Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

How mature Systematic Literature Reviews are?

This file contains 84 mitigation actions (practices) to improve SLR process summarized from Ampatzoglou (2019) and Zhou et al (2016). In addition, it contains the results from summarization of these practices.

openMar 2023View details →

Argument maps as tools to support the development of new media literacies: a systematic review.

The post-digital era is characterized by the vast presence of platforms imposing their digital affordances and algorithmic control on our behavior. This environment is challenging education and training, with implications for digital and transmedial literacy. Investigating instructional methodologies is crucial to foster critical comprehension of such novel informational environments. The argument maps (AM), which were first created and evaluated in static information contexts (analogical/old web), could be useful in the emergence of dynamic (post-digital) textual forms. The current paper describes a comprehensive literature review based on the assumptions above. We looked into state of the art in research on using AM to handle dynamic information. We found 150 papers using a PRISMA procedure and then examined 25 of them. Our review produced pertinent data about the current state of AM, including the sorts of texts on which they are used and the tools (especially digital and AI-based) that have been employed. Our research lays the groundwork for teaching the literacies needed in new informational settings, such as multimodal, dynamic, algorithmic, and data-driven contexts, with a specific focus on AM as an effective mediational tool. This Zenodo record presents the full dataset composed of the following sheets: <ol> <li>Codebook</li> <li>Italian Journals</li> <li>List of articles extracted from SCOPUS</li> <li>List of articles extracted from ERIC</li> <li>List of articles extracted from WOS</li> <li>List of articles extracted from DOAJ</li> <li>PRISMA workflow</li> <li>Analysis - First Level (classification of 25 articles selected)</li> <li>Analysis - Second Level (List of 19 articles selected)</li> <li>Final Dataset</li> <li>Interrater Agreement.</li> </ol> As for the Keywords' Map, a primo file .txt displays the text over which basis was performed the keyword maps analysis. The second .txt file shows notes relating to the analysis procedures using the software VOS-Viewer <a href="http://www.vosviewer.com/">http://www.vosviewer.com/</a>  Any comments or improvements are welcome!

opencc-by-4.0Apr 2023View details →

Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling (datasets)

Supplemental data files that include the results of complexome profiling experiments from the manuscript entitled "Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling" by Potter et al.  Supplemental Data 1: comparison of mitochondrial complexomes obtained with either Blue Native (BNE) or high resolution Clear Native (hrCNE) gel electrophoresis.  Supplemental Data 2: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented or not with DNase I.   Supplemental Data 3: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented with only DNase I or a combination of DNase I and RNase A.   Supplemental Data 4: comparison of mitochondrial complexomes obtained with hrCNE from control cells, cells treated with ethidium bromide and cells recovering after ethidium bromide treatment. Supplemental Data 5: results of LFQ-based analysis of profiles obtained from samples supplemented or not with DNase I. Supplemental Data 6: individual profiles (replicates), alignment and mass calibration results for the presented data.

opencc-zeroApr 2023View details →

Morphometric and phylogeny data for: Morphology, variation, and systematics of the late Cambrian Laurentian dikelocephalid trilobite Walcottaspis vanhornei

These pages provide details of the taxa, characters and character states used in the phylogenetic analyses of Walcottaspis vanhornei (Walcott, 1914) and relatives in the accompanying paper. Phylogenetic information included here provides details of characters and taxa used for both the parsimony-based and Bayesian analyses and documents levels of support of two types (Bremer and bootstrap) for the parsimony analysis. Also included here is the result of Bayesian maximum likelihood analysis that provides further support to the results of parsimony analysis. We include bivariate plots of the variance explained by each relative warp for the sclerites analyzed and morphometric measurement error analysis.

opencc-zeroApr 2023View details →

Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

opencc-zeroApr 2023View details →

Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, gene order variability does not predict difficulty in placing certain taxa within molecular phylogenetic studies. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why they do not always fit to the observed patterns without nuisance.

opencc-zeroDec 2022View details →

New data and systematic considerations on the Blattogryllopterida (Insecta: Grylloblattida) from the Jurassic Daohugou locality in China

The systematics of the Blattogryllopterida (Grylloblattida) from the Jurassic Daohugou locality (China) is reconsidered. The holotypes of Plesioblattogryllus magnificus and Duoduo qianae are examined, and new synonymies are proposed: Plesioblattogryllus Huang, Nel & Petrulevičius, 2008 = Duoduo Cui, 2012, syn. nov.; Plesioblattogryllus magnificus Huang, Nel & Petrulevičius, 2008 = Duoduo qianae Cui, 2012, syn. nov. The holotype of Plesioblattogryllus minor Ren & Aristov, 2011 is reinvestigated and re-documented, and a new well-preserved single wing of this rare species, also uncovered from the Jurassic Daohugou locality, is described. Besides the holotype, it is the first specimen exhibiting well-exposed wing venation characters for the species. Particular characters, such as the desclerotised MP, are better observed and complemented by Reflectance Transforming Imaging documentation. The new specimen might be a hind wing with a reduced plicatum, a trait yet unknown in grylloblattids. Based on these new data it occurs that, in contrast to P. magnificus and most Blattogryllopterida, the species possesses a long RP+MA fusion, with a long basal free part of MA and a very short basal free section of RP. Together with other characters, it justifies the erection of a new genus, Aristoviblattogryllus gen. nov., to accommodate the species Aristoviblattogryllus minor (Ren & Aristov, 2011), comb. nov.

opencc-zeroMay 2023View details →

Draining the swamp dodders: Systematics of Cuscuta gronovii s.l. (subgenus Grammica, sect. Oxycarpae)

Cuscuta gronovii species complex (sensu lato, s.l.) is a North American group of species that belong to sect. Oxycarpae of subgenus Grammica. Members of C. gronovii s.l. are often associated with riparian or wet habitats, and their delimitation has been problematic historically. DNA sequences from multiple plastid and nuclear ribosomal non-coding regions were used to reconstruct evolutionary relationships among taxa. Molecular phylogeny supported the resurrection of C. saururi, a taxon that has been treated either as C. gronovii var. latiflora or a nomenclatural synonym of C. gronovii var. gronovii. Cuscuta saururi was inferred to be sister to C. cephalanthi, but the relationships among the rest of taxa, although forming a clade with a moderate support, remained largely unresolved. Thus, the species limits of C. gronovii s.l. aggregate were also comprehensively investigated through a morphometric study. Plants with 4-merous flowers from New Brunswick and Nova Scotia, Canada, which were previously thought to be C. cephalanthi, were described as a new species, C. acadiana. Cuscuta acadiana, although fertile and producing abundant seeds, is unusual in that the majority of its pollen grains intergrade from zonocolpate, syncolpate or pantocolpate, with variously shaped or twisted ectoapertures. Cuscuta gronovii var. calyptrata, a widely accepted but virtually unknown taxon, was typified and included in all the analyses. Cuscuta umbrosa was treated as a variety of C. gronovii (var. curta), and C. rostrata was maintained as a species. An identification key, detailed descriptions, illustrations, and a summary of geographical distribution, ecology and conservation status were provided for all the members of C. gronovii s.l. The only taxon of this species complex found to be weedy, especially in cranberries, was C. gronovii var. gronovii.

The efficacy and safety of meal replacement in patients with type 2 diabetes: a systematic review and meta-analysis

There are supplemental materials for a systematic review and meta-analysis, which studied the efficacy and safety of meal replacement in patients with type 2 diabetes, with a focus on subgroup analysis of variable participant characteristics and MR prescription.

PRISMA DIAGRAM FOR ARTICLE: Lessons learned during the health crisis caused by COVID-19 in the work of the nursing professional: A systematic review

PRISMA DIAGRAM FOR ARTICLE: Lessons learned during the health crisis caused by COVID-19 in the work of the nursing professional: A systematic review

opencc-by-4.0Jan 2023View details →

Replication Package: A Systematic Mapping Study on Security in Configurable Safety-critical Systems Based on Product-Line Concepts

Welcome to the public repository for the additional content of the paper "A Systematic Mapping Study on Security in Configurable Safety-critical Systems Based on Product-Line Concepts", accepted at the ICSOFT 2023. This repository provides additional information to the conducted mapping study, including the following files: <ul> <li>fetched_results_ICSOFT2023.csv: sheet containing all papers fetched from IEEEXplore, Scopus, and the ACM Guide to Computing Literature.</li> <li>excluded_paper.csv: sheet containing all excluded papers related to safety-critical systems but not referring to security.</li> <li>analysis_sheet_ICSOFT2023.csv: sheet containing information regarding the analysis results of 44 included papers based on the extraction criteria.</li> </ul>

openother-openMay 2023View details →

Data and code for "Brehm et al. (2023) The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates"

All data and R code for Brehm, J., Ritschar, S., Laforsch, C. and Mair, M.M. (2023). The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates. Journal of Hazardous Materials 458: 131839. (<a href="https://doi.org/10.1016/j.jhazmat.2023.131839">https://doi.org/10.1016/j.jhazmat.2023.131839</a>) Abstract In recent years, the number of publications on nano- and microplastic particles (NMPs) effects on freshwater organisms has increased rapidly. Freshwater crustaceans of the genus Daphnia are widely used in ecotoxicological research as model organisms for assessing the impact of NMPs. However, the diversity of experimental designs in these studies makes conclusions about the general impact of NMPs on Daphnia challenging. To approach this, we systematically reviewed the literature on NMP effects on Daphnia and summarized the diversity of test organisms, experimental conditions, NMP properties and measured endpoints to identify gaps in our knowledge of NMP effects on Daphnia. We use a meta-analysis on mortality and immobilization rates extracted from the compiled literature to illustrate how NMP properties, study parameters and the biology of Daphnia can impact outcomes in toxicity bioassays. In addition, we investigate the extent to which the available data can be used to predict the toxicity of untested NMPs based on the extracted parameters. Based on our results, we argue that focusing on a more diverse set of NMP properties combined with a more detailed characterization of the particles in future studies will help to fill current research gaps, improve predictive models and allow the identification of NMP properties linked to toxicity.

DATABASE OF THE SYSTEMATIC MAPPING OF SOCIAL SUPPORT ANS STIGMA IN POPULATION LIVING WITH HIV

DATABASE OF THE SYSTEMATIC MAPPING OF SOCIAL SUPPORT ANS STIGMA IN POPULATION LIVING WITH HIV. IT WAS USED THE PRISMA (2020) METHODOLOGY.

Dataset for Preferred and actual involvement of caregivers in oncologic treatment decision-making: A systematic review

This dataset shows the search that was done for the publication Preferred and actual involvement of caregivers in oncologic treatment decision-making: A systematic review, which can be found at <a href="https://doi.org/10.1016/j.jgo.2023.101525">https://doi.org/10.1016/j.jgo.2023.101525</a>.

opencc-zeroMay 2023View details →

Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans

Wide-ranging species are often polytypic, span geographic dispersal barriers, and experience opportunities for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD) which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (Rana clamitans), a wide-ranging species of the Aquarana clade distributed across much of North America. Although Rana clamitans is phenotypically variable enough to previously merit description of two subspecies, patterns of genetic diversity remain unclear. Additionally, the broader phylogenetic context for R. clamitans is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Bog Frog (Rana okaloosae). Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana and unambiguously identify R. okaloosae as the sister lineage to R. clamitans. Within R. clamitans we find two well-supported and geographically divided clades which are identified as distinct species by a widely used genetic species delimitation method, BPP. However, the two clades exhibit low genealogical divergence and population genetic analyses reveal that genetic variation within R. clamitans is best described by a pattern of IBD rather than independently evolving lineages. We conclude that R. clamitans is indeed a single species and the subspecies concept is of limited use. Our analysis emphasizes how existing approaches can erroneously split species characterized by continuous genetic variation and highlights the power of combining population genetic and phylogenetic perspectives to better understand diversity within wide-ranging taxa.

Phylomitogenomics reveals mito-nuclear concordance in social wasps: the performance of mitochondrial markers and gene order for hymenopteran systematics.

Mitochondrial (mtDNA) genes have served as widely utilized genetic loci for animal phylogenetics and phylogeography studies. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analyzed mitogenomic data from social wasps, representing the four recognized tribes of Polistinae and also all Epiponini genera. Additionally, we evaluated whether mtDNA gene order in Polistinae is congruent with its tribal classification. Using concatenation phylogenetic methods, we show phylogenetic congruence between mitogenomic and nuclear data. Statistically comparing the phylogenetic performance of individual mtDNA genes, we demonstrate that for social wasps the molecular markers COI, 16S, NAD5, and NAD2 perform best, while ATP6, COII, and 12S show the worst results. Finally, we verified that the tRNA cluster close to the noncoding region is a hotspot of rearrangement in Vespidae and can be used as additional information for the systematics of this group. Together, these results indicate that mitogenomes contain robust phylogenetic signal to elucidate the evolutionary history of Vespidae. Moreover, our study identifies the best choice of mitochondrial markers for systematic investigations of social wasps.

opencc-zeroDec 2022View details →

A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data

Background The Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias. Methods This study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson's correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data. Results The method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best-performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson's correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor-performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2).

Automated diagnosis of prostate cancer using artificial intelligence. A systematic literature review. Extraction and Summary Forms.

Extraction and summary forms of a systematic literature review protocol detailed by Barbara Kitchenham for automated diagnosis of prostate cancer using artificial intelligence articles.

opencc-zeroMay 2023View details →

Data from: Relational values of nature in empirical research: A systematic review

In the past five years, scholarly and policy attention to relational values, a concept that articulates plural values of nature, has grown steadily. To date, there are no published syntheses of empirical research that explicitly address relational values. We perform a systematic literature review of n = 72 empirical studies of relational values to summarize the state of current research and to identify opportunities for future research and conceptual development. In our analysis, we categorize what authors identify as relational values and summarize study characteristics (e.g., study location, methods approach.) Authors collectively report n = 312 unique relational values. Categories of identity, social cohesion, livelihoods, connection to place/human-nature connection, and religion are most common. Scholarship that explicitly addresses relational values has increased since 2017 and exhibits substantial diversity: in how relational values are conceptualized (or not); in disciplinary associations; in geographical location; and in data collection methods. We find that most empirical research on relational values does not justify how its results reflect characteristics that establish the relational values concept as unique from other environmental values concepts. As a result, diverse interpretations of the relational values concept pose the risk of the relational values concept being so broad and inclusive that it becomes meaningless, or at least meaning-light.

TFG Systematization process of generating semantic data and ontology

<pre>Set of TALIS files, the main source of data for the investigation, in CSV format.General ontology manually and by new software. Semantic data, as well as the DSL code. Finally, the web design of the new tool.</pre>