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29 results for “nicoguaro”
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@kevinmoerman, I have read Mehrabadi and Cowin's paper before but this is my first time reading Helbig's.
I think that I get the idea that only 6 parameters are "material parameters". But then... what should we call the other parameters that "describe" de tensor?
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New blog post out!
Power analysis – A flexible simulation approach using R
https://www.nicolaromano.net/data-thoughts/power-analysis-simulation/I go through why power matters, how to use Monte Carlo simulations to estimate it, and how this approach can be useful not only to define sample size, but also to refine experimental design.
#rstats #statistics #biostats #datascience #experimentaldesign #poweranalysis -
New Python Shiny app for my image analysis course deployed!
This will accompany the lecture on edge detection methods.
https://apps.nicolaromano.net/EdgeDetection/
Source code is here, feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Apps/EdgeDetection
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New Python Shiny app for my image analysis course deployed!
This will accompany the lecture on edge detection methods.
https://apps.nicolaromano.net/EdgeDetection/
Source code is here, feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Apps/EdgeDetection
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New Python Shiny app for my image analysis course deployed!
This will accompany the lecture on edge detection methods.
https://apps.nicolaromano.net/EdgeDetection/
Source code is here, feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Apps/EdgeDetection
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New Python Shiny app for my image analysis course deployed!
This will accompany the lecture on edge detection methods.
https://apps.nicolaromano.net/EdgeDetection/
Source code is here, feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Apps/EdgeDetection
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Who’s The Masked Singer star Gargoyle? All clues and theories so far
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Who’s The Masked Singer star Gargoyle? All clues and theories so far
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Who’s The Masked Singer star Gargoyle? All clues and theories so far
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Who’s The Masked Singer star Gargoyle? All clues and theories so far
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Who’s The Masked Singer star Gargoyle? All clues and theories so far
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This is very meta... essentially someone who is in the business of writing fake papers has written a fake paper criticizing Pubpeer and post publication peer review as being vulnerable to “misuse” and “hyper-skepticism.
#RetractionWatch #AcademicIntegrity #ResearchMisconduct #ScholarlyPublishing #PostPublicationReview #PubPeer #FakeScience #MetaScience #PeerReview #ScienceFraud
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When designing a scientific experiment, a key factor is the sample size to be used for the results of the experiment to be meaningful.
How many cells do I need to measure? How many people do I interview? How many patients do I try my new drug on?
This is of great importance especially for quantitative studies, where we use statistics to determine whether a treatment or condition has an effect. Indeed, when we test a drug on a (small) number of patients, we do so in the hope our results can generalise to any patient because it would be impossible to test it on everyone.
The solution is to perform a "power analysis", a calculation that tells us whether given our experimental design, the statistical test we are using is able to see an effect of a certain magnitude, if that effect is really there. In other words, this is something that tells us whether the experiment we're planning to do could give us meaningful results.
But, as I said, in order to do a power analysis we need to decide what size of effect we would like to see. So... do scientists actually do that?
We explored this question in the context of the chronic variable stress literature.
We found that only a few studies give a clear justification for the sample size used, and in those that do, only a very small fraction used a biologically meaningful effect size as part of the sample size calculation. We discuss challenges around identifying a biologically meaningful effect size and ways to overcome them.
Read more here!
https://physoc.onlinelibrary.wiley.com/doi/10.1113/EP092884#experiments #ExperimentalDesign #effectsize #statistics #stress #research #article #power #biology
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Our #systematic #review on chronic variable #stress (CVS) procedures in rodents is now out in Journal of Neuroendocrinology!
https://onlinelibrary.wiley.com/doi/10.1111/jne.70051
A sister study to this, focussing on the reporting and justification of sample size in these studies (currently in review somewhere else) can be found on BioRXiv https://www.biorxiv.org/content/10.1101/2024.09.26.615121v1
We systematically explored the literature where behavioural tests were performed following CVS. We found extreme variability in terms of the protocols used with any hardly any study using the same CVS protocol. We then asked whether the specific protocol influenced the outcomes of the study. For instance, we would expect a longer stress to cause a larger effect than a shorter one. We found only very small correlations between the strength of the stress protocol and the effect size measured in the study. In a case (forced swim test) correlation was even negative. Overall, our analysis reveals complex relation between stress protocols and behavioural outcomes and raises important ethical questions on the design of CVS studies.
Any comments very welcome, we're working on a couple of follow up manuscripts if anyone's interested!
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And we continue today with our #workshop on #teaching #statistics to #undergraduate students in the #LifeSciences
Here's a photo of the #plenary by Dr Peter Martin "Stories for the world beyond p < 0.05"
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We're looking for someone to take over a short term (1 year) #lectureship in #microbiology, #parasitology and #epidemiology, in programmes run jointly in China by the University of Edinburgh, Zhejiang University and the University of Edinburgh-Zhejiang University Joint Institute (ZJE).
The post is based in Edinburgh but the applicant will travel up to 12 weeks to ZJE to deliver teaching there.
For more information see
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/requisitions/preview/11695/?keyword=11695&mode=location -
The second part of our exploration of chronic variable #stress studies is out!
https://www.biorxiv.org/content/10.1101/2024.09.26.615121v1
Here we look at studies employing chronic variable stress in rodents and explore how sample size was chosen. Of the 385 studies that we analysed, only one reported calculating sample size based on a biologically meaningful effect size and only 25% mention sample size at all.
A companion article where we analyse the relationship between protocols and reported effect size can be found here
https://www.biorxiv.org/content/10.1101/2024.07.04.602063v1#ResearchEthics #ThreeRs #ExperimentalDesign #StatisticalPower
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Anyone knows where can I find a list of valid types for "Dataset Type" when searching for NCBI GEO Datasets?
The help pages only mention "expression profiling by high throughput sequencing" as an example.
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Has anyone got references (or ideas/recommendations) for how to perform #data #augmentation on #scrnaseq data (to use in training #ann)?
This is the only paper I could find, but maybe I am not searching for the right thing...
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We have two tenure track #lecturer positions available at the #University of #Edinburgh, to support and develop #teaching and #research linked to the undergraduate Dual Award Honours programmes in Integrative Biomedical Sciences and Biomedical Informatics jointly developed in partnership with Zhejiang University, China.
For more info and to apply see the ads here
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/job/9999/
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/job/10000
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Do you do group #assessments for your #highered courses? How do you deal with "free-riders" who don't engage with the rest of the group?
At the moment I'm thinking of
- having students include a statement of who has done what in their final product
- having a couple of sessions (beginning of term and mid-term) where each group presents a plan first and a short progress report later, which clearly states student contributions
- stress to the students that part of the idea for a group assessment is for them to organise and work in a group. I'm a bit torn on this one as it seems unfair to put the onus for those who don't engage on those who do... but hey that's what happens in real life...Any other ideas?
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I just discovered this awesome #latex package to #annotate #equations.
https://github.com/st--/annotate-equations/tree/main
Someone is getting some snazzy lectures ready for next week...
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I just discovered this awesome #latex package to #annotate #equations.
https://github.com/st--/annotate-equations/tree/main
Someone is getting some snazzy lectures ready for next week...
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I just discovered this awesome #latex package to #annotate #equations.
https://github.com/st--/annotate-equations/tree/main
Someone is getting some snazzy lectures ready for next week...
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I just discovered this awesome #latex package to #annotate #equations.
https://github.com/st--/annotate-equations/tree/main
Someone is getting some snazzy lectures ready for next week...
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Can anyone help with understanding how to best do #modelselection in the context of #neuralnetworks ? I'm trying to understand how to reduce #bias due to the selection of a particular test set.
More details here
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We have a research assistant position to work on a study surveying how experimental study design and analysis are taught at the undergraduate level in the UK (position based at the University of Edinburgh, Scotland). The post is for four months full-time or equivalent part-time (e.g. eight. months 50%).
If you are interested or know someone who is, you can find more details here:
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/job/7014
#job #research #experimentalDesign #dataAnalysis #survey #statistics
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Can someone suggest software/pipelines for analysis of alternative #splicing from long-read #RNAseq (from #Nanopore #MinION)? Basically, I'd like to quantify abundance of different splicing variants in different samples. #bioinformatics
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Happy to share our new article, which has been in the making for a veeery long time!
https://insight.jci.org/articles/view/165763
In this study we looked at the control of the entrance of #ghrelin in the #brain
Ghrelin is a #hormone produced by the stomach, which induces hunger. In order to do so, ghrelin needs to enter the brain, to reach neurons in the arcuate nucleus of the #hypothalamus, a region of the brain important for many #endocrine responses.
Here, we explore the role of cells lining the capillaries (such as #perycytes ) at the median eminence, which is on of the "doors" of the brain, where molecules from the periphery are allowed to get in.
We used a mouse model where pericytes can be electrically excited via #optogenetics to study the dynamics of ghrelin entrance in the brain. When we excited pericytes, there was a slow-down of blood flow at the median eminence, resulting in slower entrance of ghrelin, lower and delayed food intake in response to ghrelin injection.
This shows pericytes as a potential therapeutical target for metabolic diseases.