cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3475448.v1
title: Supplemental data for the article "Contemporary sources and levels of heavy metal contamination in urban soil of Broken Hill, Australia after ad hoc land remediation"

description: Quality control results of measuring concentrations of selected heavy metals (Ca, Cr, Fe, K, Ni, Mn, Pb and Zn) in Broken Hill urban soil using a portable XRF analyser.
DOI: 10.6084/m9.figshare.3475415
title: Assessing high compositional differences of beetle assemblages across vertical woodland strata in the New Forest, Hampshire, England

description: Closed-canopy woodlands are complex ecosystems with strong vertical environmental stratification. The degree to which this vertical stratification has led to compartmentalisation in invertebrate assemblages in temperate woodlands has been researched to a limited extent, yet there are still gaps in our understanding. Here, we used five different sampling methods to sample beetles across vertical strata of nine woodland sites in the New Forest National Park, Hampshire, England. The sampling methods yielded 2412 individuals across 157 species, of which 46 were significant indicator species for one stratum or a combination of strata. Multivariate analysis of composition showed a strong separation at a subfamily level between strata, with many only found in a single stratum. This suggests a strongly compartmentalised vertical stratification of the beetle assemblages at both species and higher taxonomic levels. Our results display that multiple strata need to be sampled to obtain true estimates of overall beetle species richness in woodlands and forests. Limitations in using a single sampling method and biases using mixed sampling method protocols across a vertical transect are also discussed.
DOI: 10.6084/m9.figshare.3475415.v1
title: Assessing high compositional differences of beetle assemblages across vertical woodland strata in the New Forest, Hampshire, England

description: Closed-canopy woodlands are complex ecosystems with strong vertical environmental stratification. The degree to which this vertical stratification has led to compartmentalisation in invertebrate assemblages in temperate woodlands has been researched to a limited extent, yet there are still gaps in our understanding. Here, we used five different sampling methods to sample beetles across vertical strata of nine woodland sites in the New Forest National Park, Hampshire, England. The sampling methods yielded 2412 individuals across 157 species, of which 46 were significant indicator species for one stratum or a combination of strata. Multivariate analysis of composition showed a strong separation at a subfamily level between strata, with many only found in a single stratum. This suggests a strongly compartmentalised vertical stratification of the beetle assemblages at both species and higher taxonomic levels. Our results display that multiple strata need to be sampled to obtain true estimates of overall beetle species richness in woodlands and forests. Limitations in using a single sampling method and biases using mixed sampling method protocols across a vertical transect are also discussed.
DOI: 10.6084/m9.figshare.3475409
title: Glacial geomorphology of the terrestrial margins of the tidewater glacier, Nordenskiöldbreen, Svalbard

description: A 1:4000 scale map of the terrestrial margins of the foreland of Nordenskiöldbreen depicts a polythermal glacial landsystem containing a record of the landform signatures of individual ice flow units that operate within the glacier snout. A 1:700 map provides a detailed overview of fluted terrain, based on unmanned aerial vehicle images captured in 2014. The pattern of landforms lying inside the Little Ice Age (LIA) latero-frontal moraine on the northern side of the fjord comprises a fluted till surface, which in turn grades into ice-moulded bedrock. This signature records the recession of a single, wide ice flow unit, which was characterised by limited incorporation of subglacial material and restricted delivery of supraglacial debris. Inside the latero-frontal moraine on the south side of the fjord, a fluted surface is subordinate to a pronounced and large ice-cored moraine complex related to the confluence of five narrower ice flow units, each of which transported significant quantities of englacial and supraglacial debris at their suture zones as a series of longitudinal debris stripes. The suite of foreland landforms is diagnostic of both temperate subglacial and frozen-snout conditions, indicating the operation of a warm polythermal glacier fed by multiple flow units during the LIA.
DOI: 10.6084/m9.figshare.3475409.v1
title: Glacial geomorphology of the terrestrial margins of the tidewater glacier, Nordenskiöldbreen, Svalbard

description: A 1:4000 scale map of the terrestrial margins of the foreland of Nordenskiöldbreen depicts a polythermal glacial landsystem containing a record of the landform signatures of individual ice flow units that operate within the glacier snout. A 1:700 map provides a detailed overview of fluted terrain, based on unmanned aerial vehicle images captured in 2014. The pattern of landforms lying inside the Little Ice Age (LIA) latero-frontal moraine on the northern side of the fjord comprises a fluted till surface, which in turn grades into ice-moulded bedrock. This signature records the recession of a single, wide ice flow unit, which was characterised by limited incorporation of subglacial material and restricted delivery of supraglacial debris. Inside the latero-frontal moraine on the south side of the fjord, a fluted surface is subordinate to a pronounced and large ice-cored moraine complex related to the confluence of five narrower ice flow units, each of which transported significant quantities of englacial and supraglacial debris at their suture zones as a series of longitudinal debris stripes. The suite of foreland landforms is diagnostic of both temperate subglacial and frozen-snout conditions, indicating the operation of a warm polythermal glacier fed by multiple flow units during the LIA.
DOI: 10.6084/m9.figshare.3475361
title: Desmoglein 3 regulates membrane trafficking of cadherins, an implication in cell-cell adhesion

description: E-cadherin mediated cell-cell adhesion plays a critical role in epithelial cell polarization and morphogenesis. Our recent studies suggest that the desmosomal cadherin, desmoglein 3 (Dsg3) cross talks with E-cadherin and regulates its adhesive function in differentiating keratinocytes. However, the underlying mechanism remains not fully elucidated. Since E-cadherin trafficking has been recognized to be a central determinant in cell-cell adhesion and homeostasis we hypothesize that Dsg3 may play a role in regulating E-cadherin trafficking and hence the cell-cell adhesion. Here we investigated this hypothesis in cells with loss of Dsg3 function through RNAi mediated Dsg3 knockdown or the stable expression of the truncated mutant Dsg3ΔC. Our results showed that loss of Dsg3 resulted in compromised cell-cell adhesion and reduction of adherens junction and desmosome protein expression as well as the cortical F-actin formation. As a consequence, cells failed to polarize but instead displayed aberrant cell flattening. Furthermore, retardation of E-cadherin internalization and recycling was consistently observed in these cells during the process of calcium induced junction assembling. In contrast, enhanced cadherin endocytosis was detected in cells with overexpression of Dsg3 compared to control cells. Importantly, this altered cadherin trafficking was found to be coincided with the reduced expression and activity of Rab proteins, including Rab5, Rab7 and Rab11 which are known to be involved in E-cadherin trafficking. Taken together, our findings suggest that Dsg3 functions as a key in cell-cell adhesion through at least a mechanism of regulating E-cadherin membrane trafficking.
DOI: 10.6084/m9.figshare.3475361.v1
title: Desmoglein 3 regulates membrane trafficking of cadherins, an implication in cell-cell adhesion

description: E-cadherin mediated cell-cell adhesion plays a critical role in epithelial cell polarization and morphogenesis. Our recent studies suggest that the desmosomal cadherin, desmoglein 3 (Dsg3) cross talks with E-cadherin and regulates its adhesive function in differentiating keratinocytes. However, the underlying mechanism remains not fully elucidated. Since E-cadherin trafficking has been recognized to be a central determinant in cell-cell adhesion and homeostasis we hypothesize that Dsg3 may play a role in regulating E-cadherin trafficking and hence the cell-cell adhesion. Here we investigated this hypothesis in cells with loss of Dsg3 function through RNAi mediated Dsg3 knockdown or the stable expression of the truncated mutant Dsg3ΔC. Our results showed that loss of Dsg3 resulted in compromised cell-cell adhesion and reduction of adherens junction and desmosome protein expression as well as the cortical F-actin formation. As a consequence, cells failed to polarize but instead displayed aberrant cell flattening. Furthermore, retardation of E-cadherin internalization and recycling was consistently observed in these cells during the process of calcium induced junction assembling. In contrast, enhanced cadherin endocytosis was detected in cells with overexpression of Dsg3 compared to control cells. Importantly, this altered cadherin trafficking was found to be coincided with the reduced expression and activity of Rab proteins, including Rab5, Rab7 and Rab11 which are known to be involved in E-cadherin trafficking. Taken together, our findings suggest that Dsg3 functions as a key in cell-cell adhesion through at least a mechanism of regulating E-cadherin membrane trafficking.
DOI: 10.6084/m9.figshare.3475301
title: DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera, Papilionidae)

description: Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus <i>Parnassius</i> (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the <i>Parnassius delphius</i> species group, solving long-standing taxonomic problems.
DOI: 10.6084/m9.figshare.3475301.v1
title: DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera, Papilionidae)

description: Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus <i>Parnassius</i> (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the <i>Parnassius delphius</i> species group, solving long-standing taxonomic problems.
DOI: 10.6084/m9.figshare.3475292
title: Selecting an Orthogonal or Nonorthogonal Two-Level Design for Screening

description: This article presents a comparison of criteria used to characterize two-level designs for screening purposes. To articulate the relationships among criteria, we focus on 7-factor designs with 16–32 runs and 11-factor designs with 20–48 runs. Screening based on selected designs for each of the run sizes considered is studied with simulation using a forward selection procedure and the Dantzig selector. This article compares Bayesian D-optimal designs, designs created algorithmically to optimize estimation capacity over various model spaces, and orthogonal designs by estimation-based criteria and simulation. In this way, we furnish both general insights regarding various design approaches, as well as a guide to make a choice among a few final candidate designs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3475292.v2
title: Selecting an Orthogonal or Nonorthogonal Two-Level Design for Screening

description: This article presents a comparison of criteria used to characterize two-level designs for screening purposes. To articulate the relationships among criteria, we focus on 7-factor designs with 16–32 runs and 11-factor designs with 20–48 runs. Screening based on selected designs for each of the run sizes considered is studied with simulation using a forward selection procedure and the Dantzig selector. This article compares Bayesian D-optimal designs, designs created algorithmically to optimize estimation capacity over various model spaces, and orthogonal designs by estimation-based criteria and simulation. In this way, we furnish both general insights regarding various design approaches, as well as a guide to make a choice among a few final candidate designs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3475292.v1
title: Selecting an Orthogonal or Non-Orthogonal Two-Level Design for Screening

description: This article presents a comparison of criteria used to characterize two-level designs for screening purposes. To articulate the relationships among criteria, we focus on seven-factor designs with 16–32 runs and 11-factor designs with 20–48 runs. Screening based on selected designs for each of the run sizes considered is studied with simulation using a forward selection procedure and the Dantzig selector. This article compares Bayesian D-optimal designs, designs created algorithmically to optimize estimation capacity over various model spaces, and orthogonal designs by estimation-based criteria and simulation. In this way, we furnish both general insights regarding various design approaches, as well as a guide to make a choice among a few final candidate designs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3475274
title: SQSTM1/p62 mediates crosstalk between autophagy and the UPS in DNA repair

description: SQSTM1/p62 (sequestosome 1) selectively targets polyubiquitinated proteins for degradation via macroautophagy and the proteasome. Additionally, SQSTM1 shuttles between the cytoplasmic and nuclear compartments, although its role in the nucleus is relatively unknown. Here, we report that SQSTM1 dynamically associates with DNA damage foci (DDF) and regulates DNA repair. Upon induction of DNA damage SQSTM1 interacts with FLNA (filamin A), which has previously been shown to recruit DNA repair protein RAD51 (RAD51 recombinase) to double-strand breaks and facilitate homologous recombination (HR). SQSTM1 promotes proteasomal degradation of FLNA and RAD51 within the nucleus, resulting in reduced levels of nuclear RAD51 and slower DNA repair. SQSTM1 regulates the ratio between HR and nonhomologous end joining (NHEJ) by promoting the latter at the expense of the former. This SQSTM1-dependent mechanism mediates the effect of macroautophagy on DNA repair. Moreover, nuclear localization of SQSTM1 and its association with DDF increase with aging and are prevented by life-span-extending dietary restriction, suggesting that an imbalance in the mechanism identified here may contribute to aging and age-related diseases.
DOI: 10.6084/m9.figshare.3475274.v1
title: SQSTM1/p62 mediates crosstalk between autophagy and the UPS in DNA repair

description: SQSTM1/p62 (sequestosome 1) selectively targets polyubiquitinated proteins for degradation via macroautophagy and the proteasome. Additionally, SQSTM1 shuttles between the cytoplasmic and nuclear compartments, although its role in the nucleus is relatively unknown. Here, we report that SQSTM1 dynamically associates with DNA damage foci (DDF) and regulates DNA repair. Upon induction of DNA damage SQSTM1 interacts with FLNA (filamin A), which has previously been shown to recruit DNA repair protein RAD51 (RAD51 recombinase) to double-strand breaks and facilitate homologous recombination (HR). SQSTM1 promotes proteasomal degradation of FLNA and RAD51 within the nucleus, resulting in reduced levels of nuclear RAD51 and slower DNA repair. SQSTM1 regulates the ratio between HR and nonhomologous end joining (NHEJ) by promoting the latter at the expense of the former. This SQSTM1-dependent mechanism mediates the effect of macroautophagy on DNA repair. Moreover, nuclear localization of SQSTM1 and its association with DDF increase with aging and are prevented by life-span-extending dietary restriction, suggesting that an imbalance in the mechanism identified here may contribute to aging and age-related diseases.
DOI: 10.6084/m9.figshare.3475250
title: Interactive Instruction in Bayesian Inference

description: An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction. These principles concern coherence, personalization, signaling, segmenting, multimedia, spatial contiguity, and pretraining. Principles of self-explanation and interactivity are also applied. Four experiments on the Mammography Problem showed that these principles help participants answer the questions at significantly improved rates. Nonetheless, in novel interactivity conditions, performance was lowered suggesting that more interaction can add more difficulty for participants. Overall, a leap forward in accuracy was found, with more than twice the participant accuracy of previous work. This indicates that an instructional approach to improving human performance in Bayesian inference is a promising direction.
DOI: 10.6084/m9.figshare.3475250.v2
title: Interactive Instruction in Bayesian Inference

description: An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction. These principles concern coherence, personalization, signaling, segmenting, multimedia, spatial contiguity, and pretraining. Principles of self-explanation and interactivity are also applied. Four experiments on the Mammography Problem showed that these principles help participants answer the questions at significantly improved rates. Nonetheless, in novel interactivity conditions, performance was lowered suggesting that more interaction can add more difficulty for participants. Overall, a leap forward in accuracy was found, with more than twice the participant accuracy of previous work. This indicates that an instructional approach to improving human performance in Bayesian inference is a promising direction.
DOI: 10.6084/m9.figshare.3475250.v1
title: Interactive Instruction in Bayesian Inference

description: An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction. These principles concern coherence, personalization, signaling, segmenting, multimedia, spatial contiguity, and pre-training. Principles of self-explanation and interactivity are also applied. Four experiments on the Mammography Problem showed that these principles help participants answer the questions at significantly improved rates. Nonetheless, in novel interactivity conditions, performance was lowered suggesting that more interaction can add more difficulty for participants. Overall, a leap forward in accuracy was found, with more than twice the participant accuracy of previous work. This indicates that an instructional approach to improving human performance in Bayesian inference is a promising direction.
DOI: 10.6084/m9.figshare.3475205
title: LUBM execution on 1 mix as well as 1hour with 1 and 16 users on 20University dataset

description: Executing LUBM [1] Benchmark on 20 University dataset (generated with LUBM Data Generator [1]) <br><br>- Executing against virtuoso7, fuseki 2.3.0 (Jena tdb), blazegraoh 1.5.3 on standard settings<br>- Dataset has 20 Universities<br>- The 14 Queries can be found here [2] (be aware that iguana need each query in one own line)<br>- Upload took:<br> - Blazegraph: 78580ms<br> - Virtuoso: 10633ms<br> - Fuseki: 31000ms<br>- Querying 1 mix as well as 1 hour<br><br>File Description:<br>- lubm_1-mix_1-user_qps.pdf : 1 Query Mix of 14 queries with 1 querying user (metrics: Queries Per Second)<br>- lubm_1-mix_16-user_qps.pdf : 1 Query Mix of 14 queries with 16 querying user (metrics: Queries Per Second) <br>- lubm_small.gnumeric : gnumeric file for the figures<br>- results_lubm_small.zip : Raw results for mix benchmark<br><br>- lubm_1-hour_16-user_qps.pdf : 1 hour of 14 queries with 16 querying users (metrics Queries Per Second)<br>- lubm_1-hour_16-user_qmph.pdf : 1 hour of 14 queries with 16 querying users (metrics Query Mixes Per Hour)<br>- lubm_1-hour_16-user_no-of-queries.pdf : 1 hour of 14 queries with 16 querying users (metrics No of Queries per Hour)<br>- lubm_hour.gnumeric : gnumeric file for hour figures<br>- results_lubm_hour.zip : Raw results for hour benchmark<br><br>-------<br>[1] http://swat.cse.lehigh.edu/projects/lubm/<br>[2] http://swat.cse.lehigh.edu/projects/lubm/queries-sparql.txt <br>