bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses
Authors: Krupovic Mart , Koonin Eugene V. 
Published: June 2014

AbstractSingle-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.
Soft Nanoparticles for Biomedical Applications
Authors:   Royal Society of Chemistry
Published: June 2014

Nanoparticles are attractive for many biomedical applications such as imaging, therapeutics and diagnostics. This new book looks at different soft nanoparticles and their current and potential uses in medicine and health including magnetoliposomes, micro/nanogels, polymeric micelles, DNA particles, dendrimers and bicelles.
Each chapter provides a description of the synthesis of the particles and focus on the techniques used to characterize the size, shape, surface charge, internal structure, and surface microstructure of the nanoparticles together with modeling and simulation methods. By giving a strong physical-chemical approach to the topic, readers will gain a good background into the subject and an overview of recent developments.
The multidisciplinary point of view makes the book suitable for postgraduate students and researchers in physics, chemistry, and biology interested in soft matter and its uses.
LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface
Authors: Malojčić Goran , Andres Dorothee , Grabowicz Marcin , George Alexander H. , Ruiz Natividad , Silhavy Thomas J. , Kahne Daniel 
Published: June 2014

Significance
The outermost membrane of Gram-negative bacteria contains lipopolysaccharide (LPS), and its proper placement on the cell surface is required to establish an effective permeability barrier. The presence of LPS prevents small hydrophobic molecules from entering the cell making it difficult to develop antibiotics. LPS is synthesized inside the cell and must move across three compartments to the cell surface. The final step of LPS transport (Lpt), translocation of LPS across the outer membrane, is accomplished by a two-protein complex (LptDE) that must insert LPS into its outer leaflet. We have identified a binding site within LptE critical for the proper function of the translocon. LptE binds LPS and changes its physical state to facilitate its translocation through the outer membrane.
Normal levels of the antiprion proteins Btn2 and Cur1 cure most newly formed [URE3] prion variants
Authors: Wickner Reed B. , Bezsonov Evgeny , Bateman David A. 
Published: June 2014

Significance
The [URE3] prion (infectious protein) is an amyloid (filamentous polymer) of Ure2p. Overproduction of Btn2p or Cur1p cure this prion, and Btn2p colocalizes with Ure2p aggregates in the curing process. We show that most [URE3] variants arising in the absence of Btn2p and Cur1p are cured by restoring the normal levels of these two proteins. The variants cured by normal levels of Btn2p and Cur1p are those with low seed number, a low number of heritable particles, consistent with seed aggregation, and sequestration as the curing mechanism. These Btn2p and Cur1p antiprion proteins are members of the Hook protein family, metazoan members of which have roles in microtubule-dependent movement of organelles and aggregates in the cell.
Measurement of endo-α-mannosidase activity using a fluorescently labeled oligosaccharide derivative
Authors: Iwamoto Shogo , Kasahara Yuta , Kamei Ken-ichi , Seko Akira , Takeda Yoichi , Ito Yukishige , Matsuo Ichiro 
Published: June 2014

Abstract
Endo-α-mannosidase, a GH99-family glycoside hydrolase, cleaves α-mannoside linkages with glucose residues. This enzyme is proposed to play a critical role in N-glycan processing for deglucosylation. To measure endo-α-mannosidase activity, we synthesized a fluorescently labeled tetrasaccharide derivative (Glcα1-3Manα1-2Manα1-2Manα1-O–C3H6–NH-Dansyl) in a stereocontrolled manner. The tetrasaccharide skeleton was prepared by step-wise coupling using mannose donors 4 and 7. The 1,2-cis α-glycosidic linkage on the non-reducing end of the glucose residue was constructed by inversion of the stereochemistry of the C-2 hydroxyl group in the α-mannose residue. Finally, the dansyl group was introduced at the reducing end via an aminopropyl linker. This probe successfully measured endo-α-mannosidase activity.
Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability
Authors: Ochiai Akihito , Sugai Hiroshi , Harada Kazuki , Tanaka Seiya , Ishiyama Yohei , Ito Kosuke , Tanaka Takaaki , Uchiumi Toshio , Taniguchi Masayuki , Mitsui Toshiaki 
Published: June 2014

Abstract
AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.
Optimal Directions for Directional Distance Functions: An Exploration of Potential Reductions of Greenhouse Gases
Authors: Hampf Benjamin , Krüger Jens J. 
Published: June 2014

AbstractThis article explores the reduction potential of greenhouse gases for major pollution‐emitting countries of the world using nonparametric productivity measurement methods and directional distance functions. In contrast to the existing literature, we apply optimization methods to endogenously determine optimal directions for the efficiency analysis. These directions represent the compromise of output enhancement and emissions reduction. The results show that for reasonable directions the adoption of best practices would lead to sizable emission reductions in a range of approximately 20% compared with current levels.
DAFGA: diversity analysis of functional gene amplicons
Authors: Kim Yongkyu , Liesack Werner 
Published: June 2014

AbstractSummary: Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME.Availability and implementation: DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA .Contact: yongkyu.kim@mpi-marburg.mpg.de
Identifying international market opportunities: the case of Italian companies in Egypt
Authors: Caiazza Rosa 
Published: June 2014

Purpose
– The purpose of this paper is to investigate the differences and relations between Italy and Egypt and to identify main risks and opportunities for Italian firms that aim to operate in Egypt.

Design/methodology/approach
– The paper presents a qualitative analysis realized through some semi-structured questionnaire and a case study.

Findings
– High cultural difference, legal uncertainty and administrative instability are main problems in internationalization process of Italian firms in Egypt. Despite these problems, Italian firms still invest in Egypt because of economic opportunities and possible interactions.

Originality/value
– While interest towards Southern Mediterranean countries is increasing, there is little written on this topic. This article aims to fill the gap in literature on internationalization in emerging markets.
How not to punish your neighbour
Authors: Yang Hsu Becky 
Published: June 2014

Purpose– The paper aims to better understand why borrowers do not sanction one another in group-lending microfinance programmes.Design/methodology/approach– The paper utilises interviews conducted in 16 villages in Western China. The data were complemented by ethnographic fieldwork of an NGO in the region.Findings– The paper confirms the relevance to microfinance of existing literature showing that punishing others is costly, so people tend to wait for others to do it. It also reveals the existence of particularistic metanorms – norms of sanctioning that focus on whom one can and cannot punish. Additionally, it shows that people may punish according to whether they believe others are punishing.Research limitations/implications– The results are not immediately generalisable to all group-lending programmes.Originality/value– Fieldwork in rural China is difficult to conduct. Although cultural and social patterns are known to be important in development work, little is known about how it affects microfinance.
Factors affecting quality in the Jordanian housing sector
Authors: J. Sweis Rateb , O. Shanak Rifat , Abu El Samen Amjad , Suifan Taghrid 
Published: June 2014

Purpose
– The purpose of this study is to measure the perceptions of both architects and contractors regarding the factors affecting quality in the Jordanian housing sector.

Design/methodology/approach
– Twenty quality factors were identified from the literature and ranked by respondents. Next, the weighted indices for importance and frequency of quality variables were calculated. The quality variables were ranked according to their severity index. Finally, the principal component and factor analysis methodology was employed to arrive at the most prominent factors.

Findings
– Major factors affecting quality were human resource management, customer satisfaction, uses of technology and supplier management. Although both samples of architects and contractors chose the factor “uses of technology” as the common factor, the t-test showed statistically significant differences in the means of both samples.

Originality/value
– This study’s findings build on prior research conducted in different countries. The major factors identified in this study are compared to other similar studies’ findings, thereby adding to the available literature on factors affecting quality in the housing sector in developing countries.
Quick detection of NFC vulnerability
Authors: Azhari Firman 
Published: June 2014

Purpose
– The purpose of this research is to explain particular implementation weaknesses of near field communication (NFC) systems done by several institutions which apply for critical purposes and provide practical solutions.

Design/methodology/approach
– This research is done by literature studies of previous findings in NFC security, observations of some existing implemented systems and experimentations to provide practical solutions.

Findings
– Unintentional lack of security protection of the NFC cards and tags by some card issuers make them a vulnerable target. The outcomes of this research are proposed solutions on methods to quickly detect vulnerability in NFC tags using an Android-based mobile application. Another solution involves the assembly of a detection device using the portable, low power and powerful Raspberry Pi to analyze the NFC tags or cards and NFC reader vulnerabilities.

Research limitations/implications
– This research is conducted in Indonesia; therefore, the results and solutions may lack generalizability. However, the findings may occur in other countries which newly apply NFC technology.

Practical implications
– System implementer should become more aware about the security issue of old NFC tags like MIFARE Classic. Price should be considered after tag security. People also need to be aware of identity or money theft using NFC-enabled smartphones, as many identity cards and electronic money are now relying on NFC technology.

Social implications
– People also need to be aware of identity or money theft using NFC-enabled smartphones, as many identity cards and electronic money are now relying on NFC technology.

Originality/value
– This research fulfills an identified need to evaluate the security aspect of a system that uses NFC as one of the main technologies. The results and solutions also provides cheap, easy and practical tools to analyze NFC security.
Ontology in information studies: without, within, and withal knowledge management
Authors: Wendell Compton Bradley 
Published: June 2014

Purpose– Ontology in information studies consists of antinomic conceptions, methodologies, and emphases in both application and philosophizing. A comprehensive understanding of ontology in information studies can be achieved by employing Slavoj Žižek's parallax view which holds that reality is not only best understood by articulating conflicting perspectives on a particular phenomenon, but that given phenomena are fundamentally constrained by incommensurable perspectives that must be acknowledged accordingly. The paper aims to discuss these issues.Design/methodology/approach– Ontology in information studies, including computational ontology development, is analyzed using critical information theory based on Heideggerian, poststructuralist, and anti-postmodern philosophy. The discussion is framed by Žižek's notion of the parallax Real.Findings– A complete understanding of ontology in information studies that does not reduce ontology to a totalizing theory or sequester notions of ontology to conflicting, unrelated discourses, necessarily accepts articulating the alterity between differing ontological views as the means by which one can best allude to what “ontology in information studies really is.”Originality/value– This paper presents a comprehensive analysis of radically different ontological perspectives on the nature of reality with respect to digital technology.
HIVEing: the effect of a semantic web technology on inter-indexer consistency
Authors: White Hollie , Willis Craig , Greenberg Jane 
Published: June 2014

Purpose
– The purpose of this paper is to examine the effect of the Helping Interdisciplinary Vocabulary Engineering (HIVE) system on the inter-indexer consistency of information professionals when assigning keywords to a scientific abstract. This study examined first, the inter-indexer consistency of potential HIVE users; second, the impact HIVE had on consistency; and third, challenges associated with using HIVE.

Design/methodology/approach
– A within-subjects quasi-experimental research design was used for this study. Data were collected using a task-scenario based questionnaire. Analysis was performed on consistency results using Hooper's and Rolling's inter-indexer consistency measures. A series of t-tests was used to judge the significance between consistency measure results.

Findings
– Results suggest that HIVE improves inter-indexing consistency. Working with HIVE increased consistency rates by 22 percent (Rolling's) and 25 percent (Hooper's) when selecting relevant terms from all vocabularies. A statistically significant difference exists between the assignment of free-text keywords and machine-aided keywords. Issues with homographs, disambiguation, vocabulary choice, and document structure were all identified as potential challenges.

Research limitations/implications
– Research limitations for this study can be found in the small number of vocabularies used for the study. Future research will include implementing HIVE into the Dryad Repository and studying its application in a repository system.

Originality/value
– This paper showcases several features used in HIVE system. By using traditional consistency measures to evaluate a semantic web technology, this paper emphasizes the link between traditional indexing and next generation machine-aided indexing (MAI) tools.
Distance-to-default measures and determinants for systemically important financial institutions
Authors: A. Schenck Natalya 
Published: June 2014

Purpose
– This study aims to compare two distance-to-default methods, data-transformed maximum likelihood estimation and “naïve”, that are suitable for financial institutions. The links between these measures and asset size, Tier 1 and Tier 2 capital ratios, non-performing assets and operating efficiency have been examined and an alternative default risk measure has been introduced. Most of the market-based distance-to-default measures are not appropriate for banks due to their unique debt structure.

Design/methodology/approach
– The author has compared two distance-to-default measures and has identified their accounting determinants using Pearson’s correlation and regressions with clustered standard errors. The sample of the US-based systemically important financial institutions covers the period from 2000 to 2010.

Findings
– Non-performing assets and operating efficiency are found to be statistically and economically significant determinants of both distance-to-default measures. Tier 1 capital ratio is not a significant indicator of default risk.

Practical implications
– The results emphasize the importance of using a combination of market-based default risk measures and accounting ratios in default prediction models for the financial institutions.

Originality/value
– This paper identifies accounting determinants of two distance-to-default measures for large financial institutions, before and during the 2008 financial crisis. It introduces a spread between two measures as an alternative default risk indicator.
Knowledge sharing of academic staff
Authors: Wei Chong Chin , Yen Yuen Yee , Chew Gan Geok 
Published: June 2014

Purpose– The aim of this study is to build upon Jainet al.'s (2007) work by investigating the knowledge-sharing barriers and strategies of academic staff in public and private universities in Malaysia which have received relatively little research attention to date.Design/methodology/approach– A survey of 502 questionnaires was collected on both public and private universities in Malaysia. Data were analysed using SPSS.Findings– The overall findings show that private universities are more effective and are more willing to share knowledge. Linking knowledge sharing with non-monetary rewards and fair performance appraisals are strongly recommended in private universities, while monetary rewards, recognitions, publication of knowledge on websites and newsletters and the use of appropriate technology tools and systems are strongly recommended in public universities.Practical implications– Top management in Malaysian public and private universities must play their role and put in more effort to ensure academics have the proper platform and support to share their knowledge.Originality/value– This study is perhaps one of the first to address the comparison between knowledge sharing among lecturers in private and public universities in Malaysia.
Examining the incentives and motivations for research-based legislation in Uganda
Authors: Lugya Fredrick Kiwuwa 
Published: June 2014

Purpose
– The purpose of the paper is to discuss the factors that would increase or decrease the prospects to use research evidence in legislation in a developing country.

Design/methodology/approach
– Both qualitative and quantitative research methods were used to identify the gaps in ability to utilise research evidence among policymakers. A combination of expert analysis of five policy brief formats, 13 self-administered semi-structured interviews with policymakers, focus group discussion and literature analysis informed data collection.

Findings
– The incentives and motivations for research-based legislation are classified into three categories: those that concern legislators and researchers, those that concern legislators only and those that concern researchers only.

Originality/value
– The work discusses the need for policymakers to make decisions based on facts. The findings are a reflection of a long interaction the author had with policymakers and researchers in Uganda.
Fashion globally
Authors: G. Fowler Jie , H. Reisenwitz Timothy , R. Fowler Aubrey 
Published: June 2014

Purpose– The aim of this study is to focus on consumers’ responses towards visual fashion ideal in hybrid magazine advertisements from a cross-cultural and generational perspective.Design/methodology/approach– This exploratory qualitative focus group study showed a set of validated advertisements to 64 female participants. Half of the sample was from the USA, the other half was from China. To examine generational differences, the interviewees were split by age in each group: half of the participants were between 18 and 34, and half were between the age of 45 and 65 years.Findings– Both Chinese and American target audiences viewed the trendy advertisements with an aspirational eye in which the advertisement was interpreted as representing an ideal self to which they aspired, one that they wanted to achieve but, for some reason(s), were not capable of achieving at the time. However, the degree of aspiration varied for Chinese and American audiences.Research limitations/implications– Because of the chosen research approach, the research results may lack generalizability. Therefore, future research may use survey and experimental research approaches.Practical implications– International marketers may need to design advertisements with more “realistic” imagery, while keeping the idealized Western style in Chinese advertising. Advertisers should also be cognizant of intergenerational influences in the Chinese market; many young Chinese women still rely on their mothers regarding fashion purchase decisions.Originality/value– This paper fills a need to understand both the similarities and the differences in marketing communications across cultures.