Question on research tools

Quote from Rob

When I lookup the reference, I'd like the tool to take me directly to the relevant page of the PDF, or the relevant timestamp of the audio/video (can't see a way to do this in EndNote)

To do this, you add #page=nn to the URL. For example:

http://lenr-canr.org/acrobat/BiberianJPjcondensedx.pdf#page=74

(Accomazzi, P., Binuclear Atoms: A Model to Explain Low Energy Nuclear Reactions.)

The EndNote file I uploaded to LENR-CANR.org has all of the links to papers that are on file at LENR-CANR.org. The papers that are included in collections have the "#page=" links. You can download this file here:

http://www.lenr-canr.org/EndNoteExport.txt

Quote from Rob

The tool should have strong search capability, such as looking up all references of a particular person and allowing me to see them in chronological order, or all references of a given type

For that purpose, I prefer two programs: FileLocatorPro and Everything. (Everything is the name of the program.)

Filelocator Pro – Mythicsoft

voidtools

Quote from Rob

These sound potentially very helpful, but it looks like they're both exclusively for Windows. I know emulation exists...

Oh. So you are one of them.

See:

FileLocator Alternatives for Mac: Top 6 File Search Utilities & Similar Apps | AlternativeTo

FileLocator is not available for Mac but there are some alternatives that runs on macOS with similar functionality. The best Mac alternative is DocFetcher,…

alternativeto.net

Dieter Britz compiled bibliographies of cold fusion books, papers, patents and so on. I uploaded the database in as-received format, here:

https://lenr-canr.org/acrobat/BritzDcoldnuclea.pdf

There has been some talk of converting it to a relational database format, such as EndNote or MySQL. Below is a message I wrote about that. I could do it, or if someone else wants to go to the trouble, I can assist.

Britz also scanned the papers. He assigned titles such as Abel1990.pdf, discussed below. I have his collection of papers. The scan image quality is poor, and many of the papers are copyright, so I have not uploaded his scans. I have uploaded many of those same papers in better quality scans or digital images from authors and publishers.

CONVERTING BRITZ FILES

I think it would be best to convert to EndNote format. From there, you can go to RIS or hundreds of other formats. I wrote a program to convert from EndNote to MySQL. I use that to upload to the Library screens.

There are several different layouts in these text files. Seamus or I can write a program to convert them all to standard EndNote records. For example, here it the first Britz record for a book:

@book{B.Basi1999,

author = {A. Basile},

title = {Fusione Fredda ('Cold Fusion').

Subtitle: 'E possibile l energia nucleare senza rischi?'

('Is nuclear energy without risks possible?')},

publisher = {Avverbi Edizioni},

address = {Rome},

year = {1999},

isbn = {88-87-328-08-0},

annote = {A slim volume, roughly contemporary with that of Germano, this

one outlining in an even-handed way (and sober tone) the story of cold

fusion, especially the role played by Italian scientists. The main section on

CNF itself is on pp. 59-128, the rest is introduction to general energy

issues, fission, hot fusion and muon catalysed cold fusion. There is some

focus on science-sociological factors. Kuhn, Popper, Wolpert, Archimedes,

Galilei, Newton, Maxwell and Einstein are brought in. The new has always

assimilated the old. But is cold fusion science? The author does not decide.}

}

Here it is converted to the EndNote summary format:

Basile, A., Fusione Fredda ('Cold Fusion'). 'E possibile l energia nucleare senza rischi?' ('Is nuclear energy without risks possible?'). 1999, Rome: Avverbi Edizioni.

Here it is in EndNote export format:

%0 Book

%A Basile, A.

%D 1999

%T Fusione Fredda ('Cold Fusion'). 'E possibile l energia nucleare senza rischi?' ('Is nuclear energy without risks possible?')

%C Rome

%I Avverbi Edizioni

%! Fusione Fredda ('Cold Fusion'). 'E possibile l energia nucleare senza rischi?' ('Is nuclear energy without risks possible?')

%@ 88-87-328-08-0

%Z {A slim volume, roughly contemporary with that of Germano, this one outlining in an even-handed way (and sober tone) the story of cold fusion, especially the role played by Italian scientists. The main section on CNF itself is on pp. 59-128, the rest is introduction to general energy issues, fission, hot fusion and muon catalysed cold fusion. There is some focus on science-sociological factors. Kuhn, Popper, Wolpert, Archimedes, Galilei, Newton, Maxwell and Einstein are brought in. The new has always assimilated the old. But is cold fusion science? The author does not decide.

Anyone with the free version of EndNote can import the entire EndNote export file with no data loss. It would preserve the distinctions between books, papers, patents and so on. I can convert that file to MySQL with some loss of data. I do not preserve all of the fields. Here is the MySQL file that the EndNote records convert to:

LIBRARY

In the Britz Journal articles index, items are associated with Dieter's own scans, like this:

@article{Abel1990,

author = {G.~C. Abell and L.~K. Matson and R.~H. Steinmeyer

and R.~C. Bowman Jr and B.~M. Oliver},

title = {Helium release from aged palladium tritide},

journal = {Phys. Rev. B: Condens. Matter},

volume = {41},

year = {1990},

pages = {1220--1223},

keywords = {Experimental, helium mobility in metal, res0},

submitted = {10/1989},

published = {01/1990},

annote = {Tritium decays by beta emission and forms He; so if you let

PdT(x) stand, you accumulate He in the Pd. An interesting question for cold

fusion people looking for He, where should they look for it? In the solution

or gas outside the Pd, or inside? In other words, how fast does any He come

out? These authors examine this and find that, for small He "loadings" (<0.5

He/Pd), the He is practically not released, and that temperatures exceeding

1300 K are needed to drive it out.}

}

Where Abel1990.pdf is the scanned image. We can copy this to the URL field in the EndNote record.

Or we could add the URL for papers at LENR-CANR.org to the URL, or to another user-defined field.

I already have that Abell paper in my EndNote database. Here it is in export format:

%0 Journal Article

%A Abell, G. C. %A Matson, L. K. %A Steinmeyer, R. H. %A Bowman Jr., R. C. %A Oliver, B. M.

%D 1990

%T Helium release from aged palladium tritide

%B Phys. Rev. B: Mater. Phys.

%V 41

%N 2

%P 1220

%! Helium release from aged palladium tritide

%K Helium diffusion, PdT

I did not include the Abstract. Honestly, I just did not bother to include it. Here is a record with an Abstract and the URL in the URL field (%U):

%0 Journal Article

%A Rothwell, J.

%D 1999

%T Transistors and Cold Fusion - Part I

%B Infinite Energy

%V 5

%N 25

%P 32

%! Transistors and Cold Fusion - Part I

%K history, materials

%X The history of transistors teaches many lessons about how cold fusion might develop and what should be done to help it along. Transistors are physically similar to cold fusion devices. In fact, some of the earliest experimental transistors were immersed in electrolyte with a counter electrode to neutralize the surface barrier. . . .

%U http://lenr-canr.org/acrobat/RothwellJtransistor.pdf

Summary:

Rothwell, J., Transistors and Cold Fusion - Part I. Infinite Energy, 1999. 5(25): p. 32 http://lenr-canr.org/acrobat/RothwellJtransistor.pdf

To convert from the Britz file formats, you have to know what all those strange EndNote codes mean. %U for URL is clear. %A for Author and %D for date are clear, but many of the others are obscure, such as %X for Abstract.

I was hoping to ask orsova to do this. He's very capable.

Quote from Alan Smith

I was hoping to ask orsova to do this. He's very capable.

It is not a lot of work but I wonder if there is any point to it. Would it have advantages over the as-received version? (https://lenr-canr.org/acrobat/BritzDcoldnuclea.pdf) Here are the steps to do this:

1. Create an endnote test database.
2. Manually add one or two records from each of the Britz files to the EndNote database text files. The format and fields in each of the text files appears to be different.
3. Output the database in Export format.
4. Make note of each field type and the code EndNote assigned to it, such as %A author, %D date.
5. Write a program to parse each of the database text files, converting them to endnote export format. The program would flag any unrecognizable field, so we don't need to worry if there are one or two records with seldom used field names.

We would then have an endnote database which can be output in a variety of formats. I can convert it to MySQL with the program I already have. Then what? What would we do with this? Is there someplace we want to upload it? LENR-CANR.org already has the as-received version. I could upload a MySQL version I guess.

Quote from JedRothwell

%X for Abstract.

X is for extract...

Hello Alan and Jed,

Replying here in lieu of email.

You’ll have to forgive me, as my laptop died the other day, and so I’m working off my phone for the moment.

Consulting the bibliography mirror here:

Britz's cold nuclear fusion collection

It seems like the whole bibliography is formatted for Bibtex.

Could the path of least resistance be to reformat the text files at the mirror into .bib Bibtex files and then use Endnote’s inbuilt import functions?

The below link suggests that Endnote doesn’t handle Bibtex well, but that taking a round trip through Zotero seems to work.

How do I convert my typed bibliography in Word into reference in EndNote? - LibAnswers

There is also JabRef. The below blog (though old) suggests something similar.

https://www.jabref.org

My instinct is to first try importing the bibliography as .bib files into JabRef, and then from there, exporting out to Endnote.

Assuming it’s not time critical, I’m more than happy to take a pass at it and see if I can get it done - following my impending return from the land of the technologically dispossessed.

If the project requires a more manual parsing using some custom programming then I may need to defer back to Jed’s expertise.

Re: the value of converting to Endnote.

Would offering the bibliography in both formatted Bibtex and Endnote files at LENR-CANR.org have worth? Trying to import the bibliography from the PDF is (I think?) hampered by the PDF page numbers, which frustrate a simple copy - paste - save into .bib format.

Best,

Seamus

Quote from Alan Smith

X is for extract...

The EndNote screens call this field "Abstract."

Quote from orsova

It seems like the whole bibliography is formatted for Bibtex.

Could the path of least resistance be to reformat the text files at the mirror into .bib Bibtex files and then use Endnote’s inbuilt import functions?

So it is. I forgot that. Years ago I tried importing Britz records into EndNote using the EndNote Bibtex format. It did not work. Just now I tried again. It still does not work, but perhaps the files need some minimal adjustment. I exported a record from EndNote in Bibtex format. Here it is:

@article{RN3562,

author = {Rothwell, J.},

title = {Transistors and Cold Fusion - Part I},

journal = {Infinite Energy},

volume = {5},

number = {25},

pages = {32},

abstract = {The history of transistors teaches many lessons about how cold fusion might develop and what should be done to help it along. Transistors are physically similar to cold fusion devices. In fact, some of the earliest experimental transistors were immersed in electrolyte with a counter electrode to neutralize the surface barrier. . . .},

keywords = {history, materials},

url = {http://lenr-canr.org/acrobat/RothwellJtransistor.pdf},

year = {1999},

type = {Journal Article}

}

I will try to find out why the Britz records fail to import. If I can fix that, it will only take a few minutes to upload the entire Britz database into EndNote. From there we can do anything we like with it. That would be easier than writing a program to reformat the records into EndNote export format.

Here are two Bibtex records. This is from Britz:

@book{B.Beau2000,

author = {C. G. Beaudette },

title = {Excess Heat. Why Cold Fusion Research Prevailed},

publisher = {Oak Grove Press, LLC},

address = {South Bristol, Maine},

year = {2000},

isbn = {0-9678548-0-6 (hb), 0-9678548-1-4 (pb)},

annote = {This book strongly argues the reality of cold fusion, as

originally proposed by Fleischmann \& Pons. The author admits that there is as

yet no satisfactory theory to explain F\&P's results, and that all evidence

other than excess heat is insufficient. But the excess heat has never been

disproved and stands. Therefore, no matter the lack of theory or whether in

fact fusion is taking place, something anomalous is happening.}

}

This is output from my EndNote files for the same book:

@book{RN283,

author = {Beaudette, C. G.},

title = {Excess Heat: Why Cold Fusion Research Prevailed},

publisher = {Oak Grove Press},

address = {Concord, NH},

abstract = {This document contains extracts from the book, and the author’s description of the book: This book tells the history of the strangest event in modern science. In 1989 the University of Utah announced a new experiment by electrochemists Professors Martin Fleischmann and Stanley Pons that demonstrates table top nuclear fusion at extremely low levels, and substantial anomalous (unexplained, excess) heat energy (power) with no dangerous radiation. This story, written for the college reader without scientific training, presents the abundant replication of excess heat results by many laboratories in several countries. Excess heat research, referred to as cold fusion research, is presently an empirical science known as low energy nuclear reactions (LENR). While the book illustrates much progress, the specific reactions that produce the heat energy still await discovery. . .},

keywords = {history book},

url = {http://lenr-canr.org/acrobat/BeaudetteCexcessheat.pdf},

year = {2002},

type = {Book}

}

Some of the field names are different. There must be some difference that makes EndNote choke on the Britz files, failing to import them.

EndNote does not even want to import its own Bibtex file! Not good. However, I found a work-around. Here is an online utility that converts Bibtex to RIS:

I used this to convert the Britz Books index to RIS, and then imported it to EndNote. It looks good. Then I output all 4,755 LENR-CANR.org records to Bibtex, converted to RIS, and imported them into EndNote. I think they are all the same, but I am going to run some comparison tests to be sure.

If this works, I should be able to convert all of Britz records into just about any format we want.

. . . Okay, it sorta works. Somewhat. There are mysterious discrepancies. In some cases the EndNote version exported and then imported dropped the Date out of the record, which is a serious problem. However, the Britz records converted to RIS and then imported into EndNote seem to survive more or less intact.

I used the online utility program to convert the Britz BibTeX records RIS format. I input the RIS records into EndNote. Some of the records seem to be changed slightly, but the correct number of items show up. The Reference Types all show up as "Journal Article." I have manually changed some of the 10 groups to some other Reference Type such as Patent. I left all 1,535 Papers as Reference Type "Journal Article."

So I now have an EndNote file with 2,604 records. I can do searches for authors, titles and so on. I have attached it to this message in EndNote Export format.

I can convert it to some other format if anyone would like that. Or you can upload it to a free copy of EndNote and change it yourself. You can do all kinds of searching with EndNote. I can probably convert this file to MySQL without losing much data. I am not sure what else I might do with it. Let me know if you have suggestions.

My problems with the BibTeX format illustrate the Three Great Incompatibles:

1. In hardware stores, one-size-fits-all fits nothing.
2. Software standards are not . . . standard.
3. In his brief career doing experimental physics, Arthur Clarke said that he found the universal constants are remarkably variable.

This probably has something to do with quantum physics. Or blockchain bitcoin technology.

For what it’s worth (maybe not much), Endnote seems to have several different Bibtex import filters available for download.

Import Filters

Choose from hundreds of EndNote import filters to transfer data you previously downloaded from a library or other information provider.

endnote.com

Glad that it seems to have been possible to convert them with minimal hassle.

Am I right in understanding that this bibliography is already subsumed in the wider LENR-CANR bibliography? Ie. if I import the whole L-C biblio into a reference manager, I’ll get all of these Britz references included?

Quote from orsova

Am I right in understanding that this bibliography is already subsumed in the wider LENR-CANR bibliography? Ie. if I import the whole L-C biblio into a reference manager, I’ll get all of these Britz references included?

Most of it is subsumed. When I started in 2002, I began with Ed's EndNote files, and then I compared the entries to Dieter's files. I don't recall how I did that, but I would have used a program tool. I think I manually added all the records from Dieter that were missing. Some years later I looked again.

I will write some sort of program or use Microsoft Word file Review, Compare feature to compare them again.

Dieter also provided me and others with scanned copies of all of the papers in his bibliography. I think all of them -- there may be a few missing ones. The BibTeX files from Dieter list the acrobat filenames he assigned to them. For example:

@article{Abel1990,

author = {G.~C. Abell and L.~K. Matson and R.~H. Steinmeyer

and R.~C. Bowman Jr and B.~M. Oliver},

title = {Helium release from aged palladium tritide},

journal = {Phys. Rev. B: Condens. Matter},

volume = {41},

year = {1990},

pages = {1220--1223},

keywords = {Experimental, helium mobility in metal, res0},

submitted = {10/1989},

published = {01/1990},

annote = {Tritium decays by beta emission and forms He; so if you let

PdT(x) stand, you accumulate He in the Pd. An interesting question for cold

fusion people looking for He, where should they look for it? In the solution

or gas outside the Pd, or inside? In other words, how fast does any He come

out? These authors examine this and find that, for small He "loadings" (<0.5

He/Pd), the He is practically not released, and that temperatures exceeding

1300 K are needed to drive it out.}

}

That's the file Abel1990.pdf, 247 KB. Poor quality:

It is an image-only Acrobat file. With the latest Adobe Acrobat program, you can convert it to text format. Here is the Abstract:

Experimental studies of helium release from aged PdT% show that the helium-to-metal-atom ra-tio saturates at a value of [He]/(Pd) =0.5 under conditions of ambient-temperature storage. Below this value, very little helium release occurs. Thermal desorption experiments show that release from a sample with (Hel/[Pd)=0.3 requires temperatures in excess of ~600 K, while release from a sample with (He)/[PdJ =0.02 requires temperatures in excess of at least 1300 K. These results are related to the question of the disposition of helium that would be produced by hypothetical fusion reactions in a PdDx electrode.

This is what it looks like:

Unfortunately many of these paper are copyright, and even the ones which are not are very poor scan quality, not suitable for uploading. Although I must say, the latest version of Adobe Acrobat does a bang-up job of improving them, as you see. It would still be a lot of work to make them presentable. There are many errors in the underlying text, as you see in the Abstract above.

Someone just mailed me several boxes of printed old cold fusion papers. I will scan them. The quality should be better than Dieter's scans. Modern scanners are much better than the one he used. I have an EPSON ES-400 which produces remarkably good scans. It is double sided and very fast. Scanning all those papers will take me a while. Days, or weeks.

Here is another page from Abell. I have put red boxes around some of the problems.

I think these would all have to be corrected to make this presentable. Essentially, you have to convert the paper to text and start all over again. That is what did with all of the early papers I uploaded to LENR-CANR.org. Such as this one:

https://lenr-canr.org/acrobat/WillFGtritiumgen.pdf

You can see the original here:

https://lenr-canr.org/acrobat/EPRIproceeding.pdf#page=197

Here is the underlying text from the right side of this image:

In previous work, 19 PdTx powder was found to retain

essentially all of the helium generated by tritium decay

during ambient-temperature storage for over 1300 days

(i.e., (He}/[Pd) ratio S!i0.I). Thomas and Mintz 11 observed

bubbles with diameters 1.5-2.0 nm and a density

of about (5-lO)xI0 23 bubbles/m 3 in their TEM images

of Pd foil that had aged 66 days in the tritide phase Ci.e.,

[TJ/[Pd]a!0.6). N M R measurements 10•12 of the 3He

concentrations and relaxation times in aged PdT x samples

also indicated that helium retention is primarily in bub•

bles and that the density of helium atoms in the bubbles is

extremely high; moreover, little (if any) helium escapes

the solid when PdT x is stored at ambient temperature.

The present article provides additional information con•

cerning helium release from PdTx . Specifically, it has

been found that under conditions of ambient-temperature

storage, nearly all the helium born in the solid is retained

up to a saturation concentration of {He)/{Pd) Gl!l0.5.

Furthermore, thermal-desorption experiments show that

temperatures appreciably greater than 1300 K are re•

quired to release the trapped helium when {He]/[Pd]

a!0.02.

I may get another copy of this papers soon, which I can scan to make a much better image. As you see, this is not copyright, so I can upload it.