cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6854534.v1
title: Supplementary Material for: LOC101930370/MiR-1471 Axis Modulates the Hedgehog Signaling Pathway in Breast Cancer

description: <b><i>Background/Aims:</i></b> Non-coding RNAs (ncRNAs) play vital regulatory roles in many tumors. However, the functional roles of these transcripts responsible for their dysregulation in breast cancer (BC) are not thoroughly understood. <b><i>Methods:</i></b> We examined the expression of microRNA miR-1471 in BC specimens. Online analysis tools predicted that lncRNA LOC101930370 might act as an endogenous ‘sponge’ by competing for miR-1471 binding targets. Luciferase assays were used to prove the interaction of LOC101930370, miR-1471 and SHH. Edu, wound-healing and transwell assays were used to verify the contribution of miR-1471 and LOC101930370 on MCF-7 cells proliferation and metastasis. Gain and loss of function studies were performed to evaluate the relevance of Hedgehog pathway with LOC101930370/miR-1471 regulating axis in MCF-7 cells. <b><i>Results:</i></b> The expression of miR-1471 was markedly downregulated in BC. Inhibition of miR-1471 by LOC101930370 was proved by luciferase assay. Knockdown of LOC101930370 suppressed BC cells progression. MiR-1471 inhibitor resulted in a more aggressive metastasis of MCF-7 cells. Moreover, SHH and Gli-1 expression were significantly suppressed by LOC101930370 knockdown, and upregulated by miR-1471 inhibitor transfection. <b><i>Conclusions:</i></b> Collectively, our study reveals the interaction between LOC101930370 and miR-1471 for the first time. LOC101930370 positively regulates the expression of SHH by sponging miR-1471, which sheds new light on lncRNA-directed diagnostics and therapeutics in BC.
DOI: 10.6084/m9.figshare.6854522
title: Tortietal2018: Complete Data Table of the Indri Songs

description: Torti et al. The sound of silence. Can we reliably estimate the number of callers in a chorus? PlosONE.<br>Table reports the file name, group ID, real number of singers, unsupervised estimate of the number of singers, group size, song duration, Acoustic Diversity Index, Acoustic Complexity Index, Acoustic Entropy Index, and Acoustic Richness Index.
DOI: 10.6084/m9.figshare.6854483
title: Supplementary Material for: An FDA-Approved Drug Screen for Compounds Influencing Craniofacial Skeletal Development and Craniosynostosis

description: Neural crest stem/progenitor cells (NCSCs) populate a variety of tissues, and their dysregulation is implicated in several human diseases including craniosynostosis and neuroblastoma. We hypothesised that small molecules that inhibit NCSC induction or differentiation may represent potential therapeutically relevant drugs in these disorders. We screened 640 FDA-approved compounds currently in clinical use for other conditions to identify those which disrupt development of NCSC-derived skeletal elements that form the zebrafish jaw. In the primary screen, we used heterozygous transgenic <i>sox10:gfp </i>zebrafish to directly visualise NCSC-derived jaw cartilage. We noted partial toxicity of this transgene in relation to jaw patterning, suggesting that our primary screen was sensitised for NCSC defects, and we confirmed 10 novel, 4 previously reported, and 2 functional analogue drug hits in wild-type embryos. Of these drugs, 9/14 and 7/14, respectively, are known to target pathways implicated in osteoarthritis pathogenesis or to cause reduced bone mineral density/increased fracture risk as side effects in patients treated for other conditions, suggesting that our screen enriched for pathways targeting skeletal tissue homeostasis. We selected one drug that inhibited NCSC induction and one drug that inhibits bone mineralisation for further detailed analyses which reflect our initial hypotheses. These drugs were leflunomide and cyclosporin A, respectively, and their functional analogues, teriflunomide and FK506 (tacrolimus). We identified their critical developmental windows of activity, showing that the severity of defects observed related to the timing, duration, and dose of treatment. While leflunomide has previously been shown to inhibit NCSC induction, we demonstrate additional later roles in cartilage remodelling. Both drugs altered expression of extracellular matrix metalloproteinases. As proof-of-concept, we also tested drug treatment of disease-relevant mammalian cells. While leflunomide treatment inhibited the viability of several human NCSC-derived neuroblastoma cell lines coincident with altered expression of genes involved in ribosome biogenesis and transcription, FK506 enhanced murine calvarial osteoblast differentiation and prevented fusion of the coronal suture in calvarial explants taken from Crouzon syndrome mice.
DOI: 10.6084/m9.figshare.6854483.v1
title: Supplementary Material for: An FDA-Approved Drug Screen for Compounds Influencing Craniofacial Skeletal Development and Craniosynostosis

description: Neural crest stem/progenitor cells (NCSCs) populate a variety of tissues, and their dysregulation is implicated in several human diseases including craniosynostosis and neuroblastoma. We hypothesised that small molecules that inhibit NCSC induction or differentiation may represent potential therapeutically relevant drugs in these disorders. We screened 640 FDA-approved compounds currently in clinical use for other conditions to identify those which disrupt development of NCSC-derived skeletal elements that form the zebrafish jaw. In the primary screen, we used heterozygous transgenic <i>sox10:gfp </i>zebrafish to directly visualise NCSC-derived jaw cartilage. We noted partial toxicity of this transgene in relation to jaw patterning, suggesting that our primary screen was sensitised for NCSC defects, and we confirmed 10 novel, 4 previously reported, and 2 functional analogue drug hits in wild-type embryos. Of these drugs, 9/14 and 7/14, respectively, are known to target pathways implicated in osteoarthritis pathogenesis or to cause reduced bone mineral density/increased fracture risk as side effects in patients treated for other conditions, suggesting that our screen enriched for pathways targeting skeletal tissue homeostasis. We selected one drug that inhibited NCSC induction and one drug that inhibits bone mineralisation for further detailed analyses which reflect our initial hypotheses. These drugs were leflunomide and cyclosporin A, respectively, and their functional analogues, teriflunomide and FK506 (tacrolimus). We identified their critical developmental windows of activity, showing that the severity of defects observed related to the timing, duration, and dose of treatment. While leflunomide has previously been shown to inhibit NCSC induction, we demonstrate additional later roles in cartilage remodelling. Both drugs altered expression of extracellular matrix metalloproteinases. As proof-of-concept, we also tested drug treatment of disease-relevant mammalian cells. While leflunomide treatment inhibited the viability of several human NCSC-derived neuroblastoma cell lines coincident with altered expression of genes involved in ribosome biogenesis and transcription, FK506 enhanced murine calvarial osteoblast differentiation and prevented fusion of the coronal suture in calvarial explants taken from Crouzon syndrome mice.
DOI: 10.6084/m9.figshare.6854396
title: Input data of MIRA

description: Data for both academic levels about - the number of applications to the first recruitment session of the Italian National Scientific Qualification (NSQ); - the number of scholars that obtained the qualification after the evaluation process of the NSQ; - total number of publications available for each academic recruitment field; - average number of publications per application
DOI: 10.6084/m9.figshare.6854342
title: Trends in Community Temperature Index values for North Pacific and North Atlantic bottom trawl and plankton surveys for 5° latitude/longitude boxes from 1985 to 2014.

description: Values given are regression coefficients for trends in CTI plus covariates. Variables are described in the accompanying file.<br>Data supports: Burrows, M. T., A. E. Bates, M. J. Costello, M. Edwards, G. J. Edgar, C. J. Fox, B. S. Halpern, J. G. Hiddink, M. L. Pinsky, R. D. Batt, J. García Molinos, B. Payne, D. Schoeman, R. D. Stuart-Smith, and E. S. Poloczanska. 2018. Thermal affinities and vertical temperature gradients predict responses to warming in ocean communities. Nature, in review.
DOI: 10.6084/m9.figshare.6854342.v1
title: Trends in Community Temperature Index values for North Pacific and North Atlantic bottom trawl and plankton surveys for 5° latitude/longitude boxes from 1985 to 2014.

description: Values given are regression coefficients for trends in CTI plus covariates. Variables are described in the accompanying file.<br>Data supports: Burrows, M. T., A. E. Bates, M. J. Costello, M. Edwards, G. J. Edgar, C. J. Fox, B. S. Halpern, J. G. Hiddink, M. L. Pinsky, R. D. Batt, J. García Molinos, B. Payne, D. Schoeman, R. D. Stuart-Smith, and E. S. Poloczanska. 2018. Thermal affinities and vertical temperature gradients predict responses to warming in ocean communities. Nature, in review.
DOI: 10.6084/m9.figshare.6854312
title: Community Temperature Index values for North Pacific and North Atlantic bottom trawls and plankton in 5° latitude/longitude areas annually from 1985 to 2014

description: Data to support Burrows, M. T., A. E. Bates, M. J. Costello, M. Edwards, G. J. Edgar, C. J. Fox, B. S. Halpern, J. G. Hiddink, M. L. Pinsky, R. D. Batt, J. García Molinos, B. Payne, D. Schoeman, R. D. Stuart-Smith, and E. S. Poloczanska. 2018. Thermal affinities and vertical temperature gradients predict responses to warming in ocean communities. Nature, in review.
DOI: 10.6084/m9.figshare.6854312.v2
title: Community Temperature Index values for North Pacific and North Atlantic bottom trawls and plankton in 5° latitude/longitude areas annually from 1985 to 2014

description: Data to support Burrows, M. T., A. E. Bates, M. J. Costello, M. Edwards, G. J. Edgar, C. J. Fox, B. S. Halpern, J. G. Hiddink, M. L. Pinsky, R. D. Batt, J. García Molinos, B. Payne, D. Schoeman, R. D. Stuart-Smith, and E. S. Poloczanska. 2018. Thermal affinities and vertical temperature gradients predict responses to warming in ocean communities. Nature, in review.
DOI: 10.6084/m9.figshare.6854258
title: Supplementary Material for: Internet-Based Cognitive Behavioral Therapy for Chronic Stress: A Randomized Controlled Trial

description: <b><i>Background:</i></b> Prolonged exposure to stress can lead to substantial suffering, impairment and societal costs. However, access to psychological treatment is limited. Internet-based cognitive behavioral therapy (ICBT) can be effective in reducing symptoms of stress, but little is known of its effects in clinical samples. The aim of this study was to investigate the efficacy of ICBT for patients suffering from chronic stress, operationalized as adjustment disorder (AD) and exhaustion disorder (ED). <b><i>Methods:</i></b> A total of 100 adults diagnosed with AD or ED were randomly assigned to a 12-week ICBT (<i>n =</i> 50) or waitlist control condition (<i>n =</i> 50). Primary outcome was the level of perceived stress (PSS). Secondary outcomes included several mental health symptom domains as well as functional impairment and work ability. All outcomes were assessed at baseline, after treatment and at the 6-month follow-up. The study was preregistered at Clinicaltrials.gov: NCT02540317. <b><i>Results:</i></b> Compared to the control condition, patients in the ICBT group made large and significant improvements on the PSS (<i>d =</i> 1.09) and moderate to large improvements in secondary symptom domains. Effects were maintained at the 6-month follow-up. There was no significant between-group effect on functional impairment or work ability. <b><i>Conclusions:</i></b> A relatively short ICBT is indicated to be effective in reducing stress-related symptoms in a clinical sample of patients with AD and ED, and has the potential to substantially increase treatment accessibility. Results must be replicated, and further research is needed to understand the relationship between symptom reduction, functional impairment and work ability.
DOI: 10.6084/m9.figshare.6854312.v1
title: Community Temperature Index values for North Pacific and North Atlantic bottom trawls and plankton in 5° latitude/longitude areas annually from 1985 to 2014

description: Data to support Burrows, M. T., A. E. Bates, M. J. Costello, M. Edwards, G. J. Edgar, C. J. Fox, B. S. Halpern, J. G. Hiddink, M. L. Pinsky, R. D. Batt, J. García Molinos, B. Payne, D. Schoeman, R. D. Stuart-Smith, and E. S. Poloczanska. 2018. Thermal affinities and vertical temperature gradients predict responses to warming in ocean communities. Nature, in review.
DOI: 10.6084/m9.figshare.6854246
title: Intotheblackbox2018.zip

description: Data files accompanying journal manuscript "Into the Black Box: Using Spatially Explicit Commodity Flow Data to Map High-Resolution Urban Material Flows".
DOI: 10.6084/m9.figshare.6854189
title: Relative normalized luciferase activity for the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917

description: <br>This dataset consists of two Excel <b>.xlsx</b> spreadsheets, each containing relative luciferase activity for the recombinant vector constructs.<b>Dataset_1.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying C and T alleles for rs3218550. <br><b>Dataset_2.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying G and A alleles for rs6917.There is also one <b>.docx </b>file containing sequences of 3′UTR inserts, primer sequences, partial electropherograms of final experimental vectors and vector diagrams.The columns of each spreadsheet capture luciferase activity for firefly luciferase, renilla luciferase, and the ratio of firefly/renilla (relative luciferase activity). The rows of each spreadsheet capture the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917 SNPs, along with the pGL3P vector (lacking the insert) and the pGL3C vector (containing the SV40 promoter and enhancer). The results are expressed as relative luminescence units (RLU). The triplicate results given for each vector represent the data obtained from three independent transfections. The associated study investigates the link between two common SNPs in the XRCC2 and PHB genes and increased risk of sporadic breast cancer among Sri Lankan postmenopausal women. The putative functional effects of these two SNPs was further investigated by transfecting the recombinant vector constructs carrying the ancestral and variant alleles of these two SNPs in MCF-7 breast cancer cell lines and performing the dual-luciferase reporter gene assays to measure their bioluminescence.<br>
DOI: 10.6084/m9.figshare.6854180
title: Supplementary Material for: The Energy Density and Treatment Times Are the Main Factors That Affect the Efficacy of Long-Pulsed 1,064-nm Nd:YAG Laser Treatment for Onychomycosis Caused by <b><i>Trichophyton rubrum</i></b>

description: <b><i>Background:</i></b> No optimal regimen exists for the LPNYL (long-pulsed 1,064-nm neodymium:yttrium-aluminum-garnet laser) for treating onychomycosis. <b><i>Objective:</i></b> To establish an optimal LPNYL treatment regimen for onychomycosis caused by <i>Trichophyton rubrum</i> (OCTr). <b><i>Patients and Methods:</i></b> First, 511 infected nails of 177 patients were treated using LPNYL with orthogonally designed regimens according to various energy densities, spot sizes, pulse widths, and treatment times. The optimal treatment regimen was established by multivariate analysis. Next, 69 patients with 221 infected nails were randomized to receive oral itraconazole (drug group) and the optimal regimen of LPNYL treatment (laser group). The clinical efficacy (CE) and mycological efficacy (ME) were evaluated at 6 and 12 months following the start of treatment, and adverse reactions were recorded in both groups. <b><i>Results:</i></b> Both CE and ME were significantly correlated with the energy density (<i>p</i> &lt; 0.05) and treatment times (<i>p</i> &lt; 0.05), but not with the spot size (0.071 &lt; <i>p</i> &lt; 0.083) or pulse width (0.051 &lt; <i>p</i> &lt; 0.060), at 6 or 12<sup></sup> months. There were no significant differences at 6 or 12 months (<i>p</i> &gt; 0.05), and no significant difference was observed in CE at 12 months between the two groups (<i>p</i> &gt; 0.05). At 6 months, the CE in the laser group was significantly higher than that in the drug group (<i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> LPNYL is effective and safe for treating OCTr. The energy density and treatment times are the main factors that affect the efficacy. The optimal regimen for LPNYL is an energy density of 45 J/cm<sup>2</sup>, pulse width of 35 ms, spot size of 4 mm, frequency of 1 Hz, and 6 treatments with 1-week intervals. Laser treatment has rapid clinical recovery.
DOI: 10.6084/m9.figshare.6854180.v1
title: Supplementary Material for: The Energy Density and Treatment Times Are the Main Factors That Affect the Efficacy of Long-Pulsed 1,064-nm Nd:YAG Laser Treatment for Onychomycosis Caused by <b><i>Trichophyton rubrum</i></b>

description: <b><i>Background:</i></b> No optimal regimen exists for the LPNYL (long-pulsed 1,064-nm neodymium:yttrium-aluminum-garnet laser) for treating onychomycosis. <b><i>Objective:</i></b> To establish an optimal LPNYL treatment regimen for onychomycosis caused by <i>Trichophyton rubrum</i> (OCTr). <b><i>Patients and Methods:</i></b> First, 511 infected nails of 177 patients were treated using LPNYL with orthogonally designed regimens according to various energy densities, spot sizes, pulse widths, and treatment times. The optimal treatment regimen was established by multivariate analysis. Next, 69 patients with 221 infected nails were randomized to receive oral itraconazole (drug group) and the optimal regimen of LPNYL treatment (laser group). The clinical efficacy (CE) and mycological efficacy (ME) were evaluated at 6 and 12 months following the start of treatment, and adverse reactions were recorded in both groups. <b><i>Results:</i></b> Both CE and ME were significantly correlated with the energy density (<i>p</i> &lt; 0.05) and treatment times (<i>p</i> &lt; 0.05), but not with the spot size (0.071 &lt; <i>p</i> &lt; 0.083) or pulse width (0.051 &lt; <i>p</i> &lt; 0.060), at 6 or 12<sup></sup> months. There were no significant differences at 6 or 12 months (<i>p</i> &gt; 0.05), and no significant difference was observed in CE at 12 months between the two groups (<i>p</i> &gt; 0.05). At 6 months, the CE in the laser group was significantly higher than that in the drug group (<i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> LPNYL is effective and safe for treating OCTr. The energy density and treatment times are the main factors that affect the efficacy. The optimal regimen for LPNYL is an energy density of 45 J/cm<sup>2</sup>, pulse width of 35 ms, spot size of 4 mm, frequency of 1 Hz, and 6 treatments with 1-week intervals. Laser treatment has rapid clinical recovery.
DOI: 10.6084/m9.figshare.6854189.v2
title: Relative normalized luciferase activity for the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917

description: <br>This dataset consists of two Excel <b>.xlsx</b> spreadsheets, each containing relative luciferase activity for the recombinant vector constructs.<b>Dataset_1.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying C and T alleles for rs3218550. <br><b>Dataset_2.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying G and A alleles for rs6917.There is also one <b>.docx </b>file containing sequences of 3′UTR inserts, primer sequences, partial electropherograms of final experimental vectors and vector diagrams.The columns of each spreadsheet capture luciferase activity for firefly luciferase, renilla luciferase, and the ratio of firefly/renilla (relative luciferase activity). The rows of each spreadsheet capture the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917 SNPs, along with the pGL3P vector (lacking the insert) and the pGL3C vector (containing the SV40 promoter and enhancer). The results are expressed as relative luminescence units (RLU). The triplicate results given for each vector represent the data obtained from three independent transfections. The associated study investigates the link between two common SNPs in the XRCC2 and PHB genes and increased risk of sporadic breast cancer among Sri Lankan postmenopausal women. The putative functional effects of these two SNPs was further investigated by transfecting the recombinant vector constructs carrying the ancestral and variant alleles of these two SNPs in MCF-7 breast cancer cell lines and performing the dual-luciferase reporter gene assays to measure their bioluminescence.<br>
DOI: 10.6084/m9.figshare.6854165
title: NOVEL BROAD SPECTRUM VIRUCIDAL MOLECULES AGAINST ENVELOPED VIRUSES

description: Antiviral assays. IF assays, Binding assays
DOI: 10.6084/m9.figshare.6854189.v1
title: Relative normalized luciferase activity for the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917

description: <br>This dataset consists of two Excel <b>.xlsx</b> spreadsheets, each containing relative luciferase activity for the recombinant vector constructs.<b>Dataset_1.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying C and T alleles for rs3218550. <br><b>Dataset_2.xlsx </b>is the relative luciferase activity for the recombinant vector constructs carrying G and A alleles for rs6917.The columns of each spreadsheet capture luciferase activity for firefly luciferase, renilla luciferase, and the ratio of firefly/renilla (relative luciferase activity). The rows of each spreadsheet capture the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917 SNPs, along with the pGL3P vector (lacking the insert) and the pGL3C vector (containing the SV40 promoter and enhancer). The results are expressed as relative luminescence units (RLU). The triplicate results given for each vector represent the data obtained from three independent transfections. The associated study investigates the link between two common SNPs in the XRCC2 and PHB genes and increased risk of sporadic breast cancer among Sri Lankan postmenopausal women. The putative functional effects of these two SNPs was further investigated by transfecting the recombinant vector constructs carrying the ancestral and variant alleles of these two SNPs in MCF-7 breast cancer cell lines and performing the dual-luciferase reporter gene assays to measure their bioluminescence.<br>
DOI: 10.6084/m9.figshare.6854165.v1
title: NOVEL BROAD SPECTRUM VIRUCIDAL MOLECULES AGAINST ENVELOPED VIRUSES

description: Antiviral assays. IF assays, Binding assays
DOI: 10.6084/m9.figshare.6853961
title: Comparative analysis of B-cell receptor repertoires induced by live yellow fever vaccine in young and middle age donors

description: Immunoglobulin repertoires (top-1569 clonotypes) from healthy volunteers of two age groups, young and middle age. Plasma B cells were obtained from peripheral blood samples at 9th day after first vaccination with live YF vaccine.