bluuebunny/crossref_metadata_2025 huggingface dataset:
Advances in target normal sheath acceleration theory
Authors: Passoni M. , Perego C. , Sgattoni A. , Batani D.
Published: June 2013

A theoretical model of the Target Normal Sheath Acceleration (TNSA) process, able to go beyond the limits of available descriptions, is developed. It allows to achieve a more satisfactory interpretation of TNSA. The theory, also supported by two dimensional particle-in-cell simulations, elucidates the role played by the main laser and target parameters. Comparison between model predictions and experimental data related to the target thickness dependence of the maximum ion energy is discussed, showing satisfactory agreement. The model can be used as a simple but effective tool to guide the design of future experiments.
Controlling the sharpness of room-temperature metal-insulator transition in epitaxial Sm0.5Nd0.5NiO3 films
Authors: Lian X. K. , Chen F. , Tan X. L. , Wang L. F. , Xuan X. F. , Gao G. Y. , Jin S. W. , Wu W. B.
Published: June 2013

Sm0.5Nd0.5NiO3 (SNNO) films with metal-insulator transition (MIT) at room-temperature (∼300 K) have been grown on NdGaO3 (001) substrates by pulsed laser deposition. By modifying the parameters of oxygen pressure, substrate temperature, and film thickness, the role of oxygen vacancies and strain relaxation on the MIT of SNNO films was systematically analyzed. The strain status of the films was carefully characterized by means of high resolution x-ray diffraction. The results revealed that for the fully strained films (≤20 nm) an increment of deposition oxygen pressure (and/or temperature) would decrease the content of oxygen vacancies and Ni2+ in the films, leading to a sharp MIT. In contrast, the strain relaxation occurs in the thicker films (>20 nm) despite an optimized oxygen pressure (temperature) was adapted for the deposition, which results in an inferior transport property and surface morphology. Specifically, a broadening MIT and a doublet TMI was observed in the partially strained films, where one TMI kept a stable value around 300 K in analogues to that of fully strained film, and another one increased with the increment of the film thickness, reaching a highest value of 330 K. This might be induced by the coexistence of a fully strained part and a strain-relaxed portion in the thicker films that observed on high resolution X-ray reciprocal space mappings.
Infrared electroluminescence from GeSn heterojunction diodes grown by molecular beam epitaxy
Authors: Gupta Jay Prakash , Bhargava Nupur , Kim Sangcheol , Adam Thomas , Kolodzey James
Published: June 2013

Infrared electroluminescence was observed from GeSn/Ge p-n heterojunction diodes with 8% Sn, grown by molecular beam epitaxy. The GeSn layers were boron doped, compressively strained, and pseudomorphic on Ge substrates. Spectral measurements indicated an emission peak at 0.57 eV, about 50 meV wide, increasing in intensity with applied pulsed current, and with reducing device temperatures. The total integrated emitted power from a single edge facet was 54 μW at an applied peak current of 100 mA at 100 K. These results suggest that GeSn-based materials maybe useful for practical light emitting diodes operating in the infrared wavelength range near 2 μm.
Positive exchange bias in thin film multilayers produced with nano-oxide layer
Authors: Chun Byong Sun , Nahm Ho-Hyun , Abid Mohamed , Wu Han-Chun , Kim Yong-Sung , Chu In Chang , Hwang Chanyong
Published: June 2013

We report a positive exchange bias in thin film multilayers produced with nano-oxide layer. The positive exchange bias resulted from an antiferromagnetic interfacial exchange coupling between the ferromagnetic CoFe and the antiferromagnetic CoO layers, which spontaneously forms on top of the nano-oxide layer during the subsequent deposition of a CoFe layer. The shift in the hysteresis loop along the direction of the cooling field and the change in the sign of exchange bias are evidence of antiferromagnetic interfacial exchange coupling. The high temperature positive exchange bias observed for our system results from magnetic proximity effects between CoFe and CoO.
Catalysis of Na
+
permeation in the bacterial sodium channel Na
V
Ab
Authors: Chakrabarti Nilmadhab , Ing Christopher , Payandeh Jian , Zheng Ning , Catterall William A. , Pomès Régis
Published: June 2013

Determination of a high-resolution 3D structure of voltage-gated sodium channel Na
V
Ab opens the way to elucidating the mechanism of ion conductance and selectivity. To examine permeation of Na
+
through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of Na
V
Ab in an explicit, hydrated lipid bilayer at 0 mV in 150 mM NaCl, for a total simulation time of 21.6 μs. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na
+
through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of Na
+
between the extracellular medium and the central cavity of the channel. Analysis of Na
+
dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na
+
ions, with a computed rate of translocation of (6 ± 1) × 10
6
ions⋅s
−1
that is consistent with expectations from electrophysiological studies. The binding of Na
+
is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na
+
ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. Structural fluctuations of these ionic clusters result in a myriad of ion binding modes and foster a highly degenerate, liquid-like energy landscape propitious to Na
+
diffusion. By stabilizing multiple ionic occupancy states while helping Na
+
ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na
+
permeation.
The Impact of a Single Ward for Cohorting Patients with Infection due to Multidrug-Resistant Organisms
Authors: Stumpfs Diego Jung , de Souza Sonia Beatriz Cocaro , Konkewicz Loriane Rita , Lovatto Carem Gorniak , da Silva Cristófer Farias , Macedo Andréia Barcelos Teixeira , dos Santos Rodrigo Pires
Published: June 2013

Multidrug-resistant organisms (MDROs) are emerging and disseminating around the globe. The guidelines for the management of MDROs support the use of various interventions to reduce the burden of MDROs. We conducted a study to assess the impact of the creation of a unit for cohorting of patients with infection due to MDROs.

Hospital de Clínicas de Porto Alegre, a 795-bed university, public hospital, is located in the city of Porto Alegre in southern Brazil. In a quasi-experimental study, we assessed the impact of the creation of an MDRO unit for patient cohorting on the overall hospital incidence of infection due to MDROs.

The 34 beds of the unit were located in 16 rooms for adult MDRO-infected patients and 2 additional rooms for respiratory isolation. Patients were transferred to the unit when they were identified as infected or colonized with MDROs. The unit staff was trained for MDRO-infected patient care; unit staff, patients, and families attended weekly meetings for education about MDROs with a multidisciplinary team (doctors, nurses, pharmacists, and social assistants).
ThreaDom: extracting protein domain boundary information from multiple threading alignments
Authors: Xue Zhidong , Xu Dong , Wang Yan , Zhang Yang
Published: June 2013

Motivation: Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by sequence-based analysis, which has low accuracy. There is no efficient method for predicting discontinuous domains that consist of segments from separated sequence regions. As template-based methods are most efficient for protein 3D structure modeling, combining multiple threading alignment information should increase the accuracy and reliability of computational domain predictions.

Result: We developed a new protein domain predictor, ThreaDom, which deduces domain boundary locations based on multiple threading alignments. The core of the method development is the derivation of a domain conservation score that combines information from template domain structures and terminal and internal alignment gaps. Tested on 630 non-redundant sequences, without using homologous templates, ThreaDom generates correct single- and multi-domain classifications in 81% of cases, where 78% have the domain linker assigned within ±20 residues. In a second test on 486 proteins with discontinuous domains, ThreaDom achieves an average precision 84% and recall 65% in domain boundary prediction. Finally, ThreaDom was examined on 56 targets from CASP8 and had a domain overlap rate 73, 87 and 85% with the target for Free Modeling, Hard multiple-domain and discontinuous domain proteins, respectively, which are significantly higher than most domain predictors in the CASP8. Similar results were achieved on the targets from the most recently CASP9 and CASP10 experiments.

Availability:  http://zhanglab.ccmb.med.umich.edu/ThreaDom/.

Contact:  zhng@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Compressive genomics for protein databases
Authors: Daniels Noah M. , Gallant Andrew , Peng Jian , Cowen Lenore J. , Baym Michael , Berger Bonnie
Published: June 2013

Motivation: The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology search directly but also the huge collection of other current programs that primarily interact with large protein databases via precisely these tools.

Results: We introduce a suite of homology search tools, powered by compressively accelerated protein BLAST (CaBLASTP), which are significantly faster than and comparably accurate with all known state-of-the-art tools, including HHblits, DELTA-BLAST and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines. The key idea is that we introduce a local similarity-based compression scheme that allows us to operate directly on the compressed data. Importantly, CaBLASTP’s runtime scales almost linearly in the amount of unique data, as opposed to current BLASTP variants, which scale linearly in the size of the full protein database being searched. Our compressive algorithms will speed-up many tasks, such as protein structure prediction and orthology mapping, which rely heavily on homology search.

Availability: CaBLASTP is available under the GNU Public License at http://cablastp.csail.mit.edu/

Contact: bab@mit.edu
Stability selection for regression-based models of transcription factor–DNA binding specificity
Authors: Mordelet Fantine , Horton John , Hartemink Alexander J. , Engelhardt Barbara E. , Gordân Raluca
Published: June 2013

Motivation: The DNA binding specificity of a transcription factor (TF) is typically represented using a position weight matrix model, which implicitly assumes that individual bases in a TF binding site contribute independently to the binding affinity, an assumption that does not always hold. For this reason, more complex models of binding specificity have been developed. However, these models have their own caveats: they typically have a large number of parameters, which makes them hard to learn and interpret.

Results: We propose novel regression-based models of TF–DNA binding specificity, trained using high resolution in vitro data from custom protein-binding microarray (PBM) experiments. Our PBMs are specifically designed to cover a large number of putative DNA binding sites for the TFs of interest (yeast TFs Cbf1 and Tye7, and human TFs c-Myc, Max and Mad2) in their native genomic context. These high-throughput quantitative data are well suited for training complex models that take into account not only independent contributions from individual bases, but also contributions from di- and trinucleotides at various positions within or near the binding sites. To ensure that our models remain interpretable, we use feature selection to identify a small number of sequence features that accurately predict TF–DNA binding specificity. To further illustrate the accuracy of our regression models, we show that even in the case of paralogous TF with highly similar position weight matrices, our new models can distinguish the specificities of individual factors. Thus, our work represents an important step toward better sequence-based models of individual TF–DNA binding specificity.

Availability: Our code is available at http://genome.duke.edu/labs/gordan/ISMB2013. The PBM data used in this article are available in the Gene Expression Omnibus under accession number GSE47026.

Contact: raluca.gordan@duke.edu
Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans
Authors: Aerni Sarah J. , Liu Xiao , Do Chuong B. , Gross Samuel S. , Nguyen Andy , Guo Stephen D. , Long Fuhui , Peng Hanchuan , Kim Stuart S. , Batzoglou Serafim
Published: June 2013

Motivation: Advances in high-resolution microscopy have recently made possible the analysis of gene expression at the level of individual cells. The fixed lineage of cells in the adult worm Caenorhabditis elegans makes this organism an ideal model for studying complex biological processes like development and aging. However, annotating individual cells in images of adult C.elegans typically requires expertise and significant manual effort. Automation of this task is therefore critical to enabling high-resolution studies of a large number of genes.

Results: In this article, we describe an automated method for annotating a subset of 154 cells (including various muscle, intestinal and hypodermal cells) in high-resolution images of adult C.elegans. We formulate the task of labeling cells within an image as a combinatorial optimization problem, where the goal is to minimize a scoring function that compares cells in a test input image with cells from a training atlas of manually annotated worms according to various spatial and morphological characteristics. We propose an approach for solving this problem based on reduction to minimum-cost maximum-flow and apply a cross-entropy–based learning algorithm to tune the weights of our scoring function. We achieve 84% median accuracy across a set of 154 cell labels in this highly variable system. These results demonstrate the feasibility of the automatic annotation of microscopy-based images in adult C.elegans.

Contact: saerni@cs.stanford.edu
Information-theoretic evaluation of predicted ontological annotations
Authors: Clark Wyatt T. , Radivojac Predrag
Published: June 2013

Motivation: The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, with protein function prediction and disease gene prioritization gaining wide recognition. Although various algorithms have been proposed for these tasks, evaluating their performance is difficult owing to problems caused both by the structure of biomedical ontologies and biased or incomplete experimental annotations of genes and gene products.

Results: We propose an information-theoretic framework to evaluate the performance of computational protein function prediction. We use a Bayesian network, structured according to the underlying ontology, to model the prior probability of a protein’s function. We then define two concepts, misinformation and remaining uncertainty, that can be seen as information-theoretic analogs of precision and recall. Finally, we propose a single statistic, referred to as semantic distance, that can be used to rank classification models. We evaluate our approach by analyzing the performance of three protein function predictors of Gene Ontology terms and provide evidence that it addresses several weaknesses of currently used metrics. We believe this framework provides useful insights into the performance of protein function prediction tools.

Contact:  predrag@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inference of historical migration rates via haplotype sharing
Authors: Palamara Pier Francesco , Pe’er Itsik
Published: June 2013

Summary: Pairs of individuals from a study cohort will often share long-range haplotypes identical-by-descent. Such haplotypes are transmitted from common ancestors that lived tens to hundreds of generations in the past, and they can now be efficiently detected in high-resolution genomic datasets, providing a novel source of information in several domains of genetic analysis. Recently, haplotype sharing distributions were studied in the context of demographic inference, and they were used to reconstruct recent demographic events in several populations. We here extend the framework to handle demographic models that contain multiple demes interacting through migration. We extensively test our formulation in several demographic scenarios, compare our approach with methods based on ancestry deconvolution and use this method to analyze Masai samples from the HapMap 3 dataset.

Availability: DoRIS, a Java implementation of the proposed method, and its source code are freely available at http://www.cs.columbia.edu/∼pier/doris.

Contact: itsik@cs.columbia.edu
Efficacy and safety of ivabradine in chronic heart failure across the age spectrum: insights from the SHIFT study
Authors: Tavazzi Luigi , Swedberg Karl , Komajda Michel , Böhm Michael , Borer Jeffrey S. , Lainscak Mitja , Ford Ian ,   on behalf of the SHIFT Investigators
Published: June 2013

Aims

To test whether the efficacy and safety of the selective heart rate‐reducing agent ivabradine changes according to age in chronic heart failure (HF) patients.

Methods and results

The ivabradine and placebo arms of SHIFT, which enrolled 6505 chronic HF patients, were combined and age distribution was divided by quartiles to give four groups (<53 years, n = 1522; 53 to <60 years, n = 1521; 60 to <69 years, n = 1750; and ≥69 years, n = 1712). The effects of ivabradine on cardiovascular outcomes, changes in heart rate, and adverse events, particularly bradycardia, were evaluated according to age group. A subgroup (602 patients) underwent 24 h ambulatory ECG Holter monitoring. The relative risk of the primary endpoint (cardiovascular death or hospitalization for worsening HF) was reduced by ivabradine in all age groups, ranging from 38% [hazard ratio (HR) 0.62, 95% confidence interval (CI) 0.50–0.78, P < 0.001] in the youngest patients <53 years to 16% (HR 0.84, 95% CI 0.71–0.99, P = 0.035) in the oldest patients ≥69 years. Ivabradine up‐titration reduced heart rate similarly in all age groups, by 11 b.p.m. As anticipated, bradycardia and phosphenes occurred more frequently with ivabradine, at a similar rate whatever the age. In the Holter substudy, there were no episodes of severe bradycardia and no clinically relevant pauses with ivabradine in any age group.

Conclusions

Age does not limit the appropriate use of ivabradine in patients with chronic HF and systolic dysfunction. The safety and efficacy of ivabradine are comparable across all age groups.
Genetic characterization of a novel picornavirus distantly related to the marine mammal-infecting aquamaviruses in a long-distance migrant bird species, European roller (Coracias garrulus)
Authors: Boros Ákos , Kiss Tamás , Kiss Orsolya , Pankovics Péter , Kapusinszky Beatrix , Delwart Eric , Reuter Gábor
Published: June 2013

Despite the continuously growing number of known avian picornaviruses (family Picornaviridae), knowledge of their genetic diversity in wild birds, especially in long-distance migrant species is very limited. In this study, we report the presence of a novel picornavirus identified from one of 18 analysed faecal samples of an Afro-Palearctic migrant bird, the European roller (Coracias garrulus L., 1758), which is distantly related to the marine-mammal-infecting seal aquamavirus A1 (genus Aquamavirus). The phylogenetic analyses and the low sequence identity (P1 26.3 %, P2 25.8 % and P3 28.4 %) suggest that this picornavirus could be the founding member of a novel picornavirus genus that we have provisionally named ‘Kunsagivirus’, with ‘Greplavirus A’ (strain roller/SZAL6-KuV/2011/HUN, GenBank accession no. KC935379) as the candidate type species.
Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence
Authors: Bono Hidemasa , Ogata Hiroyuki , Goto Susumu , Kanehisa Minoru
Published: June 2013

The complete genome sequence of an organism contains information that has not been fully utilized in the current prediction methods of gene functions, which are based on piece-by-piece similarity searches of individual genes. We present here a method that utilizes a higher level information of molecular pathways to reconstruct a complete functional unit from a set of genes. Specifically, a genome-by-genome comparison is first made for identifying enzyme genes and assigning EC numbers, which is followed by the reconstruction of selected portions of the metabolic pathways by use of the reference biochemical knowledge. The completeness of the reconstructed pathway is an indicator of the correctness of the initial gene function assignment. This feature has become possible because of our efforts to computerize the current knowledge of metabolic pathways under the KEGG project. We found that the biosynthesis pathways of all 20 amino acids were completely reconstructed in Escherichia coli, Haemophilus influenzae, and Bacillus subtilis, and probably inSynechocystis and Saccharomyces cerevisiae as well, although it was necessary to assume wider substrate specificity for aspartate aminotransferases.
Kaleidaseq: A Web-Based Tool to Monitor Data Flow in a High Throughput Sequencing Facility
Authors: Dedhia Neilay N. , McCombie W. Richard
Published: June 2013

Tracking data flow in high throughput sequencing is important in maintaining a consistent number of successfully sequenced samples, making decisions on scheduling the flow of sequencing steps, resolving problems at various steps and tracking the status of different projects. This is especially critical when the laboratory is handling a multitude of projects. We have built a Web-based data flow tracking package, called Kaleidaseq, which allows us to monitor the flow and quality of sequencing samples through the steps of preparation of library plates, plaque-picking, preparation of templates, conducting sequencing reactions, loading of samples on gels, base-calling the traces, and calculating the quality of the sequenced samples. Kaleidaseq’s suite of displays allows for outstanding monitoring of the production sequencing process. The online display of current information that Kaleidaseq provides on both project status and process queues sorted by project enables accurate real-time assessment of the necessary samples that must be processed to complete the project. This information allows the process manager to allocate future resources optimally and schedule tasks according to scientific priorities. Quality of the sequenced samples can be tracked on a daily basis, which allows the sequencing laboratory to maintain a steady performance level and quickly resolve dips in quality. Kaleidaseq has a simple easy-to-use interface that allows access to all major functions and process queues from one Web page. This software package is modular and designed to allow additional processing steps and new monitoring variables to be added and tracked with ease. Access to the underlying relational database is through the Perl DBI interface, which allows for the use of different relational databases. Kaleidaseq is available for free use by the academic community from http://www.cshl.org/kaleidaseq.
Identification of Human Gene Core Promoters in Silico
Authors: Zhang Michael Q.
Published: June 2013

Identification of the 5′-end of human genes requires identification of functional promoter elements. In silico identification of those elements is difficult because of the hierarchical and modular nature of promoter architecture. To address this problem, I propose a new stepwise strategy based on initial localization of a functional promoter into a 1- to 2-kb (extended promoter) region from within a large genomic DNA sequence of 100 kb or larger and further localization of a transcriptional start site (TSS) into a 50- to 100-bp (corepromoter) region. Using positional dependent 5-tuple measures, a quadratic discriminant analysis (QDA) method has been implemented in a new program—CorePromoter. Our experiments indicate that when given a 1- to 2-kb extended promoter, CorePromoter will correctly localize the TSS to a 100-bp interval ∼60% of the time.

[Figure 3 can be found in its entirety as an online supplement at http://www.genome.org.]
Designing and testing wearable range‐vibrotactile devices
Authors: Lun Khoo Wai , Knapp Joey , Palmer Franklin , Ro Tony , Zhu Zhigang
Published: June 2013

Purpose

The purpose of this paper is to demonstrate how commercially‐off‐the‐shelf sensors and stimulators, such as infrared rangers and vibrators, can be retrofitted as a useful assistive technology in real and virtual environments.

Design/methodology/approach

The paper describes how a wearable range‐vibrotactile device is designed and tested in the real‐world setting, as well as thorough evaluations in a virtual environment for complicated navigation tasks and neuroscience studies.

Findings

In the real‐world setting, a person with normal vision who has to navigate their way around a room with their eyes closed will quickly rely on their arms and hands to explore the room. The authors’ device allows a person to “feel” their environment without touching it. Due to inherent difficulties in testing human subjects when navigating a real environment, a virtual environment affords us an opportunity to scientifically and extensively test the prototype before deploying the device in the real‐world.

Research limitations/implications

This project serves as a starting‐point for further research in benchmarking assistive technology for the visually impaired and to eventually develop a man‐machine sensorimotor model that will improve current state‐of‐the‐art technology, as well as a better understanding of neural coding in the human brain.

Social implications

Based on 2012 World Health Organization, there are 39 million blind people. This project will have a direct impact on this community.

Originality/value

The paper demonstrates a low cost design of assistive technology that has been tested and evaluated in real and virtual environments, as well as integration of sensor designs and neuroscience.
Keeping the sparkle on
Authors: Varkkey Biju , Kumar Randhir
Published: June 2013

Purpose

The Indian diamond cutting and polishing (CPD) industry enjoys a global leadership position, but at the same time is vulnerable to economic shifts in the global market. Historically, such shocks have resulted in shake down of the industry, including closures, bankruptcies, job losses and labour unrest. Most recently, the vulnerability was experienced during the economic recession of 2008, which impacted both entrepreneurs and diamond workers alike. The shock elicited different adaptation strategies from individual firms. The paper aims to understand the adaptation strategies of large and formally organized diamond enterprises in Surat, India, with particular reference to “labour hoarding” as a strategy for workforce management.

Design/methodology/approach

Using case studies of four large CPD firms, the paper investigates patterns in managerial decision making pertaining to workforce management and adaptation strategies taken during recession. The authors also traced the subject companies' performance post‐recession. The tool used for data collection was semi‐structured, in‐depth interviews with entrepreneurs and human resource managers. For additional inputs and triangulation of findings, content analysis of news reports, along with interactions with several knowledgeable persons from both industry and government, were conducted.

Findings

The authors' study of the sample firms neither supports the popular notion of “workforce retention by large diamond enterprises, in spite of recession” nor the generalized statements about “massive lay‐offs by all”, as reported in popular media. The authors found that, due to recessionary pressure, there was a deep managerial dilemma in the companies about how to strike the right trade‐off between workforce retention (labour hoarding) and downsizing. The paper argues that, post‐recession, the companies whose decisions were pro‐labour retention (hoarding) oriented were able to come back in business stronger and perform better.

Originality/value

The diamond industry of India is ethno‐bound in its functioning, where community and regional/linguistic affiliations of both workers and entrepreneurs traditionally played a vital role. Therefore, the employee management practices adopted do not strictly fall within the general realm of western management practices or popular HRM frameworks. The study shows that context‐dependent employee management strategies, suiting the need for maintaining the traditional ethno‐bound values even during recessionary pressure, created long‐term positive effects for the firm.
The impact of near field communication on tourism
Authors: Egger Roman
Published: June 2013

Purpose

– Near field communication (NFC) is currently perceived to be one of the most promising technologies for the future and will most likely become the standard in mobile devices in the years to come. Due to the novel nature of this technology, the assessment of its importance for the tourism industry is still relatively unclear. The author is one of the first to focus on NFC in tourism, with the aim of introducing NFC technology and drafting first responses to the following questions: what benefit can NFC technology have for tourism and what functionalities can it trigger? What are the possible future applications in tourism and what challenges will tourism be faced with in this respect?

Design/methodology/approach

– The potential of NFC for the tourism industry is outlined in an extensive literature research, as well as in the presentation and discussion of several pilot projects and case studies.

Findings

– The paper provides an overview of NFC functionalities and presents a first insight into the range of application for this technology in the tourism industry. The NFC ecosystem is examined and operative and strategic effects for companies, as well as the impacts for tourists, are analysed.

Practical implications

– NFC has a huge potential and offers a vast field of possible applications for the tourism industry. The technology must be seen, however, as an enabler that cannot solve problems from a supplier perspective, or increase convenience from a consumer perspective by itself. This paper helps to understand the complexity of NFC as a technology, the need for a common understanding and vision of its ecosystem, consistent business models which generate additional benefit, as well as the combination of market push-and-pull effects with regard to adoption and diffusion.

Social implications

– Modern society is virtually inconceivable without mobile devices and the consequent use of mobile services. The multitude of technologies incorporated in the tiniest space has turned mobile phones, and smart phones in particular, into the Swiss knives of our times. NFC could change the way we interact, share, exchange and retrieve information.

Originality/value

– Little research has so far been carried out on this topic and the author is one of the first to focus on NFC in tourism so far.
Portfolio margining of cleared credit default swaps
Authors: Philipp Michael M. , Sandoval Ignacio A.
Published: June 2013

Purpose

The purpose of this paper is to describe the separate but related relief issued by the Commodity Futures Trading Commission (CFTC) and the Securities and Exchange Commission (SEC) that permits the commingling and portfolio margining of centrally cleared credit default swap (CDS) positions held in customer accounts.

Design/methodology/approach

The paper provides a brief overview of the bifurcated approach taken to the regulation of CDS; explains the benefits of portfolio margining and the need for portfolio margining relief; and provides an overview of the relief provided by the SEC and CFTC.

Findings

The relief provided by the SEC and CFTC may contribute to the efficient use and allocation of capital by market participants; however, the SEC's and CFTC's orders are limited in scope only to CDS products, and the viability of the relief for CDS products will depend upon SEC approval of the margin methodology used by brokers to set margin levels for their customers.

Originality/value

The paper provides practical insights into first of its kind regulatory relief permitting commingling and portfolio margining of centrally cleared derivatives for customer accounts and the requirements incumbent on a market intermediary when implementing a program to commingle and portfolio margin centrally cleared CDS positions.
SEC lifts moratorium on actively managed ETFs' use of derivatives; moratorium continues for leveraged ETFs
Authors: Decko Kurt , Fuller Stacy
Published: June 2013

Purpose

The purpose of this paper is to explain the announcement and no‐action letter of December 11, 2012 from the Securities and Exchange Commission (“SEC”) Division of Investment Management lifting the moratorium on the use of derivatives by actively managed exchange‐traded funds (ETFs) but continuing the moratorium on use of derivatives by leveraged ETFs.

Design/methodology/approach

The paper explains the background, including the moratorium that went into effect as the SEC conducted a review of the use of derivatives by mutual funds, ETFs and other investment companies; the lifting of the moratorium; two representations ETFs that propose to use derivatives must make in their exemptive applications to the SEC; the implications for ETFs that make those representations; and the next steps for ETFs currently in the exemptive applications process.

Findings

While it does not mean the end of the SEC staff's review of derivative usage by ETFs generally, the lifting of the moratorium is a welcome development that restores actively managed ETFs' ability to compete largely on an equal footing with other vehicles in many investment strategies.

Practical implications

While the representations do not appear to impose substantive new disclosure requirements for ETFs, the difficulty, if any, could be that these representations will now be required by the terms of the exemptive relief on which they rely for all their operations.

Originality/value

The paper provides practical advice from experienced financial services lawyers.
Assessing the ability of Saccharomyces cerevisiae to bind aflatoxin B1 from contaminated medium
Authors: Sahebghalam Haleh , Mohamadi Sani Ali , Mehraban Masoumeh
Published: June 2013

Purpose

This study was conducted with the aim of examining the ability of Saccharomyces cerevisiae to remove AFB1 from liquid media in order to use data in food and feed systems.

Design/methodology/approach

The binding of AFB1 to Saccharomyces cerevisiae in the late exponential and early stationary phases was studied for viable, heat killed and acid killed yeast. AFB1 at concentrations (5, 10 and 20 μg/l) was added to the yeast culture (109 cfu/ml) in yeast mold broth medium and incubated at 25°C for 4, 12 and 24 hrs. The aflatoxin binding capacity of the strain was quantified by the amount of unbound AFB1 using ELISA technique.

Findings

The detoxification rate for different treatments reported as follows: acid treated cells > heat treated cells > viable cells. Also, the most reduction in AFB1 concentration happened within the first four hours of incubation with no significant increase in AFB1 binding on further incubation because of saturation of active sites in yeast cells. According to the results, either form of Saccharomyces cerevisiae (viable or nonviable) is effective in aflatoxin binding from medium and the binding has a physical nature.

Social implications

The findings reduce the public concern about aflatoxin B1 contamination in foods and feeds having high risk of aflatoxin contamination.

Originality/value

No research had been done to assess the ability of Saccharomyces cerevisiae in the mentioned forms to detoxify AFB1.
The good, the bad and the ugly: searching for critical research in psychology
Authors: Duckett Paul , Fryer David , Lawthom Rebecca , Nic Giolla Easpaig Brona , Radermacher Harriet
Published: June 2013

Purpose

The purpose of this paper is to answer the question “what is good research?” from the perspective of critical researchers working in the discipline of psychology.

Design/methodology/approach

The authors first look at what it means to be “good”, then what it means to be critical and then interlink these two as a means of providing a context to understand why there appears to be so little critical research around. Findings– The authors have put together a narrative that they hope is readable but that still pulls on the different ways each of them have approached the topic of defining good research and thinking about critical research.

Originality/value

The authors have personally witnessed the disappearance‐ing of critical activists, anti‐psychiatry activists, disability rights activists, trades unionists, critical scholars; and put forward a reason (among others) as to why there is so little good critical research, which is that the status quo is implacably ferocious in its efforts to close it down wherever it occurs. Indeed, if the status quo is not doing its damnedest to close down the research you are doing, you can be reasonably sure it is not good critical research.
Does venture capital portfolio size matter?
Authors: Bartkus James R. , Kabir Hassan M. , Ngene Geoffrey
Published: June 2013

Purpose

The purpose of this study is to investigate the effects of increased fund commitments on portfolio size and subsequent effects on portfolio success rates. This paper empirically analyzes the changes in average portfolio size over a 20‐year time period and how these changes affect the venture capitalists' ability to successfully exit their investments.

Design/methodology/approach

The authors utilize venture capitalists' fund level data and conduct both univariate and multivariate analysis. The multivariate analysis is conducted using a two‐limit regression tobit model. This is justified since the authors' dependent variable is a ratio bounded by zero and one, hence the tobit specification is the most appropriate methodology.

Findings

The authors find that increasing the size of portfolios not only leads to a decrease in the number of successful investments but also significantly affects portfolio success rates. They also find evidence which suggests that some optimal portfolio size exists.

Research limitations/implications

The sample was limited to independent private partnerships that raised funds specifically for investment in US portfolio companies and it represents all funds maintained in the SDC database with non‐missing data on fund size and other fund characteristics.

Practical implications

There are three main practical implications derived from this study. First, venture capitalists overextend themselves by investing in too many portfolio firms. Second, some optimal portfolio size exists beyond which success rate of the venture capitalist's portfolio declines. Third, portfolio size is an important determinant of venture capital portfolio success rates.

Originality/value

The study presents new evidence that venture capitalists have a tendency to increase their portfolio size in years following growth in fund inflows, an idea that has not been investigated earlier. The authors also use data that is not adulterated by significant economic and financial conditions such as internet bubble burst of 2000 and financial crisis of 2007/2008.
Transdermal nicotine patches for eosinophilic pustular folliculitis
Authors: Yoshifuku Asuka , Higashi Yuko , Matsushita Shigeto , Kawai Kazuhiro , Kanekura Takuro
Published: June 2013

We previously reported the clinical effectiveness of transdermal nicotine patches for the treatment of skin disorders with eosinophilic infiltration such as Kimura's disease, erythema nodosum and eosinophilic pustular folliculitis (EPF). We assessed the efficacy and safety of transdermal nicotine patches for EPF. We treated eight patients with EPF with transdermal nicotine patches and evaluated the treatment response by performing overall lesional assessment. Excellent 77and good responses were obtained in five and one patient(s), respectively. In the other two patients, the lesions remained unchanged. No severe adverse effects were observed. Our results suggest that transdermal nicotine patches may be useful and safe in the treatment of EPF.
Defensible Space on the Move: Revisiting the Urban Geography ofAliceColeman
Authors: Jacobs Jane M. , Lees Loretta
Published: June 2013

This article traces the movement of the concept of ‘defensible space’ fromNewYork City in the 1970s, where it was developed by theCanadian architect/plannerOscarNewman, toLondon in the 1980s and into design interventions inBritish public housing in the 1990s, throughBritish geographerAliceColeman, who acted as an especially powerful transfer agent. In focusing on this urban design ‘concept’ on the move we contribute to existing scholarship on policy mobility and city building in a number of ways. First, we explore an instance of the movement/mobility of a planning concept in a historical period (the recent past) largely overlooked to date. Secondly, we demonstrate that this movement was the result of a disaggregated series of expert knowledge transfers and localized translations of pre‐policy expert knowledge, generated through university‐based research work and networks. We theorize this instance of urban planning mobility by way of the interlinked insights offered by the sociology of science and policy‐mobilities literatures. As this is an instance of university research shaping public policy it also offers an opportunity to reflect upon the meaning of ‘evidence‐based policy’ and the impact agenda in contemporary higher education.
Roads as Regions, Networks and Flows: Waverley and the ‘Periphery’ of Romance
Authors: EWERS CHRIS
Published: June 2013

Sir Walter Scott's Waverley has long been regarded as the originator of the historical novel, and much critical interest in the text centres on the way it presents ‘history’. This privileging of the temporal has obscured what is perhaps an even greater achievement by Scott: the complex way in which he handles ‘space’. This article examines the way roads have been described in terms of regions or networks in the novel but adds a third spatial model, fluidity, which has important consequences for how Waverley has been read, especially in terms of the ‘periphery’ of romance and its separation from ‘history’.
Resistance of wild African ungulates to foraging by red‐billed oxpeckers (Buphagus erythrorhynchus): evidence that this behaviour modulates a potentially parasitic interaction
Authors: Bishop Anne L. , Bishop Richard P.
Published: June 2013

Field observations of the interactions between red‐billed oxpeckers (Buphagus erythrorhynchus) and wild ungulates in Nakuru National Park, Kenya, revealed that specific hosts frequently attempted to manipulate oxpecker foraging. This involved a repertoire of behaviour collectively referred to as resistance behaviour, and often resulted in the oxpeckers either changing their position on the host's body or departing. Cape buffalo (Syncerus caffer), the most frequently used host, performed little resistance behaviour. Waterbuck (Kobus ellipsiprymnus) were also popular oxpecker hosts, but frequently exhibited vigorous resistance behaviour. Impala (Aepyceros melampus), the third most widely used host species, also utilized resistance behaviours, but allowed a greater proportion of oxpeckers to forage without disturbance. The suite of resistance behaviours employed by waterbuck, impala and also the consequences for oxpecker foraging, differed significantly. Our data suggest that the oxpecker–ungulate interactions in the field are more complex than previously realized with resistance behaviour regularly employed by selected mammalian host species.
Group Segregation and Urban Violence
Authors: Bhavnani Ravi , Donnay Karsten , Miodownik Dan , Mor Maayan , Helbing Dirk
Published: June 2013

How does segregation shape intergroup violence in contested urban spaces? Should nominal rivals be kept separate or instead more closely integrated? We develop an empirically grounded agent‐based model to understand the sources and patterns of violence in urban areas, employing Jerusalem as a demonstration case and seeding our model with microlevel, geocoded data on settlement patterns. An optimal set of parameters is selected to best fit the observed spatial distribution of violence in the city, with the calibrated model used to assess how different levels of segregation, reflecting various proposed “virtual futures” for Jerusalem, would shape violence. Our results suggest that besides spatial proximity, social distance is key to explaining conflict over urban areas: arrangements conducive to reducing the extent of intergroup interactions—including localized segregation, limits on mobility and migration, partition, and differentiation of political authority—can be expected to dampen violence, although their effect depends decisively on social distance.
A journey to citizenship: Constructions of citizenship and identity in the British Citizenship Test
Authors: Gray Debra , Griffin Christine
Published: June 2013

The British Citizenship Test was introduced in 2005 as one of a raft of new procedures aimed at addressing the perceived problems of integration and social cohesion in migrant communities. In this study, we argue that this new citizenship procedure signals a shift in British political discourse about citizenship – particularly, the institutionalization of a common British citizen identity that is intended to draw citizens together in a new form of political/national community. In line with this, we examine the British Citizenship Test from a social psychological perspective to interrogate the ways in which the test constitutes identity, constitutes citizenship, and constitutes citizenship‐as‐identity. Analysis of the test and its associated documents highlights three ways in which Britishness‐as‐identity is constituted, that is, as a collective identity, as a superordinate and national identity, and finally as both a destination and a journey. These findings are discussed in terms of their implications for models of citizenship and models of identity.