bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient flexible organic solar cells with room temperature sputtered and highly conductive NiO as hole-transporting layer
Authors: Sun Nanhai , Fang Guojia , Qin Pingli , Zheng Qiao , Wang Mingjun , Fan Xi , Cheng Fei , Wan Jiawei , Zhao Xingzhong , Liu Jiwen , Carroll David L , Ye Jianming
Published: October 2010

We report efficient bulk-heterojunction [regioregular of poly(3-hexylthiophene) (P3HT) : (6,6)-phenyl C61 butyric acid methyl ester(PCBM)] solar cells with a highly transparent and electrical conductive NiO film as hole-transporting layer (HTL). The highest power conversion efficiency (PCE) of 3.26% of FTO/NiO/P3HT : PCBM/Al solar cells on glass was achieved through NiO thin film sputtering temperature, film thickness optimization and it was found that NiO with 10 nm and sputtered at room temperature shows the best photovoltaic properties. Under the optimized condition, PCE of 2.5% on flexible substrate was achieved with highly electrical conductive and room temperature sputtered NiO as HTL.
Low-cost photoelectrocatalyst based on a nanoporous oxide layer of low-carbon steel
Authors: Rangaraju Raghu R , Raja K S , Panday A , Misra M
Published: October 2010

Low-carbon steel is a commonly used structural material in a wide variety of applications. An anodic oxide layer of this inexpensive alloy has been noted to have interesting photoelectrochemical behaviour similar to that of α-Fe2O3 prepared using other expensive starting materials. An ordered nanoporous oxide layer has been grown on to the low-carbon steel surface by a simple electrochemical anodization process in different electrolytes such as ethylene glycol containing 0.05M NH4F and 3–10 vol% water and 0.5M phosphoric acid solution containing 0.05M NH4F. After anodization, the nanoporous anodic oxide layer has been transformed to α-Fe2O3 by a low-temperature annealing process. Photoelectrochemical characterization of the anodic iron oxide materials has been carried out in 1M KOH electrolyte under a solar simulated illumination using Air Mass (AM) 1.5. The ordered nanoporous oxide layer prepared in ethylene glycol-based electrolyte showed a photocurrent density of about 85 µA cm−2 at 0.4 VAg/AgCl. Whereas the anodic iron oxide prepared by anodization of the low-carbon steel in 0.5M H3PO4 + 0.05M NaF solution showed a photocurrent density of 800 µA cm−2 at 0.4 VAg/AgCl. The improved photoactivity of the phosphate-modified oxide layer could be attributed to the high charge carrier concentration, low charge transfer resistance and better ability to expend holes in the oxygen evolution reaction.
Composition dependence and reversibility of photoinduced refractive index changes in chalcogenide glass
Authors: Calvez Laurent , Yang Zhiyong , Lucas Pierre
Published: October 2010

Photoinduced refractive index changes are investigated as a function of composition in Ge–As–Se chalcogenide glass by measuring the formation of Bragg reflectors photo-imprinted in polished glass discs. It is shown that the glass network connectivity has a strong effect on the photostructural changes which decrease dramatically when the rigidity percolates through the structure at coordination numbers ⟨r⟩ > 2.4. The Bragg reflector formation is also affected by the refractive index of the glass which varies sharply with ⟨r⟩ and correlates directly with the glass density. The photoinduced refractive index change is shown to reverse upon annealing near the glass transition following a non-exponential kinetic that closely matches the kinetics of structural enthalpy relaxation. The Bragg reflectors can also be reversibly erased and readjusted to a new wavelength through subsequent irradiation with a different photon energy. The composition dependence of photosensitivity is discussed in terms of structural constraints. It is suggested that over-constrained networks remain rigid despite photoexcitation of bond constraints therefore precluding photostructural rearrangements.
Growth temperature and V/III ratio effects on the morphology and crystal structure of InP nanowires
Authors: Paiman S , Gao Q , Joyce H J , Kim Y , Tan H H , Jagadish C , Zhang X , Guo Y , Zou J
Published: October 2010

The effects of growth temperature and V/III ratio on the morphology and crystallographic phases of InP nanowires that are grown by metal organic chemical vapour deposition have been studied. We show that higher growth temperatures or higher V/III ratios promote the formation of wurtzite nanowires while zinc-blende nanowires are favourable at lower growth temperatures and lower V/III ratios. A schematic map of distribution of zinc-blende and wurtzite structures has been developed in the range of growth temperatures (400–510 °C) and V/III ratios (44 to 700) investigated in this study.
Electrical properties of multiferroic BiFeO3 ceramics synthesized by spark plasma sintering
Authors: Dai Zhonghua , Akishige Yukikuni
Published: October 2010

Single-phase multiferroic BiFeO3 powder was prepared by improved solid-state synthesis, and dense BiFeO3 ceramics were fabricated by a spark plasma sintering (SPS) process. The sintering temperature of SPS ranged from 650 to 800 °C under 50 MPa. It is found that the sample is not only single phased but also of high density when sintered at 650 °C. The dielectric constant and loss of the samples were tested between 100 Hz and 20 MHz at several temperatures. Oxygen and vacuum annealing conditions impact the dielectric behaviour of the BiFeO3 ceramics prepared by the SPS technique obviously. The piezoelectric coefficient d
33 of the sample annealed in vacuum is 4.2 pC N−1 at room temperature.
Motion control in double-walled carbon nanotube systems using a Stone–Thrower–Wales defect cluster
Authors: Liu Ping , Zhang Yong-Wei
Published: October 2010

The ability to control the motion of a single molecule will have an important impact in nano-mechanical systems. Multi-walled carbon nanotube systems, which have extremely low intertube friction and strong motion confinement, can form the basis for mechanically based motion control. We devise two molecular motion control units based on double-walled carbon nanotubes embedded with a Stone–Thrower–Wales defect cluster, and perform molecular dynamics simulations to determine the characteristics of these two control units. We show that one of the molecular control units is able to perform a logic operation on one logic input and produce three logic outputs, while the other is able to produce two logic outputs. Potential applications of the motion control units include molecular switches, shuttles and mechanically based logic devices.
Melt pool and keyhole behaviour analysis for deep penetration laser welding
Authors: Fabbro R
Published: October 2010

One usually defines the main characteristic of the welding performances of a given laser system by its ‘penetration curve’ that corresponds to the welding depth as a function of the welding speed V
w for a given set of operating parameters. Analysis of a penetration curve is interesting and gives very fruitful results. Coupled with high-speed video imaging of melt pool surface and ejected plume behaviour, the analysis of this penetration curve on a very large range of welding speeds, typically from 0 to 50 m min−1, has allowed us to observe very different and characteristic regimes. These regimes are mainly characterized by the physical processes by which they impede the laser beam penetration inside the material. We show that it is only at rather high welding speeds that these limiting processes are reduced. Consequently, the scaling law of welding depth with welding speed is in agreement with adapted modelling of this process. On the other hand, as the welding speed is reduced, different effects depending on the weld pool dynamics and plume interaction strongly disturb the keyhole stability and are responsible for the deviation of the penetration curve from the previous modelling that agrees with a 1/V
w scaling law. A corresponding criterion for the occurrence of this effect is defined.
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals
Authors: Zöllner Sebastian
Published: October 2010

Summary: The program package CopyMap identifies copy number variation from oligo-hybridization and CGH data. Using a time-dependent hidden Markov model to combine evidence of copy number variants (CNVs) across multiple carriers, CopyMap is substantially more accurate than standard hidden Markov methods in identifying CNVs and calling CNV-carriers. Moreover, CopyMap provides more precise estimates of CNV-boundaries.

Availability: The C-source code and detailed documentation for the program CopyMap is available on the Internet at http://www.sph.umich.edu/csg/szoellner/

Contact:  szoellne@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Model quality assessment for membrane proteins
Authors: Ray Arjun , Lindahl Erik , Wallner Björn
Published: October 2010

Motivation: Learning-based model quality assessment programs have been quite successful at discriminating between high- and low-quality protein structures. Here, we show that it is possible to improve this performance significantly by restricting the learning space to a specific context, in this case membrane proteins. Since these are among the most important structures from a pharmaceutical point-of-view, it is particularly interesting to resolve local model quality for regions corresponding, e.g. to binding sites.

Results: Our new ProQM method uses a support vector machine with a combination of general and membrane protein-specific features. For the transmembrane region, ProQM clearly outperforms all methods developed for generic proteins, and it does so while maintaining performance for extra-membrane domains; in this region it is only matched by ProQres. The predictor is shown to accurately predict quality both on the global and local level when applied to GPCR models, and clearly outperforms consensus-based scoring. Finally, the combination of ProQM and the Rosetta low-resolution energy function achieve a 7-fold enrichment in selection of near-native structural models, at very limited computational cost.

Availability: ProQM is available as a server at +proqm.cbr.su.se+.

Contact:  bjorn@cbr.su.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
The SMARTCyp cytochrome P450 metabolism prediction server
Authors: Rydberg Patrik , Gloriam David E. , Olsen Lars
Published: October 2010

Summary: The SMARTCyp server is the first web application for site of metabolism prediction of cytochrome P450-mediated drug metabolism.

Availability: The SMARTCyp server is freely available for use on the web at www.farma.ku.dk/smartcyp where the SMARTCyp Java program and source code is also available for download.

Contact:  smartcyp@farma.ku.dk; lo@farma.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways
Authors: Flórez Lope A. , Lammers Christoph R. , Michna Raphael , Stülke Jörg
Published: October 2010

Summary: Systems biology relies increasingly on collaborations between several groups with different expertise. Therefore, the systems biology community is adopting standards that allow effective communication of concepts, as well as transmission and processing of pathway information. The Systems Biology Graphical Notation (SBGN) is a graphical language for biological pathways that has both a biological as well as a computational meaning. The program CellDesigner allows the codification of biological phenomena in an SBGN compliant form. CellPublisher is a web server that allows the conversion of CellDesigner files to web-based navigatable diagrams based on the user interface of Google maps. Thus, CellPublisher complements CellDesigner by facilitating the understanding of complex diagrams and by providing the possibility to share any CellDesigner diagram online with collaborators and get their feedback. Due to the intuitive interface of the online diagrams, CellPublisher serves as a basis for discovery of novel properties of the modelled networks.

Availability: The freely available web server and the documentation can be accessed at: http://cellpublisher.gobics.de/. The source code and the offline version for Microsoft Windows are freely available at http://sourceforge.net/projects/cellpublisher/.

Contact:  jstuelk@gwdg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost
Authors: Vaz-Moreira Ivone , Figueira Vânia , Lopes Ana R. , De Brandt Evie , Vandamme Peter , Nunes Olga C. , Manaia Célia M.
Published: October 2010

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).
Dietzia alimentaria sp. nov., isolated from a traditional Korean food
Authors: Kim Jandi , Roh Seong Woon , Choi Jung-Hye , Jung Mi-Ja , Nam Young-Do , Kim Min-Soo , Park Eun-Jin , Shin Kee-Sun , Bae Jin-Woo
Published: October 2010

An actinobacterial strain, designated 72T, was isolated from a traditional salt-fermented seafood in Korea. Colonies were coral red and cells were Gram-reaction-positive, non-motile rods. Strain 72T grew with 0–10 % (w/v) NaCl, at pH 7–10 and at 15–37 °C. Optimum growth conditions were 2 % NaCl, pH 7.0 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 72T belonged to the genus Dietzia. The major cellular fatty acids (>5 %) were C16 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), 10-methyl C18 : 0, C17 : 0, C19 : 0 and C18 : 1ω9c. 16S rRNA gene sequence analysis and DNA–DNA hybridization, coupled with physiological and biochemical tests, revealed genotypic and phenotypic differences between strain 72T and other members of the genus Dietzia. Based on these data, strain 72T represents a novel species, for which the name Dietzia alimentaria sp. nov. is proposed. The type strain is 72T ( = JCM 16360T  = KACC 21126T).
Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil
Authors: Zhang Lei , Bai Juan , Wang Yang , Wu Gao-Lin , Dai Jun , Fang Cheng-Xiang
Published: October 2010

Two Gram-reaction-negative, rod-shaped, gliding, yellow-pigmented bacterial strains, designated ZLD-17T and ZLD-29T, were isolated from arid soil samples collected from Xinjiang Province, north-west China, and subjected to analysis using a polyphasic taxonomic approach. Both novel strains required 1.0–2.0 % (w/v) sea salts for optimal growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belong to the genus Lysobacter within the class Gammaproteobacteria. Strain ZLD-17T showed highest 16S rRNA gene sequence similarities to Lysobacter capsici KCTC 22007T (96.9 %), Lysobacter spongiicola DSM 21749T (96.8 %) and Lysobacter koreensis KCTC 12204T (96.8 %), whereas strain ZLD-29T showed highest sequence similarities to Lysobacter niastensis DSM 18481T (96.0 %) and Lysobacter enzymogenes DSM 2043T (95.9 %). 16S rRNA gene sequence similarity between ZLD-17T and ZLD-29T was 96.1 %. The DNA G+C contents of strains ZLD-17T and ZLD-29T were 67.9 and 68.2 mol%, respectively. The major cellular fatty acids of both strains were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c, iso-C16 : 0, C16 : 0 and iso-C11 : 0 3-OH; their predominant isoprenoid quinone was Q-8 and their major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and chemotaxonomic data, strains ZLD-17T ( = CCTCC AB 207174T  = KCTC 23076T) and ZLD-29T ( = CCTCC AB 207175T = KCTC 23077T) represent two novel species of the genus Lysobacter, for which the names Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov. are proposed, respectively.
Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt
Authors: Shimane Yasuhiro , Hatada Yuji , Minegishi Hiroaki , Echigo Akinobu , Nagaoka Syuhei , Miyazaki Masayuki , Ohta Yukari , Maruyama Tadashi , Usami Ron , Grant William D. , Horikoshi Koki
Published: October 2010

Strain YSM-79T was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5–5.3 M NaCl (optimum 2.5–3.0 M), pH 5.0–8.8 (optimum pH 5.2–6.3) and 20–55 °C (optimum 40 °C). Mg2+ is required for growth, with maximum growth at 200–300 mM Mg2+. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79T was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB′ gene sequence of strain YSM-79T had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79T should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79T ( = JCM 16327T  = CECT 7563T).
Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol-contaminated soil
Authors: Gomila Margarita , Tvrzová Ludmila , Teshim Andrea , Sedláček Ivo , González-Escalona Narjol , Zdráhal Zbyněk , Šedo Ondrej , González Jorge Froilán , Bennasar Antonio , Moore Edward R. B. , Lalucat Jorge , Murialdo Silvia E.
Published: October 2010

A polyphasic taxonomic approach was applied to the study of a Gram-negative bacterium (B2T) isolated from soil by selective enrichment with pentachlorophenol. 16S rRNA gene sequence analysis of strain B2T showed that the strain belongs to the genus Achromobacter within the Betaproteobacteria. The 16S rRNA gene sequence displayed more than 99 % similarity to the sequences of the type strains of all species of Achromobacter, with the highest sequence similarity to those of Achromobacter spanius CCM 7183T and A. piechaudii CCM 2986T (99.8 %). On the basis of phylogenetic analysis, genomic DNA–DNA relatedness and phenotypic characteristics, including chemotaxonomic (cellular fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2T ( = CCM 7608T  = CCUG 56371T  = CECT 7342T).
Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture
Authors: Sahin Nurettin , Tani Akio , Kotan Recep , Sedláček Ivo , Kimbara Kazuhide , Tamer Abdurrahman U.
Published: October 2010

Five isolates, designated TA2, TA4, TA25T, KOxT and NS15T were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit (gyrB) gene sequences confirmed that the isolates belonged to the genus Pandoraea and were most closely related to Pandoraea sputorum and Pandoraea pnomenusa (97.2–99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). On the basis of DNA–DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus Pandoraea, for which the names Pandoraea oxalativorans sp. nov. (TA25T  = NBRC 106091T  = CCM 7677T  = DSM 23570T), Pandoraea faecigallinarum sp. nov. (KOxT  = NBRC 106092T  = CCM 2766T  = DSM 23572T) and Pandoraea vervacti sp. nov. (NS15T  = NBRC 106088T  = CCM 7667T  = DSM 23571T) are proposed.
Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov.
Authors: Promnuan Yaowanoot , Kudo Takuji , Ohkuma Moriya , Chantawannakul Panuwan
Published: October 2010

A Gram-reaction-positive aerobic actinomycete, designated strain IM17-1T, was isolated from a honey bee (Apis mellifera) hive in Chiang Mai Province, Thailand. The strain formed a branched substrate mycelium and mature aerial mycelium bore short chains of arthrospores with warty surfaces. The cell wall contained meso-2,6-diaminopimelic acid (cell-wall type III) and the whole cell sugars were fucose, galactose, glucose, madurose, mannose and ribose. The major isoprenoid quinone was hexahydrogenated menaquinone with nine isoprene units and the predominant cellular fatty acids were C16 : 0 (33.8 %), C18 : 1ω9c (32.7 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (8.7 %) and 10-methyl C18 : 0 (8.2 %). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. These morphological and chemotaxonomic characteristics were consistent with the classification of IM17-1T within the genus Actinomadura. Based on 16S rRNA gene sequence analysis, strain IM17-1T was closely related to the type strains of Actinomadura cremea subsp. cremea (98.1 %) and Actinomadura cremea subsp. rifamycini (98.6 %); however, it represented a distinct phylogenetic lineage from the other species within this genus. The unique genetic characteristics were reaffirmed by low levels of DNA–DNA relatedness between strain IM17-1T and the two most closely related type strains, A. cremea subsp. cremea JCM 3308T (56.5±4.9 %) and A. cremea subsp. rifamycini JCM 3309T (31.0±22.6 %), and further supported the proposal of IM17-1T as a novel species. Strain IM17-1T ( = JCM 16576T  = TISTR 1980T) thus represents a novel species of the genus Actinomadura, for which the name Actinomadura apis sp. nov. is proposed. In addition, the genotypic and phenotypic data suggested the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as a separate species, Actinomadura rifamycini sp. nov., comb. nov.
Tistrella bauzanensis sp. nov., isolated from soil
Authors: Zhang De-Chao , Liu Hong-Can , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: October 2010

A Gram-reaction-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain BZ78T, was isolated from soil from an industrial site. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ78T belonged to the family Rhodospirillaceae and formed a coherent cluster with the type strain of Tistrella mobilis (98.3 % pairwise similarity). The predominant cellular fatty acids of strain BZ78T were C18 : 1ω7c (58.3 %), C19 : 0ω8c cyclo (11.5 %), C18 : 1 2-OH (10.9 %) and C14 : 0 3-OH (6.4 %). The predominant ubiquinone was Q-10. The genomic DNA G+C content of strain BZ78T was 65.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ78T is considered to represent a novel species of the genus Tistrella, for which the name Tistrella bauzanensis sp. nov. is proposed. The type strain is BZ78T ( = DSM 22817T  = CGMCC 1.10188T  = LMG 26047T).
Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments
Authors: Pohl Carolina H. , Smit Martha S. , Albertyn Jacobus
Published: October 2010

Recent rDNA sequencing of 25 isolates from a previous study, during which limonene-utilizing yeasts were isolated from monoterpene-rich environments by using 1,4-disubstituted cyclohexanes as sole carbon sources, led to the identification of four hitherto unknown Rhodotorula species. Analyses of the 26S rDNA D1/D2 region as well as the internal transcribed spacer (ITS) domain indicated that two isolates (CBS 8499T and CBS 10736) were identical and were closely related to Rhodotorula cycloclastica, a previously described limonene-utilizing yeast. These novel isolates differed from known yeast species and could be distinguished from R. cycloclastica by standard physiological tests. The other three isolates represent three novel Rhodotorula species, closely related to Sporobolomyces magnisporus. These three species could also be distinguished from other Rhodotorula species by standard physiological tests. Based on these results, we suggest that the new isolates represent novel species, for which the names Rhodotorula eucalyptica sp. nov. (type strain CBS 8499T  = NRRL Y-48408T), Rhodotorula pini sp. nov. (type strain CBS 10735T  = NRRL Y-48410T), Rhodotorula bloemfonteinensis sp. nov. (type strain CBS 8598T  = NRRL Y-48407T) and Rhodotorula orientis sp. nov. (type strain CBS 8594T  = NRRL Y-48719T) are proposed. R. eucalyptica and R. pini can also utilize limonene.
Ochrobactrum pecoris sp. nov., isolated from farm animals
Authors: Kämpfer Peter , Huber Bettina , Busse Hans-Jürgen , Scholz Holger C. , Tomaso Herbert , Hotzel Helmut , Melzer Falk
Published: October 2010

Two Gram-negative, rod-shaped, non-spore-forming strains, designated 08RB2639T and 08RB2781-1, were isolated from a sheep (Ovis aries) and a domestic boar (Sus scrofa domestica), respectively. By 16S rRNA gene sequencing, the isolates revealed identical sequences and were shown to belong to the Alphaproteobacteria. They exhibited 97.8 % 16S rRNA gene sequence similarity with Ochrobactrum rhizosphaerae PR17T, O. pituitosum CCUG 50899T, O. tritici SCII24T and O. haematophilum CCUG 38531T and 97.4 % sequence similarity with O. cytisi ESC1T, O. anthropi LMG 3331T and O. lupini LUP21T. The recA gene sequences of the two isolates showed only minor differences (99.5 % recA sequence similarity), and strain 08RB2639T exhibited the highest recA sequence similarity with Ochrobactrum intermedium CCUG 24694T (91.3 %). The quinone system was ubiquinone Q-10, with minor amounts of Q-9 and Q-11, the major polyamines were spermidine, putrescine and sym-homospermidine and the major lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine, with moderate amounts of the Ochrobactrum-specific unidentified aminolipid AL2. The major fatty acids (>20 %) were C18 : 1ω7c and C19 : 0 cyclo ω8c. These traits were in excellent agreement with the assignment of the isolates to the genus Ochrobactrum. DNA–DNA relatedness and physiological and biochemical tests allowed genotypic and phenotypic differentiation from other members of the genus Ochrobactrum. Hence, it is concluded that the isolates represent a novel species, for which the name Ochrobactrum pecoris sp. nov. is proposed (type strain 08RB2639T  = DSM 23868T  = CCUG 60088T  = CCM 7822T).
Functional Analyses of Caffeic Acid O-Methyltransferase and Cinnamoyl-CoA-Reductase Genes from Perennial Ryegrass (Lolium perenne)
Authors: Tu Yi , Rochfort Simone , Liu Zhiqian , Ran Yidong , Griffith Megan , Badenhorst Pieter , Louie Gordon V. , Bowman Marianne E. , Smith Kevin F. , Noel Joseph P. , Mouradov Aidyn , Spangenberg German
Published: October 2010

Cinnamoyl CoA-reductase (CCR) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the biosynthesis of monolignols, which serve as building blocks in the formation of plant lignin. We identified candidate genes encoding these two enzymes in perennial ryegrass (Lolium perenne) and show that the spatio-temporal expression patterns of these genes in planta correlate well with the developmental profile of lignin deposition. Downregulation of CCR1 and caffeic acid O-methyltransferase 1 (OMT1) using an RNA interference–mediated silencing strategy caused dramatic changes in lignin level and composition in transgenic perennial ryegrass plants grown under both glasshouse and field conditions. In CCR1-deficient perennial ryegrass plants, metabolic profiling indicates the redirection of intermediates both within and beyond the core phenylpropanoid pathway. The combined results strongly support a key role for the OMT1 gene product in the biosynthesis of both syringyl- and guaiacyl-lignin subunits in perennial ryegrass. Both field-grown OMT1-deficient and CCR1-deficient perennial ryegrass plants showed enhanced digestibility without obvious detrimental effects on either plant fitness or biomass production. This highlights the potential of metabolic engineering not only to enhance the forage quality of grasses but also to produce optimal feedstock plants for biofuel production.
Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 Directly Regulates the Genes That Govern Programmed Cell Death and Secondary Wall Formation during Xylem Differentiation
Authors: Ohashi-Ito Kyoko , Oda Yoshihisa , Fukuda Hiroo
Published: October 2010

Xylem consists of three types of cells: tracheary elements (TEs), parenchyma cells, and fiber cells. TE differentiation includes two essential processes, programmed cell death (PCD) and secondary cell wall formation. These two processes are tightly coupled. However, little is known about the molecular mechanisms underlying these processes. Here, we show that VASCULAR-RELATED NAC-DOMAIN6 (VND6), a master regulator of TEs, regulates some of the downstream genes involved in these processes in a coordinated manner. We first identified genes that are expressed downstream of VND6 but not downstream of SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1), a master regulator of xylem fiber cells, using transformed suspension culture cells in microarray experiments. We found that VND6 and SND1 governed distinct aspects of xylem formation, whereas they regulated a number of genes in common, specifically those related to secondary cell wall formation. Genes involved in TE-specific PCD were upregulated only by VND6. Moreover, we revealed that VND6 directly regulated genes that harbor a TE-specific cis-element, TERE, in their promoters. Thus, we found that VND6 is a direct regulator of genes related to PCD as well as to secondary wall formation.
Three‐dimensional extension of a digital library service system
Authors: Xiao Long
Published: October 2010

Purpose

The paper aims to provide an overall methodology and case study for the innovation and extension of a digital library, especially the service system.

Design/methodology/approach

Based on the three‐dimensional structure theory of the information service industry, this paper combines a comprehensive analysis with the practical experiences of Peking University Library as a case study.

Findings

The paper proposes three‐dimensional extensions of a digital library service system. It analyses the respective functions of organisations and librarians, information resources, services and methods and the interactions between them.

Originality/value

Innovatively, the theory of three‐dimensional structures is applied to the discussion of the development of the digital library service system. It is significant for the integrality of a digital library theoretical system, as well as for the practical developments, innovations and sustainability of the digital library.
E‐resources, services and user surveys in Tsinghua University Library
Authors: Min Shao , Yi Yang
Published: October 2010

Purpose

The paper aims to provide an overview of the e‐resources and services in Tsinghua University Library, Beijing, and describe five campus‐wide user surveys. It states how these user surveys play an important role in service quality enhancement.

Design/methodology/approach

Following a brief history of Tsinghua University Library, a summary of the collections and services developed in recent years is given. The library has made a great effort to learn about users' needs and to improve service delivery through a series of user surveys. The paper describes these surveys, including the conclusions and the improvement measures adopted.

Findings

Feedback gathered from user surveys provides vital information for improving library services. Through these user surveys, the library received a large amount of data to be analysed and a lot of valuable information, it promoted communication with our users, and the librarian's service literacy has also improved.

Practical implications

An overview of user surveys, including methodology, content, organisation, and implementation process, as well as data analysis, might offer reference and practical experience for other university libraries.

Originality/value

User surveys play an important role in the library's service quality enhancement. The paper provides a useful overview and practical experience of the topic.
Regional consortia for e‐resources: a case study of deals in the South China Region
Authors: Chunrong Luo , Jingfen Wang , Zhinong Zhou
Published: October 2010

Purpose

The purpose of this paper is to analyse the current situation and the social and economic benefits from the consortia acquisitions of electronic resources by the China Academic Library and Information System (CALIS) South China Regional Centre and to recommend improvements for consortia acquisitions.

Design/methodology/approach

Analyses of price and usage made within the CALIS South China region of databases from a range of suppliers including EBSCO, LexisNexis and Springer are presented.

Findings

The electronic resource acquisitions by the CALIS South China Regional Centre have yielded remarkable social and economic benefits as the range of electronic collections has been expanded and enriched, benefits have accrued, money has been saved and it has proved to be of benefit to users; however, there is room for improvement. During the last three years, the total usage of the South China Consortia has increased but the usage of the member libraries in the consortia is unbalanced and there are big gaps among the member libraries. The single download/search cost of the e‐resources has been gradually decreasing but the cost of the e‐resources purchased by the South China region consortia is higher than that of the national consortia; hence, there is a need for further reductions.

Originality/value

The study is the first of its kind ever conducted in China. The findings of this paper will be helpful in improving electronic resource consortia acquisitions in the South China region.
An evaluation of implementing Koha in a Chinese language environment
Authors: Chang Naicheng , Tsai Yuchin , Hopkinson Alan
Published: October 2010

Purpose

The purpose of this paper is to evaluate issues of different scripts in the same record (in MARC21 and Chinese machine‐readable cataloguing (CMARC)) and Chinese internal codes (i.e. double‐byte character set) when implementing Koha. It also discusses successful efforts in promoting the adoption of Koha in Taiwan, particularly the contributions from Koha‐Taiwan.

Design/methodology/approach

A Koha CMARC/MARC21 testbed was set up to discuss issues of multi‐scripts and Chinese internal codes when implementing Koha, and to determine to what extent the various features of CMARC, which are not present in MARC21, such as linking fields, can be supported in Koha and what is required to implement them if they are not available.

Findings

In contrast to western characters, Chinese internal codes cause extra work, as special programming for character conversion is required when working with Koha. This situation is commonly seen in Asian countries such as China, Japan and Korea. This paper recommends implementing CMARC, MARC21 or even any other type of MARC format in Koha with strong commercial‐level support.

Practical implications

Koha‐Taiwan serves Koha Chinese users around the world. A successful Koha‐Taiwan could be a model around the world.

Originality/value

In recent years, the concept of implementing an open‐source library management system has been coming to the fore. In Taiwan, the local‐based commercial library system covers more than one quarter of the library system market in academic libraries because the company provides better tailor‐made support, mainly in scripts and multiple internal codes, than do western‐based commercial library systems. Evaluations and conclusions from this paper will be useful to countries where multi‐scripts and double‐byte character sets are issues.
Collaboration in cultural heritage digitisation in East Asia
Authors: Lee Hyuk‐Jin
Published: October 2010

Purpose

The purpose of this paper is to review the current status of collaboration in cultural heritage preservation in East Asia, including digital projects, and to suggest practical improvements based on a cultural structuralism perspective.

Design/methodology/approach

Through exploratory research, the paper addresses aspects for successful collaboration in cultural heritage digitisation in East Asia.

Findings

The paper indicates the difference in collaboration of cultural heritage digitisation between regions such as Europe and the unique situation in East Asia.

Social implications

If collaboration between the countries of East Asia was implemented then such a community could deal with the issues of cultural heritage by having a standard scheme or policy.

Originality/value

There has been little literature published on East Asian cultural heritage initiatives, particularly in the area of digitisation and digital preservation.
Creating complex repository collections, such as journals, with Manakin
Authors: Koenig Jack (Jay) , Mikeal Adam
Published: October 2010

Purpose

The purpose of this paper is to report on a devised method of collection organisation within a DSpace repository using a Manakin theme and descriptive metadata.

Design/methodology/approach

Using a Manakin theme, a user interface for a repository collection containing the contents of a serial was created to divide the collection into individual issues and serve the user a table of contents.

Findings

The Manakin theme delivered the desired result of a browse interface that allowed the user to select and view subsets of items within a collection.

Practical implications

For complex collections that might require subdivisions, DSpace's rigid data model of communities and collections is not ideal. This new interface allows for the inclusion and proper display of such complex collections.

Originality/value

The paper should resonate with repository managers frustrated with the inflexibility of the default organisational structure of DSpace and its unsuitability for many different types of collections.
Computational determination of inner stresses in rock masses
Authors: Díaz‐Fernández M.E. , González‐Nicieza C. , Álvarez‐Fernández M.I. , Álvarez‐Vigil A.E. , Argüelles Amado A.
Published: October 2010

Purpose

This paper aims to present a computational approach which – setting off from measures obtained by using an overdrilling method – determines, automatically and accurately, stress changes undergone in terrain as a consequence of human activity.

Design/methodology/approach

The method presented uses the data from three boreholes and the elasticity theory to represent a numerical system whose resolution allows determining the stress state in a particular point. Since the system obtained is over‐dimensioned, the Levenberg‐Marquardt minimization method has been used in order to minimize errors. This paper details the analysis carried out in order to develop the computational method.

Findings

This paper provides the algorithm for determining inner stresses in a particular point of a rock mass. Besides, a method to verify obtained results is presented, including its computational encoding in C#. Furthermore, the developed methods have been integrated in a computer tool which presents the results in a graphic environment.

Research limitations/implications

The algorithms presented are applicable when using an overdrilling method to measure stresses.

Practical implications

A reliable determination of global stress state demands the use of any method that is numerically difficult to use. Thus, in practice, it is of great importance to dispose of some reliable automatic tool to calculate stress state.

Originality/value

Accuracy in the results obtained with the tool, together with the simplicity of its interface, involves a certain advantage regarding the use of a general‐scope commercial tool, since it allows – without being necessary to be an expert user – quickly obtaining results within the analysed working area.
Detecting the sensitivity of structural damage based on the Hilbert‐Huang transform approach
Authors: Chiang Wei‐Ling , Chiou Dung‐Jiang , Chen Cheng‐Wu , Tang Jhy‐Pyng , Hsu Wen‐Ko , Liu Te‐Yu
Published: October 2010

Purpose

This study aims to investigate the relationship between structural damage and sensitivity indices using the Hilbert‐Huang transform (HHT) method.

Design/methodology/approach

The relationship between structural damage and the sensitivity indices is obtained by using the HHT method. Three sensitivity indices are proposed: the ratio of rotation (RR), the ratio of shifting value (SV) and the ratio of bandwidth (RB). The nonlinear single degree of freedom and multiple degree of freedom models with various predominant frequencies are constructed using the SAP2000 program. Adjusted PGA El Centro and Chi‐Chi (TCU068) earthquake data are used as the excitations. Next, the sensitivity indices obtained using the HHT and the fast Fourier transform (FFT) methods are evaluated separately based on the acceleration responses of the roof structures to earthquakes.

Findings

Simulation results indicate that, when RR < 1, the structural response is in the elastic region, and neither the RB nor SV in the HHT and FFT spectra change. When the structural response is nonlinear, i.e. RR1, a positive trend of change occurs in RB and RR, while in the HHT spectra, SV increases with an increasing RR. Moreover, the FFT spectra reveal that SV changes only when the RR is sufficiently large. No steady relationship between the RB and the RR can be found.

Originality/value

The paper demonstrates the effectiveness of the HHT method.
Neurocomputing strategies for solving reliability‐robust design optimization problems
Authors: Lagaros Nikos D. , Plevris Vagelis , Papadrakakis Manolis
Published: October 2010

Purpose

This paper, by taking randomness and uncertainty of structural systems into account aims to implement a combined reliability‐based robust design optimization (RRDO) formulation. The random variables to be considered include the cross section dimensions, modulus of elasticity, yield stress, and applied loading. The RRDO problem is to be formulated as a multi‐objective optimization problem where the construction cost and the standard deviation of the structural response are the objectives to be minimized.

Design/methodology/approach

The solution of the optimization problem is performed with the non‐dominant cascade evolutionary algorithm with the weighted Tchebycheff metric, while the probabilistic analysis required is carried out with the Monte Carlo simulation method. Despite the computational advances, the solution of a RRDO problem for real‐world structures is extremely computationally demanding and for this reason neurocomputing estimations are implemented.

Findings

The obtained estimates with the neural network predictions are shown to be very satisfactory in terms of accuracy for performing this type of computation. Furthermore, the present numerical results manage to achieve a reduction in computational time up to four orders of magnitude, for low probabilities of violation, compared to the conventional procedure making thus feasible the reliability‐robust design optimization of realistic structures under probabilistic constraints.

Originality/value

The novel parts of the present work include the implementation of neurocomputing strategies in RRDO problems for reducing the computational cost and the comparison of the results given by RRDO and robust design optimization formulations, where the significance of taking into account probabilistic constraints is emphasized.
Stochastic sensitivity analysis using preconditioning approach
Authors: Chowdhury R. , Adhikari S.
Published: October 2010

Purpose

High‐dimensional model representation (HDMR) is a general set of quantitative model assessment and analysis tools for capturing the high‐dimensional relationships between sets of input and output model variables. It is an efficient formulation of the system response, if higher‐order cooperative effects are weak, allowing the physical model to be captured by the lower‐order terms. The paper's aim is to develop a new computational tool for estimating probabilistic sensitivity of structural/mechanical systems subject to random loads, material properties and geometry.

Design/methodology/approach

When first‐order HDMR approximation of the original high‐dimensional limit state is not adequate to provide the desired accuracy to the sensitivity analysis, this paper presents an enhanced HDMR (eHDMR) method to represent the higher‐order terms of HDMR expansion by expressions similar to the lower‐order ones with monomial multipliers. The accuracy of the HDMR expansion can be significantly improved using preconditioning with a minimal number of additional input‐output samples without directly invoking the determination of second‐ and higher‐order terms. As a part of this effort, the efficacy of HDMR, which is recently applied to uncertainty analysis, is also demonstrated. The method is based on computing eHDMR approximation of system responses and score functions associated with probability distribution of a random input. Surrogate model is constructed using moving least squares interpolation formula. Once the surrogate model form is defined, both the probabilistic response and its sensitivities can be estimated from a single probabilistic analysis, without requiring the gradients of performance functions.

Findings

The results of two numerical examples involving mathematical function and structural/solid‐mechanics problems indicate that the sensitivities obtained using eHDMR approximation provide significant accuracy when compared with the conventional Monte Carlo method, while requiring fewer original model simulations.

Originality/value

This is the first time where application of eHDMR concepts is explored in the stochastic sensitivity analysis. The present computational approach is valuable to the practical modelling and design community.