bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two decades of Ripple Down Rules research
Authors: Richards Debbie 
Published: May 2009

AbstractRipple Down Rules (RDR) were developed in answer to the problem of maintaining medium to large rule-based knowledge systems. Traditional approaches to knowledge-based systems gave little thought to maintenance as it was expected that extensive upfront domain analysis involving a highly trained specialist, the knowledge engineer, and the time-poor domain expert would produce a complete model capturing what was in the expert’s head. The ever-changing, contextual and embrained nature of knowledge were not a part of the philosophy upon which they were based. RDR was a paradigm shift, which made knowledge acquisition and maintenance one and the same thing by incrementally acquiring knowledge as domain experts directly interacted with naturally occurring cases in their domain. Cases played an integral part of the acquisition process by motivating the capture of new knowledge, framing the context in which new knowledge would apply and ensuring that previously correctly classified cases remained so by requiring that the classification of the new case distinguish it from the system’s classification and be justified by features of the new case. RDR has moved beyond its first representation which handled single classification tasks within the domain of pathology to support multiple conclusions across a wide range of domains such as help-desk support, email classification and RoboCup and problem types including configuration, simulation, planning and natural language processing. This paper reviews the history of RDR research over the past two decades with a view to its future.
The search for a human Holliday junction resolvase
Authors: West Stephen C. 
Published: May 2009

Four-way DNA intermediates, known as Holliday junctions, are formed during mitotic and meiotic recombination, and their efficient resolution is essential for proper chromosome segregation. Bacteria, bacteriophages and archaea promote Holliday junction resolution by the introduction of symmetrically related nicks across the junction, in reactions mediated by Holliday junction resolvases. In 2008, after a search that lasted almost 20 years, a Holliday junction resolvase was identified in humans. The protein, GEN1, was identified using MS following the brute-force fractionation of extracts prepared from human cells grown in tissue culture. GEN1 fits the paradigm developed from studies of prokaryotic Holliday junction resolvases, in that it specifically recognizes junctions and resolves them using a mechanism similar to that exhibited by the Escherichia coli RuvC protein.
The impact of heterochromatin on DSB repair
Authors: Goodarzi Aaron A. , Noon Angela T. , Jeggo Penny A. 
Published: May 2009

DNA NHEJ (non-homologous end-joining) is the major DNA DSB (double-strand break) repair pathway in mammalian cells. Although NHEJ-defective cell lines show marked DSB-repair defects, cells defective in ATM (ataxia telangiectasia mutated) repair most DSBs normally. Thus NHEJ functions independently of ATM signalling. However, ∼15% of radiation-induced DSBs are repaired with slow kinetics and require ATM and the nuclease Artemis. DSBs persisting in the presence of an ATM inhibitor, ATMi, localize to heterochromatin, suggesting that ATM is required for repairing DSBs arising within or close to heterochromatin. Consistent with this, we show that siRNA (small interfering RNA) of key heterochromatic proteins, including KAP-1 [KRAB (Krüppel-associated box) domain-associated protein 1], HP1 (heterochromatin protein 1) and HDAC (histone deacetylase) 1/2, relieves the requirement for ATM for DSB repair. Furthermore, ATMi addition to cell lines with genetic alterations that have an impact on heterochromatin, including Suv39H1/2 (suppressor of variegation 3–9 homologue 1/2)-knockout, ICFa (immunodeficiency, centromeric region instability, facial anomalies syndrome type a) and Hutchinson–Guilford progeria cell lines, fails to have an impact on DSB repair. KAP-1 is a highly dose-dependent, transient and ATM-specific substrate, and mutation of the ATM phosphorylation site on KAP-1 influences DSB repair. Collectively, the findings show that ATM functions to overcome the barrier to DSB repair posed by heterochromatin. However, even in the presence of ATM, γ-H2AX (phosphorylated histone H2AX) foci form on the periphery rather than within heterochromatic centres. Finally, we show that KAP-1's association with heterochromatin is diminished as cells progress through mitosis. We propose that KAP-1 is a critical heterochromatic factor that undergoes specific modifications to promote DSB repair and mitotic progression in a manner that allows localized and transient chromatin relaxation, but precludes significant dismantling of the heterochromatic superstructure.
Developing World-Class Social Marketing Standards: A Step in the Right Direction for a More Socially Responsible Marketing Profession
Authors: Fourali Chahid 
Published: May 2009

The issue of targeting best practice is a long-standing one in professional education and more particularly in marketing. It can be automatically brushed aside (because “we all know what marketing is about”), addressed in terms of general aims of marketing, or addressed systematically to identify in as much details as possible the tasks and responsibilities that marketers undertake in their daily activities. Apart from this issue of identifying what constitutes good practice, there is a relevant issue that needs addressing as a prerequisite: Whether social marketing is a separate discipline from mainstream marketing or not. How we respond to this question affects the method to be adopted for developing the benchmark of best practice standards. This article starts by addressing the latter issue, then identifies the contextual differences of social marketing, and finally presents the methodology for developing the best practice standards for social marketing, its general findings, and the way forward. It is useful to note at the outset that although the project referred to in this article was undertaken by the U.K.'s Marketing and Sales Standards Setting Body, its perspective was international and involved many contributors at international level. In the final stages of the project, the resulting best practice standards were presented for final feedback at the first international conference on social marketing held in Brighton, U.K., where several hundreds of participants from around the world took part. [Supplementary materials are available for this article. Go to the publisher's online edition of Social Marketing Quarterly for the following free supplemental resources: Appendix A: List of Social Marketing Standards of Performance; Appendix B: Example of a Unit of Performance.]
jClust: a clustering and visualization toolbox
Authors: Pavlopoulos Georgios A. , Moschopoulos Charalampos N. , Hooper Sean D. , Schneider Reinhard , Kossida Sophia 
Published: May 2009

Abstract
jClust is a user-friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity propagation, Bron–Kerbosch, MULIC, Restricted neighborhood search cluster algorithm, Markov clustering and Spectral clustering, while the supported filtering procedures are haircut, outside–inside, best neighbors and density control operations. The combination of a simple input file format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for data analysis and information extraction.
Availability: http://jclust.embl.de/
Contact: pavlopou@embl.de; rschneid@embl.de; skossida@bioacademy.gr
Supplementary information: Supplementary data are available at Bioinformatics online.
A Comprehensive Genotype and Environment Assessment of Wheat Grain Ash Content in Oregon and Washington: Analysis of Variation
Authors: Morris Craig F. , Li Shuobi , King G. E. , Engle Doug A. , Burns John W. , Ross Andrew S. 
Published: May 2009

ABSTRACTA comprehensive analysis of the variation in wheat grain ash content has not been previously conducted. This study assessed the relative contribution of genotype and environment to variation in ash content, with a particular aim of ascertaining the potential for manipulating the trait using contemporary adapted germplasm. A total of 2,240 samples were drawn from four years of multilocation field plots grown in the wheat production areas of Oregon and Washington states. Genotypes included commercial cultivars and advanced breeding lines of soft and hard winter, and soft and hard spring wheats with red and white kernel color, several soft white club wheats, and one soft white spring waxy wheat cultivar. In addition to ash, protein content, test weight, and Single Kernel Characterization System kernel hardness, weight and size were also measured. In total, 20 separate fully balanced ANOVA results were conducted. Whole model R2 values were highly significant, 0.62–0.91. Nineteen of the 20 ANOVA results indicated significant genotype effects, but the effects were not large. In contrast, environment effects were always highly significant with F values often one to two orders of magnitude larger than the genotype F values. The grand mean for all samples was 1.368% ash. For individual data sets, genotype means across environments varied ≈0.1–0.3% ash. The genotypes judged noteworthy because they had the highest least squares mean ash content were OR9900553 and ClearFirst soft white winter, NuHills hard red winter, Waxy‐Pen and Cataldo soft white spring, and WA8010 and Lochsa hard spring wheats. Genotypes with lowest least squares mean ash were Edwin (club) soft white winter, OR2040073H hard red winter, WA7952 soft white spring, and WA8038 hard spring wheats. In conclusion, wheat grain ash is more greatly influenced by crop year and location than by genotype. However, sufficient genotype variation is present to plausibly manipulate this grain trait through traditional plant breeding.
In Vitro Bile‐Acid‐Binding of Whole vs. Pearled Wheat Grain
Authors: Kahlon T. S. , Chiu M. M. , Chapman M. H. 
Published: May 2009

ABSTRACTHealth benefits of consuming whole grains are reduced risk of heart disease, stroke, and cancer. The U.S. Health and Human Services and USDA dietary guidelines recommend consumption of 6–10 oz of grain products daily and one‐half of that amount should contain whole grains. Whole grains contain vitamins, minerals, fiber, and phytonutrients. Bile‐acid‐binding capacity has been related to cholesterol lowering potential of food fractions. Lowered recirculating bile acids results in utilization of cholesterol to synthesize bile acid and reduced fat absorption. Secondary bile acids have been associated with increased risk of cancer. Bile‐acid‐binding potential has been related to lowering the risk of heart disease and that of cancer. It has been reported that bile‐acid‐binding of wheat bran is not related to its total dietary fiber (TDF) content. Whole (W) grain as well as pearled (P) hard red winter wheat (Hrw), hard white winter wheat (Hww), and durum wheat (DU) cooked grains were evaluated for in vitro, bile‐acid‐binding relative to cholestryramine (a cholesterol lowering bile‐acid‐binding drug). On dry matter basis (db) relative bile‐acid‐binding values were 7.7% WHrw; 7.5% WHww; 6.3% PHww; 6.0% PHrw; 5.5% WDU; and 5.4% PDU. On a TDF basis, binding values were 42–57% of that for cholestyramine for the whole and pearled wheat grains tested. Bile‐acid‐binding values (db) for WHrw and WHww were similar and significantly higher than those of PHww, PHrw, WDU and PDU. Similar bile‐acid‐binding of WHww to that of WHrw suggest that the red color commonly associated with whole grain may not necessarily indicate more healthful potential. Data suggest that cooked WHrw and WHww wheat have significantly higher health‐promoting potential than pearled grains. WDU or PDU wheat health‐promoting potential was similar to that of PHww or PHrw. Consumption of products containing WHrw and WHww are recommended.
Structural and Physical Changes in Ultrasound‐Assisted Frozen Wet Gluten
Authors: Song GuoSheng , Hu Song Qing , Li Lin , Chen Ping , Shen Xing 
Published: May 2009

ABSTRACTUltrasound‐assisted freezing is a novel food‐freezing technique which is of benefit to frozen food quality. Studies of the structural and physical changes in the ultrasound‐assisted frozen wet gluten system illustrate how the ultrasound irradiation improves the frozen dough quality. The microtopography of ice crystals in frozen wet gluten was observed indirectly by scanning electron microscopy; the ice crystals were smaller and more uniform in wet gluten frozen using the ultrasound‐assisted technique than in wet gluten frozen without ultrasound. Fourier transform infrared spectroscopy was used to monitor the changes in the secondary structure of a frozen gluten heavy water system during frozen storage. It was determined that there were no noticeable changes in the structure of the wet gluten frozen using the ultrasound‐assisted technique. However, the structure of the wet gluten frozen without ultrasound became unordered. The freezable water content in the frozen wet gluten was determined by differential scanning calorimetry. Compared with conventional freezing, more water was frozen using ultrasound‐assisted freezing. Furthermore, the freezable water content in the wet gluten frozen using the ultrasound‐assisted technique did not increase during frozen storage. Ultrasonic cavitation promoted the primary and secondary nucleation of ice in the wet gluten and loosened the weak interactions between the gluten and the water. Consequently, the existence of a microstructure with small and uniform ice crystals was noted, which was determined to be beneficial with regard to reducing the deterioration of the gluten network and, hence, improving the quality of the frozen food.
Association of Glutenin Subunit Composition and Dough Rheological Characteristics with Cookie Baking Properties of Soft Wheat Cultivars
Authors: HadiNezhad Mehri , Butler Francis 
Published: May 2009

ABSTRACTThe effect of flour type and dough rheology on cookie development during baking was investigated using seven different soft winter wheat cultivars. Electrophoresis was used to determine the hydrolyzing effects of a commercial protease enzyme on gluten protein and to evaluate the relationships between protein composition and baking characteristics. The SDS‐PAGE technique differentiated flour cultivars based on the glutenin subunits pattern. Electrophoresis result showed that the protease degraded the glutenin subunits of flour gluten. Extensional viscosities of cookie dough at all three crosshead speeds were able to discriminate flour cultivar and correlated strongly and negatively to baking performance (P < 0.0001). The cookie doughs exhibited extensional strain hardening behavior and those values significantly correlated to baking characteristics. Of all rheological measurements calculated, dough consistency index exhibited the strongest correlation coefficient with baking parameters. The degradation effects of the protease enzyme resulted in more pronounced improvements on baking characteristics compared with dough rheological properties. Stepwise multiple regression showed that the dough consistency index, the presence or absence of the fourth (44 kDa) subunit in LMW‐GS and the fifth subunit (71 kDa) subunit in HMW‐GS were predominant parameters in predicting cookie baking properties.
Flour Particle Size, Starch Damage, and Alkali Reagent: Impact on Uniaxial Stress Relaxation Parameters of Yellow Alkaline Noodles
Authors: Hatcher D. W. , Bellido G. G. , Anderson M. J. 
Published: May 2009

ABSTRACTThree patent flours, each possessing three different levels of starch damage were prepared from a single hard white spring wheat. Each flour was sieved to yield three flours with different particle size distributions (85–110, 110–132, 132–183 μm). Raw alkaline noodles were prepared from the nine flours using either 1% w/w kansui (sodium and potassium carbonates in 9:1 ratio) or 1% w/w sodium hydroxide. Uniaxial stress relaxation parameters percent stress relaxation (SR%), initial rate of relaxation (k1) and the extent of relaxation (k2) were measured on the raw noodles immediately after production (t = 0 min) and at 60 min. Raw noodles after resting for 60 min were optimally cooked and stress relaxation parameters were measured. Raw noodles at t = 0 min exhibited SR%, k1, and k2 that were significantly (P < 0.0001) influenced by both the degree of starch damage and the type of alkaline reagent used. Flour particle size only influenced SR% and k1 (P < 0.025) but had no impact on k2. In raw noodles aged for 60 min, both SR% and k2 were significantly influenced by alkaline reagent, particle size, and starch damage (P < 0.01) while k1 was only affected by the degree of starch damage (P < 0.0001). Cooked noodle SR parameters were all significantly (P < 0.0001) influenced by alkaline reagent, particle size, and the degree of starch damage. Cooked noodles prepared from starch with low damaged flours within any given particle size range, regardless of the type of alkali employed, yielded the most rheologically elastic‐like (firmer) noodles. Two potential mechanisms by which the degree of starch damage influences noodle elastic like texture are discussed.
Gibberellin Modulates Anther Development in Rice via the Transcriptional Regulation of GAMYB
Authors: Aya Koichiro , Ueguchi-Tanaka Miyako , Kondo Maki , Hamada Kazuki , Yano Kentaro , Nishimura Mikio , Matsuoka Makoto 
Published: May 2009

Abstract
Gibberellins (GAs) play important roles in regulating reproductive development, especially anther development. Our previous studies revealed that the MYB transcriptional factor GAMYB, an important component of GA signaling in cereal aleurone cells, is also important for anther development. Here, we examined the physiological functions of GA during anther development through phenotypic analyses of rice (Oryza sativa) GA-deficient, GA-insensitive, and gamyb mutants. The mutants exhibited common defects in programmed cell death (PCD) of tapetal cells and formation of exine and Ubisch bodies. Microarray analysis using anther RNAs of these mutants revealed that rice GAMYB is involved in almost all instances of GA-regulated gene expression in anthers. Among the GA-regulated genes, we focused on two lipid metabolic genes, a cytochrome P450 hydroxylase CYP703A3 and β-ketoacyl reductase, both of which might be involved in providing a substrate for exine and Ubisch body. GAMYB specifically interacted with GAMYB binding motifs in the promoter regions in vitro, and mutation of these motifs in promoter-β-glucuronidase (GUS) transformants caused reduced GUS expression in anthers. Furthermore, a knockout mutant for CYP703A3 showed gamyb-like defects in exine and Ubisch body formation. Together, these results suggest that GA regulates exine formation and the PCD of tapetal cells and that direct activation of CYP703A3 by GAMYB is key to exine formation.
Local Differentiation of Sugar Donor Specificity of Flavonoid Glycosyltransferase in Lamiales
Authors: Noguchi Akio , Horikawa Manabu , Fukui Yuko , Fukuchi-Mizutani Masako , Iuchi-Okada Asako , Ishiguro Masaji , Kiso Yoshinobu , Nakayama Toru , Ono Eiichiro 
Published: May 2009

Abstract
Flavonoids are most commonly conjugated with various sugar moieties by UDP-sugar:glycosyltransferases (UGTs) in a lineage-specific manner. Generally, the phylogenetics and regiospecificity of flavonoid UGTs are correlated, indicating that the regiospecificity of UGT differentiated prior to speciation. By contrast, it is unclear how the sugar donor specificity of UGTs evolved. Here, we report the biochemical, homology-modeled, and phylogenetic characterization of flavonoid 7-O-glucuronosyltransferases (F7GAT), which is responsible for producing specialized metabolites in Lamiales plants. All of the Lamiales F7GATs were found to be members of the UGT88-related cluster and specifically used UDP-glucuronic acid (UDPGA). We identified an Arg residue that is specifically conserved in the PSPG box in the Lamiales F7GATs. Substitution of this Arg with Trp was sufficient to convert the sugar donor specificity of the Lamiales F7GATs from UDPGA to UDP-glucose. Homology modeling of the Lamiales F7GAT suggested that the Arg residue plays a critical role in the specific recognition of anionic carboxylate of the glucuronic acid moiety of UDPGA with its cationic guanidinium moiety. These results support the hypothesis that differentiation of sugar donor specificity of UGTs occurred locally, in specific plant lineages, after establishment of general regiospecificity for the sugar acceptor. Thus, the plasticity of sugar donor specificity explains, in part, the extraordinary structural diversification of phytochemicals.
Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae
Authors: Yoshida Kentaro , Saitoh Hiromasa , Fujisawa Shizuko , Kanzaki Hiroyuki , Matsumura Hideo , Yoshida Kakoto , Tosa Yukio , Chuma Izumi , Takano Yoshitaka , Win Joe , Kamoun Sophien , Terauchi Ryohei 
Published: May 2009

Abstract
To subvert rice (Oryza sativa) host defenses, the devastating ascomycete fungus pathogen Magnaporthe oryzae produces a battery of effector molecules, including some with avirulence (AVR) activity, which are recognized by host resistance (R) proteins resulting in rapid and effective activation of innate immunity. To isolate novel avirulence genes from M. oryzae, we examined DNA polymorphisms of secreted protein genes predicted from the genome sequence of isolate 70-15 and looked for an association with AVR activity. This large-scale study found significantly more presence/absence polymorphisms than nucleotide polymorphisms among 1032 putative secreted protein genes. Nucleotide diversity of M. oryzae among 46 isolates of a worldwide collection was extremely low (θ = 8.2 × 10−5), suggestive of recent pathogen dispersal. However, no association between DNA polymorphism and AVR was identified. Therefore, we used genome resequencing of Ina168, an M. oryzae isolate that contains nine AVR genes. Remarkably, a total of 1.68 Mb regions, comprising 316 candidate effector genes, were present in Ina168 but absent in the assembled sequence of isolate 70-15. Association analyses of these 316 genes revealed three novel AVR genes, AVR-Pia, AVR-Pii, and AVR-Pik/km/kp, corresponding to five previously known AVR genes, whose products are recognized inside rice cells possessing the cognate R genes. AVR-Pia and AVR-Pii have evolved by gene gain/loss processes, whereas AVR-Pik/km/kp has evolved by nucleotide substitutions and gene gain/loss.
ZYGOMYCOSIS: Current approaches to management of patients with haematological malignancies
Authors: Pagano Livio , Valentini Caterina G. , Caira Morena , Fianchi Luana 
Published: May 2009

SummaryZygomycosis is an invasive infection that can occur particularly in patients with haematological malignancy. The causative fungi are members of the order Mucorales, and individual species within this group require a high level of laboratory skill to be identified. Zygomycosis can present as rhinocerebral, pulmonary, or disseminated disease, with a rapid clinical course. The optimal management of these cases requires early diagnosis, aggressive antifungal therapy and, when possible, surgical debridement. Founded on clinical experience, but without the benefit of comparative studies, liposomal amphotericin B has become the therapeutic agent of choice. Posaconazole is an orally administered triazole with a demonstrated in vitro and in vivo activity against most Zygomycetes that is comparable to that of amphotericin B. Studies on salvage therapy with posaconazole have yielded promising results, and successful case reports are also available. As an adjuvant approach, iron chelation with deferasirox has shown promising results, although clinical experience is still limited.