Category Archives: Software

More tensions at PubPeer

1.08.2024 admin

Wafik S El Deiry has now uploaded more than 40 times a rebuttal letter to PubPeer complaining about being bullied by “academic terrorism”. Thomas C Südhoff is even more aggressive with new ad hominem attacks as I just learned

https://med.stanford.edu/sudhoflab/integrity—pubpeer.html 1/8/2024

while his explanation of the numerous duplications is clearly wrong

… the tiny allegedly cloned areas of similar background signals partly overlap and are randomly distributed in the image. Besides the fact that it would make no sense to duplicate such small areas of background – a fraudster could just run a gel with empty lanes – and that such duplications do not improve the data, overlapping duplications like this are nearly impossible to manufacture.

Of course also small areas can be copied with the clone tool. If the placement is random or intentional can only be judged from the original image while an educated guess is certainly allowed. Running Photoshop is at least far more time and cost effective than running a gel with an empty lane.

A general problem here is that digital reproductions of images – both of immunoblots and of tissue sections or cells – can create artifactual microduplications especially if the image resolution is changed during reproductions.

This is outright wrong. Artifacts by capturing or stitching software is possible in theory while in practice we have found it only a few times.

So here comes my assessment of the now famous Synaptotagmin-1/Synaptopyhsin-1 immunoblot

The assessment is based on the directly extracted (inline) image from the PDF.

Identical patches were confirmed using 3 software packages Forensically, ImageDup and ICMF.

ICMF https://ipolcore.ipol.im/demo/clientApp/demo.html?id=213&key=6317E0D9603764AC6FB3A9FAF3090847

Also the manual annotation below shows 100% identical areas where the KW+ lane pixel has been copied to KW- (the other direction is less likely). Not sure what had been there, dust, dirt, text marker or another dot?

manual pixel-wise annotation, click for full view

Südhof comments on this image on his website

Mistake identified: Dr. E. Bik claims that the Suppl. Figure 6b immunoblot stripes (reproduced digitally at low resolution by the journal from a non-digital original blot) contains tiny areas of microduplications in the background pattern (not the actual signal). These areas are tiny, within a blot, randomly distributed, and only digitally identifiable. She implies that these blots are suspicious and could be manipulated.
Resolution: This is an unusually bizarre accusation since it refers to digital low resolution images in which tiny image areas would have been scrambled by a person if Dr. Bik’s accusation were correct. Even though she maintains publicly that she won’t speculate about motivations, her accusations imply a motivation that would be difficult to understand since any manipulation here would produce a partly altered background. The most likely explanation here is, like for many of the ‘mistakes’ identified by Dr. Bik’s A.I.-powered software, that these random microduplications are simply a reproduction artifact of a digitized image.
Classification: unfounded

Great story: The journal Nature Structural & Molecular Biology received the original blots and digitized them? So this is their fault? These are neither tiny spots, nor are they randomly distributed and of course, they can be seen by naked eye.

German newspapers covered the Südhof stor already (SPIEGEL, FAZ but also Science Magazine). Ulrich Dirnagel/Tagesspiegel believes that any intentional manipulation or deception cannot be recognized. I am not sure when looking at the images above.

Software

Our data are being sold

31.07.2024 admin

We are being spied on and the data are being sold.

https://x.com/RuthieClems/status/1813478033975623697Report by The Chronicle

The two reports note that Informa will explore how AI can make its internal operations more effective, specifically through Copilot, Microsoft’s AI assistant. “Like many, we are exploring new applications that will improve research and make it easier to analyze data, generate hypotheses, automate tasks, work across disciplines, and research ideas,” a Taylor & Francis spokesperson wrote in an email to The Chronicle.

Publishers neither analyze data, generate hypotheses and work on research ideas – it is just a money making scheme after the

Another publisher, Wiley, also recently agreed to sell academic content to a tech company for training AI models. The publisher completed a “GenAI content rights project” with an undisclosed “large tech company,” according to a quarterly earnings report released at the end of June.

Software

Florence Nightingale über Statistik

27.07.2024 admin

mit interessanten Details zu ihrem Rose Diagramm auf historyofinformation.com

In 1858 nurse, statistician, and reformer Florence Nightingale published “Notes on Matters Affecting the Health, Efficiency, and Hospital Administration of the British Army”. … This privately printed work contained a color statistical graphic entitled “Diagram of the Causes of Mortality in the Army of the EastOffsite Link” which showed that epidemic disease, which was responsible for more British deaths in the course of the Crimean War.

Philosophy, Software

How to ruin yourself

5.07.2024 admin

Found at futirism.com

Google researchers have come out with a new paper that warns that generative AI is ruining vast swaths of the internet with fake content — which is painfully ironic because Google has been hard at work pushing the same technology to its enormous user base.
The study, a yet-to-be-peer-reviewed paper spotted by 404 Media, found that the great majority of generative AI users are harnessing the tech to “blur the lines between authenticity and deception” by posting fake or doctored AI content, such as images or videos, on the internet. The researchers also pored over previously published research on generative AI and around 200 news articles reporting on generative AI misuse.

The authors painfully collected 200 observed incidents of misuse reported between January 2023 and March 2024 and find

– Manipulation of human likeness and falsification of evidence underlie the most prevalent tactics in real-world cases of misuse…
– The majority of reported cases of misuse do not consist of technologically sophisticated uses … requiring minimal technical expertise.
– The increased sophistication, availability and accessibility of GenAI tools seemingly introduces new and lower-level forms of misuse that are neither overtly malicious nor explicitly violate these tools’ terms of services, but still have concerning ethical ramifications.

Software

The official end of academic Twitter

11.06.2024 admin

Twitter was the #1 information source during COVID times but it is now officially declared dead in a new preprint “The Failed Migration of Academic Twitter“.

Utilizing publicly available user account data, we track the posting activity of academics on Mastodon over a one year period. Our analyses reveal significant challenges sustaining user engagement on Mastodon due to its decentralized structure as well as competition from other platforms such as Bluesky and Threads. The movement lost momentum after an initial surge of en- thusiasm as most users did not maintain their activity levels, and those who did faced lower levels of engagement compared to Twitter.

While the paper isn’t particular well designed – I would expect some Sankey plots showing the activity movement like those found after elections – the main message is clear. The paper summary also reflects my own experience as I am writing now only occasionally at my blog while my Twitter, Mastodon and Bluesky accounts are left in an orphan state.

Software

Onleihe + Brave + GoFullPage

9.06.2024 admin

Leider funktionieren die Onleihe Screenshots über GoFullPage in Brave nicht so schön wie in Chrome da zusätzliche CSS Elemente von Onleihe stören . Mit drei Regeln im Inhaltsfilter

kann man sie aber ausblenden. Die Zoom Buttons sind zwar dann auch weg aber der Zoom funktioniert weiter mit CRTL+ bzw CTRL-.

Noteworthy, Software

How to integrate wordpress in another website

7.05.2024 admin

In another website constructed more than a decade ago, I integrated WordPress pages just as iframe .This was quite common at that time but not very elegant as all the formatting had to be adjusted to the parent site for a coherent view. When revising the website last week I have chosen a radical different approach by completely silencing the WP output using a plugin

<?php
/** Plugin Name: shutup **/
add_action( 'template_redirect', function() {
  wp_die( __( 'disabled' ) ); 
});
?>

WP pages and posts are retrieved in the main website using the WP API only

$api_url = 'https://www.DOMAIN.de/BLOGNAME/wp-json/wp/v2/pages/xxxx';
$response = file_get_contents($api_url);
$posts = json_decode($response);
echo $posts->content->rendered;

Noteworthy, Software

How to lie with statistics

27.04.2024 admin

ephorie.de has a convincing re-analysis that Daniel Kahneman is wrong, who purportedly demonstrated that emotional wellbeing increases with income but plateaus at $75,000…

Software

What really matters

24.04.2024 admin

The title is clickbait as nobody really knows what is really relevant in science although some people still think that a few failed postdocs at NSC (Nature, Science, Cell) are the ultimate judges here.

Google also did not know in the 1990ies when they invented the pagerank with the now famous words “The prototype with a full text and hyperlink database of at least 24 million pages is available at http://google.stanford.edu”.

https://twitter.com/methode/status/1781357974578995315

Everybody since then believed in the authoritative power of links but according to Roger Montti they are no more relevant as at a recent conference in Bulgaria Google’s Gary Illyes confirmed that links have lost their importance. And maybe even Google at all?

Software

From start to finish programming with ChatGPT in 60s

17.04.2024 admin

Create a PHP script that can read a CSV in the form start_date, end_date, event and output as ICS file

function convertDate($date)
{
    $dateTime = DateTime::createFromFormat('m/d/Y', $date);
    if ($dateTime === false) {
        return false; // Return false if date parsing fails
    }
    return $dateTime->format('Ymd');
}

// Function to escape special characters in text
function escapeText($text)
{
    return str_replace(["\n", "\r", ",", ";"], ['\n', '\r', '\,', '\;'], $text);
}

// Read CSV file
$csvFile = 'uci.csv'; // Replace with your CSV file name
$icsFile = 'uci.ics'; // Output ICS file name

$handle = fopen($csvFile, 'r');
if ($handle !== false) {
    // Open ICS file for writing
    $icsHandle = fopen($icsFile, 'w');

    // Write ICS header
    fwrite($icsHandle, "BEGIN:VCALENDAR\r\n");
    fwrite($icsHandle, "VERSION:2.0\r\n");
    fwrite($icsHandle, "PRODID:-//Your Company//NONSGML Event Calendar//EN\r\n");

    // Read CSV line by line
    while (($data = fgetcsv($handle, 1000, ',')) !== false) {
        $startDate = convertDate($data[0]);
        $endDate = convertDate($data[1]);
        print_r($data) . PHP_EOL;
        echo $startDate;
        
        if ($startDate === false || $endDate === false) {
            continue;
        }
        $event = escapeText($data[2]);

        // Write event to ICS file
        fwrite($icsHandle, "BEGIN:VEVENT\r\n");
        fwrite($icsHandle, "UID:" . uniqid() . "\r\n"); // Unique identifier
        fwrite($icsHandle, "DTSTART;VALUE=DATE:" . $startDate . "\r\n");
        fwrite($icsHandle, "DTEND;VALUE=DATE:" . $endDate . "\r\n");
        fwrite($icsHandle, "SUMMARY:" . $event . "\r\n");
        fwrite($icsHandle, "DESCRIPTION:" . $event . "\r\n");
        fwrite($icsHandle, "END:VEVENT\r\n");
    }

    // Write ICS footer
    fwrite($icsHandle, "END:VCALENDAR\r\n");

    // Close files
    fclose($icsHandle);
    fclose($handle);

    echo "ICS file generated successfully.";
} else {
    echo "Error: Unable to open CSV file.";
}

Source data are from UCI and output is here from where it can be added as a calendar. BTW created also my first “hello world” Swift/iPhone app using this source although this took a bit more time…

Noteworthy, Software

How to cite bookends references in LaTeX

14.04.2024 admin

attn: this is the chatGPT solution

In LaTeX, you can use the biblatex package along with a bibliography management tool like BibTeX … to manage your references. To cite references generated by Bookends, you would typically export your references from Bookends to a BibTeX (.bib) file and then include that file in your LaTeX document.

Here’s a general outline of how you can cite Bookends references in LaTeX using BibTeX:
1. Export your references from Bookends to a BibTeX (.bib) file.
2. Include the BibTeX file in your LaTeX document using \bibliography{your_bibliography_file}.
3. Cite the references in your document using \cite{} or \autocite{} commands, passing the citation key corresponding to each reference in your BibTeX file.

\documentclass{article}
\usepackage[backend=biber]{biblatex}

% Include your bibliography file
\bibliography{your_bibliography_file}

\begin{document}
Some text \autocite{citation_key}.

% Your content here

\printbibliography

\end{document}

Replace your_bibliography_file with the name of your BibTeX file (without the .bib extension), and replace citation_key with the citation key of the reference you want to cite.

After compiling your LaTeX document with the appropriate compiler (usually something like pdflatex followed by biber and then pdflatex again), LaTeX will automatically format the citations and generate the bibliography according to the style specified in your document.

Make sure to choose a citation style compatible with your field or publication requirements. You can specify the citation style in the \usepackage[style=…]{biblatex} command. Popular styles include apa, ieee, chicago, etc.

Software

MacOS Pages getting line numbers

14.04.2024 admin

Mayn journals requiring consecutive line numbering which is not a problem with MS Word, Open Office or LaTeX but with Pages.

Maybe it is possible to add a new background to PDF? Acrobat can do it (which I would not recommend), there is some crazy script out there (that did not work as well as ). My initial solution

pandoc -s input.rtfd -o output.tex --template=header_template.tex | pdflatex -output-directory=output_directory

with the header_template.tex containing

---
header-includes:
- \usepackage[left]{lineno}
- \linenumbers
- \modulolinenumbers[5]
---

did not work as pandoc cannot read the rather complex rtfd format produced by Pages. Also the next try with rtf2latex2e looked terrible, so I went back to RTF export in Libre Office where I corrected the few Math formulas that were not recognized correctly.

Another option would have been Google Docs – they introduced line numbering recently which is probably the fastest and easiest way to do that.

Whenver it comes to more than one formula, it would be even better to move from Pages to Overleaf (online) or Texifier (local).

Software

htaccess nightmare

30.03.2024 admin

I have rewritten my image website last week, collapsing 25 php scripts into 1 while combining it with another 5 javascript files. The interesting point is that most of the server side layout moved now to the client side.
The website was running basically for 20 years while I felt it is too time consuming now to update it one more time always running at risk of some security flaws.
There is now now a true responsive layout, image upload is now done by a web form and no more by FTP. I am also not storing any more different image sizes while all the processing including watermarking is now done on the fly. This required however some more sophisticated rules for site access.
Writing the htaccess rules was the most complicated. thing where even chatGPT failed. Only the rules tester helped me out…

Software

Happy Birthday

16.03.2024 admin

A MUST READ by Tim Berners Lee at Medium

Three and a half decades ago, when I invented the web, its trajectory was impossible to imagine … It was to be a tool to empower humanity.The first decade of the web fulfilled that promise — the web was decentralised with a long-tail of content and options, it created small, more localised communities, provided individual empowerment and fostered huge value. Yet in the past decade, instead of embodying these values, the web has instead played a part in eroding them…

Noteworthy, Software

How does AI recognize AI text

13.03.2024 admin

The Semrush blog has a nice summary

By analyzing two main characteristics of the text: perplexity and burstiness. In other words, how predictable or unpredictable it sounds to the reader, as well as how varied or uniform the sentences are.

Perplexity is

a statistical measure of how confidently a language model predicts a text sample. In other words, it quantifies how “surprised” the model is when it sees new data. The lower the perplexity, the better the model predicts the text.

Burstiness is

is the intermittent increases and decreases in activity or frequency of an event. One of measures of burstiness is the Fano factor —a ratio between the variance and mean of counts. In natural language processing, burstiness has a slightly more specific definition… A word is more likely to occur again in a document if it has already appeared in the document. Importantly, the burstiness of a word and its semantic content are positively correlated; words that are more informative are also more bursty.

Or lets call it entropy? So we now have some criteria

- AI texts are more uniform and more predictable and often repetitive with
- lack of depth and personality
- Sometimes plagiarism checker may recognize “learned” AI phrases. Sometimes reference checkers will find “hallucinated” references
- Incorrect content and outdated information in contrast needs human experts
- An obvious, yet underappreciated downside: “AI texts have nothing to say” – “clichéd nothingness“.

Well, there appear now also AI prologue sentences in scientific literature for example like “Certainly! Here is…”