cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5982298
title: Data from: Nitrogen deposition outweighs climatic variability in driving annual growth rate of canopy beech trees: evidence from long-term growth reconstruction across a geographic gradient

description: In this study, we investigated the role of climatic variability and atmospheric nitrogen deposition in driving long-term tree growth in canopy beech trees along a geographic gradient in the montane belt of the Italian peninsula, from the Alps to the southern Apennines. We sampled dominant trees at different developmental stages (from young to mature tree cohorts, with tree ages spanning from 35 to 160 years) and used stem analysis to infer historic reconstruction of tree volume and dominant height. Annual growth volume (<i>G</i><sub>V</sub>) and height (<i>G</i><sub>H</sub>) variability were related to annual variability in model simulated atmospheric nitrogen deposition and site-specific climatic variables, (<i>i.e.</i> mean annual temperature, total annual precipitation, mean growing period temperature, total growing period precipitation, and standard precipitation evapotranspiration index) and atmospheric CO<sub>2</sub> concentration, including tree cambial age among growth predictors. Generalized additive models (<i>GAM</i>), linear mixed-effects models (<i>LMM</i>), and Bayesian regression models (<i>BRM</i>) were independently employed to assess explanatory variables. The main results from our study were as follows: i) tree age was the main explanatory variable for long-term growth variability; ii) <i>GAM</i>, <i>LMM</i>, and <i>BRM </i>results consistently indicated climatic variables and CO<sub>2</sub> effects on <i>G</i><sub>V</sub> and <i>G</i><sub>H</sub> were weak, therefore evidence of recent climatic variability influence on beech annual growth rates was limited in the montane belt of the Italian peninsula; iii) instead, significant positive nitrogen deposition (<i>N</i><sub>dep</sub>) effects were repeatedly observed in <i>G</i><sub>V</sub> and <i>G</i><sub>H</sub>; the positive effects of <i>N</i><sub>dep</sub> on canopy height growth rates, which tended to level off at <i>N</i><sub>dep</sub> values greater than approximately 1.0 g m<sup>-2</sup> y<sup>-1</sup> were interpreted as positive impacts on forest stand above-ground net productivity at the selected study sites
DOI: 10.6084/m9.figshare.5982298.v1
title: Data from: Nitrogen deposition outweighs climatic variability in driving annual growth rate of canopy beech trees: evidence from long-term growth reconstruction across a geographic gradient

description: In this study, we investigated the role of climatic variability and atmospheric nitrogen deposition in driving long-term tree growth in canopy beech trees along a geographic gradient in the montane belt of the Italian peninsula, from the Alps to the southern Apennines. We sampled dominant trees at different developmental stages (from young to mature tree cohorts, with tree ages spanning from 35 to 160 years) and used stem analysis to infer historic reconstruction of tree volume and dominant height. Annual growth volume (<i>G</i><sub>V</sub>) and height (<i>G</i><sub>H</sub>) variability were related to annual variability in model simulated atmospheric nitrogen deposition and site-specific climatic variables, (<i>i.e.</i> mean annual temperature, total annual precipitation, mean growing period temperature, total growing period precipitation, and standard precipitation evapotranspiration index) and atmospheric CO<sub>2</sub> concentration, including tree cambial age among growth predictors. Generalized additive models (<i>GAM</i>), linear mixed-effects models (<i>LMM</i>), and Bayesian regression models (<i>BRM</i>) were independently employed to assess explanatory variables. The main results from our study were as follows: i) tree age was the main explanatory variable for long-term growth variability; ii) <i>GAM</i>, <i>LMM</i>, and <i>BRM </i>results consistently indicated climatic variables and CO<sub>2</sub> effects on <i>G</i><sub>V</sub> and <i>G</i><sub>H</sub> were weak, therefore evidence of recent climatic variability influence on beech annual growth rates was limited in the montane belt of the Italian peninsula; iii) instead, significant positive nitrogen deposition (<i>N</i><sub>dep</sub>) effects were repeatedly observed in <i>G</i><sub>V</sub> and <i>G</i><sub>H</sub>; the positive effects of <i>N</i><sub>dep</sub> on canopy height growth rates, which tended to level off at <i>N</i><sub>dep</sub> values greater than approximately 1.0 g m<sup>-2</sup> y<sup>-1</sup> were interpreted as positive impacts on forest stand above-ground net productivity at the selected study sites
DOI: 10.6084/m9.figshare.5982286
title: Research Methods

description: Qualitative? Quantitative? Mixed? Research methods are the systematic tools used to conduct research. Basically, they are the rules researchers follow to collect information in order to seek an answer to their research question. In this session you will be briefly introduced to different research methodologies, and explore learning materials that will help you to design research projects, understand particular methods or identify a new method, and learn how to incorporate these into your own teaching, research, and writing. This workshop would suit those staff and researchers who want to refine or enhance their skills and those who are conducting or considering their own research. This session maps to the RDF’s sub domain of Knowledge base (A1) and Communication and dissemination (D2).
DOI: 10.6084/m9.figshare.5982268
title: Love Your Literature Search

description: You may or may not love literature searching, but you can learn how to perform it more effectively. This session will help you get started with planning a literature search and introduce you to top search tools for your area. You’ll look at techniques to improve your search results and how to source items not available at Edinburgh Napier University.The sessions at each campus will be customised for different subject areas by the Information Services Advisor/Subject Librarian for your School. This session maps to the RDF’s sub domains of Knowledge base (A1) and Cognitive abilities (A2).
DOI: 10.6084/m9.figshare.5982253
title: Dataset and Scripts "An Evaluation of Open-Source Software Microbenchmark Suites for Continuous Performance Assessment"

description: Dataset and R scripts for "An Evaluation of Open-Source Software Microbenchmark Suites for Continuous Performance Assessment" by Laaber and Leitner, published at Mining Software Repositories (MSR) in 2018
DOI: 10.6084/m9.figshare.5982181
title: Supplementary Material for: Improved Production of Highly Active and Pure Human Creatine Kinase MB

description: Human creatine kinase MB (hCKMB) is one of the most preferred biomarkers used for the diagnosis of acute coronary syndrome due to its high sensitivity and specificity. The increasing need for highly purified and biologically active hCKMB in the field of diagnostics makes its production valuable. Currently, the production of hCKMB is mainly achieved in methylotrophic yeast, <i>Pichia pastoris</i>, because the production in <i>Escherichia coli</i> is challenging and generally yields an inactive enzyme with a low quantity. With the aim of finding the best way for the high-yield production of active hCKMB in <i>E. coli</i>, an efficient strategy was developed using a construct allowing tandem expression of each subunit with 2 different tags. The strategy allowed the efficient expression and separate characterization of each subunit and 1-step purification of the heterodimeric protein into homogeneity. The heterodimeric protein displayed more than 11-fold greater specific activity than the commercially available one. The production strategy described in this study shows a clear advantage over the currently used ones and can be made available not only for laboratory scale production but also for commercial production. Our study is also a well-suited example for the studies in which novel protein expression strategies are needed to achieve greater yields with higher purities.
DOI: 10.6084/m9.figshare.5982055
title: drav_cov_est_ucln_yule.xml from A Bayesian phylogenetic study of the Dravidian language family

description: BEAST 2 xml file that was used for the best-supported analysis, relaxed covarion model with relative mutation rates estimated.
DOI: 10.6084/m9.figshare.5982055.v1
title: drav_cov_est_ucln_yule.xml from A Bayesian phylogenetic study of the Dravidian language family

description: BEAST 2 xml file that was used for the best-supported analysis, relaxed covarion model with relative mutation rates estimated.
DOI: 10.6084/m9.figshare.5982046
title: drav_cov_est_ucln_yule.mcct.trees from A Bayesian phylogenetic study of the Dravidian language family

description: The Dravidian language family consists of about 80 varieties (Hammarström H. 2016 <i>Glottolog 2.7</i>) spoken by 220 million people across southern and central India and surrounding countries (Steever SB. 1998 In <i>The Dravidian languages</i> (ed. SB Steever), pp. 1–39: 1). Neither the geographical origin of the Dravidian language homeland nor its exact dispersal through time are known. The history of these languages is crucial for understanding prehistory in Eurasia, because despite their current restricted range, these languages played a significant role in influencing other language groups including Indo-Aryan (Indo-European) and Munda (Austroasiatic) speakers. Here, we report the results of a Bayesian phylogenetic analysis of cognate-coded lexical data, elicited first hand from native speakers, to investigate the subgrouping of the Dravidian language family, and provide dates for the major points of diversification. Our results indicate that the Dravidian language family is approximately 4500 years old, a finding that corresponds well with earlier linguistic and archaeological studies. The main branches of the Dravidian language family (North, Central, South I, South II) are recovered, although the placement of languages within these main branches diverges from previous classifications. We find considerable uncertainty with regard to the relationships between the main branches.
DOI: 10.6084/m9.figshare.5982046.v1
title: drav_cov_est_ucln_yule.mcct.trees from A Bayesian phylogenetic study of the Dravidian language family

description: The Dravidian language family consists of about 80 varieties (Hammarström H. 2016 <i>Glottolog 2.7</i>) spoken by 220 million people across southern and central India and surrounding countries (Steever SB. 1998 In <i>The Dravidian languages</i> (ed. SB Steever), pp. 1–39: 1). Neither the geographical origin of the Dravidian language homeland nor its exact dispersal through time are known. The history of these languages is crucial for understanding prehistory in Eurasia, because despite their current restricted range, these languages played a significant role in influencing other language groups including Indo-Aryan (Indo-European) and Munda (Austroasiatic) speakers. Here, we report the results of a Bayesian phylogenetic analysis of cognate-coded lexical data, elicited first hand from native speakers, to investigate the subgrouping of the Dravidian language family, and provide dates for the major points of diversification. Our results indicate that the Dravidian language family is approximately 4500 years old, a finding that corresponds well with earlier linguistic and archaeological studies. The main branches of the Dravidian language family (North, Central, South I, South II) are recovered, although the placement of languages within these main branches diverges from previous classifications. We find considerable uncertainty with regard to the relationships between the main branches.
DOI: 10.6084/m9.figshare.5981926
title: Sedimentary processes and facies on a high-latitude passive continental margin, Wilkes Land, East Antarctica

description: Supplementary data file.
DOI: 10.6084/m9.figshare.5981926.v1
title: Sedimentary processes and facies on a high-latitude passive continental margin, Wilkes Land, East Antarctica

description: Supplementary data file.
DOI: 10.6084/m9.figshare.5981923
title: Search System Survey

description: We designed a survey instrument to cover the following five survey question topics: 1. System configuration (e.g., ranking model, index methods, query methods) (7 questions)2. Evaluation methods and benchmark (10 questions)a. What has been evaluated?a. What evaluation methods have been applied?b. How was the evaluation collection built?c. What is the performance under specific configurations? 3. Methods applied to boost searchability by web search engines (two questions)4. Other technologies or system configurations that have been employed (five questions)5. Wish list for future activities of the RDA relevance task force (two questions)We also asked five additional questions about the characteristics of each repository so we could assess whether there is any correlation between repository characteristics and the adoption of a certain technology or configuration. Also, we included two additional questions about survey administration.<br>
DOI: 10.6084/m9.figshare.5981905
title: Relevancy_Ranking_Systems_responses (redacted)

description: We designed a survey instrument to cover the following five survey question topics: System configuration (e.g., ranking model, index methods, query methods) (7 questions) Evaluation methods and benchmark (10 questions) a. What has been evaluated? a. What evaluation methods have been applied? b. How was the evaluation collection built? c. What is the performance under specific configurations? Methods applied to boost searchability by web search engines (two questions) Other technologies or system configurations that have been employed (five questions) Wish list for future activities of the RDA relevance task force (two questions) We also asked five additional questions about the characteristics of each repository so we could assess whether there is any correlation between repository characteristics and the adoption of a certain technology or configuration. Also, we included two additional questions about survey administration.
DOI: 10.6084/m9.figshare.5981899
title: PhD Thesis. Genomics of bovine milk fat composition. Paper3 Supplementary Tables S1 to S5

description: Tim Knutsen PhD Thesis: Genomics of bovine milk fat composition. <b>Paper III:</b>Supplementary Tables S1 to S5. Excel files.
DOI: 10.6084/m9.figshare.5981905.v1
title: Relevancy_Ranking_Systems_responses (redacted)

description: We designed a survey instrument to cover the following five survey question topics: System configuration (e.g., ranking model, index methods, query methods) (7 questions) Evaluation methods and benchmark (10 questions) a. What has been evaluated? a. What evaluation methods have been applied? b. How was the evaluation collection built? c. What is the performance under specific configurations? Methods applied to boost searchability by web search engines (two questions) Other technologies or system configurations that have been employed (five questions) Wish list for future activities of the RDA relevance task force (two questions) We also asked five additional questions about the characteristics of each repository so we could assess whether there is any correlation between repository characteristics and the adoption of a certain technology or configuration. Also, we included two additional questions about survey administration.
DOI: 10.6084/m9.figshare.5981899.v1
title: PhD Thesis. Genomics of bovine milk fat composition. Paper3 Supplementary Tables S1 to S5

description: Tim Knutsen PhD Thesis: Genomics of bovine milk fat composition. <b>Paper III:</b>Supplementary Tables S1 to S5. Excel files.
DOI: 10.6084/m9.figshare.5981854
title: TC.csv

description: Anti-angiogenic peptides - TC
DOI: 10.6084/m9.figshare.5981854.v1
title: TC.csv

description: Anti-angiogenic peptides - TC
DOI: 10.6084/m9.figshare.5981851
title: DP.csv

description: Anti-angiogenic peptides - DP
DOI: 10.6084/m9.figshare.5981851.v1
title: DP.csv

description: Anti-angiogenic peptides - DP
DOI: 10.6084/m9.figshare.5981848
title: AAC.csv

description: Anti-angiogenic sequences - AAC
DOI: 10.6084/m9.figshare.5981848.v1
title: AAC.csv

description: Anti-angiogenic sequences - AAC
DOI: 10.6084/m9.figshare.5981845
title: Supplementary data to the paper "Trematode cercariae as prey for zooplankton: effect on fitness traits of predators" by Mironova E., Gopko M., Pasternak A., Mikheev V., Taskinen J.

description: <b>Supplementary table S1</b>. Feeding experiments with different zooplankters and cercariae of <i>Diplostomum pseudospathaceum</i>.<br><b>Supplementary table S2.</b> Reproductive characteristics of females of two cyclopoid species, fed exclusively with <i>Diplostomum pseudospathaceum </i>cercariae <i>ad libitum</i> during 17 days. The longevity (h) of reproductive periods and the offspring numbers (nauplii) hatched from the each egg clutch* are shown. <br>
DOI: 10.6084/m9.figshare.5981845.v1
title: Supplementary data to the paper "Trematode cercariae as prey for zooplankton: effect on fitness traits of predators" by Mironova E., Gopko M., Pasternak A., Mikheev V., Taskinen J.

description: <b>Supplementary table S1</b>. Feeding experiments with different zooplankters and cercariae of <i>Diplostomum pseudospathaceum</i>.<br><b>Supplementary table S2.</b> Reproductive characteristics of females of two cyclopoid species, fed exclusively with <i>Diplostomum pseudospathaceum </i>cercariae <i>ad libitum</i> during 17 days. The longevity (h) of reproductive periods and the offspring numbers (nauplii) hatched from the each egg clutch* are shown. <br>
DOI: 10.6084/m9.figshare.5981833
title: Supplementary Material for: Endoscopic Removal of Two Esophageal Over-The-Scope Clips with Cold Saline Solution Technique

description: Medicine
DOI: 10.6084/m9.figshare.5981833.v1
title: Supplementary Material for: Endoscopic Removal of Two Esophageal Over-The-Scope Clips with Cold Saline Solution Technique

description: Medicine
DOI: 10.6084/m9.figshare.5981785
title: Glacio-marine iron formation deposition in a c. 700 Ma glaciated margin: insights from the Chuos Formation, Namibia

description: Full set of geochemical data.
DOI: 10.6084/m9.figshare.5981785.v1
title: Glacio-marine iron formation deposition in a c. 700 Ma glaciated margin: insights from the Chuos Formation, Namibia

description: Full set of geochemical data.
DOI: 10.6084/m9.figshare.5981719
title: A cross-sectional study of partograph utilization as a decision making tool for referral of abnormal labour in primary health care facilities of Bangladesh

description: This is the data for the study titled, "A cross-sectional study of partograph utilization as a decision making tool for referral of abnormal labour in primary health care facilities of Bangladesh"
DOI: 10.6084/m9.figshare.5981719.v1
title: A cross-sectional study of partograph utilization as a decision making tool for referral of abnormal labour in primary health care facilities of Bangladesh

description: This is the data for the study titled, "A cross-sectional study of partograph utilization as a decision making tool for referral of abnormal labour in primary health care facilities of Bangladesh"
DOI: 10.6084/m9.figshare.5981683
title: Supplementary Material for: Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome

description: <b><i>Background:/Aims:</i></b> Renal disease is a common cause of morbidity in patients with Bardet-Biedl syndrome (BBS), however the severity of kidney dysfunction is highly variable. To date, there is little information on the pathogenesis, the risk and predictor factors for poor renal outcome in this setting. The present study aims to analyze the spectrum of urinary proteins in BBS patients, in order to potentially identify 1) disease-specific proteomic profiles that may differentiate the patients from normal subjects; 2) urinary markers of renal dysfunction. <b><i>Methods:</i></b> Fourteen individuals (7 males and 7 females) with a clinical diagnosis of BBS have been selected in this study. A pool of 10 aged-matched males and 10 aged-matched females have been used as controls for proteomic analysis. The glomerular filtration rate (eGFR) has been estimated using the CKD-EPI formula. Variability of eGFR has been retrospectively assessed calculating average annual eGFR decline (ΔeGFR) in a mean follow-up period of 4 years (3-7). <b><i>Results:</i></b> 42 proteins were significantly over- or under-represented in BBS patients compared with controls; the majority of these proteins are involved in fibrosis, cell adhesion and extracellular matrix organization. Statistic studies revealed a significant correlation between urine fibronectin (u-FN) (r<sup>2</sup>=0.28; p&lt;0.05), CD44 antigen (r<sup>2</sup> =0.35; p&lt;0.03) and lysosomal alfa glucosidase ( r<sup>2</sup>0.27; p&lt;0.05) abundance with the eGFR. In addition, u-FN (r<sup>2</sup> =0.2389; p&lt;0.05) was significantly correlated with ΔeGFR. <b><i>Conclusion:</i></b> The present study demonstrates that urine proteome of BBS patients differs from that of normal subjects; in addition, kidney dysfunction correlated with urine abundance of known markers of renal fibrosis.
DOI: 10.6084/m9.figshare.5981683.v1
title: Supplementary Material for: Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome

description: <b><i>Background:/Aims:</i></b> Renal disease is a common cause of morbidity in patients with Bardet-Biedl syndrome (BBS), however the severity of kidney dysfunction is highly variable. To date, there is little information on the pathogenesis, the risk and predictor factors for poor renal outcome in this setting. The present study aims to analyze the spectrum of urinary proteins in BBS patients, in order to potentially identify 1) disease-specific proteomic profiles that may differentiate the patients from normal subjects; 2) urinary markers of renal dysfunction. <b><i>Methods:</i></b> Fourteen individuals (7 males and 7 females) with a clinical diagnosis of BBS have been selected in this study. A pool of 10 aged-matched males and 10 aged-matched females have been used as controls for proteomic analysis. The glomerular filtration rate (eGFR) has been estimated using the CKD-EPI formula. Variability of eGFR has been retrospectively assessed calculating average annual eGFR decline (ΔeGFR) in a mean follow-up period of 4 years (3-7). <b><i>Results:</i></b> 42 proteins were significantly over- or under-represented in BBS patients compared with controls; the majority of these proteins are involved in fibrosis, cell adhesion and extracellular matrix organization. Statistic studies revealed a significant correlation between urine fibronectin (u-FN) (r<sup>2</sup>=0.28; p&lt;0.05), CD44 antigen (r<sup>2</sup> =0.35; p&lt;0.03) and lysosomal alfa glucosidase ( r<sup>2</sup>0.27; p&lt;0.05) abundance with the eGFR. In addition, u-FN (r<sup>2</sup> =0.2389; p&lt;0.05) was significantly correlated with ΔeGFR. <b><i>Conclusion:</i></b> The present study demonstrates that urine proteome of BBS patients differs from that of normal subjects; in addition, kidney dysfunction correlated with urine abundance of known markers of renal fibrosis.
DOI: 10.6084/m9.figshare.5981551
title: Data from High, low, or familiar? Nest site preferences of experienced laying hens

description: Data from High, low, or familiar? Nest site preferences of experienced laying hens
DOI: 10.6084/m9.figshare.5981272
title: Additional file 9 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes at evolutionary breakpoints of great tit in comparison with zebra finch and chicken. (CSV 633 kb)
DOI: 10.6084/m9.figshare.5981272.v1
title: Additional file 9 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes at evolutionary breakpoints of great tit in comparison with zebra finch and chicken. (CSV 633 kb)