bluuebunny/crossref_metadata_2025_split huggingface dataset:
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
Authors: Li Jing-Woei , Wan Raymond , Yu Chi-Shing , Co Ngai Na , Wong Nathalie , Chan Ting-Fung 
Published: January 2013

Abstract
Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral–human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.
Availability: VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
Contact: tf.chan@cuhk.edu.hk
Supplementary information: Supplementary data are available at Bioinformatics Online
miRCancer: a microRNA–cancer association database constructed by text mining on literature
Authors: Xie Boya , Ding Qin , Han Hongjin , Wu Di 
Published: January 2013

Abstract
Motivation: Research interests in microRNAs have increased rapidly in the past decade. Many studies have showed that microRNAs have close relationships with various human cancers, and they potentially could be used as cancer indicators in diagnosis or as a suppressor for treatment purposes. There are several databases that contain microRNA–cancer associations predicted by computational methods but few from empirical results. Despite the fact that abundant experiments investigating microRNA expressions in cancer cells have been carried out, the results have remain scattered in the literature. We propose to extract microRNA–cancer associations by text mining and store them in a database called miRCancer.
Results: The text mining is based on 75 rules we have constructed, which represent the common sentence structures typically used to state microRNA expressions in cancers. The microRNA–cancer association database, miRCancer, is updated regularly by running the text mining algorithm against PubMed. All miRNA–cancer associations are confirmed manually after automatic extraction. miRCancer currently documents 878 relationships between 236 microRNAs and 79 human cancers through the processing of &gt;26 000 published articles.
Availability: miRCancer is freely available on the web at http://mircancer.ecu.edu/
Contact: dingq@ecu.edu
Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
Authors: Busby Michele A. , Stewart Chip , Miller Chase A. , Grzeda Krzysztof R. , Marth Gabor T. 
Published: January 2013

Abstract
Motivation: A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?
Results: Scotty is an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives. This design can be based on data available from either pilot samples or publicly available datasets.
Availability: Scotty can be freely accessed on the web at http://euler.bc.edu/marthlab/scotty/scotty.php
Contact: gabor.marth@bc.edu
Supplementary information: Supplementary data are is available at Bioinformatics online.
Effects of the Insect Growth Regulators Novaluron and Diflubenzuron on the Brown Marmorated Stink Bug
Authors: Kamminga Katherine L. , Kuhar Thomas P. , Wimer Adam , Herbert D. Ames 
Published: January 2013

The brown marmorated stink bug (BMSB), Halyomorpha halys (Stål), is an invasive pest from China that causes economic damage to field crops, vegetables, and tree fruit. Due to its destructive potential, applications of broad-spectrum insecticides have escalated. Researchers are trying to identify options for controlling BMSB that have less of a negative impact on non-target species. Chitin biosynthesis inhibitors are more selective than the commonly used pyrethroids and organophosphates. They are active on the larval stage of the insect and are reported as having sublethal effects such as reducing adult fecundity. In our studies, bioassays were completed with chitin biosynthesis inhibitors novaluron and diflubenzuron to evaluate the effectiveness of these insecticides on adult mortality, nymphal growth, adult fecundity, and egg hatch. Our data indicate that treatments of novaluron at 362.2 g ai/ha or diflubenzuron at 280.2 g ai/ha effectively controlled BMSB nymphs. However, the insecticides were not effective at reducing egg hatch, adult fecundity, or adult life span. If novaluron or diflubenzuron are used in agriculture for BMSB control, then the nymphal stage should be targeted. Accepted for publication 9 November 2012. Published 12 December 2012.
First Report of Pythium dissotocum Affecting Cilantro in Hydroponic Systems in Puerto Rico
Authors: Romero G. , de Jensen C. Estévez , Palmateer A. J. 
Published: January 2013

Pythium dissotocum was detected on cilantro in hydroponic systems in Puerto Rico. Isolates from stem lesions were inoculated in cilantro ‘Lonestar’ and in pea ‘Sugar Baby,’ producing soft rot 21 and 15 days after inoculation, respectively. The pathogen was re-isolated from diseased plants and it was confirmed to be Pythium dissotocum by PCR. Accepted for publication 5 December 2012. Published 14 December 2012.
Sunflower Diseases Remain Rare in California Seed Production Fields Compared to North Dakota
Authors: Gulya Thomas J. , Rooney-Latham Suzanne , Miller Jean S. , Kosta Kathleen , Murphy-Vierra Colleen , Larson Carrie , Vaccaro William , Kandel Hans , Nowatzki John F. 
Published: January 2013

The majority of United States sunflower production is in seven Midwestern states, but hybrid planting seed is almost exclusively produced in California. Due to the lack of summer rains and furrow irrigation, California-produced seed is relatively disease free and thus it regularly meets phytosanitary restrictions imposed by many countries. For the 15-year period from 1997 to 2011, 7231 seed fields in northern California were inspected and samples processed at the state diagnostic laboratory (California Department of Food and Agriculture). Rust (Puccinia helianthi) was the most prevalent quarantine disease, found in 4.3% of fields. Stalk rot (Sclerotinia sclerotiorum) and downy mildew (Plasmopara halstedii) were the only other quarantine pathogens observed, found in 2.6% and 0.5% of the 7231 fields, respectively. Many sunflower pathogens have never been recorded in California, including Phoma macdonaldii, Phomopsis helianthi, or any virus. North Dakota, the state with the highest US sunflower production, had quarantine pathogens in 88% of 1263 fields surveyed from 1995 to 2011. Phoma macdonaldii, Sclerotinia sclerotiorum, Puccinia helianthi, Phomopsis helianthi, Plasmopara halstedii, and Verticillium dahliae were recorded in 62, 54, 37, 33, 14, and 12%, respectively, of North Dakota fields. Accepted for publication 5 November 2012. Published 14 December 2012.
incurvata13, a Novel Allele of AUXIN RESISTANT6, Reveals a Specific Role for Auxin and the SCF Complex in Arabidopsis Embryogenesis, Vascular Specification, and Leaf Flatness
Authors: Esteve-Bruna David , Pérez-Pérez José Manuel , Ponce María Rosa , Micol José Luis 
Published: January 2013

Abstract
Auxin plays a pivotal role in plant development by modulating the activity of SCF ubiquitin ligase complexes. Here, we positionally cloned Arabidopsis (Arabidopsis thaliana) incurvata13 (icu13), a mutation that causes leaf hyponasty and reduces leaf venation pattern complexity and auxin responsiveness. We found that icu13 is a novel recessive allele of AUXIN RESISTANT6 (AXR6), which encodes CULLIN1, an invariable component of the SCF complex. Consistent with a role for auxin in vascular specification, the vascular defects in the icu13 mutant were accompanied by reduced expression of auxin transport and auxin perception markers in provascular cells. This observation is consistent with the expression pattern of AXR6, which we found to be restricted to vascular precursors and hydathodes in wild-type leaf primordia. AXR1, RELATED TO UBIQUITIN1-CONJUGATING ENZYME1, CONSTITUTIVE PHOTOMORPHOGENIC9 SIGNALOSOME5A, and CULLIN-ASSOCIATED NEDD8-DISSOCIATED1 participate in the covalent modification of CULLIN1 by RELATED TO UBIQUITIN. Hypomorphic alleles of these genes also display simple venation patterns, and their double mutant combinations with icu13 exhibited a synergistic, rootless phenotype reminiscent of that caused by loss of function of MONOPTEROS (MP), which forms an auxin-signaling module with BODENLOS (BDL). The phenotypes of double mutant combinations of icu13 with either a gain-of-function allele of BDL or a loss-of-function allele of MP were synergistic. In addition, a BDL:green fluorescent protein fusion protein accumulated in icu13, and BDL loss of function or MP overexpression suppressed the phenotype of icu13. Our results demonstrate that the MP-BDL module is required not only for root specification in embryogenesis and vascular postembryonic development but also for leaf flatness.
The Arabidopsis Rho of Plants GTPase AtROP6 Functions in Developmental and Pathogen Response Pathways
Authors: Poraty-Gavra Limor , Zimmermann Philip , Haigis Sabine , Bednarek Paweł , Hazak Ora , Stelmakh Oksana Rogovoy , Sadot Einat , Schulze-Lefert Paul , Gruissem Wilhelm , Yalovsky Shaul 
Published: January 2013

Abstract
How plants coordinate developmental processes and environmental stress responses is a pressing question. Here, we show that Arabidopsis (Arabidopsis thaliana) Rho of Plants6 (AtROP6) integrates developmental and pathogen response signaling. AtROP6 expression is induced by auxin and detected in the root meristem, lateral root initials, and leaf hydathodes. Plants expressing a dominant negative AtROP6 (rop6DN) under the regulation of its endogenous promoter are small and have multiple inflorescence stems, twisted leaves, deformed leaf epidermis pavement cells, and differentially organized cytoskeleton. Microarray analyses of rop6DN plants revealed that major changes in gene expression are associated with constitutive salicylic acid (SA)-mediated defense responses. In agreement, their free and total SA levels resembled those of wild-type plants inoculated with a virulent powdery mildew pathogen. The constitutive SA-associated response in rop6DN was suppressed in mutant backgrounds defective in SA signaling (nonexpresser of PR genes1 [npr1]) or biosynthesis (salicylic acid induction deficient2 [sid2]). However, the rop6DN npr1 and rop6DN sid2 double mutants retained the aberrant developmental phenotypes, indicating that the constitutive SA response can be uncoupled from ROP function(s) in development. rop6DN plants exhibited enhanced preinvasive defense responses to a host-adapted virulent powdery mildew fungus but were impaired in preinvasive defenses upon inoculation with a nonadapted powdery mildew. The host-adapted powdery mildew had a reduced reproductive fitness on rop6DN plants, which was retained in mutant backgrounds defective in SA biosynthesis or signaling. Our findings indicate that both the morphological aberrations and altered sensitivity to powdery mildews of rop6DN plants result from perturbations that are independent from the SA-associated response. These perturbations uncouple SA-dependent defense signaling from disease resistance execution.
Key CSR dimensions for the food chain
Authors: Forsman‐Hugg Sari , Katajajuuri Juha‐Matti , Riipi Inkeri , Mäkelä Johanna , Järvelä Katja , Timonen Päivi 
Published: January 2013

PurposeThis paper aims to identify and define the content of corporate social responsibility (CSR) for the food chain.Design/methodology/approachA qualitative research approach was applied in the study, based on participatory and case study research methodologies. The study drew on three different case food products and their supply chains: rye bread, broiler chicken products and margarine. The content of CSR was built through participatory workshops, the aim of which was to elicit the ideas of different stakeholder groups.FindingsThe study identified seven key dimensions of food chain CSR: environment, product safety, corporate nutritional responsibility, occupational welfare, animal health and welfare, local market presence and economic responsibility.Originality/valueThe results provide food and agribusiness companies with a better understanding of core CSR issues and their relevance in complex chains and networks. This may encourage the companies to promote their activities in a more responsible and sustainable direction and offer elements to build sustainable business cases. In addition, the results may indicate a change towards broader understanding of what is meant by corporate social responsibility.
Disclosure strategies regarding ethically questionable business practices
Authors: Aktar Ipek 
Published: January 2013

PurposeThe author's objective is to reveal the consumer responses to information disclosure strategies regarding controversial ethical issues.Design/methodology/approachThe author is interested in how voluntary disclosure of questionable business practices by chocolate manufacturers regarding child labor exploitation at cocoa plantations influences consumer behavior. A total of 120 students participated in an experimental study in which the author manipulated awareness of ethical issues in the chocolate industry and corporate disclosure strategy. The author measured willingness to pay (WTP) and consumer perceptions about the firm's commitment to corporate social responsibility.FindingsThe study found that voluntary disclosure of unethical business practices by a firm was not damaging in terms of consumer perceptions. When public awareness was limited, disclosing participation in unethical behavior did not influence WTP for the firm's products. When public awareness was high, disclosing this negative information is even more beneficial than no disclosure and generates similar responses to including only positive elements in the firm's communication, provided that the firm commits to eliminate its unethical practices.Research limitations/implicationsVoluntary negative social disclosure will not hurt a firm's performance in terms of sales, given the disclosure is transparent and this suggests a credible commitment to improve its practices regarding the issue.Originality/valueThe author investigates the optimal strategy for a firm to disclose ethical infractions. She demonstrates that being open about them does not necessarily damage a firm's reputation and suggests under which conditions this is the case.
Does hope moderate the impact of job burnout on frontline bank employees’ in‐role and extra‐role performances?
Authors: Yavas Ugur , Babakus Emin , Karatepe Osman M. 
Published: January 2013

PurposeThe purpose of this paper is to examine whether hope as a personal resource moderates the relationships between job burnout and frontline bank employees’ in‐role and extra‐role performances.Design/methodology/approachFrontline employees of several banks throughout the Turkish Republic of Northern Cyprus serve as the study setting.FindingsResults of the study reveal that burnout is significantly related to frontline employees’ in‐role and extra‐role performances and that hope moderates these relationships.Research limitations/implicationsThough common method bias does not appear to be a potential threat to the magnitude of relationships, in future studies using multiple‐informants (e.g. performance data from supervisors or customers) would be useful. In addition, replication studies among front employees in other countries would be beneficial for further generalizations.Practical implicationsManagement of the banks should consider the personality traits of the individuals during the selection process. This is important, since hope reduces the detrimental impact of burnout on performance outcomes. Management should also retain employees high in hope, because such employees can create a positive work environment and serve as role models to their colleagues with low hope.Originality/valueEmpirical research in the banks services literature pertaining to the effect of hope on extra‐role performance and hope as a moderator of the impact of burnout on in‐role and extra‐role performances is scarce. Therefore, this study adds to the literature in this research stream by investigating the aforementioned relationships.
A 3D approach to first year English education
Authors: Zeegers Margaret 
Published: January 2013

PurposeThe purpose of this paper is to explore the suggestive possibilities of an approach to undergraduate English teacher education that the author has called the 3D Approach – Develop professional knowledge, Display professional knowledge, Disseminate professional knowledge – in relation to a number of groups of first year pre‐service teachers (PSTs) engaging the teaching and learning materials of their English education course.Design/methodology/approachThe paper examines ways in which this approach has been assessed by the PSTs themselves, constructing this as an expression of their lived experience as PSTs. The author draws on Vygotsky's concept of the Zone of Proximal Development, initiates a systematic and orchestrated program of explicit scaffolding of first year PST learning and draws on University‐generated student assessment of their courses, focus groups and individual interviews to investigate ways in which the 3D approach may be considered as enhancing first year PST learning.FindingsPSTs' own informed evaluations of their own developing knowledge have made visible the teaching and learning that they have engaged and articulated. What the author outlines in this paper is not a “Eureka” moment for first year PSTs, but it is the result of careful scholarly considerations of what careful scholarly considerations by first years in Education courses may engage. For this cohort of PSTs, and for the author, it is a particular form of engagement with pedagogy. It is a pedagogy for teachers, part of active engagement on the part of the teacher and the learner, producing knowledge together.Research limitations/implicationsLack of generalisability from case study research may be considered as a limitation, but the author would argue that it is the details thrown up for careful examination in a case study which may serve to inform professional discussion and debate.Practical implicationsNegative press of inadequate teachers emerging from universities, with their specious claims will not progress reasoned discussion; research on how the PSTs are themselves taught and how they develop as professionals will. PSTs' own informed evaluations of their own developing knowledge will go some way towards enabling this to happen. This sort of research opens up possibilities for starting with the right sort of questions, a shift from asking the wrong sort of questions, which the author would argue is that sort on which the media are basing their opinion pieces.Social implicationsContinuing public discussions, usually conducted in and by the media, about teacher quality, particularly as this tends to be tied to notions of teacher pay, indicates a wider social concern about the need for quality teachers. This sort of social concern is also a major concern for teacher educators, and is to be addressed as such. This paper addresses some of those concerns.Originality/valueThe paper engages issues about teacher education raised publicly in the media and ties these to the more private domain of university practice in a given teacher education course.
Microwave permittivity and permeability of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 thick films using superstrate method
Authors: Kashid P.B. , Kulkarni D.C. , Surve V.G. , Puri Vijaya 
Published: January 2013

PurposeThe purpose of this paper is to study thickness dependent variation in microwave properties of the MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films and enhancement of power efficiency of Ag thick film EMC patch antenna.Design/methodology/approachX‐band microwave properties of the MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films were measured by superstrate technique using Ag thick film EMC patch antenna as the resonant element. The complex permittivity and permeability of these thick films were also measured by this technique. The microwave response of the EMC patch, complex permeability and permittivity of Mg0.8Mn0.1Al0.1Zn0.8Fe1.2O4 and Mg0.9Al0.1Zn0.8Fe1.2O4 thick films and their thickness dependency were investigated.FindingsThe XRD patterns reveal the cubic spinel crystal system was obtained for both compositions. The crystallite size obtained was 134.68 nm for Mg0.8Mn0.1Al0.1Zn0.8Fe1.2O4 and 155.99 nm for Mg0.9Al0.1Zn0.8Fe1.2O4 The superstrate technique has been used successfully to evaluate the complex permittivity and permeability of the ferrite thick films in the X band. The EMC patch also show thickness and composition dependent frequency agility and enhancement of power efficiency.Originality/valueThe complex permeability of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films measured by superstrate technique is reported in this paper. The superstrate of MgxMn(0.9−x)Al0.1Zn0.8Fe1.2O4 (x=0.8, 0.9) thick films makes the Ag thick film EMC patch antenna frequency agile and power amplification is obtained.
Mobile cloud computing: state of the art and outlook
Authors: Dihal Soebhaash , Bouwman Harry , de Reuver Mark , Warnier Martijn , Carlsson Christer 
Published: January 2013

PurposeThe purpose of this conceptual paper is to explore the meaning of cloud computing for mobile communication. The paper answers the question “what is mobile cloud computing?” and how is it related to the generic cloud computing concept?Design/methodology/approachThis is an explanatory conceptual paper, based on literature review and exploring potential use cases, focused on the use of mobile cloud for service, platform or infrastructure access. The authors exclude the discussion of the traditional cloud concept in back office processes of telecom operators, and service providers.FindingsWhere cloud computing is focused on pooling of resources, mobile technology is focused on pooling and sharing of resources locally enabling alternative use cases for mobile infrastructure, platforms and service delivery. The paper discusses relevant concepts and offers examples of use cases.Research limitations/implicationsThe value of mobile cloud solutions is not yet explicit, but needs further attention. Research should focus on the relation between mobile cloud computing, platforms and eco systems. From a user perspective the willingness to share pooled resources needs further attention.Practical implicationsMobile cloud computing offers the possibility that disruptive applications might impact the mobile eco system; reinforcing or weakening business models of core players like handset providers, telecom operators, and service providers.Originality/valueA lot of attention is paid to cloud computing and to platform discussions, papers on mobile cloud are scarce. This paper offers the current state of the art and a research outlook.