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opencc-by-4.0Aug 2019View details →

Map of articles about "Teaching Open Science"

This description is part of the blog post "Systematic Literature Review of teaching Open Science" https://sozmethode.hypotheses.org/839 According to my opinion, we do not pay enough attention to teaching Open Science in higher education. Therefore, I designed a seminar to teach students the practices of Open Science by doing qualitative research.About this seminar, I wrote the article ”<a href="https://osf.io/preprints/socarxiv/b3zf7">Teaching Open Science and qualitative methods</a>“. For the article ”Teaching Open Science and qualitative methods“, I started to review the literature on ”Teaching Open Science“. The result of my literature review is that certain aspects of Open Science are used for teaching. However, Open Science with all its aspects (Open Access, Open Data, Open Methodology, Open Science Evaluation and Open Science Tools) is not an issue in publications about teaching. Based on this insight, I have started a systematic literature review. I realized quickly that I need help to analyse and interpret the articles and to evaluate my preliminary findings. Especially different disciplinary cultures of teaching different aspects of Open Science are challenging, as I myself, as a social scientist, do not have enough insight to be able to interpret the results correctly. Therefore, I would like to invite you to participate in this research project! I am now looking for people who would like to join a collaborative process to further explore and write the systematic literature review on “Teaching Open Science“. Because I want to turn this project into a Massive Open Online Paper (MOOP). According to the <a href="https://osf.io/preprints/socarxiv/b3zf7">10 rules of Tennant et al (2019) on MOOPs</a>, it is crucial to find a core group that is enthusiastic about the topic. Therefore, I am looking for people who are interested in creating the structure of the paper and writing the paper together with me. I am also looking for people who want to search for and review literature or evaluate the literature I have already found. Together with the interested persons I would then define, the rules for the project (cf. Tennant et al. 2019). So if you are interested to contribute to the further search for articles and / or to enhance the interpretation and writing of results, please get in touch. For everyone interested to contribute, the list of articles collected so far is freely accessible at Zotero: <a href="https://www.zotero.org/groups/2359061/teaching_open_science">https://www.zotero.org/groups/2359061/teaching_open_science</a>. The figure shown below provides a first overview of my ongoing work. I created the figure with the free software <a href="https://www.yworks.com/products/yed">yEd</a> and uploaded the file to zenodo, so everyone can download and work with it: To make transparent what I have done so far, I will first introduce what a systematic literature review is. Secondly, I describe the decisions I made to start with the systematic literature review. Third, I present the preliminary results. Systematic literature review – an Introduction Systematic literature reviews “are a method of mapping out areas of uncertainty, and identifying where little or no relevant research has been done.” (Petticrew/Roberts 2008: 2). Fink defines the systematic literature review as a “systemic, explicit, and reproducible method for identifying, evaluating, and synthesizing the existing body of completed and recorded work produced by researchers, scholars, and practitioners.” (Fink 2019: 6). The aim of a systematic literature reviews is to surpass the subjectivity of a researchers’ search for literature. However, there can never be an objective selection of articles. This is because the researcher has for example already made a preselection by deciding about search strings, for example “Teaching Open Science”. In this respect, transparency is the core criteria for a high-quality review.  In order to achieve high quality and transparency, Fink (2019: 6-7) proposes the following seven steps: <ol> <li>Selecting a research question.</li> <li>Selecting the bibliographic database.</li> <li>Choosing the search terms.</li> <li>Applying practical screening criteria.</li> <li>Applying methodological screening criteria.</li> <li>Doing the review.</li> <li>Synthesizing the results.</li> </ol> I have adapted these steps for the “Teaching Open Science” systematic literature review. In the following, I will present the decisions I have made. Systematic literature review – decisions I made <ol> <li>Research question: I am interested in the following research questions: How is Open Science taught in higher education? Is Open Science taught in its full range with all aspects like Open Access, Open Data, Open Methodology, Open Science Evaluation and Open Science Tools? Which aspects are taught? Are there disciplinary differences as to which aspects are taught and, if so, why are there such differences?</li> <li>Databases: I started my search at the <a href="https://doaj.org/">Directory of Open Science (DOAJ)</a>. “DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals.” (https://doaj.org/) Secondly, I used the <a href="http://base-search.net">Bielefeld Academic Search Engine (base)</a>. Base is operated by Bielefeld University Library and “one of the world’s most voluminous search engines especially for academic web resources” (base-search.net). Both platforms are non-commercial and focus on Open Access publications and thus differ from the commercial publication databases, such as Web of Science and Scopus. For this project, I deliberately decided against commercial providers and the restriction of search in indexed journals. Thus, because my explicit aim was to find articles that are open in the context of Open Science.</li> <li>Search terms: To identify articles about teaching Open Science I used the following search strings: “teaching open science” OR teaching “open science” OR teach &bdquo;open science“. The topic search looked for the search strings in title, abstract and keywords of articles. Since these are very narrow search terms, I decided to broaden the method. I searched in the reference lists of all articles that appear from this search for further relevant literature. Using Google Scholar I checked which other authors cited the articles in the sample. If the so checked articles met my methodological criteria, I included them in the sample and looked through the reference lists and citations at Google Scholar. This process has not yet been completed.</li> <li>Practical screening criteria: I have included English and German articles in the sample, as I speak these languages (articles in other languages are very welcome, if there are people who can interpret them!). In the sample only journal articles, articles in edited volumes, working papers and conference papers from proceedings were included. I checked whether the journals were predatory journals – such articles were not included. I did not include blogposts, books or articles from newspapers. I only included articles that fulltexts are accessible via my institution (University of Kassel). As a result, recently published articles at Elsevier could not be included because of the special situation in Germany regarding the Project DEAL (https://www.projekt-deal.de/about-deal/). For articles that are not freely accessible, I have checked whether there is an accessible version in a repository or whether preprint is available. If this was not the case, the article was not included. I started the analysis in May 2019.</li> <li>Methodological criteria: The method described above to check the reference lists has the problem of subjectivity. Therefore, I hope that other people will be interested in this project and evaluate my decisions. I have used the following criteria as the basis for my decisions: First, the articles must focus on teaching. For example, this means that articles must describe how a course was designed and carried out. Second, at least one aspect of Open Science has to be addressed. The aspects can be very diverse (FOSS, repositories, wiki, data management, etc.) but have to comply with the principles of openness. This means, for example, I included an article when it deals with the use of FOSS in class and addresses the aspects of openness of FOSS. I did not include articles when the authors describe the use of a particular free and open source software for teaching but did not address the principles of openness or re-use.</li> <li>Doing the review: Due to the methodical approach of going through the reference lists, it is possible to create a map of how the articles relate to each other. This results in thematic clusters and connections between clusters. The starting point for the map were four articles (Cook et al. 2018; Marsden, Thompson, and Plonsky 2017; Petras et al. 2015; Toelch and Ostwald 2018) that I found using the databases and criteria described above. I used yEd to generate the network. &bdquo;yEd is a powerful desktop application that can be used to quickly and effectively generate high-quality diagrams.” (<a href="https://www.yworks.com/products/yed">https://www.yworks.com/products/yed</a>) In the network, arrows show, which articles are cited in an article and which articles are cited by others as well. In addition, I made an initial rough classification of the content using colours. This classification is based on the contents mentioned in the articles’ title and abstract. This rough content classification requires a more exact, i.e., content-based subdivision and evaluation by others, who are experts in the respective fields/disciplines.</li> </ol>

opencc-by-4.0Aug 2019View details →

Data set of the article: Ranking by relevance and citation counts, a comparative study: Google Scholar, Microsoft Academic, WoS and Scopus

Data of investigation published in the article "Ranking by relevance and citation counts, a comparative study: Google Scholar, Microsoft Academic, WoS and Scopus". Abstract of the article: Search engine optimization (SEO) constitutes the set of methods designed to increase the visibility of, and the number of visits to, a web page by means of its ranking on the search engine results pages. Recently, SEO has also been applied to academic databases and search engines, in a trend that is in constant growth. This new approach, known as academic SEO (ASEO), has generated a field of study with considerable future growth potential due to the impact of open science. The study reported here forms part of this new field of analysis. The ranking of results is a key aspect in any information system since it determines the way in which these results are presented to the user. The aim of this study is to analyse and compare the relevance ranking algorithms employed by various academic platforms to identify the importance of citations received in their algorithms. Specifically, we analyse two search engines and two bibliographic databases: Google Scholar and Microsoft Academic, on the one hand, and Web of Science and Scopus, on the other. A reverse engineering methodology is employed based on the statistical analysis of Spearman’s correlation coefficients. The results indicate that the ranking algorithms used by Google Scholar and Microsoft are the two that are most heavily influenced by citations received. Indeed, citation counts are clearly the main SEO factor in these academic search engines. An unexpected finding is that, at certain points in time, WoS used citations received as a key ranking factor, despite the fact that WoS support documents claim this factor does not intervene.

Dataset related to article "Pentraxin 3 regulates synaptic function by inducing AMPA receptor clustering via ECM remodeling and β1-integrin"

This record contains raw data related to article "Pentraxin 3 regulates synaptic function by inducing AMPA receptor clustering via ECM remodeling and β1-integrin" Abstract Control of synapse number and function in the developing central nervous system is critical to the formation of neural circuits. Astrocytes play a key role in this process by releasing factors that promote the formation of excitatory synapses. Astrocyte-secreted thrombospondins (TSPs) induce the formation of structural synapses, which however remain post-synaptically silent, suggesting that completion of early synaptogenesis may require a two-step mechanism. Here, we show that the humoral innate immune molecule Pentraxin 3 (PTX3) is expressed in the developing rodent brain. PTX3 plays a key role in promoting functionally-active CNS synapses, by increasing the surface levels and synaptic clustering of AMPA glutamate receptors. This process involves tumor necrosis factor-induced protein 6 (TSG6), remodeling of the perineuronal network, and a β1-integrin/ERK pathway. Furthermore, PTX3 activity is regulated by TSP1, which directly interacts with the N-terminal region of PTX3. These data unveil a fundamental role of PTX3 in promoting the first wave of synaptogenesis, and show that interplay of TSP1 and PTX3 sets the proper balance between synaptic growth and synapse function in the developing brain.

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions" Multiple sclerosis (MS) is the most common neurological disorder in young adults. Despite extensive studies, only a fraction of MS heritability has been explained, with association studies focusing primarily on protein-coding genes, essentially for the difficulty of interpreting non-coding features. However, non-coding RNAs (ncRNAs) and functional elements, such as super-enhancers (SE), are crucial regulators of many pathways and cellular mechanisms, and they have been implicated in a growing number of diseases. In this work, we searched for possible enrichments in non-coding elements at MS genome-wide associated loci, with the aim to highlight their possible involvement in the susceptibility to the disease. We first reconstructed the linkage disequilibrium (LD) structure of the Italian population using data of 727,478 single-nucleotide polymorphisms (SNPs) from 1,668 healthy individuals. The genomic coordinates of the obtained LD blocks were intersected with those of the top hits identified in previously published MS genome-wide association studies (GWAS). By a bootstrapping approach, we hence demonstrated a striking enrichment of non-coding elements, especially of circular RNAs (circRNAs) mapping in the 73 LD blocks harboring MS-associated SNPs. In particular, we found a total of 482 circRNAs (annotated in publicly available databases) vs. a mean of 194 ± 65 in the random sets of LD blocks, using 1,000 iterations. As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP. Finally, by evaluating RNA-seq data of two cell lines, SH-SY5Y and Jurkat cells, representing tissues relevant for MS, we identified 18 (two novel) circRNAs derived from MS-associated genes. In conclusion, this work showed for the first time that MS-GWAS top hits map in LD blocks enriched in circRNAs, suggesting circRNAs as possible novel contributors to the disease pathogenesis. GEO database URL: <a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a> Numero di accesso del dataset: GSE110525

Link to dataset related to article "Sustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage"

This record contains link to raw data related to article "Sustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage" Chronic inflammation promotes oncogenic transformation and tumor progression. Many inflammatory agents also generate a toxic microenvironment, implying that adaptive mechanisms must be deployed for cells to survive and undergo transformation in such unfavorable contexts. A paradigmatic case is represented by cancers occurring in pediatric patients with genetic defects of hepatocyte phosphatidylcholine transporters and in the corresponding mouse model (Mdr2-/- mice), in which impaired bile salt emulsification leads to chronic hepatocyte damage and inflammation, eventually resulting in oncogenic transformation. By combining genomics and metabolomics, we found that the transition from inflammation to cancer in Mdr2-/- mice was linked to the sustained transcriptional activation of metabolic detoxification systems and transporters by the Constitutive Androstane Receptor (CAR), a hepatocyte-specific nuclear receptor. Activation of CAR-dependent gene expression programs coincided with reduced content of toxic bile acids in cancer nodules relative to inflamed livers. Treatment of Mdr2-/- mice with a CAR inhibitor blocked cancer progression and caused a partial regression of existing tumors. These results indicate that the acquisition of resistance to endo- or xeno-biotic toxicity is critical for cancers that develop in toxic microenvironments. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80777 under the accession GSE80777, which comprises ChIP-seq data (GSE80775) and expression data (GSE80776).

Dataset related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"

This record contains raw data related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations" Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV-neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.

data set related to article Brainstem enlargement in preschool children with autism Results from an intermethod agreement study of segmentation algorithms

This record contains raw data related to article Brainstem enlargement in preschool children with autism Results from an intermethod agreement study of segmentation algorithms

Dataset for the article: "Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea"

Dataset used for the article: "Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea". Dataset consists on a VCF file from 471 individuals of lesser sandeel, Ammodytes marinus (L.). This VCF is the end product of the bioinformatic analysis described in the paper Jimenez-Mena et al. (2019). Data was obtained from double-digest Restriction-site Associated DNA (ddRAD) sequencing. More information can be obtained in Methods of the article. The information of each of the individuals in the VCF is also included as a separate file, as well as the supplementary tables of the article.

opencc-by-4.0Aug 2019View details →

Supplementary dataset for journal article "AC Characteristics of Low Ohmic Foil Shunts Influenced by Eddy Currents in the Mounting Body"

This is the complete simulation environment for all simulations and plots done for the paper 'AC Characteristics of Low Ohmic Foil Shunts Influenced by Eddy Currents in the Mounting Body'. The entire simulation is based on fully free software: <ul> <li>Linux</li> <li>GNU Octave</li> <li>Fast Field Solver: Fast Henry</li> </ul> All scripts and models have been copied together in one zip-archive.

opencc-by-4.0Nov 2019View details →

Supplementary dataset for SRL Data Mine article

Supplementary dataset for SRL Data Mine article by Milliner & Donnellan (2019). Titled: Using Daily Observations from Planet Labs Satellite Imagery to Separate the Surface Deformation Between the July 4th Mw 6.4 Foreshock and July 5th  Mw 7.1 Mainshock During the 2019 Ridgecrest Earthquake Sequence.

opencc-by-4.0Dec 2018View details →

Dataset for the article "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments"

This dataset contains additional material related to the article: "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments". Final version of the article is available at <a href="https://doi.org/10.1021/acs.jctc.9b00616">https://doi.org/10.1021/acs.jctc.9b00616</a> (paywall). A preprint is freely available at <a href="https://doi.org/10.26434/chemrxiv.8126912">https://doi.org/10.26434/chemrxiv.8126912</a>. See readme.md for further description.

opencc-by-4.0Nov 2019View details →

Data from the Mancoosi solver competition and articles

This directory contains the data produced in the framework of the Mancoosi european research project, and in particular: <ul> <li>the dataset used for the MISC solver competition</li> <li>the dataset used in the articles written with support from the Mancoosi project</li> </ul>

opencc-zeroMay 2024View details →

Supplemental material to the journal article "Tracing Homopolymers in Oikopleura dioica's mitogenome"

Supplemental material to the journal article “Tracing Homopolymers in Oikopleura dioica’s mitogenome”, consisting of: <ul> <li>The I25 mitochondrial genome (GenBank ID PP146516) and its annotation (not in GenBank)</li> <li>Transcript model sequences used to annotate the genome</li> <li>Nucleotide sequences of cytochrome oxidase I used to compute the tree in Figure 3</li> </ul> Updated on August 6th 2024: <ul> <li>Add raw reads used to assemble the mitogenome.</li> <li>ATP6 gene coordinate corrected (7110 -> 7104) to reach TAA stop codon.</li> </ul>

opencc-by-4.0Jul 2024View details →

Data for figures in the article "Thermal-integration in Photoelectrochemistry for Fuel and Heat Co-Generation"

This repository contains the data used to generate figures in the article "Thermal-integration in Photoelectrochemistry for Fuel and Heat Co-Generation" in 2024 in Sustainable Energy and Fuels. Authors of this data and the article are Evan F Johnson and Sophia Haussener.

Extended data of the article "Lockbox enrichment facilitates manipulative and cognitive activities for mice": Supplementary Figure

Figure and results of the distance traveled in the Free Exploratory Paradigm, Open Field Test, and Elevated Plus Maze Test during habituation are shown.

Dataset for the article Maintaining favourable carbon balance in boreal clay soil is challenging even under no-till and crop diversification

Open the record for dataset details and reuse information.

Dataset related to article "Distribution of pamiparib, a novel inhibitor of poly(ADP-ribose)-polymerase (PARP), in tumor tissue analyzed by multimodal imaging"

This record contains data related to article "Distribution of pamiparib, a novel inhibitor of poly(ADP-ribose)-polymerase (PARP), in tumor tissue analyzed by multimodal imaging" Pamiparib is a potent and selective oral PARP1/2 inhibitor (PARPi). Pamiparib has good bioavailability and showed greater cytotoxic potency and similar DNA-trapping capacity compared to olaparib. It is not affected by ATP-binding cassette transporters. Consequently, pamiparib may be useful in overcoming drug resistance caused by poor drug distribution in tumor due to overexpression of these efflux pump [1]. Mass spectrometry imaging (MSI) is a powerful technology that allows to study drugs distribution in tissues while maintaining spatial information [2]. Here, MSI was applied to visualize pamiparib in tumor in combination with spatial metabolomics and lipidomics, LC-MS/MS analysis, immunofluorescence analysis, and histological staining to gain a comprehensive understanding of how pamiparib is distributed. The results show that pamiparib was evenly distributed in ovarian tumor models, including those that overexpress P-glycoprotein (P-gp). In contrast, olaparib was not detected by MSI in any of the analyzed tumors, despite the comparable sensitivity of the analytical method. This difference in tumor distribution was confirmed by LC-MS/MS analysis.

Dataset related to article "On the extension of the use of a standard operating procedure for nicotine, glycerol and propylene glycol analysis in e-liquids using mass spectrometry"

Open the record for dataset details and reuse information.

Dataset of article: Residual capacity of RC beams subjected to impact loading: influence of reinforcement ductility. Part 4: Series I20

Part 4: Series I20 Results in this dataset are presented in Johansson et. al. (2024). Any results used from this open access data shall be cited to: Johansson M., Leppänen J., Andersson M. and Pettersson E. (2024). Residual Capacity of RC Beams Subjected to Impact Loading: Influence of reinforcement ductility. International Journal of Protective Structures. <a href="https://doi.org/10.1177/20414196241277221">https://doi.org/10.1177/20414196241277221</a> The presented data is based on Andersson and Pettersson (2019): Andersson M. and Pettersson E. (2019). Reinforced concrete beams subjected to drop-weight impact: Experimental study of the influence of reinforcement properties on the structural response. Department of Architecture and Civil Engineering. Gothenburg, Sweden: Chalmers University of Technology. Master’s Thesis ACEX30-19-27. --- This dataset consists of the following records: Part 1: General information Andersson and Pettersson 2019 - Reinforced Concrete Beams Subjected to Drop-Weight Impact Part 2: Series S Static tests – COM Correlate files Part 3: Series I10 Static tests – COM Correlate files Impact tests – High speed images Impact tests – COM Correlate files Part 4: Series I20 Static tests – COM Correlate files Impact tests – High speed images Impact tests – COM Correlate files Part 5: Result files

Dataset of article: Residual capacity of RC beams subjected to impact loading: influence of reinforcement ductility. Part 3: Series I10

Part 3: Series I10 Results in this dataset are presented in Johansson et. al. (2024). Any results used from this open access data shall be cited to: Johansson M., Leppänen J., Andersson M. and Pettersson E. (2024). Residual Capacity of RC Beams Subjected to Impact Loading: Influence of reinforcement ductility. International Journal of Protective Structures. <a href="https://doi.org/10.1177/20414196241277221">https://doi.org/10.1177/20414196241277221</a> The presented data is based on Andersson and Pettersson (2019): Andersson M. and Pettersson E. (2019). Reinforced concrete beams subjected to drop-weight impact: Experimental study of the influence of reinforcement properties on the structural response. Department of Architecture and Civil Engineering. Gothenburg, Sweden: Chalmers University of Technology. Master’s Thesis ACEX30-19-27. --- This dataset consists of the following records: Part 1: General information Andersson and Pettersson 2019 - Reinforced Concrete Beams Subjected to Drop-Weight Impact Part 2: Series S Static tests – COM Correlate files Part 3: Series I10 Static tests – COM Correlate files Impact tests – High speed images Impact tests – COM Correlate files Part 4: Series I20 Static tests – COM Correlate files Impact tests – High speed images Impact tests – COM Correlate files Part 5: Result files