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} # Linkout formatting # Raw ingredients required to build the full text URL dynamically using the following variables # collected by the plugin: type ikey_1 ckey_1 ikey_2 ckey_2 format_linkout HWIRE { return [list HighWire "http://${ckey_1}/cgi/content/abstract/${ikey_1}/${ikey_2}/${ckey_2}"] } format_linkout HIWIRE { return [list \ HighWire "http://${ckey_1}.abstract" \ "HighWire (PDF)" "http://${ckey_1}.full.pdf" \ ] } #Tests test {http://www.genetics.org/cgi/content/abstract/171/1/35} { linkout {HWIRE 171 www.genetics.org 1 35} linkout {DOI {} 10.1534/genetics.105.040634 {} {}} linkout {PMID 16183906 {} {} {}} formatted_url {HighWire http://www.genetics.org/cgi/content/abstract/171/1/35} formatted_url {DOI http://dx.doi.org/10.1534/genetics.105.040634} formatted_url {Pubmed http://view.ncbi.nlm.nih.gov/pubmed/16183906} formatted_url {Hubmed http://www.hubmed.org/display.cgi?uids=16183906} volume {171} issue {1} start_page {35} end_page {47} year {2005} month {9} day {1} title {Dissection of Arp2/3 Complex Actin Nucleation Mechanism and Distinct Roles for Its Nucleation-Promoting Factors in Saccharomyces cerevisiae} journal Genetics author {D'Agostino Jessica JL {D'Agostino, Jessica L.}} author {Goode Bruce BL {Goode, Bruce L.}} type {JOUR} url http://www.genetics.org/cgi/content/abstract/171/1/35 status ok abstract {Actin nucleation by the Arp2/3 complex is under tight control, remaining inactive until stimulation by nucleation-promoting factors (NPFs). Although multiple NPFs are expressed in most cell types, little is known about how they are coordinated and whether they perform similar or distinct functions. We examined genetic relationships among the four S. cerevisiae NPFs. Combining las17{Delta} with pan1-101 or myo3{Delta}myo5{Delta} was lethal at all temperatures, whereas combining pan1-101 with myo3{Delta}myo5{Delta} showed no genetic interaction and abp1{Delta} partially suppressed las17{Delta}. These data suggest that NPFs have distinct and overlapping functions in vivo. We also tested genetic interactions between each NPF mutant and seven different temperature-sensitive arp2 alleles and purified mutant Arp2/3 complexes to compare their activities. Two arp2 alleles with mutations at the barbed end were severely impaired in nucleation, providing the first experimental evidence that Arp2 nucleates actin at its barbed end in vitro and in vivo. Another arp2 allele caused partially unregulated ("leaky") nucleation in the absence of NPFs. Combining this mutant with a partially unregulated allele in a different subunit of Arp2/3 complex was lethal, suggesting that cells cannot tolerate high levels of unregulated activity. Genetic interactions between arp2 alleles and NPF mutants point to Abp1 having an antagonistic role with respect to other NPFs, possibly serving to attenuate their stronger activities. In support of this model, Abp1 binds strongly to Arp2/3 complex, yet has notably weak nucleation-promoting activity and inhibits Las17 activity on Arp2/3 complex in a dose-responsive manner. 10.1534/genetics.105.040634} } test {http://www.ajhp.org/cgi/content/full/62/3/239} { linkout {HWIRE 62 www.ajhp.org 3 239} linkout {PMID 15719576 {} {} {}} formatted_url {HighWire http://www.ajhp.org/cgi/content/abstract/62/3/239} formatted_url {Pubmed http://view.ncbi.nlm.nih.gov/pubmed/15719576} formatted_url {Hubmed http://www.hubmed.org/display.cgi?uids=15719576} volume {62} issue {3} start_page {239} end_page {240} year {2005} month {2} day {1} title {Nation is unprepared for bioterrorism threat, study finds} journal {Am J Health Syst Pharm} author {Young Donna D {Young, Donna}} type {JOUR} url http://www.ajhp.org status ok } test {http://sth.sagepub.com/cgi/content/refs/28/1/5} { linkout {HWIRE 28 sth.sagepub.com 1 5} linkout {DOI {} 10.1177/0162243902238803 {} {}} formatted_url {HighWire http://sth.sagepub.com/cgi/content/abstract/28/1/5} formatted_url {DOI http://dx.doi.org/10.1177/0162243902238803} volume {28} issue {1} start_page {5} end_page {14} year {2003} month {1} day {1} title {Editorial} journal {Science Technology Human Values} author {Senker Peter P {Senker, Peter}} type {JOUR} url http://sth.sagepub.com abstract {10.1177/0162243902238803} status ok } test {http://jhered.oxfordjournals.org/cgi/content/extract/95/5/II} { linkout {HWIRE 95 jhered.oxfordjournals.org 5 II} formatted_url {HighWire http://jhered.oxfordjournals.org/cgi/content/abstract/95/5/II} volume {95} issue {5} start_page {ii} year {2004} month {9} day {1} title {Erratum} journal {J Hered} type {JOUR} url http://jhered.oxfordjournals.org status ok } test {http://bioinformatics.oxfordjournals.org/cgi/screenpdf/18/4/529} { status ok linkout {HWIRE 18 bioinformatics.oxfordjournals.org 4 529} linkout {DOI {} 10.1093/bioinformatics/18.4.529 {} {}} linkout {PMID 12016050 {} {} {}} formatted_url {HighWire http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/529} formatted_url {DOI http://dx.doi.org/10.1093/bioinformatics/18.4.529} formatted_url {Pubmed http://view.ncbi.nlm.nih.gov/pubmed/12016050} formatted_url {Hubmed http://www.hubmed.org/display.cgi?uids=12016050} volume {18} issue {4} start_page {529} end_page {535} year {2002} month {4} day {1} title {Construction of optimal quality control for oligo arrays} journal {Bioinformatics} author {Colbourn Charles CJ {Colbourn, Charles J.}} author {Ling Alan ACH {Ling, Alan C. H.}} author {Tompa Martin M {Tompa, Martin}} type {JOUR} url http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/529 abstract {Motivation: Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step. Results: We describe a practical algorithm for the construction of optimal quality control designs that identify any faulty manufacturing step. The algorithm uses hillclimbing, a search technique from combinatorial optimization. We also present the results of using this algorithm on all practical quality control design sizes. Availability: On request from the authors. Contact: tompa@cs.washington.edu 10.1093/bioinformatics/18.4.529} } #AOP article included for completeness: #Links of this form work, but will likely break as articles are published #test {http://glycob.oxfordjournals.org/cgi/content/abstract/cwj046v1} { # linkout {HWIRE glycob.oxfordjournals.org cwj046v1 {} {}} # linkout {DOI {} 10.1093/glycob/cwj046 {} {}} # linkout {PMID 16207893 {} {} {}} # formatted_url {HighWire http://glycob.oxfordjournals.org/cgi/content/abstract/cwj046v1//} # formatted_url {DOI http://dx.doi.org/10.1093/glycob/cwj046} # formatted_url {PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16207893} # formatted_url {HubMed http://www.hubmed.org/display.cgi?uids=16207893} # start_page {cwj046} # year {2005} # month {10} # day {5} # title {Identification of Linkage-Specific Sequence Motifs in Sialyltransferases} # journal {Glycobiology} # author {Patel Ronak RY {Patel, Ronak Y.}} # author {Balaji Petety PV {Balaji, Petety V.}} # type {JOUR} # url http://glycob.oxfordjournals.org/cgi/content/abstract/cwj046v1 # abstract {Eukaryotic sialyltransferases (SiaTs) comprise a superfamily of enzymes catalyzing the transfer of sialic acid from a common donor substrate to various acceptor substrates in different linkages. These enzymes have been classified as ST3Gal, ST6Gal, ST6GalNAc and ST8Sia families based on linkage- and acceptor monosaccharide-specificities and sequence similarities. It was recognized early on that SiaTs contain certain well-conserved motifs and these were denoted as L (large)-, S (small)-, and VS (very small)-motifs; recently, a fourth motif, denoted as motif III, was identified recently. These four motifs are common to all the SiaTs, irrespective of the linkage- and acceptor saccharide-specificities. In the present study, the sequences of the various families have been analyzed and sequence motifs that are unique to the various families have been identified. These unique motifs are expected to contribute to the characteristic linkage- and acceptor saccharide-specificities of the family members. One of the linkage specific motifs is contiguous to L-motif. Members of ST3Gal and ST8Sia families share significant sequence similarities; in contrast, the ST6Gal family is distinct from the ST6GalNAc family. The latter consists of two subfamilies, one comprising ST6GalNAc I, ST6GalNAc II and the other comprising ST6GalNAc III, ST6GalNAc IV, ST6GalNAc V and ST6GalNAc VI. Each of these sub-families has characteristic sequence motifs, not present in the other subfamily.} # status ok #} test {http://www.sciencemag.org/cgi/content/short/sci;218/4570/348} { status ok linkout {DOI {} 10.1126/science.6289436 {} {}} linkout {PMID 6289436 {} {} {}} formatted_url {DOI http://dx.doi.org/10.1126/science.6289436} formatted_url {Pubmed http://view.ncbi.nlm.nih.gov/pubmed/6289436} formatted_url {Hubmed http://www.hubmed.org/display.cgi?uids=6289436} volume {218} issue {4570} start_page {348} end_page {353} year {1982} month {10} day {22} title {Genetic transformation of Drosophila with transposable element vectors} journal {Science} author {Rubin {} GM {Rubin, GM}} author {Spradling {} AC {Spradling, AC}} type {JOUR} url http://www.sciencemag.org/cgi/content/abstract/218/4570/348 abstract {Exogenous DNA sequences were introduced into the Drosophila germ line. A rosy transposon (ry1), constructed by inserting a chromosomal DNA fragment containing the wild-type rosy gene into a P transposable element, transformed germ line cells in 20 to 50 percent of the injected rosy mutant embryos. Transformants contained one or two copies of chromosomally integrated, intact ry1 that were stably inherited in subsequent generations. These transformed flies had wild-type eye color indicating that the visible genetic defect in the host strain could be fully and permanently corrected by the transferred gene. To demonstrate the generality of this approach, a DNA segment that does not confer a recognizable phenotype on recipients was also transferred into germ line chromosomes. 10.1126/science.6289436} }