Wednesday, June 24, 2009

2008 Journal impact factors released

2008 Journal impact factors released

Thomson Reuters has just published the 2008 Journal Citation Reports, available to UW-Madison library users. These metrics, including the "impact factor," can be used to compare journal performance. JCR includes 8,000+ highly cited, peer-reviewed journals from around the world.

New features:

  • 350+ new journals with their first published impact factor
  • Updated 5-year impact factors and Eigenfactor metrics
  • "Journal self cites" analyzes the contribution of self-citation to the impact factor (20 journals were dropped from JCR due to high self citation rates)
  • "Rank in category" for each journal's subject area, along with a box plot of impact factor distribution for all journals in that category

Top 3 in Agronomy by impact factor:

  1. Agricultural and Forest Meteorology
  2. Theoretical and Applied Genetics
  3. Advances in Agronomy

Top 3 in Entomology by impact factor:

  1. Annual Review of Entomology
  2. Advances in Insect Physiology
  3. Insect Molecular Biology

Top 3 in Horticulture by impact factor:

  1. Theoretical and Applied Genetics
  2. Tree Genetics and Genomes
  3. Postharvest Biology and Technology

Top 3 in Plant Sciences by impact factor:

  1. Annual Review of Plant Biology
  2. Annual Review of Phytopathology
  3. Plant Cell

Friday, June 19, 2009

Coming soon: Proxy changes for licensed database access

Proxy changes for licensed database access
The UW Libraries are changing how we manage access to our online, licensed resources from campus computers. These changes have already been implemented for our library computer networks and now it's time to implement them for the rest of campus.

In order to better control access and remain in compliance with our license agreements, beginning on July 1st, all links from our pages to licensed, e-resource links, will be routed through our proxy server. For computers within the campus IP space, this routing will occur without the need for any user authentication. The only thing you will notice is a URL with an "ezproxy" string embedded in it. Computers outside of the campus IP space route through the proxy as they do now, with a need to authenticate with a valid NetID and password.

Users who have direct links or bookmarks to licensed resources, such as from campus computers will continue to be able to do so in the short term, but eventually as we notify vendors to only accept sessions from our proxy server IP address, they will be denied.

The most reliable way to maintain access to resources is to access them via our library web pages where all appropriate proxying is automatic. We do however realize that some users will wish to use direct links to licensed content. In order to facilitate this, we will be promoting a simple "bookmarklet" that will insert the proxy string into any URL. Users will be able to easily insert the proxy string using this bookmarklet and then create new bookmarks for future use. Information on this "bookmarklet" can be found at:

Why are we making this change?

The main reason we're making this change is because of the increasingly dynamic nature of the campus IP space and the proliferation of VPNs. With our current system if there are changes to the campus IP range (for example, an extension of a campus subnet to Research Park) or creation of VPN ranges, we must communicate it to hundreds of resource vendors. By bringing IP control back to our proxy server, we can make the changes locally (forcing authentication or not) and only require our vendors to allow sessions from the few proxy server IPs.

Why is this so complicated?

The main complicating issue is the way in which we license resources. The vast majority of them are licensed to allow anybody to use them while physically on the UW campus. In addition, any staff, faculty or student may use them from anywhere. So, we use a proxy server to confirm if a user is on campus, and if they are not, we force them to login to ensure they are staff, faculty or students.

Please let us know if you have questions or concerns about any of these changes, or if problems arise with resource access.

Tuesday, June 16, 2009

Biotechnology Abstract database: New interface

Biotechnology Abstract moves to OvidSP, from WebSPIRS SilverPlatter

"Derwent Biotechnology Abstract is a Biotechnology Literature and Patents Information Service produced by Derwent Information Ltd. The subject coverage includes all aspects of biotechnology, from genetic manipulation to biochemical engineering and fermentation to downstream processing. All industrial uses of microorganisms, enzymes, and cell culture are covered, as well as plant micropropagation."

"Information is extracted from around 1200 major scientific publications, including primary journals and conference proceedings, and from the patents literature."

Journals indexed include:
  • Agroforestry Systems

  • Annals of Botany

  • Biodiversity & Conservation

  • Biologia Plantarum

  • Biological Invasions

  • Biological Reviews

  • Euphytica

  • European Journal of Plant Pathology

  • FEBS Journal

  • Genetic Resources & Crop Evolution

  • Journal of Agricultural & Environmental Ethics

  • Journal of Experimental Botany

  • Journal of Forensic Sciences

  • Journal of Insect Behavior

  • Medical & Veterinary Entomology

  • Nature

  • Nutrient Cycling in Agroecosystems

  • Oikos

  • Photosynthetica

  • Plant & Cell Physiology

  • Plant & Soil

  • Plant Cell Tissue & Organ Culture

  • Plant Journal

  • Plant Pathology

  • Precision Agriculture

  • Soil Science

  • Tropical Medicine & International Health

NEW e-book! Encyclopedia of Genetics, Genomics, Proteomics, and Informatics

NEW! Online reference book provided by the UW-Madison Libraries:

Encyclopedia of Genetics, Genomics, Proteomics, and Informatics

"...covers the basics and the latest in genomics, proteomics, genetic engineering, small RNAs, transcription factories, chromosome territories, stem cells, genetic networks, epigenetics, prions, hereditary diseases, and patents."

"...about 56% more words than the 1,392-page second edition of 2003. The number of illustrations increased to almost 2,000 and their quality has improved by design and four colors. In addition, cross-references among entries are expanded and the statements are supported by references: more than 14,000 journal papers and more than 3,000 books are listed."

"Target audience includes research workers in general genetics, genomics, proteomics, biochemistry, molecular biology, cell biology, evolution, cytogenetics, human genetics, ethics, natural philosophy; professors...; physicians, law professionals; students...; science administrators and journal editors..."

Selected entries:

Monday, June 8, 2009

Light harvesting in plants

24 highly-cited papers from 2003 to 2009 form a "research front" on light harvesting in plants, as reported at

Topics covered include:
  • Carotenoid and regulation of light harvesting
  • Chloroplast protein kinase
  • Light stress
  • Organization of thylakoid proteins
  • Photo-inhibition
  • Photo-protection
  • Photosystem I - crystal structure
  • Photosystem II - core phosphorylation
  • Photosystem II - light-harvesting antenna
  • Photosystem II - repair
  • Plant antenna protein
  • Proteases in chloroplasts
  • Quenching
Papers in the research front:

Title: Crystal structure of spinach major light-harvesting complex at 2.72 angstrom resolution
Journal: NATURE, 428 (6980): 287-292 MAR 18 2004
Authors: Liu, ZF; Yan, HC; Wang, KB; Kuang, TY; Zhang, JP; Gui, LL; An, XM; Chang, WR

Title: Crystal structure of plant photosystem I
Journal: NATURE, 426 (6967): 630-635 DEC 11 2003
Authors: Ben-Shem, A; Frolow, F; Nelson, N

Title: Carotenoid cation formation and the regulation of photosynthetic light harvesting
Journal: SCIENCE, 307 (5708): 433-436 JAN 21 2005
Authors: Holt, NE; Zigmantas, D; Valkunas, L; Li, XP; Niyogi, KK; Fleming, GR

Title: Supramolecular organization of thylakoid membrane proteins in green plants
Journal: BBA BIOENERGETICS, 1706 (1-2): 12-39 JAN 7 2005
Authors: Dekker, JP; Boekema, EJ

Title: Rote of chloroplast protein kinase Stt7 in LHCII phosphorylation and state transition in Chlamydomonas
Journal: SCIENCE, 299 (5612): 1572-1575 MAR 7 2003
Authors: Depege, N; Bellafiore, S; Rochaix, JD

Title: Molecular basis of photoprotection and control of photosynthetic light-harvesting
Journal: NATURE, 436 (7047): 134-137 JUL 7 2005
Authors: Pascal, AA; Liu, ZF; Broess, K; van Oort, B; van Amerongen, H; Wang, C; Horton, P; Robert, B; Chang, WR; Ruban, A

Title: Evidence for direct carotenoid involvement in the regulation of photosynthetic light harvesting
Authors: Ma, YZ; Holt, NE; Li, XP; Niyogi, KK; Fleming, GR

Title: Photoinhibition - a historical perspective
Journal: PHOTOSYNTHESIS RESEARCH, 76 (1-3): 343-370 2003
Authors: Adir, N; Zer, H; Shochat, S; Ohad, I

Title: Is PsbS the site of non-photochemical quenching in photosynthesis?
Journal: JOURNAL OF EXPERIMENTAL BOTANY, 56 (411): 375-382 JAN 2005
Authors: Niyogi, KK; Li, XP; Rosenberg, V; Jung, HS

Title: Coordinated regulation and complex formation of YELLOW VARIEGATED1 and YELLOW VARIEGATED2, chloroplastic FtsH metalloproteases involved in the repair cycle of photosystem II in Arabidopsis thylakoid membranes Journal: PLANT CELL, 15 (12): 2843-2855 DEC 2003
Authors: Sakamoto, W; Zaltsman, A; Adam, Z; Takahashi, Y

Title: Molecular design of the photosystem II light-harvesting antenna: photosynthesis and photoprotection Journal:
Authors: Horton, P; Ruban, A

Title: Dynamics of photosystem II: a proteomic approach to thylakoid protein complexes
Authors: Aro, EM; Suorsa, M; Rokka, A; Allahverdiyeva, Y; Paakkarinen, V; Saleem, A; Battchikova, N; Rintamaki, E

Title: Photosystem II core phosphorylation and photosynthetic acclimation require two different protein kinases Journal: NATURE, 437 (7062): 1179-1182 OCT 20 2005
Authors: Bonardi, V; Pesaresi, P; Becker, T; Schleiff, E; Wagner, R; Pfannschmidt, T; Jahns, P; Leister, D

Title: FtsH-mediated repair of the photosystem II complex in response to light stress
Authors: Nixon, PJ; Barker, M; Boehm, M; de Vries, R; Komenda, J

Title: Protein degradation machineries in plastids
Journal: ANNUAL REVIEW OF PLANT BIOLOGY, 57: 599-621 2006
Authors: Sakamoto, W

Title: Photoprotection in an ecological context: the remarkable complexity of thermal energy dissipation
Journal: NEW PHYTOLOGIST, 172 (1): 11-21 2006
Authors: Demmig-Adams, B; Adams, WW

Title: Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts
Journal: CURRENT OPINION IN PLANT BIOLOGY, 9 (3): 234-240 JUN 2006
Authors: Adam, Z; Rudella, A; van Wijk, KJ

Title: Identification of a mechanism of photoprotective energy dissipation in higher plants
Journal: NATURE, 450 (7169): 575-U22 NOV 22 2007
Authors: Ruban, AV; Berera, R; Ilioaia, C; van Stokkum, IHM; Kennis, JTM; Pascal, AA; van Amerongen, H; Robert, B; Horton, P; van Grondelle, R

Title: Lack of the light-harvesting complex CP24 affects the structure and function of the grana membranes of higher plant chloroplasts
Journal: PLANT CELL, 18 (11): 3106-3120 NOV 2006
Authors: Kovacs, L; Damkjaer, J;Kereiche, S; Ilioaia, C; Ruban, AV; Boekema, EJ; Jansson, S;Horton, P

Title: Psb27, a cyanobacterial lipoprotein, is involved in the repair cycle of photosystem II
Journal: PLANT CELL, 18 (11): 3121-3131 NOV 2006
Authors: Nowaczyk, MM; Hebeler, R; Schlodder, E; Meyer, HE; Warscheid, B; Rogner, M

Title: Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein
Journal: SCIENCE, 320 (5877): 794-797 MAY 9 2008
Authors: Ahn, TK; Avenson, TJ; Ballottari, M; Cheng, YC; Niyogi, KK; Bassi, R; Fleming, GR

Title: Zeaxanthin radical cation formation in minor light-harvesting complexes of higher plant antenna
Journal: JOURNAL OF BIOLOGICAL CHEMISTRY, 283 (6): 3550-3558 FEB 8 2008
Authors: Avenson, TJ; Ahn, TK; Zigmantas, D; Niyogi, KK; Li, Z; Ballottari, M; Bassi, R; Fleming, GR

Title: Interorganellar communication
Authors: Pesaresi, P; Schneider, A; Kleine, T; Leister, D

Title: How do environmental stresses accelerate photoinhibition?
Journal: TRENDS IN PLANT SCIENCE, 13 (4): 178-182 APR 2008
Authors: Takahashi, S; Murata, N