bluuebunny/crossref_metadata_2025 huggingface dataset:
Notch insensitive fracture in nanoscale thin films
Authors: Kumar S. , Haque M. A. , Gao H.
Published: June 2009

To study the effect of stress concentration at the nanoscale, we performed fracture experiments on single edge notched thin film specimens inside the transmission electron microscope. Even at about 4 GPa stress at the notch tip, the specimens failed far away from the notch at places with no apparent stress concentration. The in situ electron microscopy showed evidence of little or no plastic deformation at the notch tip. We propose that the apparent notch insensitivity arises from the breakdown of the classical fracture mechanics at the nanoscale, where materials fail by reaching a uniform rupture stress and not due to stress concentration.
Band alignments and improved leakage properties of (La2O3)0.5(SiO2)0.5/SiO2/GaN stacks for high-temperature metal-oxide-semiconductor field-effect transistor applications
Authors: Gao L. G. , Xu B. , Guo H. X. , Xia Y. D. , Yin J. , Liu Z. G.
Published: June 2009

The band alignments of (La2O3)0.5(SiO2)0.5(LSO)/GaN and LSO/SiO2/GaN gate dielectric stacks were investigated comparatively by using x-ray photoelectron spectroscopy. The valence band offsets for LSO/GaN stack and LSO/SiO2/GaN stack are 0.88 and 1.69 eV, respectively, while the corresponding conduction band offsets are found to be 1.40 and 1.83 eV, respectively. Measurements of the leakage current density as function of temperature revealed that the LSO/SiO2/GaN stack has much lower leakage current density than that of the LSO/GaN stack, especially at high temperature. It is concluded that the presence of a SiO2 buffer layer increases band offsets and reduces the leakage current density effectively.
Origin of the phase transition of AlN, GaN, and ZnO nanowires
Authors: Wu Yelong , Chen Guangde , Ye Honggang , Zhu Youzhang , Wei Su-Huai
Published: June 2009

The stabilities of AlN, GaN, and ZnO nanowires/nanorods with different structures and sizes are investigated using first-principles calculations. We found a structure transformation from the graphitelike phase to wurtzite phase as the diameter and length of the nanowire increases. We show that this is due to the competition between the bond energy, the Coulomb energy, and the energy originating from the dipole field of the wurtzite structure. A mechanism of growing uniform nanowires using a graphitelike structure as a precursor is proposed through analyzing the phase diagram of these materials.
Translesion DNA polymerases are required for spontaneous deletion formation in
Salmonella typhimurium
Authors: Koskiniemi Sanna , Andersson Dan I.
Published: June 2009

How spontaneous deletions form in bacteria is still a partly unresolved problem. Here, we show that deletion formation in
Salmonella typhimurium
requires the presence of functional translesion polymerases. First, in wild-type bacteria, removal of the known translesion DNA polymerases, PolII (
polB
), PolIV (
dinB
), PolV (
umuDC
), and SamAB (
samAB
), resulted in a 10-fold decrease in the deletion rate, indicating that 90% of all spontaneous deletions require these polymerases for their formation. Second, overexpression of these polymerases by derepression of the DNA damage-inducible LexA regulon caused a 25-fold increase in deletion rate that depended on the presence of functional translesion polymerases. Third, overexpression of the polymerases PolII and PolIV from a plasmid increased the deletion rate 12- to 30-fold, respectively. Last, in a
recBC
−
mutant where dsDNA ends are stabilized due to the lack of the end-processing nuclease RecBC, the deletion rate was increased 20-fold. This increase depended on the translesion polymerases. In
lexA
(def) mutant cells with constitutive SOS expression, a 10-fold increase in DNA breaks was observed. Inactivation of all 4 translesion polymerases in the
lexA
(def) mutant reduced the deletion rate 250-fold without any concomitant reduction in the amount of DNA breaks. Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a
lexA
(def) mutant with a concomitant 50-fold reduction in deletion rate. These findings suggest that the translesion polymerases are not involved in forming the DNA breaks, but that they require them to stimulate deletion formation.
Journals and repositories: an evolving relationship?
Authors: PINFIELD Stephen
Published: June 2009

It is now widely accepted that there are two routes to open access (OA): OA repositories and OA journals. It is often assumed these are distinct alternative parallel tracks. However, it has recently become clear that there is potential for repositories and journals to interact with each other on an ongoing basis and between them to form a coherent OA scholarly communication system. This paper puts forward three possible models of interaction between repositories and journals; services such as arXiv and PubMed Central, and the work carried out by the RIOJA project, are working exemplars and pilot implementations of these models. The key issues associated with the widespread adoption of these models include repository infrastructure development; changing ideas of the ‘journal’, ‘article’, and ‘publication’; version management; quality assurance; business and funding models; developing value‐added features; content preservation; policy frameworks; and changing roles and cultures within the research community.
Scholarly publishing and open access in the Nordic countries
Authors: HEDLUND Turid , RABOW Ingegerd
Published: June 2009

This study examines aspects of scholarly journal publishing in the Nordic countries. On average half of Nordic journals publish online. In most Nordic countries, commercial publishers predominate; however, in Finland the majority are society publishers. The number of open access journals is low, in line with international figures. There is concern to maintain local languages in journal publishing. A majority of the journals publishing in local languages are within social science, humanities, and arts; the STM sector publishes in English. English‐language publications are favoured in research assessments, international recognition, and impact, while the visibility of local‐language scholarly journals in international databases is low. The Nordbib program supports Nordic scholarly journals and fosters co‐operation with publishing companies and learned societies over migration to e‐publishing; it also supports open access. The article discusses future challenges for journal publishing, pointing out the problems of small journal publishers and the need for co‐operation between stakeholders.
A different form of editor—author interaction: the approach of university journals in China
Authors: LI Li
Published: June 2009

University journals in China exist primarily to showcase the academic research achievements of the university from which they originate. Although they do publish peer‐reviewed articles, their management, distribution, and editorial processes are different from those of regular academic journals. Because they are on campus, the editors of university journals can use face‐to‐face communication to help their authors to revise their papers. To maximize the efficiency of this communication, editors need to prepare well before giving such guidance in order to minimize publication delay, to provide useful guidance to groups of authors, and to improve their own editorial abilities and knowledge.
Creating the Mark Twain Project Online
Authors: SCHIFF Lisa
Published: June 2009

The Mark Twain Project Online (MTPO) was launched in October 2007 and, in this first phase, digitally published several thousand of Twain's letters, almost 100 facsimiles of original documents, and over 28,000 records of other correspondence. The partners involved in the building of MTPO – the Mark Twain Papers, the California Digital Library, and University of California Press – created the site on the premise that Web‐accessible versions of this content, enhanced by innovative design and site architecture and a suite of research tools, would greatly improve scholars' ability to discover and work with this unique material. Anecdotal feedback supports this premise. Early data analysis confirms the usefulness of facsimiles and browsing functionality. Users tend to prefer simple keyword over complex searches; however, those conducting advanced searches are using the tool flexibly, as we had hoped. Further analysis is expected to improve our understanding of how researchers use these tools in combination.
Using what you've got: the development of Emerald Management First
Authors: CRAVEN Alistair , DALLAS Graham
Published: June 2009

This article describes Emerald Group Publishing's development of an online library of management content for managerial training and continued professional development. Emerald Management First was launched in 2000 as a pilot and this article charts the development of the website into a commercial product, providing insights into both the content and technical develoments since its beta days.
What societies want from a publishing partner
Authors: ASHMAN Peter
Published: June 2009

Societies, whose publishing programmes are primarily mission‐driven, play a unique role in funding and disseminating research. But by their nature – often small and with limited resources – they are particularly prone to the turbulence currently affecting scholarly publishing. BMJ Journals is itself a society publisher but also publishes under contract for other societies. During 2008, we carried out research to assess societies' evolving needs from their publishing partnerships. The changing expectations and behaviours of the next generation of researchers are considered to be as much of a threat as declining revenues. Societies are planning to expand professional development activities and to maximise their use of emerging technologies to help maintain and grow membership. Although surplus is a low priority for societies and, accordingly, for their publishing programmes, a high financial return is nonetheless a key criterion when choosing publishing partners – as are reputation, technological innovation, and individual title development.
Learned society members and open access
Authors: MORRIS Sally , THORN Sue
Published: June 2009

The individual members of 35 UK learned societies were surveyed on their attitudes to open access (OA); 1,368 responses were received. Most respondents said they knew what OA was, and supported the idea of OA journals. However, although 60% said that they read OA journals and 25% that they published in them, in both cases around one‐third of the journals named were not OA. While many were in favour of increased access through OA journals, concerns were expressed about the cost to authors, possible reduction in quality, and negative impact on existing journals, publishers, and societies. By contrast, less than half knew what self‐archiving was; 36% thought it was a good idea and 50% were unsure. Just under half said they used repositories of self‐archived articles, but 13% of references were not in fact to self‐archiving repositories. 29% said they self‐archived their own articles, but 10% of references were not to publicly accessible sites of any kind. The access and convenience of self‐archiving repositories were seen as positive, but there were concerns about quality control, workload for authors and institutions, chaotic proliferation of versions, and potential damage to existing journals, publishers, and societies.
Book reviews
Authors: HAYASHI Kazuhiro
Published: June 2009

Scholarly Communication in China, Hong Kong, Japan, Korea and Taiwan
Jingfeng Xia (Editor) Chandos Publishing, Oxford, 2008, 171 pp. ISBN 978‐1‐84334‐322‐6, £59.95, hbk
Book reviews
Authors: OPPENHEIM Charles
Published: June 2009

Copyright's Paradox
Neil Weinstock Netanel Oxford University Press, Oxford, 2008, 274 pp. ISBN 978 0 19 513762 0, £18.00, $34.95, hbk
Book reviews
Authors: NIX Linda
Published: June 2009

Strategic Information Management: A Practitioner's Guide
Jela Webb Oxford, Chandos Publishing, 2008, 226 pp. ISBN 978 1 84334 376 9, £39.95, pbk ISBN 978 1 84334 377 6, £59.95, hbk
Is Placebo Acupuncture What It Is Intended to Be?
Authors: Lundeberg Thomas , Lund Irene , Sing Audrey , Näslund Jan
Published: June 2009

Randomized, placebo‐controlled clinical trials are recommended for evaluation of a treatment′s efficacy with the goal of separating the specific effects (verum) from the non‐specific ones (placebo). In order to be able to carry out placebo‐controlled acupuncture trials, minimal/sham acupuncture procedures and a sham acupuncture needle has been used with the intention of being inert. However, clinical and experimental results suggest that sham/minimal acupuncture is not inert since it is reported that both verum acupuncture and sham/minimal acupuncture induce a significant alleviation of pain. This alleviation is as pronounced as the alleviation obtained with standard treatment and more obvious than the one obtained with placebo medication or by the use of waiting list controls. These results also suggest that sham acupuncture needles evoke a physiological response. In healthy individuals sham acupuncture results in activation of limbic structures, whereas a deactivation is seen in patients with pain, i.e. results from healthy individuals do not reflect what is seen in clinical conditions. Also, depending on the etiology of pain (or any under clinical condition under investigation), the response to sham acupuncture is varying. The acupuncture ritual may also be seen as an emotional focused therapy allowing for psychological re‐orientation. Sham needling in such context may be as powerful as verum acupuncture. We recommend that the evaluated effects of acupuncture could be compared with those of standard treatment, also taking the individual response into consideration, before its use or non‐use is established.
An Angiotensin I Converting Enzyme Polymorphism Is Associated with Clinical Phenotype When Using Differentiation‐Syndrome to Categorize Korean Bronchial Asthma Patients
Authors: Jung Sung-ki , Ra Jehyeon , Seo Jungchul , Jung Hee-Jae , Choi Jun-Yong , Cho Yong-Ju , Hong Mee-Suk , Chung Joo-Ho , Kim Jinju
Published: June 2009

In this study, genetic analysis was conducted to investigate the association of angiotensin I converting enzyme (ACE) gene polymorphism with clinical phenotype based on differentiation‐syndrome of bronchial asthma patients. Differentiation‐syndrome is a traditional Korean medicine (TKM) theory in which patients are classified into a Deficiency Syndrome Group (DSG) and an Excess Syndrome Group (ESG) according to their symptomatic classification. For this study, 110 participants were evaluated by pulmonary function test. Among them, 39 patients were excluded because they refused genotyping. Of the remaining patients, 52 with DSG of asthma (DSGA) and 29 with ESG of asthma (ESGA), as determined by the differentiation‐syndrome techniques were assessed by genetic analysis. ACE insertion/deletion (I/D) polymorphism analysis was conducted using polymerase chain reaction (PCR). Student′s t, chi‐square, Fisher and Hardy‐Weinberg equilibrium tests were used to compare groups. No significant differences in pulmonary function were observed between DSGA and ESGA. The genotypic frequency of ACE I/D polymorphism was found to differ slightly between DSGA and ESGA (P = .0495). However, there were no significant differences in allelic frequency observed between DSGA and ESGA (P = .7006, OR = 1.1223). Interestingly, the allelic (P = .0043, OR = 3.4545) and genotypic (P = .0126) frequencies of the ACE I/D polymorphism in female patients differed significantly between DSGA and ESGA. Taken together, the results presented here indicate that the symptomatic classification of DSGA and ESGA by differentiation‐syndrome in Korean asthma patients could be useful in evaluation of the pathogenesis of bronchial asthma.
Abdominal Aortic Aneurysms
Authors: Knights Gayle
Published: June 2009

Ruptured abdominal aortic aneurysms (AAAs) are uncommon and difficult to diagnose, but they are also life-threatening surgical emergencies and as such the GP should always have a low threshold for suspicion and admission. In contrast, many patients have small asymptomatic aneurysms, often diagnosed by chance during investigations for other illnesses. This article aims to look at both surveillance and treatment of the asymptomatic AAA and the emergency management of the rupturing AAA.
Management of Shoulder Pain in General Practice
Authors: Murphy Richard , Carr Andrew
Published: June 2009

Shoulder pain is a common problem accounting for significant morbidity and disability in the community. As the third most frequent musculoskeletal problem presenting in primary care, shoulder pain has a prevalence of 16–26% in the UK population and around 1% of adults consult their GP with a new presentation of shoulder pain each year. The aetiology of shoulder pain is diverse and many disorders present with similar symptoms and signs. Patients with shoulder pain suffer from a spectrum of functional disability; they may have difficulty performing many essential activities of daily living and are often forced to take time off work.
Joint and Soft Tissue Injections in General Practice
Authors: Saunders Stephanie
Published: June 2009

Musculoskeletal conditions are common, accounting for 15–20% of GP consultations, are chronic disorders and are usually managed in primary care. Injection therapy is an intervention that normally involves localized administration of a corticosteroid with a local anaesthetic. It has been in use for more than 50 years, and there is plenty of anecdotal evidence of its efficacy, but few definitive studies of its application in joint and soft tissue lesions. Despite this, it is the most common therapeutic intervention in rheumatological practice and is recommended for knee and shoulder problems in national and international guidelines. Given its relative safety, ease of application, cost-effectiveness plus the frequent lack of convincing systematic evidence for the benefit of alternative treatments, injection therapy is a useful outpatient treatment modality.
Nuclear Pregnane X Receptor Single Nucleotide Polymorphism (−25385C/T) Is Not Associated With Inflammatory Bowel Disease in Pediatric Patients
Authors: Lacher Martin , Kappler Roland , Schroepf Sebastian , Berkholz Stefan , Ballauff Antje , Bufler Philip , Baurecht Hansjoerg , von Schweinitz Dietrich , Koletzko Sibylle
Published: June 2009

Objective:

Studies in adults characterized the role of the pregnane X receptor (PXR) in the pathophysiology of inflammatory bowel disease (IBD) with conflicting results; pediatric studies are still lacking.

Patients and Methods:

Genotyping for the −25385C/T polymorphism of the PXR gene in 187 white children with IBD and 185 controls. Determination of colonic PXR expression in selected patients with IBD.

Results:

Minor allele frequency was seen in 35.6% patients with IBD and 40.5% controls (P = 0.174), although no significant differences were seen between the genotypes (P = 0.366). PXR was underexpressed in colonic tissue of 7 out of 11 Crohn disease and in 4 out of 5 patients with ulcerative colitis.

Conclusions:

We could not confirm an association of the −25385C/T polymorphism in pediatric patients with IBD.
Defensins Are Differentially Expressed With Respect to the Anatomic Region in the Upper Gastrointestinal Tract of Children
Authors: Vordenbäumen Stefan , Pilic Denisa , Otte Jan‐Michel , Schmitz Frank , Schmidt‐Choudhury Anjona
Published: June 2009

Defensins are antimicrobial peptides expressed on various epithelial surfaces. Although they are believed to contribute to intestinal homeostasis, their expression pattern in children is not well characterized. As determined by real‐time polymerase chain reaction, amount of human alpha‐defensins (hD)‐5 and ‐6 mRNA in duodenal biopsies were significantly higher than in biopsies taken from the gastric mucosa. On the contrary, expression of human beta‐defensins (hBD)‐1 and ‐2 mRNA showed a significantly higher expression in the stomach. Expression of hBD3 to 6 was inconsistently detected. These results suggest a distinct role for various defensins in host defense in the upper gastrointestinal tract of children.
Bilirubin Impairs Intestinal Regrowth Following Massive Small Bowel Resection in a Rat Model
Authors: Sukhotnik Igor , Shaoul Ron , Lieber Michael , Coran Arnold G , Abassi Zaid , Shiloni Eitan , Mogilner Jorge G
Published: June 2009

Objectives:

The purpose of the present study was to evaluate the effects of exogenous bilirubin on structural intestinal adaptation, cell proliferation, and apoptosis in a rat model of short bowel syndrome (SBS).

Materials and Methods:

Male Sprague‐Dawley rats were divided into 5 experimental groups: Sham rats underwent bowel transection and reanastomosis, sham multiple doses of bilirubin (MDB) rats underwent bowel transection and were treated with bilirubin, SBS rats underwent a 75% small bowel resection, SBS‐SDB (single dose bilirubin) rats underwent a bowel resection and were treated with a single dose of bilirubin, and SBS‐MDB underwent a bowel resection and were treated with 3 doses of bilirubin. Bilirubin was administered intraperitoneally from the 7th day through the 14th day postoperatively. Serum total bilirubin concentration over time was evaluated in 5 SBS‐SDB rats following a single intraperitoneal dose. Total bilirubin, alanine aminotransferase, and aspartate aminotransferase in serum and parameters of intestinal adaptation, enterocyte proliferation, and enterocyte apoptosis were determined on day 15.

Results:

SBS‐SDB and SBS‐MDB animals demonstrated lower ileal bowel and mucosal weights, jejunal mucosal DNA and ileal mucosal protein, and jejunal and ileal villus height and crypt depth (vs SBS animals). Bilirubin‐treated rats showed a lower apoptotic index in jejunum and ileum and a trend toward an increase in cell proliferation in jejunum and ileum (vs SBS group).

Conclusions:

In a rat model of SBS, exogenous bilirubin inhibits structural intestinal adaptation. Increased cell proliferation and decreased apoptosis may be considered adaptive mechanisms that maintain cell mass.
Comparative genomics of protoploid Saccharomycetaceae
Authors:   The Génolevures Consortium, Souciet Jean-Luc , Dujon Bernard , Gaillardin Claude , Johnston Mark , Baret Philippe V. , Cliften Paul , Sherman David J. , Weissenbach Jean , Westhof Eric , Wincker Patrick , Jubin Claire , Poulain Julie , Barbe Valérie , Ségurens Béatrice , Artiguenave François , Anthouard Véronique , Vacherie Benoit , Val Marie-Eve , Fulton Robert S. , Minx Patrick , Wilson Richard , Durrens Pascal , Jean Géraldine , Marck Christian , Martin Tiphaine , Nikolski Macha , Rolland Thomas , Seret Marie-Line , Casarégola Serge , Despons Laurence , Fairhead Cécile , Fischer Gilles , Lafontaine Ingrid , Leh Véronique , Lemaire Marc , de Montigny Jacky , Neuvéglise Cécile , Thierry Agnès , Blanc-Lenfle Isabelle , Bleykasten Claudine , Diffels Julie , Fritsch Emilie , Frangeul Lionel , Goëffon Adrien , Jauniaux Nicolas , Kachouri-Lafond Rym , Payen Célia , Potier Serge , Pribylova Lenka , Ozanne Christophe , Richard Guy-Franck , Sacerdot Christine , Straub Marie-Laure , Talla Emmanuel
Published: June 2009

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call “protoploid” because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
Authors: Li Jin Billy , Gao Yuan , Aach John , Zhang Kun , Kryukov Gregory V. , Xie Bin , Ahlford Annika , Yoon Jung-Ki , Rosenbaum Abraham M. , Zaranek Alexander Wait , LeProust Emily , Sunyaev Shamil R. , Church George M.
Published: June 2009

Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From ∼3 million reads derived from a single Illumina Genome Analyzer lane, ∼94% (∼50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%–100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human–chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.
BT2, a BTB Protein, Mediates Multiple Responses to Nutrients, Stresses, and Hormones in Arabidopsis
Authors: Mandadi Kranthi K. , Misra Anjali , Ren Shuxin , McKnight Thomas D.
Published: June 2009

The Arabidopsis (Arabidopsis thaliana) gene BT2 encodes a 41-kD protein that possesses an amino-terminal BTB domain, a central TAZ domain, and a carboxyl-terminal calmodulin-binding domain. We previously demonstrated that BT2 could activate telomerase expression in mature Arabidopsis leaves. Here, we report its distinct role in mediating diverse hormone, stress, and metabolic responses. We serendipitously discovered that steady-state expression of BT2 mRNA was regulated diurnally and controlled by the circadian clock, with maximum expression in the dark. This pattern of expression suggested that BT2 mRNA could be linked to the availability of photosynthate in the plant. Exogenous sugars decreased BT2 expression, whereas exogenous nitrogen increased expression. bt2 loss-of-function mutants displayed a hypersensitive response to both sugar-mediated inhibition of germination and abscisic acid (ABA)-mediated inhibition of germination, thus supporting a role of ABA in sugar signaling in germination and development. Moreover, constitutive expression of BT2 imparted resistance to both sugars and ABA at germination, suggesting that BT2 suppresses sugar and ABA responses. In support of the previously described antagonistic relationship between ABA and auxin, we found that BT2 positively regulated certain auxin responses in plants, as revealed by knocking down BT2 expression in the high-auxin mutant yucca. Accumulation of BT2 mRNA was affected by a variety of hormones, nutrients, and stresses, and BT2 was required for responses to many of these same factors. Together, these results suggest that BT2 is a central component of an interconnected signaling network that detects and responds to multiple inputs.
Resistance to the Pseudomonas syringae Effector HopA1 Is Governed by the TIR-NBS-LRR Protein RPS6 and Is Enhanced by Mutations in SRFR1
Authors: Kim Sang Hee , Kwon Soon Il , Saha Dipanwita , Anyanwu Nkemdi C. , Gassmann Walter
Published: June 2009

The Pseudomonas syringae-Arabidopsis (Arabidopsis  thaliana) interaction is an extensively studied plant-pathogen system. Arabidopsis possesses approximately 150 putative resistance genes encoding nucleotide binding site (NBS) and leucine-rich repeat (LRR) domain-containing proteins. The majority of these belong to the Toll/Interleukin-1 receptor (TIR)-NBS-LRR (TNL) class. Comparative studies with the coiled-coil-NBS-LRR genes RPS2, RPM1, and RPS5 and isogenic P. syringae strains expressing single corresponding avirulence genes have been particularly fruitful in dissecting specific and common resistance signaling components. However, the major TNL class is represented by a single known P. syringae resistance gene, RPS4. We previously identified hopA1 from P. syringae pv syringae strain 61 as an avirulence gene that signals through ENHANCED DISEASE SUSCEPTIBILITY1, indicating that the corresponding resistance gene RPS6 belongs to the TNL class. Here we report the identification of RPS6 based on a forward-genetic screen and map-based cloning. Among resistance proteins of known function, the deduced amino acid sequence of RPS6 shows highest similarity to the TNL resistance protein RAC1 that determines resistance to the oomycete pathogen Albugo candida. Similar to RPS4 and other TNL genes, RPS6 generates alternatively spliced transcripts, although the alternative transcript structures are RPS6 specific. We previously characterized SRFR1 as a negative regulator of avrRps4-triggered immunity. Interestingly, mutations in SRFR1 also enhanced HopA1-triggered immunity in rps6 mutants. In conclusion, the cloning of RPS6 and comparisons with RPS4 will contribute to a closer dissection of the TNL resistance pathway in Arabidopsis.
CYP86B1 Is Required for Very Long Chainω-Hydroxyacid andα,ω-Dicarboxylic Acid Synthesis in Root and Seed Suberin Polyester
Authors: Compagnon Vincent , Diehl Patrik , Benveniste Irène , Meyer Denise , Schaller Hubert , Schreiber Lukas , Franke Rochus , Pinot Franck
Published: June 2009

Suberin composition of various plants including Arabidopsis (Arabidopsis thaliana) has shown the presence of very long chain fatty acid derivatives C20 in addition to the C16 and C18 series. Phylogenetic studies and plant genome mining have led to the identification of putative aliphatic hydroxylases belonging to the CYP86B subfamily of cytochrome P450 monooxygenases. In Arabidopsis, this subfamily is represented by CYP86B1 and CYP86B2, which share about 45% identity with CYP86A1, a fatty acid ω-hydroxylase implicated in root suberin monomer synthesis. Here, we show that CYP86B1 is located to the endoplasmic reticulum and is highly expressed in roots. Indeed, CYP86B1 promoter-driven β-glucuronidase expression indicated strong reporter activities at known sites of suberin production such as the endodermis. These observations, together with the fact that proteins of the CYP86B type are widespread among plant species, suggested a role of CYP86B1 in suberin biogenesis. To investigate the involvement of CYP86B1 in suberin biogenesis, we characterized an allelic series of cyp86B1 mutants of which two strong alleles were knockouts and two weak ones were RNA interference-silenced lines. These root aliphatic plant hydroxylase lines had a root and a seed coat aliphatic polyester composition in which C22- and C24-hydroxyacids and α,ω-dicarboxylic acids were strongly reduced. However, these changes did not affect seed coat permeability and ion content in leaves. The presumed precursors, C22 and C24 fatty acids, accumulated in the suberin polyester. These results demonstrate that CYP86B1 is a very long chain fatty acid hydroxylase specifically involved in polyester monomer biosynthesis during the course of plant development.
A Cell Wall–Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice
Authors: Aparna Gudlur , Chatterjee Avradip , Sonti Ramesh V. , Sankaranarayanan Rajan
Published: June 2009

Xanthomonas oryzae pv oryzae (Xoo) causes bacterial blight, a serious disease of rice (Oryza sativa). LipA is a secretory virulence factor of Xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. Here, we present the high-resolution structural characterization of LipA that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalytic domain. We demonstrate that the enzyme binds to a glycoside ligand through a rigid pocket comprising distinct carbohydrate-specific and acyl chain recognition sites where the catalytic triad is situated 15 Å from the anchored carbohydrate. Point mutations disrupting the carbohydrate anchor site or blocking the pocket, even at a considerable distance from the enzyme active site, can abrogate in planta LipA function, exemplified by loss of both virulence and the ability to elicit host defense responses. A high conservation of the module across genus Xanthomonas emphasizes the significance of this unique plant cell wall–degrading function for this important group of plant pathogenic bacteria. A comparison with the related structural families illustrates how a typical lipase is recruited to act on plant cell walls to promote virulence, thus providing a remarkable example of the emergence of novel functions around existing scaffolds for increased proficiency of pathogenesis during pathogen-plant coevolution.
Modelling and simulation of mechanical transmission in roller‐screw electromechanical actuators
Authors: Karam Wissam , Mare Jean‐Charles
Published: June 2009

Purpose

The purpose of this paper is to develop accurate model and simulation of mechanical power transmission within roller‐screw electromechanical actuators with special attention to friction, compliance and inertia effects. Also, to propose non‐intrusive experiments for the identification of model parameters with an integrator or system‐oriented view.

Design/methodology/approach

At system design level, the actuation models need to reproduce with confidence the energy losses and the main dynamic effects. The adopted modelling methodology is based on non‐intrusive measurements taken on a standard actuator test‐bench. The actuator model is first structured with respect to the bond‐graph formalism that allows a clear identification of the considered effects and associated causalities for model implementation. Various approaches are then combined, mixing blocked or moving load, position or torque control and time or frequency domains analysis. The friction representation model is suggested using a step‐by‐step approach that covers a wide domain of operation. The model is validated under varying torque and speed conditions.

Findings

A structured model is introduced with support of the bond‐graph formalism. Combining blocked/moving load and time/frequency domain experiments allows the development of progressive model identification. An advanced friction representation model is proposed including the effects of speed, transmitted force, quadrant of operation and roller‐screw preload.

Originality/value

Mechanical transmission energy losses and dynamics are modelled in a system‐oriented view without massive need to confidential design parameters. Not only speed but also load and operation quadrant effects are reproduced by the proposed friction model. The non‐intrusive experimental procedure is made consistent with use of a standard actuator test‐bench.
Robust attitude acquisition for micro‐satellite
Authors: Chen Weiyue , Jing Wuxing
Published: June 2009

Purpose

The purpose of this paper is to investigate the problem of the initial attitude detumbling and acquisition for micro‐satellite using geomagnetism with the aid of the pitch momentum bias, and the application of the feedback linearization method, H∞ and μ‐synthesize control theory in the robust attitude acquisition controller design.

Design/methodology/approach

The pitch flywheels establish the momentum bias state in the beginning of the detumbling stage and keep the momentum bias state thereafter. The geomagnetic change rate feedback detumbling controller is used to detumble the micro‐satellite and the gyroscope rigidity is utilized to capture orbital negative normal orientation in the detumbling and attitude acquisition phase. Feedback linearization method is adopted to obtain the linear attitude dynamics. Based on the feedback linearization model, a quasi proportion differential (PD) controller is designed, meanwhile H∞ and μ‐synthesis control theories are adopted to synthesis the robust attitude acquisition controllers.

Findings

The pitch momentum bias‐aided attitude detumbling and acquisition method make the capture of the orbital negative normal orientation faster and more accurate than the classical initial operation process. Quasi PD and H∞ have greater robustness than the classical PD attitude acquisition controller in normal geomagnetic case; quasi PD and μ‐synthesis have greater robustness than the classical PD attitude acquisition controller in magnetic storm case.

Originality/value

Provides pitch momentum bias‐aided attitude detumbling and acquisition method for the micro‐satellite and the robust attitude acquisition controller design technology.
Active vibration control of a laminated composite plate subjected to blast load
Authors: Uyanık Haydar , Mecitoğlu Zahit
Published: June 2009

Purpose

The purpose of this paper is to develop a structural vibration control system by using a state observer which estimates system states using displacements measured from sensors.

Design/methodology/approach

Friedlander's exponential decay function is used for expressing the blast load model. A semiloof shell element is developed in order to account for piezoelectric effects. The composite plate is discretized by using the semiloof shell elements, and stiffness and mass matrices of the plate are obtained from the finite element model. In order to reduce the degrees of freedom of the finite element model, mode summation method is used with weighted modal vector including initial dominant modes in the dynamic behavior.

Findings

The structural vibrations are suppressed successfully and in an optimal way by using a state observer control system which estimates system states using displacements measured from sensors.

Originality/value

This paper shows, for the first time, that vibrations of a cantilevered composite plate subjected to blast loading are suppressed by the use of piezoelectric actuators. The state observer and optimal linear quadratic regulator are both used at the same time to suppress the vibrations.
The turbo fan aircraft minimum cost climb technique
Authors: Mirosavljević P. , Gvozdenović S. , Čokorilo O.
Published: June 2009

Purpose

The purpose of this paper is to define minimum cost technique of turbo fan transport aircraft in the presence of dynamic change of aircraft performance. Results can be practical applicable in airlines for achieving minimal operation costs.

Design/methodology/approach

Logarithmic differential is applied for defining conditions in order to achieve optimal Mach number for minimal climb cost. This condition is solved numerically by using Newton‐Ramphson method, to obtain optimal Mach number distribution with altitude. Conclusion about optimal top of climb (TOC) is defined after analyses for different aircraft mass and cost indexes.

Findings

Proposed method of minimum cost climb resulting in potential savings up to 5 per cent compared to Aircraft Flight Manual climb law. Proposed method also made correction of climb law and optimal TOC under existence of aircraft performance degradation.

Practical implications

Use of defined climb law and optimal TOC will minimize cost of en route flight profile.

Originality/value

At present, there is no definition of climb technique for minimum cost of en route flight profile, under dynamic degradation of aircraft performance. Final results are standardized to become applicable and easy to use with modern and old type of flight management system.
Redundancy handling – a key training need
Authors: Rees W. David , Porter Christine
Published: June 2009

Purpose

The purpose of this paper is to identify and explain key training needs regarding redundancy handling which is increasingly affecting people, often for the first time

Design/methodology approach

The authors use their background in the employee relations area to identify and explain key skills that are involved in redundancy handling. While knowledge of relevant law is part of what is required, it is only one aspect. Managers can suddenly find that they are thrust into a complicated conflict situation, in a deteriorating workplace atmosphere when they may also be unsure about their own job security.

Findings

Staff surpluses do not automatically mean redundancy. Options can include re‐deployment, short‐time working, temporary lay‐offs and temporary closure and pay cuts. However, in these situations, as with redundancy, managers may find that the situation may be very stressful. This may be aggravated by a collapse in morale combined with a need to maintain a reduced level of production and/or services. Policies of multi‐skilling may both help avoid redundancy in the first place and failing that help with the re‐deployment of surplus staff. Training and development may also have a crucial role in helping an organisation adapt to the circumstances that caused a staff surplus. Adaptation is likely to need to include the positive management of redundancy survivors.

Originality/value

There are two main features of the paper – it explains the key issues in redundancy handling for people who may be unexpectedly involved in it – which is increasingly likely; it also focuses on the training issues – especially for those having to implement redundancy.
Leadership, beyond project management
Authors: Clarke Prudence A.
Published: June 2009

Purpose

The purpose of this paper is to raise awareness of the need to understand the differences between management and leadership within the project environment.

Design/methodology/approach

First stage research involved data analysis from forum, workshops, group to one, one to one interviews. Second stage research involves a five‐year PhD study undertaken by the author.

Findings

The paper highlights the need not only to understand the difference between project management and leadership, but also to use this differentiation in the identification, assessment and development of project services providers and as an integral part of organisational and people development for all companies involved in sponsoring, supporting or delivering projects.

Practical implications

The premise is that the emphasis needs to be on project leadership to achieve a successful project

Originality/value

The paper includes research within a specific industry based on identification of a market niche.
The Google Book settlement and academic libraries
Authors: Joint Nicholas
Published: June 2009

Purpose

The purpose of this paper is to illustrate issues surrounding the Google Book settlement in 2009, and its relevance to libraries by general discussion and examples from library practice.

Design/methodology/approach

A set of projections and speculations that are both conceptual and practical in nature, based on early reactions and comments about this development.

Findings

There are many philosophical and moral objections to the consequences of the Google Book settlement, and that the practical effects for academic libraries could be both positive and/or negative. The practical examples of such outcomes are designed to help clarify the implications for library and information practitioners and generate further debate.

Research limitations/implications

The fact that the Book settlement is a legal arrangement between parties in a civil court makes in depth research analysis of a public nature very difficult – which is in itself one of the main themes of the paper.

Practical implications

The teasing out of the real‐life consequences of the settlement are intended be helpful to the library practitioner.

Originality/value

This paper tries to offer an early insight into an important new development in information retrieval history from the point of view of academic librarians, in contrast to much contemporary comment, which has come from authors and rights holders.
Inferential information‐seeking
Authors: Shenton Andrew K.
Published: June 2009

Purpose

Using a variety of evidence this paper aims to develop the concept of “inferential information‐seeking”. The term itself is new and the type of phenomena it addresses has been the subject of limited attention.

Design/methodology/approach

The author considers inferential information‐seeking in the context of three distinct scenarios, each of which has come to the writer's attention through either the literature or his own direct experience.

Findings

Exploration of the identified instances of inferential information‐seeking reveals that the strategy is a circuitous one employed by individuals when faced with barriers that impede their use of more obvious methods of finding information. Substantial mental effort may be required on the user's part to exploit the information elicited in such a way as to satisfy the information need stimulating the action.

Research limitations/implications

The notion of inferential information‐seeking postulated here is based on a very small number of cases, none of which has come to light in research specially undertaken to investigate the phenomenon.

Practical implications

Even though knowledge of inferential information‐seeking is still in its infancy, it would appear appropriate to incorporate some provision for it in the teaching of information literacy.

Originality/value

Intended for information practitioners and academics alike, the paper synthesizes a new concept through examination of actual information‐seeking episodes with reference to a wide‐ranging body of source material. An understanding of inferential information‐seeking offers the potential to increase our comprehension of how individuals find information, as well as to add a further dimension to information literacy instruction.