cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5325010
title: Supplementary Material for: Heterologous Expression of Spinosyn Biosynthetic Gene Cluster in Streptomyces Species Is Dependent on the Expression of Rhamnose Biosynthesis Genes

description: Spinosyns are a group of macrolide insecticides produced by <i>Saccharopolyspora spinosa</i>. Although <i>S. spinosa</i> can be used for industrial-scale production of spinosyns, this might suffer from several limitations, mainly related to its long growth cycle, low fermentation biomass, and inefficient utilization of starch. It is crucial to generate a robust strain for further spinosyn production and the development of spinosyn derivatives. A BAC vector, containing the whole biosynthetic gene cluster for spinosyn (74 kb) and the elements required for conjugal transfer and site-specific integration, was introduced into different <i>Streptomyces</i> hosts in order to obtain heterologous spinosyn-producing strains. The exconjugants of different <i>Streptomyces</i> strains did not show spinosyn production unless the rhamnose biosynthesis genes from <i>S. spinosa</i> genomic DNA were present and expressed under the control of a strong constitutive <i>ermE</i>*<i>p</i> promoter. Using this heterologous expression system resulted in yields of 1 μg/mL and 1.5 μg/mL spinosyns in <i>Streptomyces coelicolor</i> and <i>Streptomyces lividans</i>, respectively. This report demonstrates spinosyn production in 2 <i>Streptomyces</i> strains and stresses the essential role of rhamnose in this process. This work also provides a potential alternative route for producing spinosyn analogs by means of genetic manipulation in the heterologous hosts.
DOI: 10.6084/m9.figshare.5324995
title: Liver of adult Xenopus laevis

description: Hematoxylin-eosin staining of paraffin embedded sections. Scale bar 50 micrometers.
DOI: 10.6084/m9.figshare.5324983
title: Pancreas of adult Xenopus laevis

description: Hematoxylin-eosin staining of paraffin embedded sections. Scale bar 50 micrometers.
DOI: 10.6084/m9.figshare.5324995.v1
title: Liver of adult Xenopus laevis

description: Hematoxylin-eosin staining of paraffin embedded sections. Scale bar 50 micrometers.
DOI: 10.6084/m9.figshare.5324986
title: Fat body of adult Xenopus laevis

description: Hematoxylin-eosin staining of paraffin embedded sections. Scale bar 50 micrometers.
DOI: 10.6084/m9.figshare.5324986.v1
title: Fat body of adult Xenopus laevis

description: Hematoxylin-eosin staining of paraffin embedded sections. Scale bar 50 micrometers.
DOI: 10.6084/m9.figshare.5324914
title: Microarray data for single rabbit immunization with black mamba SN-1

description: The reposotory contains four files:<br>1) A list of Uniprot accesion numbers<br>2) A fasta file contaning the sequence of the investigted toxins<br>3) A data file containing the observed signals after binding of the naive rabbit serum<br>4) A data file containing the observed signals after binding of rabbit anti-SN-1 antiserum <br>
DOI: 10.6084/m9.figshare.5324908
title: Widespread release of dissolved organic carbon from anoxic boreal lake sediments

description: Sediments in boreal lakes are important components of the carbon cycle because they receive and store large amounts of organic carbon (OC) and at the same time are a source of greenhouse gases. Under anoxic conditions, sediment OC can be lost through dissolution from the solid phase and subsequent diffusion to the water column. Although this process may have implications for sediment OC budgets, it has yet to be studied systematically. We combined laboratory sediment incubation experiments from 4 boreal lakes in central Sweden that differed widely in their biogeochemical conditions with data from the Swedish monitoring program covering &gt;100 lakes to analyze the frequency of occurrence of sediment DOC loss in boreal lakes and identify lake characteristics and the conditions related to high DOC fluxes from anoxic sediments. We found DOC diffusion from anoxic sediments in all the anoxic sediment incubations but at different mean rates (0.7–3.7 mmol m<sup>−2</sup> d<sup>−1</sup>). Similarly, 16 of 17 of the monitoring lakes that developed anoxic bottom water exhibited an increase in bottom-water DOC concentration, corresponding to a mean (and standard deviation) DOC diffusion flux from anoxic sediment of 11.1 (35.4) mmol m<sup>−2</sup> d<sup>−1</sup>. The observed variability between lakes was related to particularly large DOC fluxes in humic-rich lakes, which we attribute to their low pH and high share of terrestrial OC favoring the formation of OC-iron aggregates. Accordingly, increasing pH might facilitate the dissolution of sediment OC because high dissolved OC fluxes from anoxic sediments were accompanied by high microbial iron and sulfate reduction, resulting in concomitant pH increase.
DOI: 10.6084/m9.figshare.5324908.v1
title: Widespread release of dissolved organic carbon from anoxic boreal lake sediments

description: Sediments in boreal lakes are important components of the carbon cycle because they receive and store large amounts of organic carbon (OC) and at the same time are a source of greenhouse gases. Under anoxic conditions, sediment OC can be lost through dissolution from the solid phase and subsequent diffusion to the water column. Although this process may have implications for sediment OC budgets, it has yet to be studied systematically. We combined laboratory sediment incubation experiments from 4 boreal lakes in central Sweden that differed widely in their biogeochemical conditions with data from the Swedish monitoring program covering &gt;100 lakes to analyze the frequency of occurrence of sediment DOC loss in boreal lakes and identify lake characteristics and the conditions related to high DOC fluxes from anoxic sediments. We found DOC diffusion from anoxic sediments in all the anoxic sediment incubations but at different mean rates (0.7–3.7 mmol m<sup>−2</sup> d<sup>−1</sup>). Similarly, 16 of 17 of the monitoring lakes that developed anoxic bottom water exhibited an increase in bottom-water DOC concentration, corresponding to a mean (and standard deviation) DOC diffusion flux from anoxic sediment of 11.1 (35.4) mmol m<sup>−2</sup> d<sup>−1</sup>. The observed variability between lakes was related to particularly large DOC fluxes in humic-rich lakes, which we attribute to their low pH and high share of terrestrial OC favoring the formation of OC-iron aggregates. Accordingly, increasing pH might facilitate the dissolution of sediment OC because high dissolved OC fluxes from anoxic sediments were accompanied by high microbial iron and sulfate reduction, resulting in concomitant pH increase.
DOI: 10.6084/m9.figshare.5324914.v1
title: Microarray data for single rabbit immunization with black mamba SN-1

description: The reposotory contains four files:<br>1) A list of Uniprot accesion numbers<br>2) A fasta file contaning the sequence of the investigted toxins<br>3) A data file containing the observed signals after binding of the naive rabbit serum<br>4) A data file containing the observed signals after binding of rabbit anti-SN-1 antiserum <br>
DOI: 10.6084/m9.figshare.5324881
title: Ballot structure, list flexibility and policy representation

description: There is a growing body of research on the impact of the electoral system ‘ballot structure’ on the behaviour of politicians. We offer a clear, ordinal and rules-based three-way coding (closed, flexible, open) of the electoral systems used in European Parliament elections, taking into account both the ballot type and the intra-party seat-allocation rules. For the notoriously difficult group of flexible list-systems, we show how these operated in the 2004, 2009 and 2014 elections, and introduce an additional behavioural distinction between ‘weakly flexible’ and ‘strongly flexible’ subtypes at the party-list-level. We then illustrate how the type of ballot used in an election can influence individual policy representation by looking at the vote-splits between Members of the European Parliament (MEPs) in the European People’s Party in a vote on tackling homophobia.
DOI: 10.6084/m9.figshare.5324875
title: Supplementary Material for: The Effect of Tegafur-Uracil on Survival in T Categories as Defined in the Eighth Edition of the TNM Classification: An Exploratory Analysis of Postoperative Adjuvant Tegafur-Uracil on Survival in Patients with Adenocarcinoma of the Lung

description: <b><i>Background:</i></b> Tegafur-uracil (UFT) improves survival in patients with stage I adenocarcinoma of the lung. We evaluated the effect of UFT on survival in maximum primary tumor diameter (T) categories as defined in the eighth edition of the TNM Classification (TNM8). <b><i>Methods:</i></b> Tumors were subgrouped on the basis of T category (TNM8) as follows: T1a, T ≤1 cm; T1b, 1 &lt; T ≤2 cm; T1c, 2 &lt; T ≤3 cm; T2a, 3 &lt; T ≤4 cm; T2b , 4 &lt; T ≤5 cm; T3, 5 &lt; T ≤7 cm. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated by Cox proportional hazard models. <b><i>Results:</i></b> UFT was associated with improved survival. The adjusted HRs were as follows: for T1a, 0.79 (95% CI 0.14-4.50); for T1b, 1.16 (95% CI 0.63-2.12); for T1c, 0.74 (95% CI 0.43-1.27); for T2a, 0.45 (95% CI 0.21-0.96); for T2b, 0.55 (95% CI 0.10-3.07), and for T3, 0.70 (95% CI 0.20-2.50). <b><i>Conclusions:</i></b> The adjuvant chemotherapy with UFT tended to improve survival in patients with adenocarcinoma of the lung of each T category based on TNM8, except T1b.
DOI: 10.6084/m9.figshare.5324878
title: No participation without representation

description: How does the degree to which European citizens see themselves represented by political parties relate to their willingness to participate in an election? We argue that the closer citizens are to the parties running in an election in terms of the socio-economic left-right conflict and the European integration policy dimension, the more likely they participate in elections to the European Parliament. The analysis, which is based on the 2009 and 2014 European Election Studies datasets, indicates that the ideological left-right distance between citizens and parties mattered for participation in both EP elections under study. Moreover, the European integration dimension has become relevant for citizens’ turnout decision over the course of the European economic and sovereign debt crisis, but only in countries that are part of the Eurozone. These findings have implications for the nature of European elections and representative democracy on the European level, and indicate that missing policy responsiveness can lead to lower voter turnout.
DOI: 10.6084/m9.figshare.5324872
title: Supplementary Material for: Practical Value of Anti-Xa Activity in the Evaluation of Extracorporeal Circuit Anticoagulation during Haemodialysis: Results of a Cross-Sectional Single-Centre Study

description: <b><i>Background/Aims:</i></b> Anticoagulation of the extracorporeal circuit is essential for adequate haemodialysis (HD). Low molecular weight heparins (LMWHs) are safe and sufficient towards achieving this goal. In the Netherlands, dosage is based on bodyweight and adjusted based on clinical events. LMWH levels during dialysis can be quantified through measurement of the anti-Xa activity and a target range of 0.5-1.0 IU/mL has been proposed. We aimed to evaluate the practical value of the anti-Xa activity to guide LMWH dosage in HD patients. Additionally, the value of the activated partial thromboplastin time (APTT) was investigated. <b><i>Methods:</i></b> All prevalent adult HD patients of our dialysis clinic were included. APTT and anti-Xa activity were measured before, during and after 2 dialysis sessions. Clinical and dialysis characteristics, including LMWH dosage, were derived from digital patient charts. <b><i>Results:</i></b> Our final study cohort consisted of 83 patients. LMWH dosage during dialysis was appropriate for bodyweight in 61% of cases, of which 50% reached an anti-Xa activity within the putative target range of 0.5-1.0 IU/mL. Forty-six percent of patients had an anti-Xa activity &gt;1.0 IU/mL. Anti-Xa levels during and after dialysis were significantly correlated (<i>r</i> = 0.803, <i>p</i> &lt; 0.01). No thrombotic or haemorrhagic complications were observed in this study. Correlation of APTT with anti-Xa activity was poor. <b><i>Conclusion:</i></b> Anti-Xa activity measurements during dialysis can identify patients in whom LMWH dosage should be lowered in a subsequent dialysis session. Whether such an intervention leads to a decrease in haemorrhagic complications needs to be evaluated in prospective studies.
DOI: 10.6084/m9.figshare.5324875.v1
title: Supplementary Material for: The Effect of Tegafur-Uracil on Survival in T Categories as Defined in the Eighth Edition of the TNM Classification: An Exploratory Analysis of Postoperative Adjuvant Tegafur-Uracil on Survival in Patients with Adenocarcinoma of the Lung

description: <b><i>Background:</i></b> Tegafur-uracil (UFT) improves survival in patients with stage I adenocarcinoma of the lung. We evaluated the effect of UFT on survival in maximum primary tumor diameter (T) categories as defined in the eighth edition of the TNM Classification (TNM8). <b><i>Methods:</i></b> Tumors were subgrouped on the basis of T category (TNM8) as follows: T1a, T ≤1 cm; T1b, 1 &lt; T ≤2 cm; T1c, 2 &lt; T ≤3 cm; T2a, 3 &lt; T ≤4 cm; T2b , 4 &lt; T ≤5 cm; T3, 5 &lt; T ≤7 cm. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated by Cox proportional hazard models. <b><i>Results:</i></b> UFT was associated with improved survival. The adjusted HRs were as follows: for T1a, 0.79 (95% CI 0.14-4.50); for T1b, 1.16 (95% CI 0.63-2.12); for T1c, 0.74 (95% CI 0.43-1.27); for T2a, 0.45 (95% CI 0.21-0.96); for T2b, 0.55 (95% CI 0.10-3.07), and for T3, 0.70 (95% CI 0.20-2.50). <b><i>Conclusions:</i></b> The adjuvant chemotherapy with UFT tended to improve survival in patients with adenocarcinoma of the lung of each T category based on TNM8, except T1b.
DOI: 10.6084/m9.figshare.5324881.v1
title: Ballot structure, list flexibility and policy representation

description: There is a growing body of research on the impact of the electoral system ‘ballot structure’ on the behaviour of politicians. We offer a clear, ordinal and rules-based three-way coding (closed, flexible, open) of the electoral systems used in European Parliament elections, taking into account both the ballot type and the intra-party seat-allocation rules. For the notoriously difficult group of flexible list-systems, we show how these operated in the 2004, 2009 and 2014 elections, and introduce an additional behavioural distinction between ‘weakly flexible’ and ‘strongly flexible’ subtypes at the party-list-level. We then illustrate how the type of ballot used in an election can influence individual policy representation by looking at the vote-splits between Members of the European Parliament (MEPs) in the European People’s Party in a vote on tackling homophobia.
DOI: 10.6084/m9.figshare.5324878.v1
title: No participation without representation

description: How does the degree to which European citizens see themselves represented by political parties relate to their willingness to participate in an election? We argue that the closer citizens are to the parties running in an election in terms of the socio-economic left-right conflict and the European integration policy dimension, the more likely they participate in elections to the European Parliament. The analysis, which is based on the 2009 and 2014 European Election Studies datasets, indicates that the ideological left-right distance between citizens and parties mattered for participation in both EP elections under study. Moreover, the European integration dimension has become relevant for citizens’ turnout decision over the course of the European economic and sovereign debt crisis, but only in countries that are part of the Eurozone. These findings have implications for the nature of European elections and representative democracy on the European level, and indicate that missing policy responsiveness can lead to lower voter turnout.
DOI: 10.6084/m9.figshare.5324872.v1
title: Supplementary Material for: MicroRNA-200a Inhibits Transforming Growth Factor β1-Induced Proximal Tubular Epithelial-Mesenchymal Transition by Targeting β-Catenin

description: <b><i>Background:</i></b> The epithelial-mesenchymal transition (EMT) is a crucial event in the development of renal interstitial fibrosis (RIF). A growing body of evidence indicates that β-catenin plays an important role in various types of fibrosis. Although members of the microRNA (miRNA)-200 family have been suggested to suppress EMT in cancer and fibrosis, the function of miRNA-200a in regulating the progression of RIF is unknown. We speculate that miRNA-200a may hinder this progression through the suppression of β-catenin. <b><i>Methods:</i></b> Transforming growth factor β1 (TGF β1) was used to induce EMT of proximal tubule epithelial (HK-2) cells in vitro, quantitative real time polymerase chain reaction (qPCR) and Western Blot analysis measured the miRNA-200a and β-catenin expression. qPCR, Western Blot analysis, Migration Assay and cell immunofluorescence were applied to detect the influence of up- and downregulated miRNA-200a expression and β-catenin siRNA on β-catenin and EMT. Dual luciferase report plasmid (CTNNB1 UTR WT/MT) verifies the target relationship between miRNA-200a and CTNNB1 (β-catenin gene). <b><i>Results:</i></b> miRNA-200a is downregulated and β-catenin is upregulated during TGF β1-induced EMT. Upregulation of miRNA-200a inhibits β-catenin and attenuates TGF β1-induced EMT and cell migration, while its downregulation increases β-catenin and induces EMT and HK-2 cell migration. Further, knocking down β-catenin suppressed the EMT induced by miRNA-200a downregulation. miRNA-200a directly targets for CTNNB1. <b><i>Conclusions:</i></b> miRNA-200a inhibits TGF β1-induced EMT by directly targeting β-catenin in proximal tubule epithelial cells.
DOI: 10.6084/m9.figshare.5324878.v2
title: No participation without representation. Policy distances and abstention in European Parliament elections

description: How does the degree to which European citizens see themselves represented by political parties relate to their willingness to participate in an election? We argue that the closer citizens are to the parties running in an election in terms of the socio-economic left-right conflict and the European integration policy dimension, the more likely they participate in elections to the European Parliament. The analysis, which is based on the 2009 and 2014 European Election Studies datasets, indicates that the ideological left-right distance between citizens and parties mattered for participation in both EP elections under study. Moreover, the European integration dimension has become relevant for citizens’ turnout decision over the course of the European economic and sovereign debt crisis, but only in countries that are part of the Eurozone. These findings have implications for the nature of European elections and representative democracy on the European level, and indicate that missing policy responsiveness can lead to lower voter turnout.
DOI: 10.6084/m9.figshare.5324848
title: An open-source model and solution method to predict co-contraction in the finger

description: A novel open-source biomechanical model of the index finger with an electromyography (EMG)-constrained static optimization solution method are developed with the goal of improving co-contraction estimates and providing means to assess tendon tension distribution through the finger. The Intrinsic model has four degrees of freedom and seven muscles (with a 14 component extensor mechanism). A novel plugin developed for the OpenSim modelling software applied the EMG-constrained static optimization solution method. Ten participants performed static pressing in three finger postures and five dynamic free motion tasks. Index finger 3D kinematics, force (5, 15, 30 N), and EMG (4 extrinsic muscles and first dorsal interosseous) were used in the analysis. The Intrinsic model predicted co-contraction increased by 29% during static pressing over the existing model. Further, tendon tension distribution patterns and forces, known to be essential to produce finger action, were determined by the model across all postures. The Intrinsic model and custom solution method improved co-contraction estimates to facilitate force propagation through the finger. These tools improve our interpretation of loads in the finger to develop better rehabilitation and workplace injury risk reduction strategies.
DOI: 10.6084/m9.figshare.5324857
title: Supplementary Material for: Predictors of Postoperative Non-Chylous Massive Discharge after Pancreaticoduodenectomy for Pancreatic Ductal Adenocarcinoma

description: <b><i>Background:</i></b> Pancreaticoduodenectomy (PD) is performed for pancreatic ductal adenocarcinoma (PDA) located at the pancreas head/body. Non-chylous massive discharge after PD is frequently encountered and can cause a vicious cycle of complications associated with severe dehydration and protein loss. <b><i>Methods:</i></b> From August 2008 to June 2015, 102 patients who underwent PD for PDA were retrospectively reviewed. High non-chylous discharge was defined as postoperative daily serous discharge exceeding 10 mL/kg. Predictive factors for high non-chylous discharge were assessed using multivariable analysis. <b><i>Results:</i></b> Fifty-one patients (50%) developed high non-chylous discharge. Body mass index (BMI) and hemoglobin, total protein, and cholinesterase levels were significantly lower in the high-discharge group compared to the corresponding levels in the low-discharge group. The incidence of postoperative pancreatic fistula and delayed gastric emptying was significantly lower and higher in the high-discharge group than in the low-discharge group, respectively. Multivariable analysis revealed that BMI &lt;22.0 kg/m<sup>2</sup>, hemoglobin &lt;12.0 g/dL and intraoperative blood loss ≥800 mL were independent predictive factors for high non-chylous discharge. <b><i>Conclusions:</i></b> Preoperative low levels of BMI and hemoglobin and intraoperative high blood loss were independent predictive factors for high non-chylous discharge. Improvement of preoperative general and nutritional condition may reduce the incidence of high non-chylous discharge.
DOI: 10.6084/m9.figshare.5324848.v1
title: An open-source model and solution method to predict co-contraction in the finger

description: A novel open-source biomechanical model of the index finger with an electromyography (EMG)-constrained static optimization solution method are developed with the goal of improving co-contraction estimates and providing means to assess tendon tension distribution through the finger. The Intrinsic model has four degrees of freedom and seven muscles (with a 14 component extensor mechanism). A novel plugin developed for the OpenSim modelling software applied the EMG-constrained static optimization solution method. Ten participants performed static pressing in three finger postures and five dynamic free motion tasks. Index finger 3D kinematics, force (5, 15, 30 N), and EMG (4 extrinsic muscles and first dorsal interosseous) were used in the analysis. The Intrinsic model predicted co-contraction increased by 29% during static pressing over the existing model. Further, tendon tension distribution patterns and forces, known to be essential to produce finger action, were determined by the model across all postures. The Intrinsic model and custom solution method improved co-contraction estimates to facilitate force propagation through the finger. These tools improve our interpretation of loads in the finger to develop better rehabilitation and workplace injury risk reduction strategies.
DOI: 10.6084/m9.figshare.12900920
title: images256

description: dataset for samples256
DOI: 10.6084/m9.figshare.12900920.v1
title: images256

description: dataset for samples256