cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6099458
title: Identification and expression analysis of 11 <i>MADS-box</i> genes in peach (<i>Prunus persica</i> var. <i>nectarina</i> ‘Luxing’)

description: MADS-box genes play a central role in the development of flowers in plants. In this study, 11 <i>PpMADS</i>s were isolated from ‘Luxing’ peach, and the expression levels were detected in different tissues and fruit development. Eleven <i>PpMADS</i>s, designated as <i>PpMADS13, 14, 18, 23, 24, 25, 32, 33, 34, 35</i>, and <i>39</i> were isolated. Phylogenetic analysis revealed that <i>PpMADS13, 14</i>, and <i>18</i> belonged to SVP, AGL15, and MIKC* group respectively; <i>PpMADS23, 24, 25</i>, and <i>39</i> were in the Mα group; <i>PpMADS32, 33, 34</i>, and <i>35</i> belonged to the Mγ group. Predictions from subcellular localization showed that 10 PpMADS were located in the nucleus. RT-PCR revealed that <i>PpMADS13</i> was expressed in stems, leaves, and during fruit development (70d); <i>PpMADS14</i> was expressed in sepals, stamens, petals, and during flower development; <i>PpMADS18</i> was expressed in roots, stems, leaves, sepals, ovaries, stamens, petals, and during flower and fruit development; all MADS-box genes (expect for <i>PpMADS33</i>) in the Mα and Mγ group were expressed in roots, stems, leaves, sepals, ovaries, stamens, petals, and during flower development; few genes were expressed during fruit development. These results indicated that <i>PpMADS</i> may play a crucial regulatory role in vegetative growth and development processes of flowers and fruits in peaches.
DOI: 10.6084/m9.figshare.6099458.v1
title: Identification and expression analysis of 11 <i>MADS-box</i> genes in peach (<i>Prunus persica</i> var. <i>nectarina</i> ‘Luxing’)

description: MADS-box genes play a central role in the development of flowers in plants. In this study, 11 <i>PpMADS</i>s were isolated from ‘Luxing’ peach, and the expression levels were detected in different tissues and fruit development. Eleven <i>PpMADS</i>s, designated as <i>PpMADS13, 14, 18, 23, 24, 25, 32, 33, 34, 35</i>, and <i>39</i> were isolated. Phylogenetic analysis revealed that <i>PpMADS13, 14</i>, and <i>18</i> belonged to SVP, AGL15, and MIKC* group respectively; <i>PpMADS23, 24, 25</i>, and <i>39</i> were in the Mα group; <i>PpMADS32, 33, 34</i>, and <i>35</i> belonged to the Mγ group. Predictions from subcellular localization showed that 10 PpMADS were located in the nucleus. RT-PCR revealed that <i>PpMADS13</i> was expressed in stems, leaves, and during fruit development (70d); <i>PpMADS14</i> was expressed in sepals, stamens, petals, and during flower development; <i>PpMADS18</i> was expressed in roots, stems, leaves, sepals, ovaries, stamens, petals, and during flower and fruit development; all MADS-box genes (expect for <i>PpMADS33</i>) in the Mα and Mγ group were expressed in roots, stems, leaves, sepals, ovaries, stamens, petals, and during flower development; few genes were expressed during fruit development. These results indicated that <i>PpMADS</i> may play a crucial regulatory role in vegetative growth and development processes of flowers and fruits in peaches.
DOI: 10.6084/m9.figshare.6099389
title: A zinc knuckle gene on the Y chromosome (zkY) determines sex in Atlantic cod (Gadus morhua) - Supporting files

description: gadMor2.1 - Atlantic cod gadMor2.1 genome assembly.<br>long-range PCR miseq Illumina R1 and R2 - The long-range miseq illumina data.<br>
DOI: 10.6084/m9.figshare.12894197
title: R0191_20171003a_videos

description: Rat 0191, skilled reaching data collected on 10/3/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12894197.v1
title: R0191_20171003a_videos

description: Rat 0191, skilled reaching data collected on 10/3/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.6098972
title: freebayes.ALL.VAR.Q40.DP4_30_max_miss_5.recode.edit.annotated.names.SNPs.AA.common.vcf.gz

description: Common SNPs in corkwing wrasses (n=65) from Northern Europe with ancestral state
DOI: 10.6084/m9.figshare.6098852
title: Supplementary Material for: Identifying Risk Factors Shared by Bronchopulmonary Dysplasia, Severe Retinopathy, and Cystic Periventricular Leukomalacia in Very Preterm Infants for Targeted Intervention

description: <b><i>Background:</i></b> Bronchopulmonary dysplasia (BPD), severe retinopathy of prematurity (sROP), and cystic periventricular leukomalacia (cPVL) are 3 major morbidities with long-term neurodevelopmental impairments in preterm infants. <b><i>Objective:</i></b> To investigate the strength of associations and identify key risk factors shared by BPD, sROP, and cPVL for targeted intervention. <b><i>Methods:</i></b> We studied the Taiwanese very-preterm-infant registry data on 3,507 infants admitted to neonatal intensive care units and discharged at postmenstrual age ≥36 weeks between 2008 and 2013. <b><i>Results:</i></b> Of 3,507 infants, 1,497 presented with at least 1 morbidity (26 [1.7%], 386 [25.8%], and 1,085 [72.5%] exhibited 3, 2, and 1 morbidities, respectively). BPD was strongly associated with sROP (odds ratio 5.93; 95% confidence interval 5.02–7.03), followed by cPVL (2.08; 1.63–2.64), but sROP and cPVL were weakly associated (1.59; 1.17–2.13). Most risk factors contributed to BPD, which shared risk factors with sROP and cPVL. A birth weight of &lt; 1,000 g, male sex, and prolonged mechanical ventilation (MV) were shared by BPD and sROP, and chorioamnionitis, severe respiratory distress syndrome, and prolonged MV specifically contributed to BPD and cPVL. Prolonged MV was the single risk factor common to BPD, sROP, and cPVL. Avoiding prolonged MV reduced the risk of having at least 1 of the 3 morbidities by 37%. <b><i>Conclusions:</i></b> BPD and sROP were most strongly associated. Most risk factors contributed to BPD, with differentially shared effects on sROP and cPVL. Prolonged MV was the only risk factor shared by all 3 morbidities, and avoiding it potentially reduced the risk of having at least 1 of them.
DOI: 10.6084/m9.figshare.6098321
title: crAss-like phage genome and protein sequences

description: Updated 15/01/2019:<br>249 crAss-like phage contigs detected in metagenomic sequencing data of human faecal virome/phageome studies.<br>Includes prodigal protein predictions of genome sequences, with candidate genus 7 and 8 predictions performed using genetic code 15.
DOI: 10.6084/m9.figshare.6098321.v2
title: crAss-like phage genome and protein sequences

description: Updated 15/01/2019:<br>249 crAss-like phage contigs detected in metagenomic sequencing data of human faecal virome/phageome studies.<br>Includes prodigal protein predictions of genome sequences, with candidate genus 7 and 8 predictions performed using genetic code 15.
DOI: 10.6084/m9.figshare.6098321.v1
title: crAss-like_contigs.fasta.tar.gz

description: 245 crAss-like phage contigs detected in metagenomic sequencing data of human faecal virome/phageome studies
DOI: 10.6084/m9.figshare.6098255
title: Supplementary Material for: Age, Loss Minimization, and the Role of Probability for Decision-Making

description: <b><i>Background:</i></b> Older adults are stereotypically considered to be risk averse compared to younger age groups, although meta-analyses on age and the influence of gain/loss framing on risky choices have not found empirical evidence for age differences in risk-taking. <b><i>Objective:</i></b> The current study extends the investigation of age differences in risk preference by including analyses on the effect of the probability of a risky option on choices in gain versus loss situations. <b><i>Methods:</i></b> Participants (<i>n</i> = 130 adults aged 19–80 years) chose between a certain option and a risky option of varying probability in gain- and loss-framed gambles with actual monetary outcomes. <b><i>Results:</i></b> Only younger adults displayed an overall framing effect. Younger and older adults responded differently to probability fluctuations depending on the framing condition. Older adults were more likely to choose the risky option as the likelihood of avoiding a larger loss increased and as the likelihood of a larger gain decreased. Younger adults responded with the opposite pattern: they were more likely to choose the risky option as the likelihood of a larger gain increased and as the likelihood of avoiding a (slightly) larger loss decreased. <b><i>Conclusion:</i></b> Results suggest that older adults are more willing to select a risky option when it increases the likelihood that larger losses be avoided, whereas younger adults are more willing to select a risky option when it allows for slightly larger gains. This finding supports expectations based on theoretical accounts of goal orientation shifting away from securing gains in younger adulthood towards maintenance and avoiding losses in older adulthood. Findings are also discussed in respect to the affective enhancement perspective and socioemotional selectivity theory.
DOI: 10.6084/m9.figshare.6098219.v2
title: ELLPMDA: Ensemble learning and link prediction for miRNA-disease association prediction

description: Recently, accumulating evidences have indicated miRNAs play critical roles in the progression and development of various human complex diseases, which pointed out that identifying miRNA-disease association could enable us to understand diseases at miRNA level. Thus, revealing more and more potential miRNA-disease associations is a vital topic in biomedical domain. However, it will be extremely expensive and time-consuming if we examine all the possible miRNA-disease pairs. Therefore, more accurate and efficient methods are being highly requested to detect potential miRNA-disease associations. In this study, we developed a computational model of Ensemble Learning and Link Prediction for miRNA-Disease Association prediction (ELLPMDA) to achieve this goal. By integrating miRNA functional similarity, disease semantic similarity, miRNA-disease association and Gaussian profile kernel similarity for miRNAs and diseases, we constructed a similarity network and utilized ensemble learning to combine rank results given by three classic similarity-based algorithms. To evaluate the performance of ELLPMDA, we exploited global and local Leave-One-Out Cross Validation (LOOCV), 5-fold Cross Validation (CV) and three kinds of case studies. As a result, the AUCs of ELLPMDA is 0.9181, 0.8181 and 0.9193+/−0.0002 in global LOOCV, local LOOCV and 5-fold CV, respectively, which significantly exceed almost all the previous methods. Moreover, in three distinct kinds of case studies for Kidney Neoplasms, Lymphoma, Prostate Neoplasms, Colon Neoplasms and Esophageal Neoplasms, 88%, 92%, 86%, 98% and 98% out of the top 50 predicted miRNAs has been confirmed, respectively. Besides, ELLPMDA is based on global similarity measure and applicable to new diseases without any known related miRNAs.
DOI: 10.6084/m9.figshare.6098219.v1
title: ELLPMDA: Ensemble Learning and Link Prediction for miRNA-Disease Association prediction

description: Recently, accumulating evidences have indicated miRNAs play critical roles in the progression and development of various human complex diseases, which pointed out that identifying miRNA-disease association could enable us to understand diseases at miRNA level. Thus, revealing more and more potential miRNA-disease associations is a vital topic in biomedical domain. However, it will be extremely expensive and time-consuming if we examine all the possible miRNA-disease pairs. Therefore, more accurate and efficient methods are being highly requested to detect potential miRNA-disease associations. In this study, we developed a computational model of Ensemble Learning and Link Prediction for miRNA-Disease Association prediction (ELLPMDA) to achieve this goal. By integrating miRNA functional similarity, disease semantic similarity, miRNA-disease association and Gaussian profile kernel similarity for miRNAs and diseases, we constructed a similarity network and utilized ensemble learning to combine rank results given by three classic similarity-based algorithms. To evaluate the performance of ELLPMDA, we exploited global and local Leave-One-Out Cross Validation (LOOCV), 5-fold Cross Validation (CV) and three kinds of case studies. As a result, the AUCs of ELLPMDA is 0.9181, 0.8181 and 0.9193+/-0.0002 in global LOOCV, local LOOCV and 5-fold CV, respectively, which significantly exceed almost all the previous methods. Moreover, in three distinct kinds of case studies for Kidney Neoplasms, Lymphoma, Prostate Neoplasms, Colon Neoplasms and Esophageal Neoplasms, 88%, 92%, 86%, 98% and 98% out of the top 50 predicted miRNAs has been confirmed, respectively. Besides, ELLPMDA is based on global similarity measure and applicable to new diseases without any known related miRNAs.
DOI: 10.6084/m9.figshare.6097718.v1
title: Is the Maturation of Arteriovenous Fistulas a Mechanical or Biological Problem? IMECE 2016, Phoenix: Supplementary materials

description: Changes of parameters recorded in the first 30 s of the arteriovenous fistula maturation process
DOI: 10.6084/m9.figshare.6097718.v2
title: ASME 2016 Is the Maturation of Arteriovenous Fistulas a Mechanical or Biological Problem?

description: IMECE 2016, Phoenix: Supplementary materials<br><br>Changes of parameters recorded in the first 30 s of the arteriovenous fistula maturation process
DOI: 10.6084/m9.figshare.6097718.v3
title: ASME 2016 Is the Maturation of Arteriovenous Fistulas a Mechanical or Biological Problem? IMECE 2016, Phoenix: Supplementary materials

description: Changes of parameters recorded in the first 30 s of the arteriovenous fistula maturation process<br>
DOI: 10.6084/m9.figshare.6097685
title: Supplementary Material for: Peripheral Retinal Imaging Biomarkers for Alzheimer’s Disease: A Pilot Study

description: <b><i>Purpose:</i></b> To examine whether ultra-widefield (UWF) retinal imaging can identify biomarkers for Alzheimer’s disease (AD) and its progression. <b><i>Methods:</i></b> Images were taken using a UWF scanning laser ophthalmoscope (Optos P200C AF) to determine phenotypic variations in 59 patients with AD and 48 healthy controls at baseline (BL). All living participants were invited for a follow-up (FU) after 2 years and imaged again (if still able to participate). All participants had blood taken for genotyping at BL. Images were graded for the prevalence of age-related macular degeneration-like pathologies and retinal vascular parameters. Comparison between AD patients and controls was made using the Student <i>t</i> test and the χ<sup>2</sup> test. <b><i>Results:</i></b> Analysis at BL revealed a significantly higher prevalence of a hard drusen phenotype in the periphery of AD patients (14/55; 25.4%) compared to controls (2/48; 4.2%) [χ<sup>2</sup> = 9.9, df = 4, <i>p</i> = 0.04]. A markedly increased drusen number was observed at the 2-year FU in patients with AD compared to controls. There was a significant increase in venular width gradient at BL (zone C: 8.425 × 10<sup>–3</sup> ± 2.865 × 10<sup>–3</sup> vs. 6.375 × 10<sup>–3</sup> ± 1.532 × 10<sup>–3</sup>, <i>p</i> = 0.008; entire image: 8.235 × 10<sup>–3</sup> ± 2.839 × 10<sup>–3</sup> vs. 6.050 × 10<sup>–3</sup> ± 1.414 × 10<sup>–3</sup>, <i>p</i> = 0.004) and a significant decrease in arterial fractal dimension in AD at BL (entire image: 1.250 ± 0.086 vs. 1.304 ± 0.089, <i>p</i> = 0<b><i>.</i></b>049) with a trend for both at FU. <b><i>Conclusions:</i></b> UWF retinal imaging revealed a significant association between AD and peripheral hard drusen formation and changes to the vasculature beyond the posterior pole, at BL<sub></sub> and after clinical progression over 2 years, suggesting that monitoring pathological changes in the peripheral retina might become a valuable tool in AD monitoring.
DOI: 10.6084/m9.figshare.6097685.v1
title: Supplementary Material for: Peripheral Retinal Imaging Biomarkers for Alzheimer’s Disease: A Pilot Study

description: <b><i>Purpose:</i></b> To examine whether ultra-widefield (UWF) retinal imaging can identify biomarkers for Alzheimer’s disease (AD) and its progression. <b><i>Methods:</i></b> Images were taken using a UWF scanning laser ophthalmoscope (Optos P200C AF) to determine phenotypic variations in 59 patients with AD and 48 healthy controls at baseline (BL). All living participants were invited for a follow-up (FU) after 2 years and imaged again (if still able to participate). All participants had blood taken for genotyping at BL. Images were graded for the prevalence of age-related macular degeneration-like pathologies and retinal vascular parameters. Comparison between AD patients and controls was made using the Student <i>t</i> test and the χ<sup>2</sup> test. <b><i>Results:</i></b> Analysis at BL revealed a significantly higher prevalence of a hard drusen phenotype in the periphery of AD patients (14/55; 25.4%) compared to controls (2/48; 4.2%) [χ<sup>2</sup> = 9.9, df = 4, <i>p</i> = 0.04]. A markedly increased drusen number was observed at the 2-year FU in patients with AD compared to controls. There was a significant increase in venular width gradient at BL (zone C: 8.425 × 10<sup>–3</sup> ± 2.865 × 10<sup>–3</sup> vs. 6.375 × 10<sup>–3</sup> ± 1.532 × 10<sup>–3</sup>, <i>p</i> = 0.008; entire image: 8.235 × 10<sup>–3</sup> ± 2.839 × 10<sup>–3</sup> vs. 6.050 × 10<sup>–3</sup> ± 1.414 × 10<sup>–3</sup>, <i>p</i> = 0.004) and a significant decrease in arterial fractal dimension in AD at BL (entire image: 1.250 ± 0.086 vs. 1.304 ± 0.089, <i>p</i> = 0<b><i>.</i></b>049) with a trend for both at FU. <b><i>Conclusions:</i></b> UWF retinal imaging revealed a significant association between AD and peripheral hard drusen formation and changes to the vasculature beyond the posterior pole, at BL<sub></sub> and after clinical progression over 2 years, suggesting that monitoring pathological changes in the peripheral retina might become a valuable tool in AD monitoring.
DOI: 10.6084/m9.figshare.6097619
title: Monitoring of forest cover dynamics in eastern area of Béni-Mellal Province using ASTER and Sentinel-2A multispectral data

description: This study aimed to monitor and analyze the spatial and temporal dynamic of forest cover in Eastern area of Beni-Mellal Province (Morocco), using multispectral ASTER and Sentinel-2A MIS images acquired in 2001 and 2015, respectively. The supervised classification algorithm and NDVI were combined within a GIS environment to quantify the extent and density change of forest cover stands, i.e., Holm oak, Aleppo pine, Thya, Zea oak, Crops & others and Bare ground. The classification overall accuracy was 97.76 and 95.80% in 2001 and 2015 images, respectively. The result revealed an overall forest cover change with an increase in forested area. All species stands showed expansion at the expense of the bare ground and crops & others classes. The density maps showed a net density change with an expansion of dense forest class. The observed forest cover expansion may be due to the favourable climate in the examined period, the protection, the reforestation programs and the regeneration through clandestine cutting. These results constituted the first attempt at mapping and monitoring of forest cover change in the study region that used a remote sensing-based product. They will help authorities and forest managers for the development of sustainable forest conservation and management decisions.
DOI: 10.6084/m9.figshare.6097619.v1
title: Monitoring of forest cover dynamics in eastern area of Béni-Mellal Province using ASTER and Sentinel-2A multispectral data

description: This study aimed to monitor and analyze the spatial and temporal dynamic of forest cover in Eastern area of Beni-Mellal Province (Morocco), using multispectral ASTER and Sentinel-2A MIS images acquired in 2001 and 2015, respectively. The supervised classification algorithm and NDVI were combined within a GIS environment to quantify the extent and density change of forest cover stands, i.e., Holm oak, Aleppo pine, Thya, Zea oak, Crops & others and Bare ground. The classification overall accuracy was 97.76 and 95.80% in 2001 and 2015 images, respectively. The result revealed an overall forest cover change with an increase in forested area. All species stands showed expansion at the expense of the bare ground and crops & others classes. The density maps showed a net density change with an expansion of dense forest class. The observed forest cover expansion may be due to the favourable climate in the examined period, the protection, the reforestation programs and the regeneration through clandestine cutting. These results constituted the first attempt at mapping and monitoring of forest cover change in the study region that used a remote sensing-based product. They will help authorities and forest managers for the development of sustainable forest conservation and management decisions.
DOI: 10.6084/m9.figshare.6097616
title: Supplementary Material for: Skin Barrier Restoration and Moisturization Using Horse Oil-Loaded Dissolving Microneedle Patches

description: <b><i>Background:</i></b> Horse oil (HO) has skin barrier restoration and skin-moisturizing effects. Although cream formulations have been used widely and safely, their limited penetration through the stratum corneum is a major obstacle to maximizing the cosmetic efficacy of HO. Therefore, we aimed to encapsulate HO in a cosmetic dissolving microneedle (DMN) for efficient transdermal delivery. <b><i>Methods:</i></b> To overcome these limitations of skin permeation, HO-loaded DMN (HO-DMN) patches were developed and evaluated for their efficacy and safety using in vitro and clinical studies. <b><i>Results:</i></b> Despite the lipophilic nature of HO, the HO-DMN patches had a sharp shape and uniform array, with an average length and tip diameter of 388.36 ± 16.73 and 38.54 ± 5.29 µm, respectively. The mechanical strength of the HO-DMN patches was sufficient (fracture force of 0.29 ± 0.01 N), and they could successfully penetrate pig skin. During the 4-week clinical evaluation, HO-DMN patches caused significant improvements in skin and dermal density, skin elasticity, and moisturization. Additionally, a brief safety assessment showed that the HO-DMN patches induced negligible adverse events. <b><i>Conclusion:</i></b> The HO-DMNs are efficient, safe, and convenient for wide use in cosmetic applications for skin barrier restoration and moisturization.
DOI: 10.6084/m9.figshare.6097436
title: przepiora_rawdata

description: przepiora_rawdata
DOI: 10.6084/m9.figshare.6097436.v1
title: przepiora_rawdata

description: przepiora_rawdata
DOI: 10.6084/m9.figshare.6097343
title: bla

description: blabla
DOI: 10.6084/m9.figshare.6097343.v1
title: Row data Coral planulae

description: Material supporting the manuscript "<b>Boat noise prevents soundscape-based habitat selection by coral planulae</b>" submitted to Proc. R. Soc. B. by Lecchini et al.
DOI: 10.6084/m9.figshare.6097307
title: Results of parameter estimation for Ambrosia artemisiifolia simulations

description: The NetCDF files in this dataset contain annual results of the 100 best "runs" from a Latin-Hupercube-Sampling over the parameter space in North America (NAM) and transferred those results to Europe (EUR). The Excel sheet contains the parameter combination for those.<br><br> Leiblein-Wild, M. C., Steinkamp, J., Hickler, T. and Tackenberg, O.: Modelling the potential distribution, net primary production and phenology of common ragweed with a physiological model, J. Biogeogr., 43(3), 544–554, doi:10.1111/jbi.12646, 2016.
DOI: 10.6084/m9.figshare.6097307.v1
title: Results of parameter estimation for Ambrosia artemisiifolia simulations

description: The NetCDF files in this dataset contain annual results of the 100 best "runs" from a Latin-Hupercube-Sampling over the parameter space in North America (NAM) and transferred those results to Europe (EUR). The Excel sheet contains the parameter combination for those.<br><br> Leiblein-Wild, M. C., Steinkamp, J., Hickler, T. and Tackenberg, O.: Modelling the potential distribution, net primary production and phenology of common ragweed with a physiological model, J. Biogeogr., 43(3), 544–554, doi:10.1111/jbi.12646, 2016.