bluuebunny/crossref_metadata_2025 huggingface dataset:
The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins
Authors: Feige Matthias J. , Gräwert Melissa A. , Marcinowski Moritz , Hennig Janosch , Behnke Julia , Ausländer David , Herold Eva M. , Peschek Jirka , Castro Caitlin D. , Flajnik Martin , Hendershot Linda M. , Sattler Michael , Groll Michael , Buchner Johannes
Published: May 2014

Significance

Sharks are among the evolutionary oldest living organisms with an immune system that possesses a number of elements similar to ours, including antibodies. In this article, we present structural insights into one of the most ancient antibodies, shedding light on the molecular evolution of the immune system and the structural features of heavy chain-only antibodies. Sharks enrich urea in their blood to prevent osmotic loss of water in the marine environment. Urea, however, denatures proteins if they are not sufficiently stable. Indeed, we find that shark antibodies are particularly stable. We pinpointed specific features responsible for their high stability and found that transplanting them into a human antibody increased its secretion.
Heterologous production, purification, and immunodetection of Magnaporthe oryzae avirulence protein AVR-Pia
Authors: Satoh Yuki , Miki Shinsuke , Ose Toyoyuki , Oikawa Azusa , Maenaka Katsumi , Terauchi Ryouhei , Asano Kozo , Sone Teruo
Published: May 2014

The avirulence gene AVR-Pia of Magnaporthe oryzae, which induces a hypersensitive reaction in rice cultivars containing the resistance gene Pia, was expressed in Escherichia coli. AVR-Pia protein was collected as inclusion bodies, denatured, and refolded. Finally, recombinant AVR-Pia (rAVR-Pia) protein was purified by column chromatography. Infiltration of rAVR-Pia triggered cell browning in the leaves of rice cultivar Aichiasahi (Pia), with accumulation of H2O2 and induction of PR1a expression in rice. On the other hand, these reactions were not observed in Shin-2 (pia) leaves after the same treatment. This observation indicated that rAVR-Pia had the function of an avirulence protein. rAVR-Pia was used for immunization of a rabbit, and anti-AVR-Pia antiserum was prepared. The specificity of this antibody was appraised by detecting native AVR-Pia in the inoculated leaf sheath extract using Western blotting in combination with immunoprecipitation. Native AVR-Pia was successfully detected, and its molecular weight was estimated to be 7.4 kDa, indicating signal peptide cleavage. Additionally, secreted native AVR-Pia was quantified as 3.7 ng/g rice sheath.
RNASeqExpressionBrowser—a web interface to browse and visualize high-throughput expression data
Authors: Nussbaumer Thomas , Kugler Karl G. , Bader Kai C. , Sharma Sapna , Seidel Michael , Mayer Klaus F. X.
Published: May 2014

Motivation: RNA-seq techniques generate massive amounts of expression data. Several pipelines (e.g. Tophat and Cufflinks) are broadly applied to analyse these datasets. However, accessing and handling the analytical output remain challenging for non-experts.

Results: We present the RNASeqExpressionBrowser, an open-source web interface that can be used to access the output from RNA-seq expression analysis packages in different ways, as it allows browsing for genes by identifiers, annotations or sequence similarity. Gene expression information can be loaded as long as it is represented in a matrix-like format. Additionally, data can be made available by setting up the tool on a public server. For demonstration purposes, we have set up a version providing expression information from the barley genome.

Availability and implementation: The source code and a show case are accessible at http://mips.helmholtz-muenchen.de/plant/RNASeqExpressionBrowser/.

Contact:  k.mayer@helmholtz-muenchen.de
RiboMaker: computational design of conformation-based riboregulation
Authors: Rodrigo Guillermo , Jaramillo Alfonso
Published: May 2014

Motivation: The ability to engineer control systems of gene expression is instrumental for synthetic biology. Thus, bioinformatic methods that assist such engineering are appealing because they can guide the sequence design and prevent costly experimental screening. In particular, RNA is an ideal substrate to de novo design regulators of protein expression by following sequence-to-function models.

Results: We have implemented a novel algorithm, RiboMaker, aimed at the computational, automated design of bacterial riboregulation. RiboMaker reads the sequence and structure specifications, which codify for a gene regulatory behaviour, and optimizes the sequences of a small regulatory RNA and a 5′-untranslated region for an efficient intermolecular interaction. To this end, it implements an evolutionary design strategy, where random mutations are selected according to a physicochemical model based on free energies. The resulting sequences can then be tested experimentally, providing a new tool for synthetic biology, and also for investigating the riboregulation principles in natural systems.

Availability and implementation: Web server is available at http://ribomaker.jaramillolab.org/. Source code, instructions and examples are freely available for download at http://sourceforge.net/projects/ribomaker/.

Contact:  Guillermo.Rodrigo@issb.genopole.fr or Alfonso.Jaramillo@warwick.ac.uk
Memory-efficient RNA energy landscape exploration
Authors: Mann Martin , Kucharík Marcel , Flamm Christoph , Wolfinger Michael T.
Published: May 2014

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches.

Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes.

Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/ .

Contact:  mmann@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data
Authors: Wang Weixin , Wang Panwen , Xu Feng , Luo Ruibang , Wong Maria Pik , Lam Tak-Wah , Wang Junwen
Published: May 2014

Summary: Recent advances in high-throughput sequencing technologies have enabled us to sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cell contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and an accurate somatic single-nucleotide variations (SNVs) detection program, FaSD-somatic. The performance of FaSD-somatic is extensively assessed on various types of cancer against several state-of-the-art somatic SNV detection programs. Benchmarked by somatic SNVs from either existing databases or de novo higher-depth sequencing data, FaSD-somatic has the best overall performance. Furthermore, FaSD-somatic is efficient, it finishes somatic SNV calling within 14 h on 50X whole genome sequencing data in paired samples.

Availability and implementation: The program, datasets and supplementary files are available at http://jjwanglab.org/FaSD-somatic/.

Contact:  wangdatou2009@gmail.com.

Supplementary information:  Supplementary Data are available at Bioinformatics online
Can ice breeding seals adapt to habitat loss in a time of climate change?
Authors: Stenson G. B. , Hammill M. O.
Published: May 2014

Climate change associated declines in sea ice will have serious impact on species that rely on ice for reproduction and/or feeding. Little is known about the impacts on ice-dependent, sub-Arctic species or on how these species may adapt, although the ecosystem changes are likely to be most rapid along the ice edge. Harp seals (Pagophilus groenlandicus) require stable ice for pupping, nursing and the first weeks after weaning when the young develop the capacity to swim and feed. Although ice conditions in the Northwest Atlantic have varied over the past 40 years, in 2010 and 2011, the total extent of ice suitable for whelping harp seals was at, or near, the lowest ever recorded. These years of exceptionally poor ice provided us with an opportunity to improve our understanding about how ice breeding seals may respond to the conditions expected in the future. Harp seals responded to poor ice conditions differently, depending on the presence or absence of ice at the beginning of the pupping period. If no ice was present, females moved away from their traditional whelping areas to find suitable ice. If small amounts of ice were present, females gave birth even if the ice was too thin to sustain the pups, resulting in high pup mortality. There was no evidence to indicate that harp seals pupped on land even in areas where ice was absent. Young seals that drifted to shore had high levels of abandonment and mortality. If the predicted warming trends continue, ice-breeding harp seals will encounter more years with poor ice conditions and may eventually adapt by moving north. Until then, they will continue to have increased levels of mortality that could result in the disappearance of the most southern breeding component in the Gulf of St Lawrence.
First Report of Meloidogyne marylandi Infecting Bermudagrass in Oklahoma
Authors: Walker N.
Published: May 2014

Meloidogyne marylandi is a nematode commonly associated with turfgrasses and has been reported to occur in Texas and Arkansas (1,3). In the fall of 2013, a stand of ultradwarf bermudagrass (Cynodon dactylon × C. transvaalensis) plants in a sand-based, research putting green in Stillwater, Oklahoma, exhibited symptoms of decline. Roots of the affected plants had small galls and upon staining of the root system, numerous egg masses were evident. Egg masses were collected, placed in water, and the morphology of 20 hatched, second-stage juveniles were examined. The characteristics of the juveniles were: body length averaged 393.1 ± 19.87 (range: 361 to 425) μm, mean width averaged 16.6 ± 0.7 (15.6 to 17.8) μm, stylet lengths averaged 12.1 ± 0.7 (10.4 to 12.9) μm, dorsal gland orifice from stylet base averaged 2.9 ± 0.4 (2.5 to 3.6) μm, tail lengths averaged 53.7 ± 3.8 (46.2 to 60.4) μm, and the hyaline region of the tails averaged 10.4 ± 1.1 (8.4 to 12.7) μm. Genomic DNA was extracted from six females that were removed from roots. Amplification and sequencing of the mitochondrial DNA region between COII and 16S rRNA genes was performed with primers 1RNAF (5′-TACCTTTGACCAATCACGCT-3′) and CO11R (5′-GGTCAATGTTCAGAAATTTGTGG-3′) as previously described (2). A PCR product approximately 510 bp in length was obtained and sequenced at the Oklahoma State University Core Facility. Sequences were compared with those in NCBI's nucleotide database using BLAST and had 97% identity with two sequences from M. marylandi (KC473862.1 and KC473863.1) and the next most similar species being M. graminis (JN241898.1) with 83% identity. To our knowledge, this is the first report of the root-knot nematode M. marylandi in Oklahoma. As bermudagrass becomes more commonly used for putting greens in the turfgrass transition zone, M. marylandi may become a more common and damaging pathogen in the region.

References: (1) A. A. Elmi et al. Grass For. Sci. 55:166, 2000. (2) M. A. McClure et al. Plant Dis. 96:635, 2012. (3) J. L. Starr et al. Nematrop. 37:43, 2007.
Sensitivity of Monilinia fructicola from Peach Farms in China to Four Fungicides and Characterization of Isolates Resistant to Carbendazim and Azoxystrobin
Authors: Chen S. N. , Shang Y. , Wang Y. , Schnabel G. , Lin Y. , Yin L. F. , Luo C. X.
Published: May 2014

Brown rot of peach caused by Monilinia fructicola can cause considerable preharvest and postharvest losses in China. Fungicides are increasingly utilized to minimize such losses. Eighty isolates of M. fructicola were collected from commercial peach orchards located in five provinces in China and the sensitivity to carbendazim, azoxystrobin, tebuconazole, and boscalid was determined. Resistance to carbendazim was detected only in the Yunnan province in 15 of 16 isolates. Characterization of carbendazim-resistant isolates revealed stable resistance, no fitness penalty, and negative cross resistance to diethofencarb. Resistant isolates produced disease symptoms on detached fruit sprayed with label rates of formulated carbendazim and possessed the amino acid mutation E198A in β-tubulin. Resistance to azoxystrobin was detected in 3 of 10 isolates from Fujian. In contrast to carbendazim resistance, however, azoxystrobin resistance was unstable, associated with a fitness penalty, and not associated with mutations in the target gene cytochrome b. The concentration at which mycelial growth is inhibited 50% (EC50) values of the azoxystrobin-sensitive isolates were 0.02 to 1.94 μg/ml, with a mean value of 0.54 μg/ml. All isolates were sensitive to tebuconazole, with a mean EC50 value of 0.03 μg/ml. The EC50 values for boscalid were 0.01 to 3.85 μg/ml, with a mean value of 1.02 μg/ml. Our results indicate that methyl benzimidazole carbamates (MBCs), quionon outside inhibitors, demethylation inhibitor fungicides, and succinate dehydrogenase inhibitors are likely to be very effective in controlling brown rot in many peach production areas in China, but that resistance to MBCs is emerging.
RNA Interference of Effector GeneMc16D10LConfers Resistance AgainstMeloidogyne chitwoodiinArabidopsisand Potato
Authors: Dinh Phuong T. Y. , Brown Charles R. , Elling Axel A.
Published: May 2014

Meloidogyne chitwoodi, a quarantine pathogen, is a significant problem in potato-producing areas worldwide. In spite of considerable genetic diversity in wild potato species, no commercial potato cultivars with resistance to M. chitwoodi are available. Nematode effector genes are essential for the molecular interactions between root-knot nematodes and their hosts. Stable transgenic lines of Arabidopsis and potato (Solanum tuberosum) with resistance against M. chitwoodi were developed. RNA interference (RNAi) construct pART27(16D10i-2) was introduced into Arabidopsis thaliana and potato to express double-stranded RNA complementary to the putative M. chitwoodi effector gene Mc16D10L. Plant-mediated RNAi led to a significant level of resistance against M. chitwoodi in Arabidopsis and potato. In transgenic Arabidopsis lines, the number of M. chitwoodi egg masses and eggs was reduced by up to 57 and 67% compared with empty vector controls, respectively. Similarly, in stable transgenic lines of potato, the number of M. chitwoodi egg masses and eggs was reduced by up to 71 and 63% compared with empty vector controls, respectively. The relative transcript level of Mc16D10L was reduced by up to 76% in M. chitwoodi eggs and infective second-stage juveniles that developed on transgenic pART27(16D10i-2) potato, suggesting that the RNAi effect is systemic and heritable in M. chitwoodi.
Generation of Aggregates of Mouse ES Cells that Show Symmetry Breaking, Polarisation and Emergent Collective Behaviourin vitro
Authors: Baillie-Johnson Peter , van den Brink Susanne C. , Balayo Tina , Turner David A. , Arias Alfonso Martinez
Published: May 2014

Dissociated mouse embryonic stem (ES) cells were cultured to form aggregates in small volumes of basal medium in U-bottomed, non tissue-culture-treated 96-well plates and subsequently maintained in suspension culture. After growth for 48 hours, the aggregates are competent to respond to ubiquitous experimental signals which result in their symmetry-breaking and generation of defined polarised structures by 96 hours. It is envisaged that this system can be applied both to the study of early developmental events and more broadly to the processes of self-organisation and cellular decision-making. It may also provide a suitable niche for the generation of cell types present in the embryo but unobtainable from conventional adherent culture.
1-(4-Chlorobutanoyl)-3-(3-chlorophenyl)thiourea
Authors: Abosadiya Hamza M. , Hasbullah Siti Aishah , Yamin Bohari M. , Fadzil Adibatul H.
Published: May 2014

The two independent molecules in the asymmetric unit of the title compound, C11H12Cl2N2OS, exhibit different conformations, with the benzene ring and the N2CS thiourea group forming dihedral angles of 87.40 (18) and 69.42 (15)°. An intramolecular N—H...O hydrogen bond is present in each molecule. Two further N—H...O hydrogen bonds link the independent molecules into a dimer. In the crystal, the dimers are linked by N—H...S and C—H...S hydrogen bonds, forming chains parallel to thecaxis.
(2,2′-Bipyridine-κ2N,N′)dichloridopalladium(II) 1,4-dioxane hemisolvate
Authors: Gutiérrez Márquez Ricardo Alfredo , Crisóstomo-Lucas Carmela , Morales-Morales David , Hernández-Ortega Simón
Published: May 2014

The asymmetric unit of the title compound, [PdCl2(C10H8N2)]·0.5C4H8O2, consists of one PdIIcomplex molecule and a half-molecule of 1,4-dioxane, the complete molecule being generated by inversion symmetry. The PdIIatom has an almost square-planar coordination formed by the 2,2′-bipyridine ligand and two chloride ligands. Two intramolecular C—H...Cl hydrogen bonds occur. In the crystal, the PdIIcomplex and 1,4-dioxane molecules are connected by C—H...O hydrogen bonds, forming a layer parallel to (10-1). Within the layer, weak π–π interactions [centroid–centroid distance = 3.817 (4) Å] are observed between the pyridine rings.
Bis{μ-N-[(E)-4-benzyloxy-2-oxidobenzylidene]-4-nitrobenzenecarbohydrazidato}bis[diaquanickel(II)] dimethylformamide tetrasolvate
Authors: Joseph Bibitha , Sithambaresan M. , Kurup M. R. Prathapachandra , Ng Seik Weng
Published: May 2014

The molecule of the title complex, [Ni2(C21H15N3O5)2(H2O)4]·4C3H7NO, is located on an inversion centre. This results in a dimeric NiIIcomplex, with the two NiIIatoms bridged by phenolate O atoms. The tridentate ligand is chelated to each NiIIatomviaone N and two O atoms of the iminolate form of the hydrazide moiety, which has the same conformation as the free ligand. The coordination geometry around each NiIIion is slightly distorted octahedral. A supramolecular three-dimensional architecture is created by dominant intermolecular O—H...N, O—H...O and C—H...O hydrogen-bonding interactions. These are augmented by two C—H...π interactions and a π–π interaction with a centroid–centroid distance of 3.681 (2) Å.
9-Allyl-9H-fluoren-9-ol
Authors: Knight Kyle S. , Wood Harvey B.
Published: May 2014

The asymmetric unit of the title compound, C16H14O, contains two independent molecules differing in the orientations of the allyl groups; the corresponding O—C—C(H2)—C(H) torsion angles are −61.01 (13) and −177.43 (10)°. In the crystal, O—H...O hydrogen bonds link four molecules into a centrosymmetric tetramer, in which each hydroxy group acts as a donor and an acceptor of hydrogen bonds.
9-(3-Bromo-5-chloro-2-hydroxyphenyl)-10-(2-hydroxyethyl)-3,6-diphenyl-3,4,9,10-tetrahydroacridine-1,8(2H,5H)-dione
Authors: Akkurt Mehmet , Mohamed Shaaban K. , Abdelhamid Antar A. , Gaber Abdel-Aal M. , Albayati Mustafa R.
Published: May 2014

In the title compound, C33H27BrClNO4, the dihydropyridine ring adopts a flattened boat conformation. The molecular conformation is stabilized by an intramolecular O—H...O hydrogen bond, with anS(8) ring motif. In the crystal, O—H...O, C—H...O and C—H...Cl hydrogen bonds, and C—H...π interactions link the molecules, forming a three-dimensional network. In the acridinedione ring system, the two ring C atoms at the 2- and 3-positions, and the C atom at the 6-position and the atoms of the phenyl ring attached to the C atom at the 6-position are disordered over two sets of sites with occupancy ratios of 0.783 (5):0.217 (5) and 0.526 (18):0.474 (18), respectively.
Ba4GaN3O
Authors: Hashimoto Takayuki , Yamane Hisanori
Published: May 2014

Red transparant platelet-shaped single crystals of tetrabarium gallium trinitride oxide, Ba4GaN3O, were synthesized by the Na flux method. The crystal structure is isotypic with Sr4GaN3O, containing isolated triangular [GaN3]6−anionic groups. O2−atoms are inserted between the slabs of [Ba4GaN3]2+, in which the [GaN3]6−groups are surrounded by Ba2+atoms.
Di-μ-chlorido-bis(chlorido{N′-[phenyl(pyridin-2-yl-κN)methylidene]pyridine-2-carbohydrazide-κ2N′,O}cadmium)
Authors: Akkurt Mehmet , Khandar Ali Akbar , Tahir Muhammad Nawaz , Afkhami Farhad Akbari , Yazdi Seyed Abolfazl Hosseini
Published: May 2014

The title compound, [Cd2Cl4(C18H14N4O)2], was obtained from the reaction of Cd(NO3)2·4H2O with 2-phenylpyridineketon picolinoyl hydrazone and sodium chloride. Each Cd2+cation is coordinated by two N atoms and one O atom of the tridentate ligand and three chloride anions, forming a distorted CdNOCl3octahedron. Each pair of adjacent metal cations is linked by two bridging chloride ligands, resulting in a dinuclear complex unit. The molecular conformation is stabilized by intramolecular N—H...N and C—H...O hydrogen bonds. In the crystal, molecules are linked by nonclassical C—H...O and C—H...Cl hydrogen bonds into a three-dimensional network. In addition, π–π stacking interactions [centroid–centroid distances = 3.777 (2) and 3.631 (2) Å] contribute to the stabilization of the crystal packing.
Chlorido{2-[(dimethylamino)methyl]benzeneselenolato-κ2N,Se}(triphenylphosphane-κP)palladium(II)
Authors: Takaluoma Esther M. , Oilunkaniemi Raija , Laitinen Risto S.
Published: May 2014

The asymmetric unit of the title compound, [PdCl(C9H12NSe)(C18H15P)], contains two independent molecules. In both cases, the Pd2+cations are coordinated by the Se and N atoms of the chelating bidentate 2-[(dimethylamino)methyl]benzeneselenolate ligand. The chloride ligand liestransto selenium and the triphenylphosphane ligand istransto nitrogen. The Pd—Se bond lengths in the two independent coordination environments of Pd are 2.3801 (4) and 2.3852 (4) Å, the Pd—P bond lengths are 2.2562 (8) and 2.2471 (8) Å, the Pd—N bond lengths are 2.172 (2) and 2.158 (2) Å, and the Pd—Cl bond lengths are 2.3816 (8) and 2.3801 (8) Å. The square-planar coordination around one Pd2+cation is less distorted than that around the other.
2-(5-Iodo-2-oxoindolin-3-ylidene)hydrazinecarbothioamide including an unknown solvate
Authors: Conceição Duarte de Bittencourt Viviane , Carratu Gervini Vanessa , Rosa de Menezes Vicenti Juliano , Maciel Velasques Jecika , Jussiane Zambiazi Priscilla
Published: May 2014

The molecule of the title compound, C9H7IN4OS, is almost planar (r.m.s. deviation = 0.0373 Å). In the molecule, N—H...N and N—H...O hydrogen bonds generate, respectively,S(5) andS(6) ring motifs. In the crystal, molecules are linkedviaN—H...O hydrogen bonds, forming chains propagating along [010]. These chains are linkedviaS...I contacts [3.4915 (16) Å], forming sheets lying parallel to (100). A region of disordered electron density, probably a disordered tetrahydrofuran solvent molecule, was treated using the SQUEEZE routine inPLATON[Spek (2009).Acta Cryst.D65, 148–155]. The formula mass and unit-cell characteristics were not taken into account during refinement.
N-(3-Chloro-4-ethoxy-1-methyl-1H-indazol-5-yl)-4-methoxybenzenesulfonamide
Authors: Chicha Hakima , Rakib El Mostapha , Hannioui Abdellah , Saadi Mohamed , El Ammari Lahcen
Published: May 2014

The indazole ring system of the title compound, C17H18ClN3O4S, is almost planar (r.m.s. deviation = 0.0113 Å) and forms dihedral angles of 32.22 (8) and 57.5 (3)° with the benzene ring and the mean plane through the 4-ethoxy group, respectively. In the crystal, molecules are connected by pairs of N—H...O hydrogen bonds into inversion dimers, which are further linked by π–π interactions between the diazole rings [intercentroid distance = 3.4946 (11) Å], forming chains parallel to [101].
Preparation and X-ray analysis of potassium (2,3-dichlorophenyl)glucosinolate
Authors: Vo Quan V. , Trenerry Craige , Rochfort Simone , White Jonathan , Hughes Andrew B.
Published: May 2014

There has been much interest in obtaining crystals for crystallographic analysis of biologically active glucosinolates. Crystals of potassium (2,3-dichlorophenyl)glucosinolate were obtained as a dual solvate, containing one methanol and one ethanol molecule of crystallization, K+·C13H14Cl2NO9S2−·CH3OH·C2H5OH. The three-dimensional polymeric network consists of chains containing the potassium ions coordinated and bridged by sugar O atoms, which run parallel to theaaxis and are further crosslinked through the sugar molecules. The channels of this network are occupied by the dichlorophenyl substituents and the ethanol and methanol solvent molecules. The structure of theS-(2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl)-2,3-dichlorophenylacetothiohydroxymate, C21H23Cl2NO10S, precursor has also been determined and the β-configuration andZisomer of the thiohydroximate substituent is confirmed.
Hydrogen ADPs with CuKα data? Invariom and Hirshfeld atom modelling of fluconazole
Authors: Orben Claudia M. , Dittrich Birger
Published: May 2014

For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with CuKα radiation to a resolution of sin θ/λ of 0.6 Å−1. The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å−1, but requires good low-order data.
Unveiling the origin of a nonequilibrium dynamic process detected by X-ray photon correlation spectroscopyviaa finite element analysis approach
Authors: Ma Li , Zhang Fan , Allen Andrew , Levine Lyle
Published: May 2014

It is a scientific and engineering challenge to characterize materials under nonequilibrium conditions. In recent years, X-ray photon correlation spectroscopy (XPCS), a synchrotron-based coherent X-ray scattering technique, has been found useful in determining the timescales associated with various nonequilibrium processes, with detailed descriptions of the underlying processes lacking. Here, both static ultra small angle X-ray scattering (USAXS) and dynamic USAXS-based XPCS were used to investigate a transient structural change (a nonequilibrium process) associated with an isothermal anneal in a glass polymer composite system. While the bulk USAXS technique lacked the required sensitivity to detect the change in the microstructures, the local structural reorganization was apparent in the XPCS study. The structural changes were modeled using a three-dimensional finite element analysis approach and wave-propagation theory was used to simulate the resulting reciprocal-space coherent scattering intensity. Qualitative agreement was found between the modeling and experimental results, which validates that stress relaxation in the viscous polymer matrix was responsible for the observed changes. This analysis demonstrates that multi-physics modeling of complex systems can be used to interpret XPCS measurements of nonequilibrium processes.
Changes of physical properties in multiferroic phase transitions
Authors: Litvin Daniel B.
Published: May 2014

The physical property coefficients that arise in a phase transition which are zero in the high-symmetry phase and nonzero in the low-symmetry phase are calledspontaneous coefficients. For all 1601 Aizu species of phase transitions, matrices have been constructed which show the nonzero coefficients of a wide variety of magnetic and nonmagnetic physical properties including toroidal property coefficients in the high-symmetry phase and their corresponding spontaneous coefficients in the low-symmetry phase. It is also shown that these spontaneous coefficients provide for the distinction of and switching between nonferroelastic domain pairs.
The staurolite enigma solved
Authors: Marzouki Mohamed Amine , Souvignier Bernd , Nespolo Massimo
Published: May 2014

Staurolite has been long considered an enigma because of its remarkable pseudosymmetry and the frequent twinning. Staurolite gives two twins whose occurrence frequency seems to contradict the condition of lattice restoration requested by the reticular theory of twinning, in that the more frequent one (Saint Andrews cross twin) has a twin index of 12, whereas the less frequent one (Greek cross twin) has a twin index of 6. The hybrid theory of twinning shows that the former is actually a hybrid twin with two concurrent sublattices and an effective twin index of 6.0. However, this is still not sufficient to explain the observed higher occurrence frequency of the Saint Andrews twin. The (pseudo)-eigensymmetry of the crystallographic orbits of staurolite has been analysed and it was found that the whole substructure built on anions is restored (with small deviations) by both twin laws, which explains why twinning is frequent in staurolite. On the other hand, 45% of the cation sites are quasi-restored in the Saint Andrews cross twin, against only 19% for the Greek cross twin: this difference finally explains the different occurrence frequencies of the two twins.
Do environmental collaboration and monitoring enhance organizational performance?
Authors: Green Kenneth W. , Zelbst Pamela J. , Bhadauria Vikram S. , Meacham Jeramy
Published: May 2014

Purpose

The purpose of this paper is to contribute significantly to the first wave of empirical investigations related to the impact of green supply chain management practices on environmental and organizational performance from a manufacturer's perspective within a supply chain context.

Design/methodology/approach

An environmental collaboration and monitoring performance model is theorized and assessed following a structural equation methodology. Data were collected from 159 manufacturing managers through an on‐line survey.

Findings

Environmental collaboration and monitoring practices among supply chain partners are found to lead to improved environmental performance and organizational performance.

Research limitations/implications

As a first wave investigation of the impact of green supply chain management practices on performance, the study is somewhat exploratory.

Practical implications

Practitioners are provided with a framework for assessing the impact of environmental collaboration and monitoring practices among supply chain partners on environmental performance and organizational performance. The study provides evidence that green supply chain practices lead to improved environmental and organizational performance.

Social implications

The results also have important societal implications. While green supply chain management practices enhance the economic sustainability of the firm, they also positively impact society through improvements to the overall environment.

Originality/value

The results of this investigation support the proposition that implementation of environmental collaboration and monitoring practices by supply chain partners are both environmentally necessary and good business. The paper provides manufacturing managers with a structured approach to improving both environmental and organizational performance through environmental collaboration and monitoring with customers and suppliers.
Managerial attention and antecedents of knowledge source exploitation in MNCs
Authors: Kumar Nishant , Demir Robert
Published: May 2014

Purpose

The purpose of this paper is to address the limitations of prior views regarding knowledge source exploitation by proposing a phenomenological approach to managerial attention and the antecedents of exploiting knowledge sources within the multinational corporations (MNC) network.

Design/methodology/approach

A phenomenological approach to attention is taken to explain the antecedents of managerial attention in knowledge source exploitation behavior. This approach provides an alternative way of conceiving of knowledge source remoteness and familiarity, on the one hand, and exclusion and inclusion on the other.

Findings

Drawing on a phenomenological approach to attention, the merits and limits of prior studies of attention and knowledge seeking/exchange behavior are addressed and three modes of managerial attention are proposed – relative attention, mimetic attention, implicit attention – to explain the antecedents of managerial attention to MNC knowledge sources.

Originality/value

This approach to knowledge source exploitation and attention provides a rich conceptualization of taken‐for‐granted assumptions in extant literature on managerial attention and knowledge‐seeking behavior. The framework offered here builds on a conceptually rigid foundation of attention that overcomes dualisms such as mind‐body, subject‐object, and thinking‐acting that are often embedded in other mainstream approaches to managerial attention.
Remote sensing and spatial multi-criteria analysis for tsunami vulnerability assessment
Authors: Bakar Sambah Abu , Miura Fusanori
Published: May 2014

Purpose

– The purpose of this paper is to assess the vulnerability of the Kesennuma area in Japan to a tsunami disaster and to map the area of inundation.

Design/methodology/approach

– Digital elevation model (DEM) data and ALOS image were used to create maps of the parameters of this study area: elevation, slope, coastal proximity, river, and land use. An analytical hierarchy process was used to assign weights to each parameter and a spatial multi-criteria analysis was applied through cell-based modelling for vulnerability mapping.

Findings

– The vulnerability map shows that 17.679 km2 of the area could be inundated by a tsunami. High vulnerability areas were mostly found in coastal areas with a sloping coast and a cape area. A low elevation and the presence of rivers or water channels are factors that increase the impact of tsunamis. Inundation areas were predicted to spread in areas identified as having either high vulnerability or slightly high vulnerability.

Research limitations/implications

– Because of the limited geospatial data, the authors encourage further studies using DEM data with a high spatial resolution.

Practical implications

– The results of this research can be used as basic information for disaster mitigation and urban planning in coastal areas.

Originality/value

– This research creates a new approach for assessing which areas could be inundated by tsunamis, based on the vulnerability map generated through remote sensing and spatial multi-criteria analysis. Moreover, the parameters used are very close to those of actual inundation maps.
Framing disaster resilience
Authors: Aldunce Paulina , Beilin Ruth , Handmer John , Howden Mark
Published: May 2014

Purpose

– To confront the increasingly devastating impacts of disasters and the challenges that climate change is posing to disaster risk management (DRM) there is an imperative to further develop DRM. The resilience approach is emerging as one way to do this, and in the last decade has been strongly introduced into the policy arena, although it is not new for DRM practitioners and researchers. Nevertheless, resilience is a highly contested issue, and there is no agreed definition of it, which has resulted in confusion for stakeholders when applying it to practice. Therefore, the purpose of this paper is to investigate how resilience is framed by researchers and DRM practitioners.

Design/methodology/approach

– The analytical framework used was Hajer's “social-interactive discourse theory”, combined with analysis of government documents, in-depth interviews with practitioners and observation of field and practices within the context of the Natural Disaster Resilience Program in Queensland, Australia.

Findings

– One of the key findings is that the idea of “bouncing back” is central to the resilience discourse but different interpretations of this idea results in real-world implications. Three different ways (storylines) in which practitioners construct the meaning of disaster resilience emerge from this study. Importantly the divergences between these storylines reveal possibilities for reframing to occur and these could lead to different policy options and practices.

Originality/value

– The results presented in this paper offer empirical evidence on how resilience is understood on the ground, contributing to extending resilience theory and informing DRM and resilience practice.
The transformation of people, processes, and IT in e-recruiting
Authors: Eckhardt Andreas , Laumer Sven , Maier Christian , Weitzel Tim
Published: May 2014

Purpose

– There is only scarce research about the transformation of e-HRM in general, and of the e-recruiting function in particular. Further, there is not much known of the transformational implications for the related people, process, and information technology (IT). The paper aims to discuss these issues.

Design/methodology/approach

– To analyze the transformation of e-recruiting caused by external influences outside of the organization, the authors report the results of an eight-year case with a media corporation in order to derive and describe five consecutive steps of an e-recruiting transformation model.

Findings

– The paper comes up with five stages (transformation of tools, transformation of systems, transformation of workflows, transformation of tasks, and transformation of communication), each influenced by external developments and market tendencies (War for Talent, increasing number of applications, job market switch, globalization of job market, changing communication behavior).

Research limitations/implications

– This research contributes to literature by explaining the drivers of an e-HRM transformation and the different stages of this transformation process differentiated by the affected people, processes, and IT. However, it only observes the transformation in one company, hence the transformation of further e-HRM functions in other companies might differ.

Practical implications

– The paper highlights both the transformation of e-recruiting and for the related people, processes, and IT, so companies could observe their current status of e-recruiting transformation.

Originality/value

– This paper represents the first longitudinal approach observing the transformation of e-recruiting by describing different stages and external influences.
Institutional context and e-recruitment practices of Danish organizations
Authors: B. Holm Anna
Published: May 2014

Purpose

– Up to now, there has been little research on the impact of the external environment on recruitment practices of organizations, and in part it lags behind practice. The purpose of this paper is to rectify this by studying recent changes in recruitment practices of Danish organizations and the adoption of e-recruitment from a macro organizational perspective.

Design/methodology/approach

– The study employs new institutional theory as a theoretical lens in order to understand how external pressures impact upon recruitment professionals and their practices. The empirical part is based on interpretive methods and the inductive analysis of data. The data were collected from a number of sources, such as exploratory interviews, observations, web sites, and other secondary material from 2008 to 2013.

Findings

– The findings indicate that recruitment practices are strongly influenced by changes stemming from functional and social pressures of the wider society, such as the labour market and the penetration of the internet into Danish society. That is reflected in the widespread use of digital HRM in general, and e-recruitment in particular. The study concludes that the recruitment field has transformed and reviewed its practices to a great extent due to the changes in how individuals search for employment and expect to be hired.

Research limitations/implications

– The empirical part of this study is limited to Denmark, and its economic, social, and cultural domains, yet the research design can be applied elsewhere.

Originality/value

– The paper contributes to a better understanding of HRM in context, the pressures and mechanisms for adoption of new recruitment practices, and more specifically the rationale for adopting e-recruitment practices. Additionally, it offers a novel research framework for future research on recruitment from the neoinstitutional perspective.
Tipping the scales: ambidexterity practices on e-HRM projects
Authors: Tansley Carole , Kirk Susan , Williams Hazel , Barton Harry
Published: May 2014

Purpose

– The purpose of this paper is to examine and conceptualise the ways in which a balance can be achieved between optimising the efficiency and effectiveness of electronic human resource management (e-HRM) systems for human resource management (HRM) and enabling innovation to occur during the system implementation.

Design/methodology/approach

– An interpretive case study of a UK local authority e-HRM system implementation is examined using the notion of ambidexterity as an analytical device. Ambidexterity relates to how an organisation develops the ability to operate efficiently in the now, while at the same time being able to adapt to environmental changes around and ahead of them in order to grow into the future.

Findings

– As an intra-organisational capability, ambidexterity is found to derive from the simultaneous interplay and balancing of dual capabilities: exploitation and exploration. e-HRM exploitation concerned the capability to generate new knowledge with innovatory effects, created through the everyday practices performed by practitioners at all levels in the organisation. e-HRM exploration, rather than being a purposeful act, was found to be an accidental consequence of engaging in exploitation to maintain the status quo.

Research limitations/implications

– The notion of ambidexterity was originally constructed within strategic management and studies in the field have previously been confined to this area. This makes this study theoretically and empirically experimental, making it a challenging research endeavour. Another limitation is that the authors only sought views from the interviewees on how external forces might limit or facilitate their ambidexterity, as opposed to actually studying those forces themselves.

Practical implications

– The authors suggest that those in organisations who are responsible for strategic HRM need to consider ways in which “intentional” opportunities for ambidexterity in e-HRM systems implementation can be identified and harnessed to ensure better balances between exploitation and exploration in such endeavours and to guard against innovation only occurring through chance.

Originality/value

– There is a lack of detailed investigation of how organisations actually achieve ambidexterity, particularly in three under-researched areas: ambidexterity in the public sector, at human resourcing functional level and e-HRM systems implementation. Bundling these three areas into an integrated examination allows us to both identify how exploitation and exploration play out in the ambidextrous practices of an e-HRM project and also to identify the dimensions of ambidexterity in balancing e-HRM work.
Structural integrity assessment for a component of the bucket-wheel excavator
Authors: Cernescu Anghel , Marsavina Liviu , Dumitru Ion
Published: May 2014

Purpose

– The purpose of this paper is to present a methodology for assessing the structural integrity of a tie member from a bucket-wheel excavator, ESRC 470 model, which was in operation for about 20 years. The tie member is made of S355J2N structural steel. Following the period of operation, the occurrence of microcracks which can propagate by fatigue is almost inevitable. It is therefore necessary to analyze the structural integrity and the remaining life of the component analyzed.

Design/methodology/approach

– In principle, the assessment methodology is based on three steps: first, the evaluation of mechanical properties of the material component; second, a BEM analysis using FRANC 3D software package to estimate the evolution of the stress intensity factor based on crack length and applied stress; third, risk factor estimation and remaining fatigue life predictions based on failure assessment diagram and fatigue damage tolerance concept.

Findings

– Following the evaluation procedure were made predictions of failure risk factor and remaining fatigue life function of crack length and variable stress range, for a high level of confidence.

Originality/value

– As results of this analysis was implemented a program for verification and inspection of the tie member for the loading state and development of small cracks during operation.
An experimental study of initial flaws in thin sheets of 2024 aircraft aluminium alloy
Authors: Zhuang Wyman , Liu Qianchu , Smith Cathy
Published: May 2014

Purpose

– One of the challenges in the prediction of fatigue crack growth is to identify representative initial flaws and defects that can cause fatigue crack initiation and subsequent crack growth. Representative initial flaws identified from this experimental study provided an essential input for the fatigue life assessment programme of the PC-9/A training aircraft currently in service. The paper aims to discuss these issues.

Design/methodology/approach

– This paper addresses this challenge with a critical literature review and experimental assessment of initial flaw types that may cause fatigue crack initiation, by fatigue testing and fractography analysis using optical microscope and scanning electron microscopy (SEM).

Findings

– With a focus on aluminium alloy (AA) 2024-T3 thin sheet, the results cover various discontinuities from microstructural constituent particles inherent from the material process to macrostructural defects and surface discontinuities (such as burrs and machining marks) introduced during the production of airframes. It was found that most fatigue cracks originated from the bore surface discontinuities of rivet holes in the PC-9 vertical stabiliser thin panels rather than microstructural material defects of AA2024-T3 inherent from the material process.

Research limitations/implications

– The experimental study has found that quantifying fatigue initial flaw sizes which resulted from poorly finished fastener holes with arbitrary discontinuities at the surface is a challenging topic. This topic is under the current investigation using a statistics based analysis of initial flaws in the prediction of fatigue crack growth.

Practical implications

– The results obtained from this experimental study provided an essential input for the empennage and aft fuselage recertification and life assessment programme for the PC-9/A training aircraft currently in service.

Originality/value

– This experimental study examined AA2024-T3 thin skin panels from two different PC-9/A aircraft. The post-test failure analysis using optical microscope and SEM found that machining defects dominate fatigue crack initiation that can result in subsequent crack propagation.