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@devezer

Underlying problem is that we literally have college courses in noise mining (we call them Stats 101) so millions of scientists are out there noise mining, and so we have a lot of papers that really do have low evidentiary value. It's not because they're not preregistered, it's because the people doing the analysis wouldn't know what a good analysis looked like, and in fact would likely fight a good analysis tooth and nail.

I wrote a script that takes as input a gene of interest:

```console
./script/plot_heatmap.sh -p 10 TP53
```

and generates a gene expression heatmap with genes that have correlated expression patterns.

Behind the scenes is a Bash script (calling `gget`) and a #Rstats script available at github.com/davetang/archs4_hea

@marilenharo @nature @tatsuya_amano and then there's always the dumb reviewer that complains a priori about the quality of English, just because they see a non-English sounding name...

Scientists whose first language is not English spend much longer to read and write papers in English and prepare for international conferences. @tatsuya_amano and colleagues worked to measure this invisible struggle. I wrote about their work for @nature nature.com/articles/d41586-023

@devezer I always tell students that reading papers (e.g. for a journal club) is about critiquing, not criticizing.

That is not to say one should ignore the negatives, but you should be looking at those with a positive attitude. How could this have been improved? Was it possible to do it? Does it really affect the conclusions of the article?

One of my professors during PhD used to say “you can drive a truck through the holes in any given paper. so you look for what you *can* learn instead.” and being the smartass grad students we used to think driving that truck was fun. After so many years, I now appreciate her wisdom more than ever. All scholarly work has limitations but it’s refreshing when people critically evaluate what’s the actual value of the research. It's about humility, honesty, rigorous intellectual work.

Very happy to share our newly published "Sex differences in pituitary corticotroph excitability".

It is well known that sex differences exist in stress-related disorders, with women having twice the lifetime rate of depression compared to men and most anxiety disorders.

Corticotroph cells in the pituitary gland are a key player in the generation of hormonal stress responses. However, their contribution to sexually differential responses of the stress axis (which might underlie differences in stress-related disorders) is very poorly understood.

We found sex differences in the electrical activity of these cells, which could be related to differences in their gene expression pattern.

These findings shed light on the cellular mechanisms underlying sex differences in stress responses, contributing to a better understanding of stress-related disorders and potential avenues for diagnosis and treatment.

frontiersin.org/articles/10.33

New posting! This addresses the recent controversy at the 2023 Lindau Nobel Laureate meeting, where one of the speakers used his time to complain that he felt discriminated against as a white man.

To my mind, that isn't what's surprising and shocking about the episode.

The surprising thing is that on this occasion, a courageous young female scientist actually called him out on it.

The shocking thing is that despite such sexist, chauvinistic comments still being commonplace, such interventions basically never happen. And they should.

totalinternalreflectionblog.co

Many prominent anti-vaccine influencers claim biomedical credentials. In a new pre-print, we quantify the size & influence of the group of perceived experts in the anti-vaccine community on Twitter.

medrxiv.org/content/10.1101/20

The role and influence of perceived experts in an anti-vaccine misinformation community

The role of perceived experts (i.e., medical professionals and biomedical scientists) as potential anti-vaccine influencers has not been characterized systematically. We describe the prevalence and importance of anti-vaccine perceived experts by constructing a coengagement network based on a Twitter data set containing over 4.2 million posts from April 2021. The coengagement network primarily broke into two large communities that differed in their stance toward COVID-19 vaccines, and misinformation was predominantly shared by the anti-vaccine community. Perceived experts had a sizable presence within the anti-vaccine community and shared academic sources at higher rates compared to others in that community. Perceived experts occupied important network positions as central anti-vaccine nodes and bridges between the anti- and pro-vaccine communities. Perceived experts received significantly more engagements than other individuals within the anti- and pro-vaccine communities and there was no significant difference in the influence boost for perceived experts between the two communities. Interventions designed to reduce the impact of perceived experts in spreading anti-vaccine misinformation may be warranted. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Protocols <https://osf.io/6u3rn> ### Funding Statement MJH was funded by the Achievement Rewards for College Scientists Scholarship, the National Institutes of Health (R35GM133439), the University of Washington's Center for an Informed Public, and the John S. and James L. Knight Foundation. RM was funded by the Bryce and Bonnie Nelson Fellowship . EAM was funded by the National Science Foundation (DEB-2011147, with the Fogarty International Center), the National Institutes of Health (R35GM133439, R01AI168097, and R01AI102918), the Stanford King Center on Global Development, Woods Institute for the Environment, Center for Innovation in Global Health, and the Terman Award. JDW was funded by the Knight Foundation and the National Science Foundation grants 2120496 and 2230616. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Institutional Review Board of Washington University determined that this study (STUDY00017030) was exempt. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Code and data used to conduct main analyses and reproduce figures are available on Github at: https://github.com/mjharris95/perceived-experts. As explained in the repository, users were anonymized throughout the analysis and in the dataset. Additionally information may be provided by the corresponding author on reasonable request. <https://github.com/mjharris95/perceived-experts>

www.medrxiv.org

@mzan

Bad values dont me new values... A good person encouraging education to children is just as good a person regardless if they wear pants or a dress... THAT is a good value to teach kids.

@admitsWrongIfProven @iDoobyLeaves@noagendasocial.com

Microsoft "confirmed Tuesday that its validation procedure had been manipulated to digitally sign dozens of pieces of software."

Microsoft, Adobe, these firms have autoupdaters, installed on so many of our machines, that will run without question code signed by the mothership.

That's bad enough. How much should you trust Microsoft, both its intentions and internal security?

It's absolutely terrifying that hostile third parties have managed it. washingtonpost.com/national-se

ht @GossiTheDog

Hey #RStats folks. For the coming R Sprint I'm thinking of proposing a project to improve documentation (in particular, examples, but it could be anything). So hit me with functions with bad, confusing or incomplete documentation in R base.

@rstats

Just came across this very interesting about in detectors (surprise, surprise...).

Weixin Liang et al. - GPT detectors are biased against non-native English writers - 2023

arxiv.org/abs/2304.02819

"Our results call for a broader conversation about the ethical implications of deploying ChatGPT content detectors and caution against their use in evaluative or educational settings, particularly when they may inadvertently penalize or exclude non-native English speakers from the global discourse."

GPT detectors are biased against non-native English writers

The rapid adoption of generative language models has brought about substantial advancements in digital communication, while simultaneously raising concerns regarding the potential misuse of AI-generated content. Although numerous detection methods have been proposed to differentiate between AI and human-generated content, the fairness and robustness of these detectors remain underexplored. In this study, we evaluate the performance of several widely-used GPT detectors using writing samples from native and non-native English writers. Our findings reveal that these detectors consistently misclassify non-native English writing samples as AI-generated, whereas native writing samples are accurately identified. Furthermore, we demonstrate that simple prompting strategies can not only mitigate this bias but also effectively bypass GPT detectors, suggesting that GPT detectors may unintentionally penalize writers with constrained linguistic expressions. Our results call for a broader conversation about the ethical implications of deploying ChatGPT content detectors and caution against their use in evaluative or educational settings, particularly when they may inadvertently penalize or exclude non-native English speakers from the global discourse. The published version of this study can be accessed at: www.cell.com/patterns/fulltext/S2666-3899(23)00130-7

arXiv.org

Please boost/forward/tape to lab fridge etc.

Are you currently working on a #scientificwriting project such as a manuscript, grant proposal, job application, or research/teaching statement? Struggle to find place/time to write? Interested in learning how to improve the clarity and effectiveness of your professional writing? If so, consider applying to the CSHL Scientific Writing Retreat!

DM me with any questions. See interview with us here:
currentexchange.cshl.edu/blog/

meetings.cshl.edu/courses.aspx

Enjoyed reading "Using prototyping to choose a #bioinformatics workflow management system". Paper describes authors' 10 day experience searching and implementing a workflow. Summary: Need to decide which tool to use? Shortlist a list of potentially useful tools based on your needs. Start using each tool on a simpler problem. Assess the suitability of each tool. Paper contains useful tips for building reproducible workflows and links to many useful resources. journals.plos.org/ploscompbiol

Using prototyping to choose a bioinformatics workflow management system

Author summary Data analysis involves many steps, as data are wrangled, processed, and analysed using a succession of unrelated software packages. Running the right steps, in the right order, and putting the right outputs in the right places, is a major source of frustration. Workflow management systems require that each data analysis step be “wrapped” in a structured way, describing its inputs, parameters, and outputs. By writing these wrappers, the scientist can focus on the meaning of each step, and how they fit together, which is the interesting part. The system uses these wrappers to decide what steps to run and how to run these and takes charge of running the steps, including reporting on errors. This makes it much easier to repeatedly run the analysis and to run it transparently upon different computers. To select a workflow management system, we surveyed available tools and chose 4 in which we developed prototype implementations to evaluate their suitability for our project. We conclude that many similar multistep data analysis workflows can be rewritten in a workflow management system, and we advocate prototyping as a low-cost (both time and effort) way of making an informed selection of software for use within a research project.

journals.plos.org

@GatekeepKen @donniecash818 Don't think a supposedly private conversation about something that must have been devastating can be classified as bragging...

Read an article today about why Americans think alcohol has health benefits and it's apparently another "well the French are healthy and they do X so it's healthy to do X."

So here's your periodic reminder that France (and Italy, and Sweden, and Japan, and basically every country you've seen in a "this country is so healthy, what's their secret?" headline) has universal health care.

The secret is access to health care. It's always access to health care.

Last term, I had a final assignment option having students use #ChatGPT to write their final essay, then critique the results. It was great, and I'll be doing it again. Everyone in #academia should do something like this with their class if they can. Short 🧵 on what we found.

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