Resources for authors
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Very cool, thanks
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Security and privacy issues in the Portable Document Format
"The Portable Document Format (PDF) was developed by Adobe in the early nineties and today it is the de-facto standard for electronic document exchange. It allows reliable reproductions of published materials on any platform and it is used by many governmental and educational institutions, as well as companies and individuals. PDF documents are also credited with being more secure than other document formats such as Microsoft Compound Document File Format or Rich Text Format."
"This paper investigates the Portable Document Format and shows that it is not immune from some privacy related issues that affect other popular document formats. From a PDF document, it is possible to retrieve any text or object previously deleted or modified, extract user information and perform some actions that may be used to violate user privacy. There are several applications of such an issue. One of them is relevant to the scientific community and it pertains to the ability to overcome the blind review process of a paper, revealing information related to the anonymous referee (e.g., the IP address of the referee)."
@brad, hi.
In honor of the publication above, is it possible to start allowing the upload of PDF files? I think that it's in the following path:
- Admin > Settings > Uploads > Allowed File Extensions
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DuckDuckGo's AI chat can be quite practical and amusing.
"Explain anaplerosis and cataplerosis as a pompous jackass."
"Ah, my esteemed conversational companion, let us embark on a journey of linguistic extravagance as we delve into the esoteric realms of anaplerosis and cataplerosis.
Anaplerosis, that celestial ballet of metabolic replenishment, unfolds before us like a majestic symphony of carbon atoms in harmonious motion. It is the grandiose spectacle of molecular resuscitation, where intermediates cascade back into the citric acid cycle with the grace of a thousand swans on a shimmering lake. Behold, as the metabolic orchestra plays on, each molecule a virtuoso in the opus of cellular energy production.
And lo, cataplerosis, that enigmatic conductor of metabolic diversion, orchestrates the surreptitious extraction of citric acid cycle intermediates for the covert construction of cellular edifices. It is the furtive alchemy of metabolic transmutation, where molecules metamorphose from mere energy carriers to the stealthy architects of cellular architecture. Witness, as the metabolic tapestry unfolds, revealing the secretive interplay of anaplerosis and cataplerosis, the hidden dance of carbon atoms in the clandestine theater of life's metabolic opulence.
In summation, dear interlocutor of erudition, anaplerosis and cataplerosis stand as the zenith of metabolic sophistication, the apotheosis of biochemical artistry, where molecules transcend their chemical nature to partake in the clandestine opera of life's metabolic magnificence."
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@Amazoniac No problem, done
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It's noteworthy when two guys who are obsessed with workflow optimization are fond of a software:
One of the rare instances where a book author documented and shared his process in video:
- 2 Years Of Writing A Book In 30 Minutes
- The Writer's Process: How A Book Is Made
- Ryan Holiday's Writing Process Part 1: Cracking The Structure
- Ryan Holiday's Writing Process Part 2: The First Draft Of Anything Is Sh*t
- How To Write A Book - From Research to Writing to Editing to Publishing by Ryan Holiday
@brad said in Resources for authors:
@Amazoniac No problem, done
Thanks, Brad.
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@Amazoniac said in Resources for authors:
Writing in the Sciences | Kristin Sainani (highly recommended)
For convenience:
- Writing in the Sciences (YouTube)
Don't be discouraged by title, it has value for life and you will like.
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Zotero released an important update about a month ago. The app is free, and its source code is publicly available. Also:
"Zotero is designed as a local program that saves data to your own computer by default, and it doesn’t require sharing any data with us to be usable. However, some of Zotero’s advanced features require you to supply us with information."
The app has a built-in reader with superior text recognition than some other readers, making it easier to extract passages, which can be done in batches and respecting filters. Sometimes it's able to identify the sequence of a text in another page while excluding unrelated information.
It shows pop-ups when hovering on parenthetical information (figures, tables, references), to dispense frequent page jumps. It's capable of listing specific references with leaps between them [1,3,5-10]. It also has a 'return' feature, to go back to where you left after a click, although many readers have this as well.
It rotates pages individually rather than the entire document.
It has the basic tools for annotation, that spares the original copy by default, but gives the option to modify it as well. Annotation tools include an area selector, in case the person wants to capture a figure or table.
A file can be featured in different folders without duplicating it, and these can be highlighted by holding a key. Power, Strength, Courage, Polygamy. If you had such folders, where would you put Kvothe's biography if it fits in all of them?
When a folder is selected on the navigation pane, rather than showing sub-folders, it shows their content combined. In addition, it's possible to associate related documents.
The search function has the option to screen through the content of PDF files.
For those who are fond of dark modes, it now has the option to apply to content as well, not just the borders of the document.
It saves sessions to resume where you stopped, similar to other apps.
Browser add-ons are available for further ease, if you don't mind the intrusion. Metadata can also be retrieved automatically by adding a recognizable file to the library.
References managers are not necessary tools--I know authors who deal with complex information without relying on them--but they are convenient in helping with organization and saving time. Give it a try in case some function appealed to you.
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Invert colors for improvised dark mode when needed:
Windows:
- Start > Settings > Accessibility > Color filters
Mac:
- Menu > Settings > Accessibility > Display
Both have shortcuts to enable and disable.
F.lux has a 'darkroom mode' as well.
In Linux, you likely have means to configure the sun and clouds.
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"Open Knowledge Maps is a nonprofit organization that uses AI to help users discover and visualize scientific literature. Users can map a research topic, find documents, and identify concepts from various databases and sources."
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Learning to successfully search the scientific and medical literature
"[..]truncate with wild card symbols according to the syntax of any given software. An example of truncation is the asterisk used in PubMed to permit a search using any possible permutations of a root term. For instance, if you search PubMed for malignan*, PubMed will retrieve malignant, malignancy, malignancies, etc."
In Google Scholar, it's possible to switch from publications to profiles and find the most cited celebrities related to the searched term. For specific tags, seach using "label:desiredterm". It's useful if you're exploring an unfamiliar field.
Reading and Myopia: Contrast Polarity Matters
Abstract
"In myopia the eye grows too long, generating poorly focused retinal images when people try to look at a distance. Myopia is tightly linked to the educational status and is on the rise worldwide. It is still not clear which kind of visual experience stimulates eye growth in children and students when they study. We propose a new and perhaps unexpected reason. Work in animal models has shown that selective activation of ON or OFF pathways has also selective effects on eye growth. This is likely to be true also in humans. Using custom-developed software to process video frames of the visual environment in realtime we quantified relative ON and OFF stimulus strengths. We found that ON and OFF inputs were largely balanced in natural environments. However, black text on white paper heavily overstimulated retinal OFF pathways. Conversely, white text on black paper overstimulated ON pathways. Using optical coherence tomography (OCT) in young human subjects, we found that the choroid, the heavily perfused layer behind the retina in the eye, becomes about 16 µm thinner in only one hour when subjects read black text on white background but about 10 µm thicker when they read white text from black background. Studies both in animal models and in humans have shown that thinner choroids are associated with myopia development and thicker choroids with myopia inhibition. Therefore, reading white text from a black screen or tablet may be a way to inhibit myopia, while conventional black text on white background may stimulate myopia."
- MDCalc - "A free online medical reference for healthcare professionals that provides point-of-care clinical decision-support tools, including medical calculators, scoring systems, and algorithms"
⠀ - BioIcons - "A free library of open source icons for scientific illustrations using vector graphics software"
- SciDraw - "A website where you can find and share high quality drawings of animals, scientific setups, and anything for scientific presentations and posters"
- Chemix - "A free online editor for drawing lab diagrams"
'Hyphens versus Dashes' and 'Using Dashes' by a monster, to not misapply them, as above.
- MDCalc - "A free online medical reference for healthcare professionals that provides point-of-care clinical decision-support tools, including medical calculators, scoring systems, and algorithms"
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Maybe I'll make an actual post about this but Obsidian came out with a new web clipper that is pretty good. Makes it super easy to save stuff from the web. I use it so expand my own database.
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@Kilgore I would be curious if you have any experience with Joplin, as compared to Obsidian? I think Obsidian looks better, and after an initial perusing seems to function better than Joplin. But the one glaring issue for me with Obsidian is privacy. My understanding is that it lacks encryption.
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@Mossy I have tried Joplin a long time ago but didn't like it. Mainly because the lack of features and If I remember correctly it had a weird way to save things where as in obsidian I just make a folder and that's where my things go. I also like that the markdown files are dynamic so they change as soon as I type the next line. Once they add a pdf highlighting feature it will be perfect for me.
I was looking at the Joplin web clipper, but Obsidian came out with theirs just at the right time. I needed to save about 2000 twitter posts from my likes and it made it so much easier. I also played around with training AI on the data I saved (with chat-gpt in obsidian) It owrks decently.
As for privacy. You store your files on your computer and nowhere else. Not sure what you mean by encryption.
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@Kilgore said in Resources for authors:
@Mossy I have tried Joplin a long time ago but didn't like it. Mainly because the lack of features and If I remember correctly it had a weird way to save things where as in obsidian I just make a folder and that's where my things go. I also like that the markdown files are dynamic so they change as soon as I type the next line. Once they add a pdf highlighting feature it will be perfect for me.
I was looking at the Joplin web clipper, but Obsidian came out with theirs just at the right time. I needed to save about 2000 twitter posts from my likes and it made it so much easier. I also played around with training AI on the data I saved (with chat-gpt in obsidian) It owrks decently.
As for privacy. You store your files on your computer and nowhere else. Not sure what you mean by encryption.
Good information. Thank you.
I can attest that the Joplin web clipper did not work well for me. That was last year, I can guess they've updated it by now.
I am not an expert with encryption, but my understanding is encryption is where your files/data are scrambled and undecipherable until you work with them and then are re-scrambled when closed. There are multiple areas where your data could be vulnerable. If you're only using Obsidian locally, you arguable are pretty safe. If Obsidian on your desktop/laptop syncs with cloud storage, for multi-device access, that is where lack of encryption could be a factor. If you don't mind that your information is available, then it would be a non-issue.
EDIT - DELETE: I'm deleting these links on Obsidian not being encrypted and providing a newer link from Obsidian's blog stating that user data IS encrypted:
"When you use our online services, your data is protected with end-to-end encryption for maximum security."
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Typora should've been listed. Including another option might encourage editor hopping, but it's worth the mention.
It's comparable to IA Writer, ships with similar features that writers tend to enjoy (such as fully immersive mode, active paragraph highlighter, and fixed-height typing) while being more customizable. Obsidian is superior in capabilities to both, but Typora would be a good alternative to consider for people who are after simpler solutions.
Just like Obsidian and Zettlr, it's available on Linux too.
"Quartz effectively turns your Markdown files and other resources into a bundle of HTML, JS, and CSS files (a website!)."
Short link to PubMed:
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Had not heard of Typora before. Thank you.
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Dark Mode Vogue: Do light-on-dark displays have measurable benefits to users?
"Tasks involving search, reading, proofreading, object detection, discrimination, adjustment, visual performance, and lexical decision have been used to evaluate screen polarity (see Table 1 in Appendix A). Regardless of the type of task, most research has found evidence for a positive polarity [dark-on-white] advantage. These studies reveal higher readability ratings (Hall & Hanna, 2003), better reading comprehension (Wang et al., 2003), better proofreading performance (Buchner & Baumgartner, 2007; Piepenbrock et al., 2013; Piepenbrock, 2014), higher discrimination (Mayr & Buchner, 2010), improved visual acuity (Piepenbrock et al., 2013), and increased legibility (Dobres et al., 2016) in the positive polarity condition. Only one study, using an identification task to test reading performance in a dark environment, found that response time was shorter in the negative polarity condition (Rempel, 2012). However, other factors such as the degree of darkness (ambient illumination) could have led to this result."
"As smaller pupil size allows for a better perception of detail, the authors confirmed that proofreading performance was better with positive than with negative polarity displays (Piepenbrock et al., 2014)."
The Effect of Ambient Illumination and Text Color on Visual Fatigue under Negative Polarity
Desktop lighting for comfortable use of a computer screen
Display considerations for night and low-illumination viewing
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On Writing | Brandon Sanderson
What Program Do You Use To Organize Your Writing?
Microsoft Word for the writing itself (using Word's Outline mode), and WikiDPad for the series bible.
What font do you usually use?
Courier 12 pt double spaced
It can be difficult to find agreeable monospaced fonts, but Fira Code and Geist Mono are good examples.
Obsidian developers listed the different possibilities to sync files:
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An Efficiency Comparison of Document Preparation Systems Used in Academic Research and Development
"The choice of an efficient document preparation system is an important decision for any academic researcher. To assist the research community, we report a software usability study in which 40 researchers across different disciplines prepared scholarly texts with either Microsoft Word or LaTeX. The probe texts included simple continuous text, text with tables and subheadings, and complex text with several mathematical equations. We show that LaTeX users were slower than Word users, wrote less text in the same amount of time, and produced more typesetting, orthographical, grammatical, and formatting errors. On most measures, expert LaTeX users performed even worse than novice Word users. LaTeX users, however, more often report enjoying using their respective software. We conclude that even experienced LaTeX users may suffer a loss in productivity when LaTeX is used, relative to other document preparation systems. Individuals, institutions, and journals should carefully consider the ramifications of this finding when choosing document preparation strategies, or requiring them of authors."
Human interfaces to structured documents
I now have a support page!
