cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8850668.v1
title: Load vs displacement data from Statistical properties of defect-dependent detachment strength in bioinspired dry adhesives

description: Dry adhesives using surface microstructures inspired by climbing animals have been recognized for their potentially novel capabilities, with relevance to a range of applications including pick-and-place handling. Past work has suggested that performance may be strongly dependent on variability in the critical defect size among fibrillar sub-contacts. However, it has not been directly verified that the resulting adhesive strength distribution is well described by the statistical theory of fracture used. Using <i>in situ</i> contact visualization, we characterize adhesive strength on a fibril-by-fibril basis for a synthetic fibrillar adhesive. Two distinct detachment mechanisms are observed. The fundamental, design-dependent mechanism involves defect propagation from within the contact. The secondary mechanism involves defect propagation from fabrication imperfections at the perimeter. The existence of two defect populations complicates characterization of the statistical properties. This is addressed by using the mean order ranking method to isolate the fundamental mechanism. The statistical properties obtained are subsequently used within a bimodal framework, allowing description of the secondary mechanism. Implications for performance are discussed, including the improvement of strength associated with elimination of fabrication imperfections. This statistical analysis of defect-dependent detachment represents a more complete approach to the characterization of fibrillar adhesives, offering new insight for design and fabrication.
DOI: 10.6084/m9.figshare.8850626
title: Continuous tracking of startled <i>Drosophila</i> as an alternative to the negative geotaxis climbing assay

description: The fruit fly, <i>Drosophila,</i> is commonly used to study late-onset neurodegenerative diseases due to the combination of powerful genetic tools, cheap and simple husbandry and short lifespan. One widely-used measure of disease progression is the age-dependent decline in motor performance that manifests in most <i>Drosophila</i> neurodegeneration models. This is usually quantified using a simple climbing assay. However, the standard climbing assay lacks sensitivity and suffers from high variability meaning large numbers of flies are needed or bespoke apparatus and software solutions. Here, we present a modification of the open-source, MATLAB-based, DART software to measure the decline in “startle response” with age. We demonstrate that the DART setup is more sensitive to the motor performance decline induced by adult-onset neuronal expression of amyloid beta (Aβ) peptides than a traditional climbing assay despite using smaller cohorts of flies. DART also has the potential to generate multiple metrics of motor behaviour during the startle response. The software requires no coding skills to operate and the required apparatus can be purchased commercially. Therefore, DART is a more useful method than the climbing assay for longitudinal assays of motor performance and will enable higher-throughput screen for genetic and pharmacological modifiers of neurodegeneration. In our proof-of-concept screen for modifiers of Aβ-dependent phenotypes, we identified that <i>in vivo</i> knock-down of <i>p53</i> in adult neurons is neuroprotective. This supports recent work targeting <i>p53 in vitro</i> and demonstrates the potential for DART to be used to screen for targets that ameliorate neurodegeneration.
DOI: 10.6084/m9.figshare.8850593
title: Supplementary Material for: Catheter-Based Renal Denervation Attenuates Kidney Interstitial Fibrosis in a Canine Model of High-Fat Diet-Induced Hypertension

description: <b><i>Background/Aims:</i></b> Catheter-based renal denervation (RDN) has emerged as an innovative interventional approach for reducing blood pressure (BP), suppressing ventricular substrate remodeling, and attenuating heart failure, which suggests that it might reduce kidney fibrosis in a canine model of high-fat diet-induced hypertension. This study thus sought to assess whether RDN could reduce kidney fibrosis and halt the progression of renal impairment in a canine model of high-fat diet-induced hypertension. <b><i>Methods:</i></b> Thirty-two beagles were randomized into either the normal control group (normal diet, <i>n</i> = 10) or the hypertension group (high-fat diet, <i>n</i> = 22). After successful establishment of the model, the hypertension model group was randomized to either the RDN group (<i>n</i> = 9) or the sham-surgery group (<i>n</i> = 8). Renal artery angiography, BP, heart rate (HR), and blood and urine biochemistry results were assessed at 1, 3, and 6 months after surgery. Canines were sacrificed at 6 months after surgery. The extent of kidney interstitial fibrosis, transforming growth factor-beta 1, alpha-smooth muscle actin, connective tissue growth factor, and E-cadherin protein were measured. <b><i>Results:</i></b> The group fed a high-fat diet had significantly (<i>p</i> ˂ 0.05) increased body weight, BP, and HR and higher levels of urine albumin, serum noradrenaline (NE), and angiotensin II (AngII) than the control group. The sham-surgery group and RDN group also had higher levels than the control group (<i>p</i> ˂ 0.05). Compared with the sham-surgery group, the RDN group had lower BP, urine albumin, serum NE, and AngII and less fibrotic tissue (all <i>p</i> ˂ 0.05). <b><i>Conclusion:</i></b> RDN reduced BP, slowed progression of albuminuria, and suppressed renal remodeling in a canine model of high-fat diet-induced hypertension.
DOI: 10.6084/m9.figshare.8850626.v1
title: Continuous tracking of startled <i>Drosophila</i> as an alternative to the negative geotaxis climbing assay

description: The fruit fly, <i>Drosophila,</i> is commonly used to study late-onset neurodegenerative diseases due to the combination of powerful genetic tools, cheap and simple husbandry and short lifespan. One widely-used measure of disease progression is the age-dependent decline in motor performance that manifests in most <i>Drosophila</i> neurodegeneration models. This is usually quantified using a simple climbing assay. However, the standard climbing assay lacks sensitivity and suffers from high variability meaning large numbers of flies are needed or bespoke apparatus and software solutions. Here, we present a modification of the open-source, MATLAB-based, DART software to measure the decline in “startle response” with age. We demonstrate that the DART setup is more sensitive to the motor performance decline induced by adult-onset neuronal expression of amyloid beta (Aβ) peptides than a traditional climbing assay despite using smaller cohorts of flies. DART also has the potential to generate multiple metrics of motor behaviour during the startle response. The software requires no coding skills to operate and the required apparatus can be purchased commercially. Therefore, DART is a more useful method than the climbing assay for longitudinal assays of motor performance and will enable higher-throughput screen for genetic and pharmacological modifiers of neurodegeneration. In our proof-of-concept screen for modifiers of Aβ-dependent phenotypes, we identified that <i>in vivo</i> knock-down of <i>p53</i> in adult neurons is neuroprotective. This supports recent work targeting <i>p53 in vitro</i> and demonstrates the potential for DART to be used to screen for targets that ameliorate neurodegeneration.
DOI: 10.6084/m9.figshare.8850593.v1
title: Supplementary Material for: Catheter-Based Renal Denervation Attenuates Kidney Interstitial Fibrosis in a Canine Model of High-Fat Diet-Induced Hypertension

description: <b><i>Background/Aims:</i></b> Catheter-based renal denervation (RDN) has emerged as an innovative interventional approach for reducing blood pressure (BP), suppressing ventricular substrate remodeling, and attenuating heart failure, which suggests that it might reduce kidney fibrosis in a canine model of high-fat diet-induced hypertension. This study thus sought to assess whether RDN could reduce kidney fibrosis and halt the progression of renal impairment in a canine model of high-fat diet-induced hypertension. <b><i>Methods:</i></b> Thirty-two beagles were randomized into either the normal control group (normal diet, <i>n</i> = 10) or the hypertension group (high-fat diet, <i>n</i> = 22). After successful establishment of the model, the hypertension model group was randomized to either the RDN group (<i>n</i> = 9) or the sham-surgery group (<i>n</i> = 8). Renal artery angiography, BP, heart rate (HR), and blood and urine biochemistry results were assessed at 1, 3, and 6 months after surgery. Canines were sacrificed at 6 months after surgery. The extent of kidney interstitial fibrosis, transforming growth factor-beta 1, alpha-smooth muscle actin, connective tissue growth factor, and E-cadherin protein were measured. <b><i>Results:</i></b> The group fed a high-fat diet had significantly (<i>p</i> ˂ 0.05) increased body weight, BP, and HR and higher levels of urine albumin, serum noradrenaline (NE), and angiotensin II (AngII) than the control group. The sham-surgery group and RDN group also had higher levels than the control group (<i>p</i> ˂ 0.05). Compared with the sham-surgery group, the RDN group had lower BP, urine albumin, serum NE, and AngII and less fibrotic tissue (all <i>p</i> ˂ 0.05). <b><i>Conclusion:</i></b> RDN reduced BP, slowed progression of albuminuria, and suppressed renal remodeling in a canine model of high-fat diet-induced hypertension.
DOI: 10.25375/uct.8850533
title: APPENDIX B_Recalibrating the breakup history of SW Gondwana: U-Pb radioisotopic constraints from the southern Cape of South Africa

description: Concordia plots for U-Pb radioisotopic data acquired by LA-ICPMS for samples from the Suurberg and Uitenhage Group.<br>The data were collected from 2015 to 2017.<br>LA-ICPMS: This was achieved using an <b>ASI Resolution M-50-LR Excimer laser to ablate zircon grains within a Laurin Technic M-50 dual-volume cell, both coupled to a Thermo Scientific Element 2 single collector mass spectrometer. </b>All analyses were performed at the Central Analytical Facility at the University of Stellenbosch, South Africa. <br><br><br>
DOI: 10.25375/uct.8850533.v1
title: APPENDIX B_Recalibrating the breakup history of SW Gondwana: U-Pb radioisotopic constraints from the southern Cape of South Africa

description: Concordia plots for U-Pb radioisotopic data acquired by LA-ICPMS for samples from the Suurberg and Uitenhage Group.<br>The data were collected from 2015 to 2017.<br>LA-ICPMS: This was achieved using an <b>ASI Resolution M-50-LR Excimer laser to ablate zircon grains within a Laurin Technic M-50 dual-volume cell, both coupled to a Thermo Scientific Element 2 single collector mass spectrometer. </b>All analyses were performed at the Central Analytical Facility at the University of Stellenbosch, South Africa. <br><br><br>
DOI: 10.25375/uct.8850485
title: APPENDIX A (Data Tables)_Recalibrating the breakup history of SW Gondwana: U-Pb radioisotopic constraints from the southern Cape of South Africa

description: U-Pb radioisotopic data for the Suurberg and Uitenhage Groups acquired by ICPMS and TIMS.<br>The data were collected from 2015 to 2017. There are two types of data acquired from two different mass spectrometers, (1) LA-ICPMS and (2) CA-TIMS: <br> (1) LA-ICPMS: This was achieved using an <b>ASI Resolution M-50-LR Excimer laser to ablate zircon grains within a Laurin Technic M-50 dual-volume cell, both coupled to a Thermo Scientific Element 2 single collector mass spectrometer. </b>All analyses were performed at the Central Analytical Facility at the University of Stellenbosch, South Africa. <br><br>(2) CA-TIMS: Following chemical abrasion pre-treatments, analysis was performed on a <b>Micromass Sector54 thermal-ionisation mass spectrometer</b> at the Berkeley Geochronology Center in California, USA.
DOI: 10.25375/uct.8850485.v1
title: APPENDIX A (Data Tables)_Recalibrating the breakup history of SW Gondwana: U-Pb radioisotopic constraints from the southern Cape of South Africa

description: U-Pb radioisotopic data for the Suurberg and Uitenhage Groups acquired by ICPMS and TIMS.<br>The data were collected from 2015 to 2017. There are two types of data acquired from two different mass spectrometers, (1) LA-ICPMS and (2) CA-TIMS: <br> (1) LA-ICPMS: This was achieved using an <b>ASI Resolution M-50-LR Excimer laser to ablate zircon grains within a Laurin Technic M-50 dual-volume cell, both coupled to a Thermo Scientific Element 2 single collector mass spectrometer. </b>All analyses were performed at the Central Analytical Facility at the University of Stellenbosch, South Africa. <br><br>(2) CA-TIMS: Following chemical abrasion pre-treatments, analysis was performed on a <b>Micromass Sector54 thermal-ionisation mass spectrometer</b> at the Berkeley Geochronology Center in California, USA.
DOI: 10.6084/m9.figshare.8850212
title: Supplement Table 1-tissue.docx

description: Supplement Table 1. Tissues or cells used to obtain the chromatin states information for intronic or intergenic SNPs.
DOI: 10.6084/m9.figshare.8850161
title: soil evaporation Data.rar

description: the data and code are used in Wang et al.,2019 for the E_FILM model
DOI: 10.6084/m9.figshare.8850212.v1
title: Supplement Table 1-tissue.docx

description: Supplement Table 1. Tissues or cells used to obtain the chromatin states information for intronic or intergenic SNPs.
DOI: 10.6084/m9.figshare.8850119
title: Subsoil AMF_1

description: Illumina MiSeq dataset containing partial LSU sequences from Glomeromycota, belonging to a Top- Subsoil fungal diversity study. <br>Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil. <br>https://doi.org/10.1016/j.soilbio.2017.11.009<br>
DOI: 10.6084/m9.figshare.8850143
title: Hox.cds.fasta

description: This fast file contains all the sequences of Hox genes of the sterlet
DOI: 10.6084/m9.figshare.8850101
title: Deciphering the role of reproductive investment, pollination success and predispersal seed predation on reproductive output in <i>Juniperus thurifera</i>

description: <b>Background</b>: Plant reproductive output is determined by a complex set of factors including resource availability, pollination success and pre-dispersal predation. Disentangling the relative contribution of each factor is critical to underpin the factors determining plant fitness. <b>Aims</b>: To unravel the relative contributions of initial reproductive effort, pollination success and pre-dispersal seed predation to plant reproductive success in the fleshy-fruited, wind-pollinated <i>Juniperus thurifera</i>. <b>Methods</b>: We conducted an experiment including pollen addition and pesticide application on 40 female juniper trees for 20 months. Flower production was used as a proxy for resource levels. <b>Results</b>: Main fruit loss occurs in early stages of fruit development. Initial flower number affected fruit and seed set by (a) increasing the rate of fruit formation and the number of viable seeds within fruits and (b) modifying the incidence of low-mobile predators through a satiation effect. Pollination did not limit fruit set, although hand pollinated fruits had more viable seeds. Pre-dispersal seed predation by different arthropods was critical in defining final fruit set. <b>Conclusions</b>: Fruit set in <i>J. thurifera</i> was determined by the interaction of initial reproductive effort and pre-dispersal seed predation. Pollination was not a limiting factor in this relatively dense juniper forests during a year of high flower production.
DOI: 10.6084/m9.figshare.8850101.v1
title: Deciphering the role of reproductive investment, pollination success and predispersal seed predation on reproductive output in <i>Juniperus thurifera</i>

description: <b>Background</b>: Plant reproductive output is determined by a complex set of factors including resource availability, pollination success and pre-dispersal predation. Disentangling the relative contribution of each factor is critical to underpin the factors determining plant fitness. <b>Aims</b>: To unravel the relative contributions of initial reproductive effort, pollination success and pre-dispersal seed predation to plant reproductive success in the fleshy-fruited, wind-pollinated <i>Juniperus thurifera</i>. <b>Methods</b>: We conducted an experiment including pollen addition and pesticide application on 40 female juniper trees for 20 months. Flower production was used as a proxy for resource levels. <b>Results</b>: Main fruit loss occurs in early stages of fruit development. Initial flower number affected fruit and seed set by (a) increasing the rate of fruit formation and the number of viable seeds within fruits and (b) modifying the incidence of low-mobile predators through a satiation effect. Pollination did not limit fruit set, although hand pollinated fruits had more viable seeds. Pre-dispersal seed predation by different arthropods was critical in defining final fruit set. <b>Conclusions</b>: Fruit set in <i>J. thurifera</i> was determined by the interaction of initial reproductive effort and pre-dispersal seed predation. Pollination was not a limiting factor in this relatively dense juniper forests during a year of high flower production.
DOI: 10.6084/m9.figshare.8850143.v1
title: Hox.cds.fasta

description: This fast file contains all the sequences of Hox genes of the sterlet
DOI: 10.6084/m9.figshare.8850119.v1
title: Drilosphere_Round_1.rar

description: Illumina MiSeq dataset containing partial LSU sequences from Glomeromycota, belonging to a Top- Subsoil fungal diversity study. <br>Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil. <br>https://doi.org/10.1016/j.soilbio.2017.11.009<br>
DOI: 10.6084/m9.figshare.8849945
title: yeast ref coding sequences

description: yeast ref orfs for angus 2019
DOI: 10.6084/m9.figshare.8849945.v2
title: yeast ref coding sequences

description: yeast ref orfs for angus 2019
DOI: 10.6084/m9.figshare.8849945.v1
title: yeast ref coding sequences

description: yeast ref orfs for angus 2019
DOI: 10.6084/m9.figshare.8849921
title: yeast ref for angus 2019

description: yeast ref for angus 2019
DOI: 10.6084/m9.figshare.8849921.v1
title: yeast ref for angus 2019

description: yeast ref for angus 2019
DOI: 10.6084/m9.figshare.8849645
title: Additional file 6: of Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies

description: BPC3 pruned top 200-union. BPC3 pruned top-200 union, sorted by decreasing extraction number followed by increasing average position. For each SNP in this list, its extraction number and average position in the ranking are indicated. For each approach, a 0 indicates that the SNP was not in the top 200, a non-zero value occurs if the SNP was in the top 200 and indicates how well the SNP ranks with 200 being the best ranking and 1 the worst. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.8849645.v1
title: Additional file 6: of Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies

description: BPC3 pruned top 200-union. BPC3 pruned top-200 union, sorted by decreasing extraction number followed by increasing average position. For each SNP in this list, its extraction number and average position in the ranking are indicated. For each approach, a 0 indicates that the SNP was not in the top 200, a non-zero value occurs if the SNP was in the top 200 and indicates how well the SNP ranks with 200 being the best ranking and 1 the worst. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.8849624
title: Additional file 3: of Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies

description: GENEVA pruned top-1000 union. GENEVA pruned top-1000 union, sorted by decreasing extraction number followed by increasing average position. For each SNP in this list, its extraction number and average position in the ranking are indicated. For each approach, a 0 indicates that the SNP was not in the top 1000, a non-zero value occurs if the SNP was in the top 1000 and indicates how well the SNP ranks with 1000 being the best ranking and 1 the worst. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.8849624.v1
title: Additional file 3: of Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies

description: GENEVA pruned top-1000 union. GENEVA pruned top-1000 union, sorted by decreasing extraction number followed by increasing average position. For each SNP in this list, its extraction number and average position in the ranking are indicated. For each approach, a 0 indicates that the SNP was not in the top 1000, a non-zero value occurs if the SNP was in the top 1000 and indicates how well the SNP ranks with 1000 being the best ranking and 1 the worst. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.8849609
title: Additional file 6: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: Univariate survival analysis identified 43 genes as independent prognostic biomarkers. (XLS 20 kb)
DOI: 10.6084/m9.figshare.8849609.v1
title: Additional file 6: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: Univariate survival analysis identified 43 genes as independent prognostic biomarkers. (XLS 20 kb)
DOI: 10.6084/m9.figshare.8849597
title: Additional file 4: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: KEGG and GO enrichment analyses for 1064 DEGs. (XLS 378 kb)
DOI: 10.6084/m9.figshare.8849603
title: Additional file 5: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: The details of GO functional enrichment analysis for each module. (XLS 51 kb)
DOI: 10.6084/m9.figshare.8849594
title: Additional file 6: of Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

description: Table S3. Semantic coordinates of the GOs represented in the graphic depiction of the favored or disfavored GO categories in multiple diseases (Detailed list of coordinates). (XLSX 41 kb)
DOI: 10.6084/m9.figshare.8849600
title: Additional file 7: of Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

description: Table S4. Published data from multiple studies analyzed in this work (References for the studies used in this work). (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8849603.v1
title: Additional file 5: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: The details of GO functional enrichment analysis for each module. (XLS 51 kb)
DOI: 10.6084/m9.figshare.8849594.v1
title: Additional file 6: of Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

description: Table S3. Semantic coordinates of the GOs represented in the graphic depiction of the favored or disfavored GO categories in multiple diseases (Detailed list of coordinates). (XLSX 41 kb)
DOI: 10.6084/m9.figshare.8849597.v1
title: Additional file 4: of A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

description: KEGG and GO enrichment analyses for 1064 DEGs. (XLS 378 kb)
DOI: 10.6084/m9.figshare.8849600.v1
title: Additional file 7: of Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

description: Table S4. Published data from multiple studies analyzed in this work (References for the studies used in this work). (XLSX 16 kb)