scholarly journals VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joachim Goedhart ◽  
Martijn S. Luijsterburg
Keyword(s):  
Effect Size ◽  
Statistical Significance ◽  
Data Repository ◽  
Online Data ◽  
Comparative Genome ◽  
Volcano Plot ◽  
Volcano Plots ◽  
Data Points ◽  
Web App ◽  
The Web

AbstractComparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/Shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots (https://huygens.science.uva.nl/VolcaNoseR). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.

scholarly journals VolcaNoseR – a web app for creating, exploring, labeling and sharing volcano plots

2020 ◽  
Author(s):  
Joachim Goedhart ◽  
Martijn S. Luijsterburg
Keyword(s):  
Effect Size ◽  
Statistical Significance ◽  
Data Repository ◽  
Online Data ◽  
Comparative Genome ◽  
Volcano Plot ◽  
Volcano Plots ◽  
Data Points ◽  
Web App ◽  
The Web

AbstractComparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots (https://huygens.science.uva.nl/VolcaNoseR). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.

scholarly journals Potential Therapeutic Effects of Curcumin on Glycemic and Lipid Profile in Uncomplicated Type 2 Diabetes—A Meta-Analysis of Randomized Controlled Trial

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 404
Author(s):  
Emma Altobelli ◽  
Paolo Matteo Angeletti ◽  
Ciro Marziliano ◽  
Marianna Mastrodomenico ◽  
Anna Rita Giuliani ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Lipid Profile ◽  
Effect Size ◽  
Meta Analysis ◽  
Statistical Significance ◽  
Glycosylated Hemoglobin ◽  
Cochrane Library ◽  
Therapeutic Effects ◽  
Model Assessment

Diabetes mellitus is an important issue for public health, and it is growing in the world. In recent years, there has been a growing research interest on efficacy evidence of the curcumin use in the regulation of glycemia and lipidaemia. The molecular structure of curcumins allows to intercept reactive oxygen species (ROI) that are particularly harmful in chronic inflammation and tumorigenesis models. The aim of our study performed a systematic review and meta-analysis to evaluate the effect of curcumin on glycemic and lipid profile in subjects with uncomplicated type 2 diabetes. The papers included in the meta-analysis were sought in the MEDLINE, EMBASE, Scopus, Clinicaltrials.gov, Web of Science, and Cochrane Library databases as of October 2020. The sizes were pooled across studies in order to obtain an overall effect size. A random effects model was used to account for different sources of variation among studies. Cohen’s d, with 95% confidence interval (CI) was used as a measure of the effect size. Heterogeneity was assessed while using Q statistics. The ANOVA-Q test was used to value the differences among groups. Publication bias was analyzed and represented by a funnel plot. Curcumin treatment does not show a statistically significant reduction between treated and untreated patients. On the other hand, glycosylated hemoglobin, homeostasis model assessment (HOMA), and low-density lipoprotein (LDL) showed a statistically significant reduction in subjects that were treated with curcumin, respectively (p = 0.008, p < 0.001, p = 0.021). When considering HBA1c, the meta-regressions only showed statistical significance for gender (p = 0.034). Our meta-analysis seems to confirm the benefits on glucose metabolism, with results that appear to be more solid than those of lipid metabolism. However, further studies are needed in order to test the efficacy and safety of curcumin in uncomplicated type 2 diabetes.

Significance tests: Necessary but not sufficient

1998 ◽  
Vol 21 (2) ◽  
pp. 221-222
Author(s):  
Louis G. Tassinary
Keyword(s):  
Effect Size ◽  
Scientific Community ◽  
Statistical Significance ◽  
Significance Tests ◽  
Experimental Control

Chow (1996) offers a reconceptualization of statistical significance that is reasoned and comprehensive. Despite a somewhat rough presentation, his arguments are compelling and deserve to be taken seriously by the scientific community. It is argued that his characterization of literal replication, types of research, effect size, and experimental control are in need of revision.

scholarly journals Alpha Is Not the False Alarm Rate: An Activity to Dispel a Common Statistical Misconception

2018 ◽  
Vol 46 (1) ◽  
pp. 72-79 ◽  
Author(s):  
W. Burt Thompson
Keyword(s):  
False Alarm ◽  
False Alarm Rate ◽  
Research Finding ◽  
Statistical Power ◽  
Prior Probability ◽  
Statistical Significance ◽  
Statistical Test ◽  
Test Results ◽  
Web App ◽  
New Research

When a psychologist announces a new research finding, it is often based on a rejected null hypothesis. However, if that hypothesis is true, the claim is a false alarm. Many students mistakenly believe that the probability of committing a false alarm equals alpha, the criterion for statistical significance, which is typically set at 5%. Instructors should take specific steps to dispel this belief because it leads students to misinterpret statistical test results and it reinforces the more general misconception that results can be interpreted in isolation, without reference to theory or prior research. In the present study, students worked with a web app that shows how the false alarm rate is a function of the prior probability of an effect, statistical power, and alpha. Quiz scores suggest the activity helps correct the misconception, which can improve how students conduct and interpret research.

scholarly journals The Other Half of the Story: Effect Size Analysis in Quantitative Research

2013 ◽  
Vol 12 (3) ◽  
pp. 345-351 ◽  
Author(s):  
Jessica Middlemis Maher ◽  
Jonathan C. Markey ◽  
Diane Ebert-May
Keyword(s):  
Educational Research ◽  
Effect Size ◽  
Quantitative Research ◽  
Statistical Significance ◽  
The Other ◽  
Practical Significance ◽  
Significance Testing ◽  
Size Analysis ◽  
Significance Tests ◽  
Statistical Significance Testing

Statistical significance testing is the cornerstone of quantitative research, but studies that fail to report measures of effect size are potentially missing a robust part of the analysis. We provide a rationale for why effect size measures should be included in quantitative discipline-based education research. Examples from both biological and educational research demonstrate the utility of effect size for evaluating practical significance. We also provide details about some effect size indices that are paired with common statistical significance tests used in educational research and offer general suggestions for interpreting effect size measures. Finally, we discuss some inherent limitations of effect size measures and provide further recommendations about reporting confidence intervals.

scholarly journals Florence RockinArt

2020 ◽  
Author(s):  
Elena Pecchioni ◽  
Alba Patrizia Santo
Keyword(s):  
Close Link ◽  
Artificial Materials ◽  
Stone Materials ◽  
Geographical Position ◽  
Web App ◽  
Materials Used ◽  
Surrounding Areas ◽  
Stone Walls ◽  
The City ◽  
The Web

The city of Firenze represents, for the variety of its artistic and architectural heritage, a kind of open-air museum. Works of art and monuments are mainly made of the rocks outcropping in Firenze and in the surrounding areas; indeed, a close link exists between monuments, geographical position of the city and its history. Florence, is characterised by the color of its stone-built cultural heritage, mainly by the warm ochraceous color of the Medieval Pietraforte sandstone and the cerulean grey of the Renaissance Pietra Serena sandstone together with other natural and artificial materials used to complete or cover the stone walls. The web-app Florence RockinArt was created to deepen the knowledge of the stone materials. It is addressed to all those who are interested in discovering the monuments of Florence by carefully observing the stone materials that make up them. The web-app contains short historical notes on the main monuments and detailed geological, mineralogical and petrographic characteristics of the natural and artificial materials of which they are constituted.

scholarly journals The use of effect size indices to determine practical significance

2006 ◽  
Vol 25 (3) ◽  
Author(s):  
H. S. Styn ◽  
S. M. Ellis
Keyword(s):  
Effect Size ◽  
Statistical Significance ◽  
Empirical Studies ◽  
Research Literature ◽  
Effect Sizes ◽  
Practical Significance ◽  
Significance Tests ◽  
Statistical Application ◽  
Significant Difference

The determination of significance of differences in means and of relationships between variables is of importance in many empirical studies. Usually only statistical significance is reported, which does not necessarily indicate an important (practically significant) difference or relationship. With studies based on probability samples, effect size indices should be reported in addition to statistical significance tests in order to comment on practical significance. Where complete populations or convenience samples are worked with, the determination of statistical significance is strictly speaking no longer relevant, while the effect size indices can be used as a basis to judge significance. In this article attention is paid to the use of effect size indices in order to establish practical significance. It is also shown how these indices are utilized in a few fields of statistical application and how it receives attention in statistical literature and computer packages. The use of effect sizes is illustrated by a few examples from the research literature.

scholarly journals Measuring Global Awareness of Nature

2021 ◽  
Author(s):  
Gabriel Henrique de Oliveira Caetano ◽  
Uri Roll ◽  
Diogo Veríssimo
Keyword(s):  
Global Awareness ◽  
Online Data ◽  
Biodiversity Crisis ◽  
The Public ◽  
Use Patterns ◽  
The Past ◽  
Conservation Actions ◽  
Data Points ◽  
Effective Use ◽  
Digital Channels

While there is general skepticism regarding the progress made towards the 20 CBD targets set in 2010, there has been no comprehensive analysis of the progress towards this first target at the global and the national levels. We harnessed vast and readily available online data to gain insight into trends of people’s interest towards biodiversity and potential conservation actions to sustain it. Specifically, we analyzed people’s Google use patterns in the past decade, across 193 countries globally, exploring about 550 terms relating to wildlife; biomes; biodiversity concepts; and conservation actions. This yielded about 2 million data points from 2013 to 2020. We found that when combined across terms and averaged across countries internet searches for biodiversity have increased worldwide in the last decade. However, this is predominantly driven by an increase in interest in a small number of charismatic animals. The interest in conservation actions has however not shown a similar overall increase in the past decade. Nevertheless, 29 countries, harboring 35% of the world’s population, did show increases for both awareness of biodiversity and the actions needed to safeguard it, thus showing progress towards this CBD target. Our results show that there was some success in achieving the first part of Aichi target 1 — “people are aware of the values of biodiversity”. However, the second part of target 1 — “people are aware of the steps they can take to conserve and use it sustainably” — has been largely missed. These results suggest that we need new ways to better communicate the importance of biodiversity and the ongoing biodiversity crisis to the public. These are likely to include more effective use of more future proof digital channels, such as mobile games and social media, which can have a wide reach while retaining the ability to target.

scholarly journals reductus: a stateless Python data reduction service with a browser front end

2018 ◽  
Vol 51 (5) ◽  
pp. 1500-1506 ◽  
Author(s):  
Brian Maranville ◽  
William Ratcliff II ◽  
Paul Kienzle
Keyword(s):  
Data Reduction ◽  
Open Data ◽  
Reduction Process ◽  
Flow Diagram ◽  
Data Repository ◽  
Accurate Estimation ◽  
Experimental Science ◽  
Online Data ◽  
Source Data ◽  
Estimation Of Uncertainties

The online data reduction service reductus transforms measurements in experimental science from laboratory coordinates into physically meaningful quantities with accurate estimation of uncertainties from instrumental settings and properties. This reduction process is based on a few well known transformations, but flexibility in the application of the transforms and algorithms supports flexibility in experiment design, enabling a broader range of measurements than a rigid reduction scheme for data. The user interface allows easy construction of arbitrary pipelines from well known data transforms using a visual data flow diagram. Source data are drawn from a networked, open data repository. The Python back end uses intelligent caching to store intermediate results of calculations for a highly responsive user experience. The reference implementation allows immediate reduction of measurements as they are recorded for the three neutron reflectometry instruments at the NIST Center for Neutron Research, without the need for visiting scientists to install additional software on their own computers.

Linked Data, Towards Realizing the Web of Data

2018 ◽  
pp. 292-312
Author(s):  
Leila Zemmouchi-Ghomari
Keyword(s):  
Semantic Web ◽  
Linked Data ◽  
Web Applications ◽  
Online Data ◽  
Web Of Data ◽  
Promising Solution ◽  
Basic Ideas ◽  
Online Sources ◽  
Significant Effort ◽  
The Web

Data play a central role in the effectiveness and efficiency of web applications, such as the Semantic Web. However, data are distributed across a very large number of online sources, due to which a significant effort is needed to integrate this data for its proper utilization. A promising solution to this issue is the linked data initiative, which is based on four principles related to publishing web data and facilitating interlinked and structured online data rather than the existing web of documents. The basic ideas, techniques, and applications of the linked data initiative are surveyed in this paper. The authors discuss some Linked Data open issues and potential tracks to address these pending questions.

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