bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magneto-Plasmons in Periodic Nanoporous Structures
Authors: Song Yujun , Yin Weiting , Wang Ying-Hui , Zhang Jun-Pei , Wang Yan , Wang Rongming , Han Junbo , Wang Wu , Nair Selvakumar V. , Ruda Harry E. 
Published: May 2014

AbstractWe report on ordered nanoporous films exhibiting a unique magneto-plasmon based response, fabricated by nanosphere-assisted physical deposition. This work focuses on multi-layer Ag/CoFeB/Ag films as examples of such structures. Their microstructure dependent magnetic properties, localized surface plasmon resonance (LSPR) and magneto-optical Kerr effect were investigated. The observed effects of nanopores and Ag layers on the magnetic properties indicate the synergistic interaction between nanopores and Ag layers leading to an enhancement of the ferromagnetic character of the CoFeB film. LSPR spectra reveal that the introduction of Ag layers enhances the light transmission in the nanoporous CoFeB films (having pore sizes exceeding the wavelength of light) due to an enhanced interaction of light with surface plasmons. Periodic nanoporous Ag/CoFeB/Ag films covered by Ag capped nanospheres show a much larger extinction than uncovered nanoporous Ag/CoFeB/Ag films. The correlation between the magneto-optical Kerr effect and the nanostructures suggests a field-tunable Kerr effect owing to the magneto-electric coupling between the magnetic layer and the Ag layers, which is enhanced by the nanopores. These hybrid nanostructures are expected to offer potential applications in photovoltaic cells and for magneto-optic sensors.
Role of plasma matrix-metalloproteases (MMPs) and their polymorphisms (SNPs) in sepsis development and outcome in ICU patients
Authors: Martin Guadalupe , Asensi Víctor , Montes A. Hugo , Collazos Julio , Alvarez Victoria , Carton José A. , Taboada Francisco , Valle-Garay Eulalia 
Published: May 2014

AbstractMatrix-metalloproteases (MMPs) and their tissue-inhibitors (TIMPs), modulated by different single nucleotide polymorphisms (SNPs), are critical in sepsis development. Ninety ICU severely septic and 91 ICU uninfected patients were prospectively studied.MMP-1 (−1607 1G/2G),MMP-3 (−1612 5A/6A),MMP-8 (−799 C/T),MMP-9 (−1562 C/T)andMMP-13 (−77A/G) SNPs were genotyped. Plasma MMPs (-1, -2, -3, -8, -9, -10, -13) and TIMPs (-1,-2,-4) were measured.AAhomozygotes andAallele carriers ofMMP-13(−77 A/G) and1G2Gcarriers of theMMP-1 (−1607 1G/2G)SNPs frequencies were different between septic and uninfected patients (p < 0.05), as well as plasma MMP-3, -8, -9 -10 and TIMP-2 levels (p < 0.04). No differences in MMPs levels amongMMP-13orMMP-1SNPs genotypes carriers were observed. The area under the ROC curve for MMP-8 in the diagnosis of sepsis was 0.87 (95% CI 0.82–0.92) and that of CRP was 0.98 (0.94–0.998), whereas the area of MMP-9 in the detection of non-septic state was 0.73 (0.65–0.80), p < 0.0001 for all curves. Sepsis associated with increased MMP-8 and decreased MMP-9 levels in multivariate analysis (p < 0.0002). We report for the first time an association betweenMMP-13andMMP-1SNPs and sepsis. An independent association of MMP-8 and MMP-9 levels with sepsis was also observed.
Identification and characterization of a mirror-image oligonucleotide that binds and neutralizes sphingosine 1-phosphate, a central mediator of angiogenesis
Authors: Purschke Werner G. , Hoehlig Kai , Buchner Klaus , Zboralski Dirk , Schwoebel Frank , Vater Axel , Klussmann Sven 
Published: May 2014

The sphingolipid S1P (sphingosine 1-phosphate) is known to be involved in a number of pathophysiological conditions such as cancer, autoimmune diseases and fibrosis. It acts extracellularly through a set of five G-protein-coupled receptors, but its intracellular actions are also well documented. Employing in vitro selection techniques, we identified an L-aptamer (Spiegelmer®) to S1P designated NOX-S93. The binding affinity of NOX-S93 to S1P had a Kd value of 4.3 nM. The Spiegelmer® shows equal binding to dihydro-S1P, but no cross-reactivity to the related lipids sphingosine, lysophosphatidic acid, ceramide, ceramide-1-phosphate or sphingosine phosphocholine. In stably transfected CHO (Chinese-hamster ovary) cell lines expressing the S1P receptors S1PR1 or S1PR3, NOX-S93 inhibits S1P-mediated β-arrestin recruitment and intracellular calcium release respectively, with IC50 values in the low nanomolar range. The pro-angiogenic activity of S1P, and of the growth factors VEGF-A (vascular endothelial growth factor-A), FGF-2 (fibroblast growth factor-2) and IGF-1 (insulin-like growth factor-1), was effectively blocked by NOX-S93 in a cellular angiogenesis assay employing primary human endothelial cells. These data provide further evidence for the relevance of extracellular S1P as a central mediator of angiogenesis, suggesting pharmacological S1P neutralization as a promising treatment alternative to current anti-angiogenesis approaches.
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

Abstract
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

Abstract
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
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.
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

AbstractDissociated 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.
Do environmental collaboration and monitoring enhance organizational performance?
Authors: Green Kenneth W. , Zelbst Pamela J. , Bhadauria Vikram S. , Meacham Jeramy 
Published: May 2014

PurposeThe 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/approachAn 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.FindingsEnvironmental collaboration and monitoring practices among supply chain partners are found to lead to improved environmental performance and organizational performance.Research limitations/implicationsAs a first wave investigation of the impact of green supply chain management practices on performance, the study is somewhat exploratory.Practical implicationsPractitioners 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 implicationsThe 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/valueThe 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

PurposeThe 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/approachA 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.FindingsDrawing 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/valueThis 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.