This is the link of the example: https://www.researchgate.net/publication/313478425_BIDUM_32_full_-_Part_A_-_17_pages_-_10022017_-_working_paper_A_Bio-Info-Digital_Universe_toy-Model_-_towards_a_transdisciplinary_TOE_centered_on_life_phenomenon_-_Part_A?ev=prf_high

Working Paper (BIDUM 3.2 full - Part A - 18 pages - last update on: 23.02....

It is likely that your pdf will download in the format you intended, but this does not necessarily mean your pdf will display on the Research Gate site in the same way. It will be converted for display on the website, using HTML code rather than the original pdf format, and the formats are not always compatible.

Not sure what system you are using when you added the references, but they are not in alphabetical order (which is unusual) and you are using both roman and non-roman numerals (which is unusual) and you have periods after the author name (which is unusual).

It may be that the system used for the ResearchGate website has tried to recognise the system you are using but can't identify it as it doesn't appear to be either APA or Harvard style. The website software may, for example, think each period is the end of a sentence or end of a paragraph.

It may be that if the references are changed to APA or Harvard style it may solve your problem. Have you tried asking on the Research Gate "Contact us" link?

I use Windows 7: however, from what I know, the pdf format is compatible (and probably exactly conserves its inner structure) with any operating system. I have listed Reference in the order in which they are mentioned in the paper (I shall mention this fact explicitly in the next version of the paper). I have used roman numbering for the other BIDUM variants cited in my paper and then continued to usual Arabic numbering for the non-self articles from the Reference section. I have changed the periods to commas (in the APA style): to test your (although I use the Harvard style where the period is used after the author and year; besides, it should have to generate errors for almost all the reference, not just for a minority of reference papers). It is a good idea to try the Contact us service. Thank you for you prompt and detailed answer!

My hypothesis was correct: even replacing periods with commas didn't solve the problem. I shall search for a rule.

"I use Windows 7: however, from what I know, the pdf format is compatible (and probably exactly conserves its inner structure) with any operating system".

Your computer uses Windows software.  Others may have a Mac which uses Mac software, or a linux computer which uses Linux software.  Unless you have a Windows phone, most phones also use a form of  Linux software called Android.  All these operating systems should convert pdf files properly.

However, when you use a web browser, on a computer or a phone, you are not using the operating system you are using the the Microsoft browser, or the Chrome browser, or the Firefox browser, or whichever browser you happen to be using.  These browsers do not display the page in Windows,  Mac, Linux or Android.  They display the page in the browser using HTML and CSS code, and sometimes other code, and they may display pdf differently. 

What this means is that if you upload a pdf file to RN and then download the same pdf file onto your computer it will look identical to your pdf when you read it in a pdf viewer, or even if you read the pdf you have downloaded in a browser..

However, if you download the same pdf to a server (which is what you do when you download pdf to RN), and then look at that file on RN you are not viewing the pdf.  Your pdf is put on one site so that it can be downloaded.  What you are  looking at on the RN website is your pdf which has been converted to HTML.  It is that conversion process that allows different HTML systems to display pdf differently.  All websites use HTML, not windows.  When you look at a website on your Windows computer, you are looking at HTML which is converted by Windows into a form you can understand.  The actual pdf is converted from pdf to HTML in order for the website to display it in the browser,

In short,

1) pdf is pdf, and it should display the same way on a computer or phone. 

2) when you view a pdf file you download, it should still look the same way.

3) However, when you view a web page in a browser you are not viewing pdf, you are viewing pdf that has been changed into HTML, and that is completely different.

I now perfectly understand what you have meant: however, this departs from the problem (which is a problem of RG scanning the reference list of my paper from a pdf)

I have partially solved the problem, which was partially generated by some more than one pair of parantheses in the titles. The conclusion from testing is that RG scans the titles of articles listed in the Reference section and then compares those title with its database of citation: if they match, RG gives a correct result. If they math just partially, RG lists those fragments from References that match (probably to) other paper contents. After correcting my pdf, these fragments still remain: 

Information heat engine: converting information to energy by feedback control. S Toyabe. 2010.

J Bain. 2014.

Le tiers inclus De la physique quantique à l'ontologie See also. B Nicolescu, Lupasco. 1999.

J E Brenner. 1900.243-285.

Question One:  If you click on the RG link to upload it back to your computer, is it correct after you have uploaded it?

Question Two:  Instead of uploading the file, if you view it on the RG site and click on the "show more" link, is that when it is not displaying properly?

1. Yes.

2. Yes, but only in the case of those papers that cannot be found on RG when specifically using those fragments as search words:

https://www.researchgate.net/search.Search.html?query=converting%20information%20to%20energy%20by%20feedback%20control&type=researcher

https://www.researchgate.net/search.Search.html?query=Le%20tiers%20inclus%20De%20la%20physique%20quantique%20%C3%A0%20l%27ontologie%20&type=researcher

https://www.researchgate.net/search.Search.html?query=J%20E%20Brenner.%201900.243-285&type=researcher

In conclusion, I have solved the problem to the limits of the RG database!

Your answer implies that the RG system cannot recognise your references.

I notice you are a pediatrician. Prescriptions are written in a strict format so they can be understood by anyone reading them, and so there are no mistakes. References, too, are usually written in a strict format because they need to enable anyone who reads them to find the book or article concerned, and because universities, colleges, and referencing software can all recognise those formats.

The Toyabe S. et al. (2010) reference may have not been recognised because you havn't provided all the authors. et al. is OK in the body of the text, but all authors/editors should be listed in full in the reference section, so that may be why the RG software hasn't recognised it.

The Brenner J.E. (2010) reference may not have been recognised becaust the title is all in capital letters. It is the only reference in all caps, so presumably, if the software has recognised a format, it will have also recognised that the capital letters do not conform to that format.

The Nicolescu B. (1999) reference may not have been recognised because half of the reference you have written in English, and half in French. The whole reference probably needs to be one or the other. The RG software would presumably be looking for English and not recognising the French, or looking for French and not recognising the English.

Hope this helps.

Thank you for your message. You are a mountain of patience AND I strongly appreciate this quality of yours! it's a good idea to also verify al these issues and try to correct them in my next version of BIDUM 3.2 - part A. Stimulated by your answer, I have also found Mr. Joseph Brenner on RG, which was a very pleasant surprise for me! I shall try to modify each citation in reference according to your indications/suggestions and verify if it will work. My main focus on content has an adverse reaction: I often do not offer much attention of these formal rules (which I realize that are important, especially for machines and programmers).

Thank you again!