarps are characterised by very small genomes with a mean 1<i>C</i> value of 0.416 pg (sd = 0.075) and five polyploids are recorded. The ancestral genome size for dipterocarps was reconstructed as 1<i>C</i><i>x</i> = 0.481 pg (95% CI = 0.433–0.534). <b><i>Conclusions</i></b>: Genome size variation in dipterocarps was characterised by very small values with a narrow range. Overall, genome size reduction from the ancestral state is a general trend in Dipterocarpaceae.
DOI: 10.6084/m9.figshare.4547200.v1
title: Genome size variation and evolution in Dipterocarpaceae

description: <b><i>Background</i></b>: Dipterocarpaceae is a pantropical tree family that plays an important role in our understanding of the ecology of Asian tropical rain forests. However, genome sizes for members of the Dipterocarpaceae are still poorly known. <b><i>Aims</i></b>: To report the genome size of 115 dipterocarp species and examine the variation and evolution of genome size in this family. <b><i>Methods</i></b>: Genome size was estimated using flow cytometry. Both the <i>rpoB</i> and <i>trn</i>L intron were sequenced to uncover the evolution of genome size within a phylogenetic framework. <b><i>Results</i></b>: The 1<i>C</i> genome size varied between 0.267 and 0.705 pg in <i>Shorea hemsleyana</i> and <i>Shorea ovalis</i>, respectively, a 2.64-fold variation across the family. Most dipterocarps are characterised by very small genomes with a mean 1<i>C</i> value of 0.416 pg (sd = 0.075) and five polyploids are recorded. The ancestral genome size for dipterocarps was reconstructed as 1<i>C</i><i>x</i> = 0.481 pg (95% CI = 0.433–0.534). <b><i>Conclusions</i></b>: Genome size variation in dipterocarps was characterised by very small values with a narrow range. Overall, genome size reduction from the ancestral state is a general trend in Dipterocarpaceae.
DOI: 10.6084/m9.figshare.4547149
title: Supplementary Material for: Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases

description: <strong><em>Objectives:</em></strong> Different types of ‘-omics' data are becoming available in the post-genome era; still a single -omics assessment provides limited insights to understand the biological mechanism of complex diseases. Genomics, epigenomics and transcriptomics data provide insight into the molecular dysregulation of neoplastic diseases, among them urothelial bladder cancer (UBC). Here, we propose a detailed analytical framework necessary to achieve an adequate integration of the three sets of -omics data to ultimately identify previously hidden genetic mechanisms in UBC. <b><i>Methods:</i></b> We built a multi-staged framework to study possible pair-wise combinations and integrated the data in three-way relationships. SNP genotypes, CpG methylation levels and gene expression levels were determined for a total of 70 individuals with UBC and with fresh tumour tissue available. <b><i>Results:</i></b> We suggest two main hypothesis-based scenarios for gene regulation based on the -omics integration analysis, where DNA methylation affects gene expression and genetic variants co-regulate gene expression and DNA methylation. We identified several three-way trans-association ‘hotspots' that are found at the molecular level and that deserve further studies. <b><i>Conclusions:</i></b> The proposed integrative framework allowed us to identify relationships at the whole-genome level providing some new biological insights and highlighting the importance of integrating -omics data.
DOI: 10.6084/m9.figshare.4547137
title: Towards a short questionnaire for stepwise assessment of upper limb function, pain and stiffness in Duchenne muscular dystrophy

description: <b>Purpose:</b> Duchenne muscular dystrophy can lead to upper extremity limitations, pain and stiffness. In a previous study, these domains have been investigated using extensive questionnaires, which are too time-consuming for clinical practice. This study aimed at gaining insight into the underlying dimensions of these questionnaires, and to construct a short questionnaire that can be used for clinical assessment. <b>Methods:</b> Exploratory factor analysis was performed on the responses of 213 participants to a web-based survey to find the underlying dimensions in the Capabilities of Upper Extremity questionnaire, the ABILHAND questionnaire, and questionnaires regarding pain and stiffness. Based on these underlying dimensions, a stepwise approach was formulated. In addition, construct validity of the factors was investigated. <b>Results:</b> In total, 14 factors were identified. All had high internal consistency (Cronbach's alpha &gt;0.89) and explained 80–88% of the variance of the original questionnaires. Construct validity was supported, because participants in the early ambulatory stage performed significantly better (<i>p</i> <b>Conclusion:</b> The factors identified from the set of questionnaires provide a valid representation of upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on the factor commonalities, the Upper Limb Short Questionnaire was formulated. Implications for RehabilitationNew insights into the underlying dimensions of upper extremity function, pain and stiffness in Duchenne muscular dystrophy are gained.Fourteen factors, with good internal consistency and construct validity, are identified regarding upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on these factors, the Upper Limb Short Questionnaire is presented.The Upper Limb Short Questionnaire can be used as an identifier of arm-hand limitations and the start of more thorough clinical investigation. New insights into the underlying dimensions of upper extremity function, pain and stiffness in Duchenne muscular dystrophy are gained. Fourteen factors, with good internal consistency and construct validity, are identified regarding upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on these factors, the Upper Limb Short Questionnaire is presented. The Upper Limb Short Questionnaire can be used as an identifier of arm-hand limitations and the start of more thorough clinical investigation.
DOI: 10.6084/m9.figshare.4547137.v1
title: Towards a short questionnaire for stepwise assessment of upper limb function, pain and stiffness in Duchenne muscular dystrophy

description: <b>Purpose:</b> Duchenne muscular dystrophy can lead to upper extremity limitations, pain and stiffness. In a previous study, these domains have been investigated using extensive questionnaires, which are too time-consuming for clinical practice. This study aimed at gaining insight into the underlying dimensions of these questionnaires, and to construct a short questionnaire that can be used for clinical assessment. <b>Methods:</b> Exploratory factor analysis was performed on the responses of 213 participants to a web-based survey to find the underlying dimensions in the Capabilities of Upper Extremity questionnaire, the ABILHAND questionnaire, and questionnaires regarding pain and stiffness. Based on these underlying dimensions, a stepwise approach was formulated. In addition, construct validity of the factors was investigated. <b>Results:</b> In total, 14 factors were identified. All had high internal consistency (Cronbach's alpha &gt;0.89) and explained 80–88% of the variance of the original questionnaires. Construct validity was supported, because participants in the early ambulatory stage performed significantly better (<i>p</i> <b>Conclusion:</b> The factors identified from the set of questionnaires provide a valid representation of upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on the factor commonalities, the Upper Limb Short Questionnaire was formulated. Implications for RehabilitationNew insights into the underlying dimensions of upper extremity function, pain and stiffness in Duchenne muscular dystrophy are gained.Fourteen factors, with good internal consistency and construct validity, are identified regarding upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on these factors, the Upper Limb Short Questionnaire is presented.The Upper Limb Short Questionnaire can be used as an identifier of arm-hand limitations and the start of more thorough clinical investigation. New insights into the underlying dimensions of upper extremity function, pain and stiffness in Duchenne muscular dystrophy are gained. Fourteen factors, with good internal consistency and construct validity, are identified regarding upper extremity function, pain and stiffness in Duchenne muscular dystrophy. Based on these factors, the Upper Limb Short Questionnaire is presented. The Upper Limb Short Questionnaire can be used as an identifier of arm-hand limitations and the start of more thorough clinical investigation.
DOI: 10.6084/m9.figshare.4547047
title: Supplementary Material for: Parkinson's Disease Case Ascertainment in the EPIC Cohort: The NeuroEPIC4PD Study

description: <strong><em>Background/Aims:</em></strong> Large epidemiological prospective studies represent an important opportunity for investigating risk factors for rare diseases such as Parkinson's disease (PD). Here we describe the procedures we used for ascertaining PD cases in the EPIC (European Prospective Investigation into Cancer and Nutrition) study. <b><i>Methods:</i></b> The following three-phase procedure was used: (1) elaboration of a NeuroEPIC4PD template for clinical data collection, (2) identification of all potential PD cases via record linkage and (3) validation of the diagnosis through clinical record revision, in a population of 220,494 subjects recruited in 7 European countries. All cases were labelled with the NeuroEPIC4PD diagnoses of ‘definite', ‘very likely', ‘probable', or ‘possible' PD. <b><i>Results:</i></b> A total of 881 PD cases were identified, with over 2,741,780 person-years of follow-up (199 definite, 275 very likely, 146 probable, and 261 possible). Of these, 734 were incident cases. The mean age at diagnosis was 67.9 years (SD 9.2) and 458 patients (52.0%) were men. Bradykinesia was the most frequent presenting motor sign (76.5%). Tremor-dominant and akinetic rigid forms of PD were the most common types of PD. A total of 289 patients (32.8%) were dead at the time of the last follow-up. <b><i>Conclusions:</i></b> This exercise proved that it is feasible to ascertain PD in large population-based cohort studies and offers a potential framework to be replicated in similar studies.
DOI: 10.6084/m9.figshare.4547047.v1
title: Supplementary Material for: Parkinson's Disease Case Ascertainment in the EPIC Cohort: The NeuroEPIC4PD Study

description: <strong><em>Background/Aims:</em></strong> Large epidemiological prospective studies represent an important opportunity for investigating risk factors for rare diseases such as Parkinson's disease (PD). Here we describe the procedures we used for ascertaining PD cases in the EPIC (European Prospective Investigation into Cancer and Nutrition) study. <b><i>Methods:</i></b> The following three-phase procedure was used: (1) elaboration of a NeuroEPIC4PD template for clinical data collection, (2) identification of all potential PD cases via record linkage and (3) validation of the diagnosis through clinical record revision, in a population of 220,494 subjects recruited in 7 European countries. All cases were labelled with the NeuroEPIC4PD diagnoses of ‘definite', ‘very likely', ‘probable', or ‘possible' PD. <b><i>Results:</i></b> A total of 881 PD cases were identified, with over 2,741,780 person-years of follow-up (199 definite, 275 very likely, 146 probable, and 261 possible). Of these, 734 were incident cases. The mean age at diagnosis was 67.9 years (SD 9.2) and 458 patients (52.0%) were men. Bradykinesia was the most frequent presenting motor sign (76.5%). Tremor-dominant and akinetic rigid forms of PD were the most common types of PD. A total of 289 patients (32.8%) were dead at the time of the last follow-up. <b><i>Conclusions:</i></b> This exercise proved that it is feasible to ascertain PD in large population-based cohort studies and offers a potential framework to be replicated in similar studies.
DOI: 10.6084/m9.figshare.4546906
title: Raw Data from Long-term memory of relative reward values

description: Long-term memory can be adaptive as it allows animals to retain information that is crucial for survival, such as the appearance and location of key resources. This is generally examined by comparing choices of stimuli that have value to the animal with those that do not; however, in nature choices are rarely so clear cut. Animals are able to assess the relative value of a resource via direct comparison, but it remains unclear whether they are able to retain this information for a biologically meaningful amount of time. To test this, captive red-footed tortoises (<i>Chelonoidis carbonaria</i>) were first trained to associate visual cues with specific qualities and quantities of food, and their preferences for the different reward values determined. They were then retested after an interval of 18 months. We found that the tortoises were able to retain the information they had learned about the cues as indicators of relative reward values over this interval, demonstrating a memory for the relative quantity and quality of food over an extended period of time. This is likely to impact directly on an animal's foraging decisions, such as the exploitation of seasonally varying resources, with obvious fitness implications for the individual; however, the implications may also extend to the ecological interactions in which the animal is involved, affecting processes such as herbivory and seed dispersal.
DOI: 10.6084/m9.figshare.4546903
title: Appendix from Larval antlions with more pronounced behavioural asymmetry show enhanced cognitive skills

description: Data on the behaviour of antlion larvae
DOI: 10.6084/m9.figshare.4546888
title: 2017 cafe du mRcredi : import and clean data

description: A toy dataset to illustrate data cleaning and importing with tidyverse packages.
DOI: 10.6084/m9.figshare.4546888.v1
title: 2017-01-13-cafe-du-mercredi-shuffled.vcf

description: A toy dataset to illustrate data cleaning and importing with tidyverse packages.
DOI: 10.6084/m9.figshare.4546888.v2
title: 2017-01-13-cafe-du-mercredi-shuffled.vcf

description: A toy dataset to illustrate data cleaning and importing with tidyverse packages.
DOI: 10.6084/m9.figshare.4546888.v4
title: 2017 cafe du mRcredi : import and clean data

description: A toy dataset to illustrate data cleaning and importing with tidyverse packages.
DOI: 10.6084/m9.figshare.4546888.v3
title: 2017 cafe du mRcredi : import and clean data

description: A toy dataset to illustrate data cleaning and importing with tidyverse packages.