OSE3: Obhajoby interpretacíVe dnech 24.11. a 8.12.

• Začněte posílat mailem (vlhavlic@biomed.cas.cz) svoje PPT, deadline je čtvrteční půlnoc 19.11.

• Pořadí obhajob bude podle doručenky, pořadí v rámci prvního oponentního dne sdělím nejpozději v pondělí 23.11.

• Měli bychom stihnout za 90 minut 11 prezentací…• Max. pětiminutová prezentace s popisem spekter

a navrženou strukturou. Následují rýpavé dotazy (M. Kuzma, D. Milde, já)

“Some see this asa threat, a way todisprove something.That’s not whatthis is about.”Timothy Errington, ReproducibilityProject: Cancer Biology

“You can’t give meand Julia Childthe same recipe andexpect an equallygood meal.”Jeff Settleman,Calico Life Sciences

Repeat failures

6 of 53Cancer papers thatAmgen couldreproduce

14 of 67Biomedical papersthat Bayer completelyreproduced

26 JUNE 2015 SCIENCE sciencemag.org • VOL 348 ISSUE 6242

on 1 July, Dong-Pyou Han, a formerbiomedical scientist at Iowa StateUniversity in Ames, was sentenced to 57months in prison for fabricating andfalsifying data in HIV vaccine trials. Hanhas also been fined US$7.2 million and willbe subject to three years of supervisedrelease after he leaves prison.

N AT U R E | VO L 5 2 3 | 9 J U LY 2 0 1 5

Han was forced to resign from Iowa Statein 2013, after the university concluded thathe had falsified the results of severalvaccine experiments supported by grantsfrom the US National Institutes of Health(NIH). In some cases, Han spiked rabbitblood samples with human HIV antibodiesso that the vaccine seemed to havecaused the animals to develop immunity tothe virus.

Databázové zdroje v literatuřePirátské konference

Vladimír Havlíček

Universita Palackého v Olomouci

• Literatura, osoby, nově i patenty• Additional Resources

http://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch

http://d360prx.biomed.cas.cz:2199/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch

Web of Science

Pro každou instituci: jiné VPN nastavení pro přístup zvenku, př.:http://portal.upol.cz/wcmfiles/CVT/InformaceNavody/PocSit/VPN_XP.pdf

• nutná primární registrace ze školní domény

• https://scifinder.cas.org/registration/index.html?corpKey=95E28B1BX86F35055X194125D419D39576E7

zadává se mj. email jméno.příjmení@upol.cz, na který přichází konfirmační mail

Pak se do SciFinderu lze dostat odkudkoli ze školy (VPN)• https://scifinder.cas.org

SciFinder

SciFinder Scholar (Web Version)

SciFinder Scholar is the premier database to abstracts of the chemical literature, but also has extensive coverage of all chemically related sciences.•Limited licence:

4 simultaneous usersIf you can’t get on try again later

•Scope:Chemical Abstracts from the Chemical Abstracts Service (CAS)(including related substance and reaction databases).Medline from 1950-PATENTS!!!…………

The top menu options:

Explore allows direct searches of the references or abstracts:•Research topic (default search)Allows keyword/subject searching. However it uses a natural language algorithm, so just enter your query as a sentence and see what happens. (This works best if you use words like ‘in’ ‘with’ or ‘of’ between your keywords/phrases. For example, search on: mass imaging by DESI)•Author NameAuthor entries are not uniform. However you can check for variants of names. (Example: enter Havlicek, Vladimir)•Company NameSearches relevant address fields (For example: Institute of Microbiology Prague)Document Identifier

Enter specific CAS document numbers to locate specific abstracts•JournalUse to find a specific article abstract where you know the details (title, journal, volume, pages, date, etc.)

• Substance IdentifierThis is the easiest way to find specific compounds. Search on the substance’s common name, trade name, CAS Registry number or whatever. The results you get are compounds from the Registry file. Select the desired compound(s) and click Get References to get to the list of References that mention the compound(s).

• Chemical StructureSciFinder allows the literature to be searched and linked by chemical structures that CAS has indexed. Basic instructions are online

• Molecular FormulaAllows formulas to be given but they have to be precise and in the correct format (Carbons, Hydrogens, then alphabetical). Many compounds can have the same formulas. As a result it is generally better to use the Substance Identifier option for specific compounds.

Viewing Reference Results

To export to Endnote, select the Tagged format and save the file to your computer. To load the references into your EndNote Library, open your library and select the tagged file using File:Import and the SciFinder filter.Note: If no references are selected SciFinder defaults to exporting the first 100 in the list.

• Reaction Structure SearchingSciFinder allows substances structures in reactions to be searched (e.g.: for products, catalysts, etc.)

Software pro reference• http://www.endnote.com/enhome.asp• Standard, současná verze X7 64 bit• Zdarma: EndnoteWeb, JABREF….

Takže pro koho se to hodí

• Disertační práce po školitelově revizi (redukce na 30 procent původního objemu)

• Nature-Science-PNAS-JBC-Indian Journal ofNegative Results

http://endnote.com/support/faqs/endnote

• Windows 8 and later•• 1. Close all open programs.

2. Go to the EndNote program folder. This is typicallyC:\Program Files\EndNote XXorC:\Program Files (x86)\EndNote XXWhere XX represents your version of EndNote

3. Right click on EndNote.exe and select "Run as administrator."4. With EndNote open, Go to Start Screen (clicking the Windows key on the keyboard brings up this window).5. On the Start Screen type "regedit" (without quotes) and hit enter on your keyboard to launch the Registry Editor.6. Expand the "HKEY_CLASSES_ROOT" folder and locate the key:

"EndNote11.AddinServer" (for X1)"EndNote12.AddinServer" (for X2)"EndNote13.AddinServer" (for X3)"EndNote14.AddinServer" (for X4)"EndNote15.AddinServer" (for X5)"EndNote16.AddinServer" (for X6)"EndNote17.AddinServer" (for X7)

7. Right Click on the AddinServer key and select Permissions.8. Select Advanced.9. Under "Permission Entries" choose Add.10. On the Permission Entry Screen Next to Principal choose "Select a Principal"11. In object name, type "Everyone" (without quotes) and select Ok.12. To the Right of Basic permissions, click "Show advanced permissions"13. Select the "Full Control" box to check all the boxes.14. Select the "Delete" box to remove the check from Delete. (This will also remove the check next to full control, this is expected)15. Choose OK. Choose OK again.16. Close the Registry Editor and close EndNote.17. Start EndNote and Word normally.

Invalid class stringChybný řetězec třídy

How to Get Endnote to Abbreviate Journal Names: Journal Term List

Some citation formats use abbreviations for journal name rather than the full journal name.Endnote uses Journal Term Lists to substitute abbreviated journal titles for full journal titles.See the video link at left for an excellent 4 1/2 minute explanation of how to do this.Or, follow the steps below to import a term list, and modify the Output Style of your choice to use it.

1. Import and Edit the Journal Term ListThe Term List allows Endnote to substitute the abbreviated title for the full journal title.This step creates the journal term list you need.

In Endnote, select:Tools > Open Term Lists > Journals Term List

If Journals are already present in the list,delete them (some may have info in wrong column)To do this: Select all journals, then click DELETE TERM

Select LISTS tabSelect JOURNALSSelect IMPORT LIST

Open Terms List folder in (usually found at: C://Program Files/Endnote/Term Lists)Double Click on the list you want to importClick the OK button

The list you imported may not have all the journals you want.You can update the list to add journal titles from the citations in your libraryYou can edit the list to add or modify journal names/abbreviations

To Update the List:Click UPDATE LIST BUTTONClick OK button

To Edit the List:Select TERMS tab: You will see a list of full journal names and their abbreviationsIf information is missing or incorrect, edit or add it hereSelect the journal you want to editClick on EDIT TERM button, correct each field, and hit OKIf you are not sure of the appropriate journal abbreviation for Chemistry journals,Use CASSI (CAS Source Index Search Tool) to find out the correct abbreviation

2. Modify The Output Style So The Abbreviated Journal Name Is Used:The step modifies the Output Style of your choice to use the abbreviated journal name.

Select the Output Style you want to modify so journal abbreviations are used.Edit > Output Styles > Name of Style you want to edit.If the Output Style you want is not shown, select OPEN STYLE MANAGER and select it from

there.

Select JOURNAL NAMES at the far left.Under “Journal Name Format” select the field you want used, usually this will be

“Abbreviation 1”Save the output style with a new name

Finally: add the new output style you created to the Output Style Window, select it and journals titles should display as abbreviations.

Pokud tvoříte vlastní journal term list

• Sloučit Chemistry, Physics, Medical• Vyházet duplicity (pokud je na jednom řádku

nezkrácený název časopisu, přestane to fungovat)

• Exportovat si vlastní term list a ten používat

Odkaz na článek v periodiku: 1. Mestek O.: Collect. Czech. Chem. Commun 63, 347 (1998). 2. Lon X., Mffler D.J., Hawthome S.B.: Anal. Chem. 72, 481 (2000).

Odkaz na článek autora zcela nepřístupného: 3. Bauderowski J.: Zesz. Politech. Slask. Energ. 1964, 1. Citováno podle Chem. Abstr. 66,

14410 (1967).

Odkaz na knihu: 4. Malát M.: Absorpční anorganická fotometrie. Academia, Praha 1973.

Odkaz na stať v knize: 5. Vláčil F. a kolektiv: Příklady z chemické a instrumentální analýzy, 4. vydání, kap. 17.

Informatorium, Praha 1991.

Odkaz na článek ve sborníku: 6. Tatarkovičová V.: Možnosti extrakce a čištění extraktů při analýzách organických polutantů, str.

52. In: Sborník přednášek z kurzu Analýza organických látek, Ed. Ing. Václav Helán - 2 Theta, Český Těšín 1999.

Odkaz na disertační práci: 7. Novotný K.: Využití membránových technik pro zkoncentrování a speciaci prvků v

AAS. Doktorská disertační práce, Masarykova Univerzita, Brno 2000.

Templát Chemických listů

Odkaz na článek v periodiku: 1. Mestek O.: Collect. Czech. Chem. Commun 63,

347 (1998). 2. Lon X., Mffler D.J., Hawthome S.B.: Anal.

Chem. 72, 481 (2000).

Open Access

Science 4 October 2013: 58-59.

New ACS Open Access Initiatives

Important because of OA policies required by funding sources in other countries Four main components of how ACS is open • ACS Central Science – journal to be launched late 2014, free to readers and authors • ACS Editors’ Choice – 1 article chosen each day, free public access to new research

of importance, (Editors) selection can be made before acceptance in ACS Paragon Plus, also change manuscript type to Editors’ Highlight

• ACS Author Rewards – vouchers to be used in future submissions (2015-2017), encourages ACS authors to choose open access

• ACS Author Choice – includes new options to help authors meet open access requirements

What is the impact of OA? There are a few studies showing the impact of OA (although statistically intensive and hard to comprehend) – studies published in OA journals concluded that OA provides a positive impact, whereas studies published in non-OA journals concluded opposite results

Science 4 October 2013: 58-59.

Location of a journal's publisher, editor, and bank account are often continents apart

J Bohannon Science 2013;342:60-65

Science 4 October 2013: 58-59.

Who's Afraid of Peer Review?

A spoof paper conducted by Science reveals little or no scrutiny at many open-access journals.

The Power of Negative Thinking

Gaining ground in the ongoing struggle to coax researchers to share negative results.

Journal of Negative Results: Ecology & Evolutionary Biology. A group of postdocs at the University of Helsinki conceived of the journal in the early 2000s and launched it in 2004. Its publication record is paltry; it gets only two or three submissions a year.

Jonathan SweedlerAnal. Chem. 2013, 85, 9983−9983