bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Authors: Liu Qian , Mackey Aaron J. , Roos David S. , Pereira Fernando C. N. 
Published: January 2008

Abstract
Motivation: The increasing diversity and variable quality of evidence relevant to gene annotation argues for a probabilistic framework that automatically integrates such evidence to yield candidate gene models.
Results: Evigan is an automated gene annotation program for eukaryotic genomes, employing probabilistic inference to integrate multiple sources of gene evidence. The probabilistic model is a dynamic Bayes network whose parameters are adjusted to maximize the probability of observed evidence. Consensus gene predictions are then derived by maximum likelihood decoding, yielding n-best models (with probabilities for each). Evigan is capable of accommodating a variety of evidence types, including (but not limited to) gene models computed by diverse gene finders, BLAST hits, EST matches, and splice site predictions; learned parameters encode the relative quality of evidence sources. Since separate training data are not required (apart from the training sets used by individual gene finders), Evigan is particularly attractive for newly sequenced genomes where little or no reliable manually curated annotation is available. The ability to produce a ranked list of alternative gene models may facilitate identification of alternatively spliced transcripts. Experimental application to ENCODE regions of the human genome, and the genomes of Plasmodium vivax and Arabidopsis thaliana show that Evigan achieves better performance than any of the individual data sources used as evidence.
Availability: The source code is available at http://www.seas.upenn.edu/~strctlrn/evigan/evigan.html
Contact: qianliu@seas.upenn.edu
Stamen Abscission Zone Transcriptome Profiling Reveals New Candidates for Abscission Control: Enhanced Retention of Floral Organs in Transgenic Plants Overexpressing ArabidopsisZINC FINGER PROTEIN2
Authors: Cai Suqin , Lashbrook Coralie C. 
Published: January 2008

AbstractOrgan detachment requires cell separation within abscission zones (AZs). Physiological studies have established that ethylene and auxin contribute to cell separation control. Genetic analyses of abscission mutants have defined ethylene-independent detachment regulators. Functional genomic strategies leading to global understandings of abscission have awaited methods for isolating AZ cells of low abundance and very small size. Here, we couple laser capture microdissection of Arabidopsis thaliana stamen AZs and GeneChip profiling to reveal the AZ transcriptome responding to a developmental shedding cue. Analyses focus on 551 AZ genes (AZ551) regulated at the highest statistical significance (P ≤ 0.0001) over five floral stages linking prepollination to stamen shed. AZ551 includes mediators of ethylene and auxin signaling as well as receptor-like kinases and extracellular ligands thought to act independent of ethylene. We hypothesized that novel abscission regulators might reside in disproportionately represented Gene Ontology Consortium functional categories for cell wall modifying proteins, extracellular regulators, and nuclear-residing transcription factors. Promoter-β-glucuronidase expression of one transcription factor candidate, ZINC FINGER PROTEIN2 (AtZFP2), was elevated in stamen, petal, and sepal AZs. Flower parts of transgenic lines overexpressing AtZFP2 exhibited asynchronous and delayed abscission. Abscission defects were accompanied by altered floral morphology limiting pollination and fertility. Hand-pollination restored transgenic fruit development but not the rapid abscission seen in wild-type plants, demonstrating that pollination does not assure normal rates of detachment. In wild-type stamen AZs, AtZFP2 is significantly up-regulated postanthesis. Phenotype data from transgene overexpression studies suggest that AtZFP2 participates in processes that directly or indirectly influence organ shed.
Elucidation of the Final Reactions of DIMBOA-Glucoside Biosynthesis in Maize: Characterization ofBx6andBx7
Authors: Jonczyk Rafal , Schmidt Holger , Osterrieder Anne , Fiesselmann Andreas , Schullehner Katrin , Haslbeck Martin , Sicker Dieter , Hofmann Diana , Yalpani Nasser , Simmons Carl , Frey Monika , Gierl Alfons 
Published: January 2008

AbstractBenzoxazinoids were identified in the early 1960s as secondary metabolites of the grasses that function as natural pesticides and exhibit allelopathic properties. Benzoxazinoids are synthesized in seedlings and stored as glucosides (glcs); the main aglucone moieties are 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA). The genes of DIBOA-glc biosynthesis have previously been isolated and the enzymatic functions characterized. Here, the enzymes for conversion of DIBOA-glc to DIMBOA-glc are identified. DIBOA-glc is the substrate of the dioxygenase BENZOXAZINLESS6 (BX6) and the produced 2,4,7-trihydroxy-2H-1,4-benzoxazin-3-(4H)-one-glc is metabolized by the methyltransferase BX7 to yield DIMBOA-glc. Both enzymes exhibit moderate K m values (below 0.4 mm) and k cat values of 2.10 s−1 and 0.25 s−1, respectively. Although BX6 uses a glucosylated substrate, our localization studies indicate a cytoplasmic localization of the dioxygenase. Bx6 and Bx7 are highest expressed in seedling tissue, a feature shared with the other Bx genes. At present, Bx6 and Bx7 have no close relatives among the members of their respective gene families. Bx6 and Bx7 map to the cluster of Bx genes on the short arm of chromosome 4.
Indole-3-Acetonitrile Production from Indole Glucosinolates Deters Oviposition byPieris rapae
Authors: de Vos Martin , Kriksunov Ksenia L. , Jander Georg 
Published: January 2008

AbstractLike many crucifer-specialist herbivores, Pieris rapae uses the presence of glucosinolates as a signal for oviposition and larval feeding. Arabidopsis thaliana glucosinolate-related mutants provide a unique resource for studying the in vivo role of these compounds in affecting P. rapae oviposition. Low indole glucosinolate cyp79B2 cyp79B3 mutants received fewer eggs than wild type, confirming prior research showing that indole glucosinolates are an important oviposition cue. Transgenic plants overexpressing epithiospecifier protein, which shifts glucosinolate breakdown toward nitrile formation, are less attractive to ovipositing P. rapae females. Exogenous application of indol-3-ylmethylglucosinolate breakdown products to cyp79B2 cyp79B3 mutants showed that oviposition was increased by indole-3-carbinol and decreased by indole-3-acetonitrile (IAN). P. rapae larvae tolerate a cruciferous diet by using a gut enzyme to redirect glucosinolate breakdown toward less toxic nitriles, including IAN, rather than isothiocyanates. The presence of IAN in larval regurgitant contributes to reduced oviposition by adult females on larvae-infested plants. Therefore, production of nitriles via epithiospecifier protein in cruciferous plants, which makes the plants more sensitive to generalist herbivores, may be a counter-adaptive mechanism for reducing oviposition by P. rapae and perhaps other crucifer-specialist insects.
Arabidopsis Stromal 70-kD Heat Shock Proteins Are Essential for Plant Development and Important for Thermotolerance of Germinating Seeds
Authors: Su Pai-Hsiang , Li Hsou-min 
Published: January 2008

AbstractThe 70-kD heat shock proteins (Hsp70s) have been shown to be important for protein folding, protein translocation, and stress responses in almost all organisms and in almost all subcellular compartments. However, the function of plastid stromal Hsp70s in higher plants is still uncertain. Genomic surveys have revealed that there are two putative stromal Hsp70s in Arabidopsis thaliana, denoted cpHsc70-1 (At4g24280) and cpHsc70-2 (At5g49910). In this study, we show that cpHsc70-1 and cpHsc70-2 could indeed be imported into the chloroplast stroma. Their corresponding T-DNA insertion knockout mutants were isolated and designated as Δcphsc70-1 and Δcphsc70-2. No visible phenotype was observed in the Δcphsc70-2 mutant under normal growth conditions. In contrast, Δcphsc70-1 mutant plants exhibited variegated cotyledons, malformed leaves, growth retardation, and impaired root growth, even though the protein level of cpHsc70-2 was up-regulated in the Δcphsc70-1 mutant. After heat shock treatment of germinating seeds, root growth from Δcphsc70-1 seeds was further impaired, indicating that cpHsc70-1 is important for thermotolerance of germinating seeds. No Δcphsc70-1 Δcphsc70-2 double mutant could be obtained, suggesting that the Δcphsc70 double knockout was lethal. Genotype analyses of F1 seedlings from various crosses indicated that double-knockout mutation was lethal to the female gametes and reduced the transmission efficiency of the male gametes. These results indicate that cpHsc70s are essential for plant development and the two cpHsc70s most likely have redundant but also distinct functions.
Tailoring the Specificity of a Plant Cystatin toward Herbivorous Insect Digestive Cysteine Proteases by Single Mutations at Positively Selected Amino Acid Sites
Authors: Goulet Marie-Claire , Dallaire Cindy , Vaillancourt Louis-Philippe , Khalf Moustafa , Badri Amine M. , Preradov Andreja , Duceppe Marc-Olivier , Goulet Charles , Cloutier Conrad , Michaud Dominique 
Published: January 2008

Abstract
Plant cystatins, similar to other defense proteins, include hypervariable, positively selected amino acid sites presumably impacting their biological activity. Using 29 single mutants of the eighth domain of tomato (Solanum lycopersicum) multicystatin, SlCYS8, we assessed here the potential of site-directed mutagenesis at positively selected amino acid sites to generate cystatin variants with improved inhibitory potency and specificity toward herbivorous insect digestive cysteine (Cys) proteases. Compared to SlCYS8, several mutants (22 out of 29) exhibited either improved or lowered potency against different model Cys proteases, strongly suggesting the potential of positively selected amino acids as target sites to modulate the inhibitory specificity of the cystatin toward Cys proteases of agronomic significance. Accordingly, mutations at positively selected sites strongly influenced the inhibitory potency of SlCYS8 against digestive Cys proteases of the insect herbivore Colorado potato beetle (Leptinotarsa decemlineata). In particular, several variants exhibited improved potency against both cystatin-sensitive and cystatin-insensitive digestive Cys proteases of this insect. Of these, some variants also showed weaker activity against leaf Cys proteases of the host plant (potato [Solanum tuberosum]) and against a major digestive Cys protease of the two-spotted stinkbug Perillus bioculatus, an insect predator of Colorado potato beetle showing potential for biological control. Overall, these observations suggest the usefulness of site-directed mutagenesis at positively selected amino acid sites for the engineering of recombinant cystatins with both improved inhibitory potency toward the digestive proteases of target herbivores and weaker potency against nontarget Cys proteases in the host plant or the environment.
CENL1Expression in the Rib Meristem Affects Stem Elongation and the Transition to Dormancy inPopulus
Authors: Ruonala Raili , Rinne Päivi L.H. , Kangasjärvi Jaakko , van der Schoot Christiaan 
Published: January 2008

AbstractWe investigated the short day (SD)–induced transition to dormancy in wild-type hybrid poplar (Populus tremula × P. tremuloides) and its absence in transgenic poplar overexpressing heterologous PHYTOCHROME A (PHYA). CENTRORADIALIS-LIKE1 (CENL1), a poplar ortholog of Arabidopsis thaliana TERMINAL FLOWER1 (TFL1), was markedly downregulated in the wild-type apex coincident with SD-induced growth cessation. By contrast, poplar overexpressing a heterologous Avena sativa PHYA construct (P35S:AsPHYA), with PHYA accumulating in the rib meristem (RM) and adjacent tissues but not in the shoot apical meristem (SAM), upregulated CENL1 in the RM area coincident with an acceleration of stem elongation. In SD-exposed heterografts, both P35S:AsPHYA and wild-type scions ceased growth and formed buds, whereas only the wild type assumed dormancy and P35S:AsPHYA showed repetitive flushing. This shows that the transition is not dictated by leaf-produced signals but dependent on RM and SAM properties. In view of this, callose-enforced cell isolation in the SAM, associated with suspension of indeterminate growth during dormancy, may require downregulation of CENL1 in the RM. Accordingly, upregulation of CENL1/TFL1 might promote stem elongation in poplar as well as in Arabidopsis during bolting. Together, the results suggest that the RM is particularly sensitive to photoperiodic signals and that CENL1 in the RM influences transition to dormancy in hybrid poplar.
People management – be bold!
Authors: Smith Ian 
Published: January 2008

PurposeThis paper aims to encourage managers in the rapidly changing library and information services environment to be bold in people management.Design/methodology/approachThe paper outlines four aspects of people management where it is particularly important to be bold: staff selection and recruitment; training development and workplace learning; performance management, and; organisational change.FindingsThe study reveals pointers to good management practice in the four areas which are outlined.Originality/valueThe paper provides useful information for those in people management.
Wa! Thewú wéiacademic librarian
Authors: Liu Anita M.M. 
Published: January 2008

PurposeThis paper seeks to examine the integration of the Western concept of dynamic equilibrium andwa, the Eastern concept of harmony, and howwú wéi(maintainingcentrality, hence, stability, in a dynamic environment) is fundamental to the sustainable development of the library system in a harmonious manner.Design/methodology/approachThe Western concept of self and the Chinese Taoist concepts of change and stability are used to examine the role of the human being – the librarian – in the constantly evolving environment.FindingsThe paper finds that four competing values faced by the librarian are based on the needs to adopt internal focus, external focus, flexibility and control. The four competing values generate issues confronting the academic librarian. Frustration – what challenges and pressures do academic librarians currently face in the university environment specifically? History and destiny – what lessons can the history of libraries in universities give us about their future role in the scholarly community? Constraints – what are the possible environmental barriers which might prevent librarians working dynamically in parallel with or ahead of university “strategists”, to secure their vision as key players in tomorrow's academy? Conflicting forces from library stakeholders are analysed in a competing values model which encompasses the elements of organisation systems and organisational culture.Originality/valueThe competing values framework provides the basis for formulating a research agenda to investigate the central role played by university libraries in the societal development of human‐kind.
Institutional antecedents to research productivity in operations: the US perspective
Authors: Smith Jeffery S. , Fox Gavin L. , “Sunny” Park Sung‐Hee , Lee Lorraine 
Published: January 2008

PurposeThe purpose of this paper is to examine the institutional factors that affect the productivity of individuals in the field of operations.Design/methodology/approachThis study identifies a sample of graduates from PhD programs in operations and utilizes a partial least squares analysis to examine the effect of academic origin, academic affiliation, and advisor productivity on each individual's research productivity.FindingsThe results of the analysis indicate that the productivity of an individual is directly influenced by the aggregate prestige of the institutions where the individual was employed during article publication and indirectly influenced by the prestige of the institution where the individual received the terminal degree. Additionally, differences were found between groups when the sample was divided by focus (operations management (OM) versus operations research (OR). The OM model held the same relationships as the combined model, while the OR model included significant direct effects of academic origin and indirect effects of the advisor's productivity on the individual's productivity.Originality/valueThis research is the first to fully evaluate the institutional antecedents to research productivity of individuals in operations. In doing so, valuable insights are gained as to how to facilitate the success of researchers in operations. Additionally, factors are highlighted that should be considered by institutions looking at hiring freshly minted PhDs. Finally, these results can benefit practitioners when considering working with academics as a source of emerging information or consulting.
Strategic capabilities and internet resources in procurement
Authors: Ordanini Andrea , Rubera Gaia 
Published: January 2008

PurposeThis paper seeks to adopt a resource‐based approach to investigate the link between procurement capabilities, internet resources, and performance. It aims to cover two gaps in the operations management literature: the missing links between procurement capabilities and the performance of a firm, and the role of internet resources in shaping such links.Design/methodology/approachAfter the identification of two key capabilities in procurement and the introduction of internet resources, the relationships with performance are empirically tested in a sample of 93 firms in the textile and clothing industry in Italy. Data were analysed using a partial least‐squares technique and main and interaction effects were investigated.FindingsFirst, process efficiency and process integration capabilities provide a significant (and equally important) contribution to firm performance, but there are no complementary effects between them. Second, and contrary to expectations, the internet has been found to enhance the effect of process integration capability, but not that of process efficiency capability. Third, a new finding reveals that the internet not only interacts with each of these capabilities in procurement separately, but it also enhances the synergistic effect between them.Research limitations/implicationsThe investigation is based on a self‐reported cross‐sectional analysis, and it is specific to a single industry and the procurement of one type of material. Nonetheless, it suggests a number of different implications. Achieving excellence in procurement requires the development of distinct capabilities, because the management of core purchasing activities and the integration of procurement in the supply chain are not complementary. Contrary to common expectations, employing the internet in procurement has little power to reduce transaction costs, although it can be fruitful for improving inter‐functional coordination. The internet can also help in “putting the pieces together” by exploiting the otherwise latent complementary effects between procurement capabilities.Originality/valueThis paper is unique in that it employs a strategic management theory – the resource‐based view – to unpack the mechanisms through which procurement activities contribute to performance. It represents a first response to the call for research into the use of such theoretical frameworks which has recently been made in the operations management literature. The paper also offers the first empirical test of how the internet interacts with existing capabilities in the procurement domain, providing clear guidance on how to exploit its often undervalued potential.
Three outcomes of service recovery
Authors: Johnston Robert , Michel Stefan 
Published: January 2008

PurposeBased on a review of the literature, this paper sets out to suggest that an organisation's service recovery procedures lead to three distinct outcomes; customer, process, and employee recoveries. The objective of the paper is to investigate the impact of service recovery procedures (i.e. the way service recovery is managed and executed) on these three outcomes and their relative impact on an organisation's financial performance.Design/methodology/approachA model, linking recovery procedures to the outcomes of recovery and financial performance, is tested using empirical data from a detailed survey of 60 organisations in the UK.FindingsIt would appear that many organisations and academic researchers have focused their efforts on customer recovery and have, to some extent, ignored the potentially higher impact outcomes of process and employee recovery. The main finding was that service recovery procedures have a greater impact on employees and process improvement than on customers. Furthermore, while many organisations appear to be concerned with service recovery few seem to be good at it or gaining the benefits of recovered customers, improved processes or recovered employees.Research limitations/implicationsThis paper tries to encourage wider research into the impact of service recovery. The main limitations were sample size and selection.Practical implicationsIt challenges the way some organisations have focused their recovery procedures on satisfying or delighting customers and suggests that by doing so they are missing out on substantial benefits. It also suggests that many organisations have a long way to go to develop their recovery procedures.Originality/valueThis work proposes three outcomes of service recovery and finds that the impact of process and employee recoveries may be more significant than customer recovery.
The impact of learning goals on emotional, social, and cognitive intelligence competency development
Authors: Leonard David C. 
Published: January 2008

PurposeThe purpose of this research is to empirically examine the efficacy of setting multiple goals targeting complex competencies with a variety of time horizons pursued across a number of years. Most research conducted in the areas of goal setting examines an individual's ability to achieve a single goal targeting a simple skill or behavioral change within a short time period.Design/methodology/approachIn this longitudinal study competency development is assessed over time periods ranging from nine months to four and half years and examined using both self‐reported change and behavior change demonstrated through critical incident interviews.FindingsProgress over the study reveals that establishing learning goals is particularly important to the development of competencies. Subjects developed significantly more on competencies for which they set goals than on other competencies. They also demonstrated greater competency development when goals were remembered.Research limitations/implicationsSubjects were studied during a specific life change event – completion of an MBA program. Their particular education environment was designed to support and encourage change. It undoubtedly contributed to their development during the study. Results therefore may not generalize to broader populations. However, the results reveal clear implications for management education in both academic and corporate education settings.Practical implicationsThis study highlights important elements in the development process that when included enhance competency development and provide insight into the mechanisms underlying intentional change theory.Originality/valueThe research evaluates the complexity and difficulty involved in competency development. It provides empirical evidence to support goal setting and intentional change theories.