How a simple botanist is collecting his readings, Latest revision: February 1, 2015

1. How a simple botanist is collecting his readings, Latest revision: February 1, 2015 Klaus Ammann, emeritus University of Bern, klaus.ammann@ips.unibe.ch Literature search and citation, for Manuscripts, Publications and Slideshows

2. First the simple tricks, no need to go over the Bibliographic programmes, direct access via Google Scholar www.scholar.google.org: Here you do not need access through a priviledged IP, see next slide for more google details. Just type part of the publication title and add at the beginning the first author name (if necessary) in order to clearly identify the paper you are looking for. You will get in the majority of the cases the full link to the publication journal website And if you are lucky you can click at the right to the pdf link directly) If not successful in this first attempt, you need a privileged access with a university IP with access to the journals to read the full pdf. Using the internet from inside a University institution, there is no problem sicne you are automatically linked to a Priviledged IP http://en.wikipedia.org/wiki/IP_address (see first overview of services for University of Bern in German http://www.ub.unibe.ch/content/index_ger.html You can get the priviledged University IP from home or travel over the VPN-Service (various programmes available, Universities use often Cisco) http://www.id.unibe.ch/content/services/virtual_private_networking_vpn/auf_einen_blick/index_ger.html Usually, the journal websites automatically recognise privileged IP addresses of the Universities and grant direct access. The Swiss University Network has access to some 80’000 Journals online for the full texts back to 1996.

3. An easy way to collect correct citations: The direct way over Google Scholar Get Google Scholar, if you do not have yet a direct button: Search for «Google Scholar» in the Google window Write in the Google search line Author (no first name necessary) and title (often only 4-7 words are enough) You get usually the bold title and to the right the link to the pdf or html, Sometimes the appropriate link is not on the first line, then scroll down to lowest line, leading directly to the Journals website, or another link for downloading the citation in your Endnote or other literature database. Then continue by producing a link to the pdf as described further on. This way you can often avoid to use the tedious way over the Web of Science and the journals website searching for the volume etc.

4. Web of Science, Web of Knowledge Most Universities and many public institutions have access to the Web of Science over the privileged University IP, over which you prefer to to your literature research. The later versions of the WOS have direkt buttons and links for the full text of the citations found, but again you need to be on the priviliged IP of a public institution (which you need anyway to have access to the Web of Science) JUST CLICK THE ISI- or DOI-LINK (WOS active!) of the reference looking like <Go to ISI>://WOS:000329636800001 or direct links by WOS like: http://dx.doi.org/10.1111/pbi.12305 As staff member or student you can also get access to the priviledged institutional IP inside the institution or by logging into the priviledged network by VPN (Virtual Private Networking) see procedure example:access through the University of Bern http://www.id.unibe.ch/content/services/virtual_private_networking_vpn/auf_einen_blick/index_ger.html

5. Web of Science, all databases Access only through priviledged IP from Institution participating In the consortium of University libraries. Staff and Students of most European University have access, also from outside with VPN (virtual private networking), see Example of the University of Bern: http://apps.webofknowledge.com/select_databases.do?highlighted_tab=select_databases&product=UA&SID=V1nGOzsBX8TpwOkXN7d&last_ prod=WOS&cacheurl=no Web of Science, all databases

6. Web of Knowledge, additional resources: http://apps.webofknowledge.com/additional_resources.do?highlighted_tab=additional_resources&p roduct=UA&SID=V1nGOzsBX8TpwOkXN7d&cacheurl=no Web of Knowledge, analytical tools and websites

7. Main search mode „biofuel AND crops“ in Topic http://apps.webofknowledge.com/UA_GeneralSearch_input.do?highlighted_tab=UA&product=UA &search_mode=GeneralSearch&SID=V1nGOzsBX8TpwOkXN7d&last_prod=WOS&highlighted_t ab=UA&cacheurl=no Web of Knowledge search mode

8. Web of Science: Search result: «biofuel and crops» first page 2224 references» The list as pdf: Full text window: direct download http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-20130906.pdf Web of Knowledge, results

9. Biofuels AND crops: Window of some reference examples (out of 2224), collected with Web of Science

10. Biofuel / crops from Web of Science and other Sources klaus.ammann@ips.unibe.ch 20130906 2224 references Abbadi, A. and G. Leckband (2011), Rapeseed breeding for oil content, quality, and sustainability, European Journal of Lipid Science and Technology, 113, 10, pp. 1198-1206, <Go to ISI>://WOS:000297012300004 Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2009), Promoting branching of a potential biofuel crop Jatropha curcas L. by foliar application of plant growth regulators, Plant Growth Regulation, 58, 3, pp. 287-295, <Go to ISI>://WOS:000266455600008 Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2009), Pollinator effectiveness, breeding system, and tests for inbreeding depression in the biofuel seed crop, Jatropha curcas, Journal of Horticultural Science & Biotechnology, 84, 3, pp. 319-324, <Go to ISI>://WOS:000272389300013 Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2012), Pollen viability, pollen germination and pollen tube growth in the biofuel seed crop Jatropha curcas (Euphorbiaceae), South African Journal of Botany, 79, pp. 132-139, <Go to ISI>://WOS:000302978900019 Abrahamson, L. P., D. J. Robison, T. A. Volk, E. H. White, E. F. Neuhauser, W. H. Benjamin and J. M. Peterson (1998), Sustainability and environmental issues associated with willow bioenergy development in New York (USA), Biomass & Bioenergy, 15, 1, pp. 17-22, <Go to ISI>://WOS:000074996000003 Abramson, M., O. Shoseyov and Z. Shani (2010), Plant cell wall reconstruction toward improved lignocellulosic production and processability, Plant Science, 178, 2, pp. 61-72, <Go to ISI>://WOS:000274877700001 Abreu, I. S., C. R. Carvalho, G. M. A. Carvalho and S. Y. Motoike (2011), First karyotype, DNA C-value and AT/GC base composition of macaw palm (Acrocomia aculeata, Arecaceae) - a promising plant for biodiesel production, Australian Journal of Botany, 59, 2, pp. 149- 155, <Go to ISI>://WOS:000288863200005 Acaroglu, M. and H. Aydogan (2012), Biofuels energy sources and future of biofuels energy in Turkey, Biomass & Bioenergy, 36, pp. 69- 76, <Go to ISI>://WOS:000300469700008 Window example biofuels AND crops, formatted references Ammann Klaus (20130906), Bibliography Biofuels AND crops: out of Web of Science and other Sources, 2224 references, in: ASK-FORCE, 131, Klaus Ammann, Neuchâtel, http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-0130906.pdf

11. Endnote 6 directories of .enl databases Klaus Ammann, 2006 (program see www.endnote.org ) Endnote library, part of directory

12. Endnote library, first page of the libraries of Klaus Ammann 2006 Endnote library, details

13. Endnote library, contents, selection references transgenic Poplars Status 2006 Endnote library, contents, GM poplars

14. Below: how to find a specific full text reference (formatted out of the Web of science): Gatehouse, A. M. R., N. Ferry and R. J. M. Raemaekers (2002), The case of the monarch butterfly: a verdict is returned, Trends in Genetics, 18, 5, pp. 249-251, http://www.botanischergarten.ch/Bt/Gatehouse-Case-Monarch-2002.pdf 1) If you do not have priviledged access through an acacemic Institution IP, then try the trick over google scholar described in the first slides, you often find an open pdf link. 2) if you have such a priviledged institutional IP, then you have the Option a) over the journal and download directly the pdf, if this (rarely) does not work, then option b) go over the Web of Science with a search or MUCH quicker over the doi-link of the reference, then the Web of Science shows directly the detailed reference with the full text button, (at least the recent versions are providing this button), often it also offers a direct link to google scholar with a direct pdf link.

15. Web of Science: Search result: «biofuel and crops» first page 2224 references» The list as pdf: a) Full text window: direct download b) Use DOI – link from any citation, go to ISI...but with WOS active http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-20130906.pdf Web of Knowledge, results

16. Pdf document on screen, you need store it on your system and it is recommended to produce an external link, see the recommended example www.hostpoint.com and buy space For 50 Gigabyte 14.90.- Fr. per month with daily backup, get a domain name (example ask-force.org), create an ftp link with password. Note: you have the Choice to make ftp files public or not, in my case I prefer it accessible only with a password.

17. Load up program Total Commander http://www.ghisler.com/ and pay a modest licence fee. You must program a connection to your ftp file to point left side to your host, right side to your hard disk site with the documents you want to transfer to the ftp-host Follow instructions in Total Commander when not connected over the button «connect to ftp server»

18. Draw the document name to your right to the ftp server of your host to the left with the Total Commander Copy-paste the link you have drawn to the ftp-host on the left ftp://server-010.hostpoint.ch/www/yourdomain.org/web/Bt1/Gatehouse-Case-Monarch- 2002.pdf to your endnote list under URL ftp://server.....hostpoint.ch/www/yourdomain.org/web/Bt1/Gatehouse-Case-Monarch-2002.pdf (only accessible with your password, but you may choose open access for everybody) Bt1 here the folder you have named for such documents on the host. To produce a single link which is publicly accessible through email: Replace on endnote citation «ftp://yourserver-.... Hostpoint.ch/www with http://www.domain-name.org The citation will be ready for any purpose: copy paste formated, also working with cite while you write, it will create with your bibliography format a bibliography list at the bottom of your manuscript automatically in some 3000 different formats for virtually all journals Gatehouse, A. M. R., N. Ferry and R. J. M. Raemaekers (2002), The case of the monarch butterfly: a verdict is returned, Trends in Genetics, 18, 5, pp. 249-251, http://www.ask-force.org/web/Bt1/Gatehouse-Case-Monarch-2002.pdf

19. If it is not possible to find on Google Scholar or Web of Science a full text link, then you have two possiblities: 1. Go to http://sv2qt7zb3k.search.serialssolutions.com/?paramdict=en-US Follow the instructions when the journal is listed, usually full text links are available back to 1996, there are numerous exceptions for availabilities back to No. 1 volume. It might also lead your search automatically to the big journal archive Istor, with priviledged IP you have generous access. 1. Go to NEBIS, information and instructions below http://www.nebis.ch/

20. How to access full text samples of journals, (since 2012) NEBIS offers to participants with login some 80’000 journals back to 1996 or earlier Regensburg System since 2012 replaced by NEBIS Netzwerk von Bibliotheken und Informationsstellen in der Schweiz http://www.nebis.ch/ EBZ Regensburg

21. Part of the result of a search for «Trends in Genetics»

22. Search entry «Trends in Genetics» then choice either NEBIS or direct access SFX Trends in Genetics free for NEBIS participants with login Trends in Genetics free for EZB participants

23. Choice of «Trends in Genetics» in NEBIS Overview of possibilities and volumes available Upper part

24. Choice of «Trends in Genetics» in NEBIS Overview of possibilities and volumes available Lower part, all available volumes

25. Gatehouse The Case of the Monarch butterfly full access to pdf With VPN (Virtual Private Networking) Login NEBIS or SFX, example of IP of University of Bern on Laptop Gatehouse The Case of the Monarch butterfly full access with VPN

26. Gatehouse, A.M.R., Ferry, N., & Raemaekers, R.J.M. (2002) The case of the monarch butterfly: a verdict is returned. Trends in Genetics, 18, 5, pp 249-251 http://www.botanischergarten.ch/Bt/Gatehouse-Case-Monarch-2002.pdf Gatehouse pdf document

27. Upload of pdf files to Bern server www.botanischergarten.ch Upload of pdf files to Bern server

28. Palm Desktop Memo: list of links, poplar, biofuel, (Hardware no more in use, programs still running ) Palm Desktop links poplar biofuel

29. Endnote library, contents, section of transgenic Poplars Endnote library, contents, GM poplars

30. Manuscript citations with authors in text

31. Manuscript citations with numbers

32. Literature alphabetic, with links to pdf Literature alphabetic, with links to pdf

33. Literature numbered, without links to pdfs Literature numbered, without links to pdf

34. Ammann, K. (2005), Effects of biotechnology on biodiversity: herbicide-tolerant and insect- resistant GM crops Trends in Biotechnology, 23, 8, pp. 388-394, <Go to ISI>://000231342700005 AND http://www.botanischergarten.ch/TIBTECH/Ammann-TIBTECH-Biodiversity-2005.pdf Effects Publication

35. Example of a recent publication: Ammann Klaus (20130415), Genomic Misconception. A fresh look at the biosafety regulation of transgenic and conventional crops: a plea for a process of agnostic regulation, open source, final version, in: New Biotechnology, 30, 50 and typeset 17pp, Ammann K., Neuchatel, http://www.sciencedirect.com/science/article/pii/S1871678413000605 AND With full text link-references, not for publication http://www.ask-force.org/web/NewBiotech/Genomic-Misconception-20130415-names-links.pdf AND typeset corrected: only publicly available full text links http://www.ask-force.org/web/NewBiotech/Ammann-Genomic-Misconception-corrected-final-20130514.pdf AND German Abstract http://www.ask-force.org/web/NewBiotech/Ammann-German-Abstract-Highlights-20130415.pdf Recently product oriented regulation has been proposed also by DEFRA from the UK http://www.ask-force.org/web/Genomics/Ammann-Progress-in-Genomic-Misconception-View-20130906.pdf

36. Werner Arber, Nobel Laureate 1978: Interestingly, naturally occurring molecular evolution, i.e. the spontaneous generation of genetic variants has been seen to follow exactly the same three strategies as those used in genetic engineering14. These three strategies are: (a) small local changes in the nucleotide sequences, (b) internal reshuffling of genomic DNA segments, and (c) acquisition of usually rather small segments of DNA from another type of organism by horizontal gene transfer. Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf Arber

37. However, there is a principal difference between the procedures of genetic engineering and those serving in nature for biological evolution. While the genetic engineer pre-reflects his alteration and verifies its results, nature places its genetic variations more randomly and largely independent of an identified goal. Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf Arber

38. Scatter plot representation of transcriptome comparisons, Baudo et al. 2006 Transgenic Wheat: Where Do We Stand after the First 12 Years? Annals of Applied Biology, 147, 1, Baudo, M.M., Lyons, R., Powers, S., Pastori, G.M., Edwards, K.J., Holdsworth, M.J., & Shewry, P.R. Transgenesis Has Less Impact on the Transcriptome of Wheat Grain Than Conventional Breeding. Plant transgenic vs. control endosperm 14 dpa 28 dpa 8 dpg http://www.botanischergarten.ch/Organic/Shewry-Performance-2006.pdf 2 conventional lines Endosperm 14 dpa 28 dpa leaf at 8 dpg http://www.botanischergarten.ch/Organic/Baudo-Impact-2006.pdf Biotechnology Journal, 4, 4, pp 369-380 Shewry, P.R. & Jones, H.D. (2005) transgenic vs. conventional Endosperm 14 dpa 28 dpa leaf at 8 dpg pp 1-14 (2006) Baudo: comparison in genomic disturbance: GM crops are less disturbed (black dots) than classic breeds

39. EU-Project Wider Fields, Ammann-Kovacovsky-2008 Huesken, A., Ammann, K., Messeguer, J., Papa, R., Robson, P., Schiemann, J., G., S., Stamp, P., J., S., & Wilhelm, R. (2007) A major European synthesis of data on pollen and seed mediated gene flow in maize in the SIGMEA project. In GMCC-07, Third International Conference on Coexistence between Genetically Modified (GM) and non-GM based Agricultural Supply Chains, Seville Spain http://www..botanischergarten.ch/SIGMEA/Huesken-Synthesis-2007.pdff Wider Fields

40. A real health problem, But not discussed, Since it does not Concern transgenic crops Bilsborrow, P.E., Evans, E.J., Bowman, J., & Bland, B.F. (1998) Contamination of edible double-low oilseed rape crops via pollen transfer from high erucic cultivars. Journal of the Science of Food and Agriculture, 76, 1, pp 17-22 http://www.botanischergarten.ch/Brassica/Bilsborr ow-Contamination-Edible-1998.pdf Real health problem

41. Phylogenesis Maize and Teosinte Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, G.J., Buckler, E., & Doebley, J. (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America, 99, 9, pp 6080-6084 http://www.botanischergarten.ch/Bt/Matsuoka-Single-Domestication-2002.pdf

42. in the US maize yields have accelerated in the last ten years • actual breeding plus cultural practice gain Troyer, A.F. (2006) Adaptedness and Heterosis in Corn and Mule Hybrids. Crop Science, 46, 2, pp 528-543 http://crop.scijournals.org/cgi/content/abstract/cropsci;46/2/528 AND http://www.botanischergarten.ch/Bt/Troyer- Adaptedness-Heterosis-2006.pdf

43. corn yields in France and Italy in the last 10 years fail to show the same trend http://epp.eurostat.ec.europa.eu/portal/page?_pageid=0,1136206,0_45570464&_dad=portal&_schema=PORTAL