bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunity to Bovine Herpesvirus 1: I. Viral lifecycle and innate immunity
Authors: Levings Randall L. , Roth James A. 
Published: June 2013

AbstractBovine herpesvirus 1 (BHV-1) causes a variety of diseases and is globally distributed. It infects via mucosal epithelium, leading to rapid lytic replication and latent infection, primarily in sensory ganglia. Large amounts of virus can be excreted by the host on primary infection or upon recrudescence of latent infection, resulting in disease spread. The bovine immune response to BHV-1 is rapid, robust, balanced, and long-lasting. The innate immune system is the first to respond to the infection, with type I interferons (IFNs), inflammatory cytokines, killing of infected host cells, and priming of a balanced adaptive immune response. The virus possesses a variety of immune evasion strategies, including inhibition of type I IFN production, chemokine and complement binding, infection of macrophages and neutrophils, and latency. BHV-1 immune suppression contributes to the severity of its disease manifestations and to the bovine respiratory disease complex, the leading cause of cattle death loss in the USA.
Synthesis and tribological properties of hexagonal NbSe2 nanoplates
Authors: Sun Jianrong , Tang Guogang , Li Changsheng , Ji Xiaorui , Liang Wei , Tang Hua 
Published: June 2013

Hexagonal NbSe2 nanoplates have been successfully prepared via solid‐state reaction by a ball‐milled mixture of Nb and Se powders. The as‐prepared products are characterised by an X‐ray diffractometer, scanning electron microscopy and transmission electron microscopy. The results showed that the NbSe2 nanoplates have a hexagonal structure and the sizes of nanoplates are about 1 μm in diameter and 100–300 nm in thickness. The tribological properties of hexagonal NbSe2 nanoplates as a lubrication additive in paraffin base oil were investigated by a UMT‐2 ball‐on‐plate friction and wear tester. The wear scars were measured by a VEECO WYKO NT1100 non‐contact optical profile testing instrument. The study shows that under determinate conditions, the friction coefficient of the base oil containing NbSe2 nanoplates is lower than that of pure base oil, and it decreases with the increase of mass percent of NbSe2 powders when its proportion is lower than 2 wt%.
Do Beaver Dams Impede the Movement of Trout?
Authors: Lokteff Ryan L. , Roper Brett B. , Wheaton Joseph M. 
Published: June 2013

AbstractDams created by North American beavers Castor canadensis (hereafter, “beavers”) have numerous effects on stream habitat use by trout. Many of these changes to the stream are seen as positive, and many stream restoration projects seek either to reintroduce beavers or to mimic the habitat that they create. The extent to which beaver dams act as movement barriers to salmonids and whether successful dam passage differs among species are topics of frequent speculation and warrant further research. We investigated beaver dam passage by three trout species in two northern Utah streams. We captured 1,375 trout above and below 21 beaver dams and fitted them with PIT tags to establish whether fish passed the dams and to identify downstream and upstream passage; 187 individual trout were observed to make 481 passes of the 21 beaver dams. Native Bonneville Cutthroat Trout Oncorhynchus clarkii utah passed dams more frequently than nonnative Brown Trout Salmo trutta and nonnative Brook Trout Salvelinus fontinalis. We determined that spawn timing affected seasonal changes in dam passage for each species. Physical characteristics of dams, such as height and upstream location, affected the passage of each species. Movement behaviors of each trout species were also evaluated to help explain the observed patterns of dam passage. Our results suggest that beaver dams are not acting as movement barriers for Bonneville Cutthroat Trout or Brook Trout but may be impeding the movements of invasive Brown Trout.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations
Authors: Chowdhury Salim Akhter , Shackney Stanley E. , Heselmeyer-Haddad Kerstin , Ried Thomas , Schäffer Alejandro A. , Schwartz Russell 
Published: June 2013

Abstract
Motivation: Development and progression of solid tumors can be attributed to a process of mutations, which typically includes changes in the number of copies of genes or genomic regions. Although comparisons of cells within single tumors show extensive heterogeneity, recurring features of their evolutionary process may be discerned by comparing multiple regions or cells of a tumor. A useful source of data for studying likely progression of individual tumors is fluorescence in situ hybridization (FISH), which allows one to count copy numbers of several genes in hundreds of single cells. Novel algorithms for interpreting such data phylogenetically are needed, however, to reconstruct likely evolutionary trajectories from states of single cells and facilitate analysis of tumor evolution.
Results: In this article, we develop phylogenetic methods to infer likely models of tumor progression using FISH copy number data and apply them to a study of FISH data from two cancer types. Statistical analyses of topological characteristics of the tree-based model provide insights into likely tumor progression pathways consistent with the prior literature. Furthermore, tree statistics from the resulting phylogenies can be used as features for prediction methods. This results in improved accuracy, relative to unstructured gene copy number data, at predicting tumor state and future metastasis.
Availability: Source code for software that does FISH tree building (FISHtrees) and the data on cervical and breast cancer examined here are available at ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees.
Contact: sachowdh@andrew.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein threading using context-specific alignment potential
Authors: Ma Jianzhu , Wang Sheng , Zhao Feng , Xu Jinbo 
Published: June 2013

Abstract
Motivation: Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related.
Results: We present a novel context-specific alignment potential for protein threading, including alignment and template selection. Our alignment potential measures the log-odds ratio of one alignment being generated from two related proteins to being generated from two unrelated proteins, by integrating both local and global context-specific information. The local alignment potential quantifies how well one sequence residue can be aligned to one template residue based on context-specific information of the residues. The global alignment potential quantifies how well two sequence residues can be placed into two template positions at a given distance, again based on context-specific information. By accounting for correlation among a variety of protein features and making use of context-specific information, our alignment potential is much more sensitive than the widely used context-independent or profile-based scoring function. Experimental results confirm that our method generates significantly better alignments and threading results than the best profile-based methods on several large benchmarks. Our method works particularly well for distantly related proteins or proteins with sparse sequence profiles because of the effective integration of context-specific, structure and global information.
Availability: http://raptorx.uchicago.edu/download/.
Contact: jinboxu@gmail.com
Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM
Authors: Sedgewick Andrew J. , Benz Stephen C. , Rabizadeh Shahrooz , Soon-Shiong Patrick , Vaske Charles J. 
Published: June 2013

Abstract
High-dimensional ‘-omics’ profiling provides a detailed molecular view of individual cancers; however, understanding the mechanisms by which tumors evade cellular defenses requires deep knowledge of the underlying cellular pathways within each cancer sample. We extended the PARADIGM algorithm (Vaske et al., 2010, Bioinformatics, 26, i237–i245), a pathway analysis method for combining multiple ‘-omics’ data types, to learn the strength and direction of 9139 gene and protein interactions curated from the literature. Using genomic and mRNA expression data from 1936 samples in The Cancer Genome Atlas (TCGA) cohort, we learned interactions that provided support for and relative strength of 7138 (78%) of the curated links. Gene set enrichment found that genes involved in the strongest interactions were significantly enriched for transcriptional regulation, apoptosis, cell cycle regulation and response to tumor cells. Within the TCGA breast cancer cohort, we assessed different interaction strengths between breast cancer subtypes, and found interactions associated with the MYC pathway and the ER alpha network to be among the most differential between basal and luminal A subtypes. PARADIGM with the Naive Bayesian assumption produced gene activity predictions that, when clustered, found groups of patients with better separation in survival than both the original version of PARADIGM and a version without the assumption. We found that this Naive Bayes assumption was valid for the vast majority of co-regulators, indicating that most co-regulators act independently on their shared target.
Availability: http://paradigm.five3genomics.com
Contact: charlie@five3genomics.com
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Squash vein yellowing virus Affecting Watermelon and Bitter Gourd in Puerto Rico
Authors: Acevedo V. , Rodrigues J. C. V. , de Jensen C. E. , Webster C. G. , Adkins S. , Wessel-Beaver L. 
Published: June 2013

In 2005, symptoms of watermelon vine decline (WVD) were observed on a 200-acre watermelon farm in Santa Isabel, on the south central coast of Puerto Rico. WVD symptoms included leaf curling, mosaics, and internode necrosis. In early growth stages of WVD, reduced vigor and plant stunting occurred. At flowering, symptoms progressed to necrosis and wilting of vines. A 2006 to 2007 survey demonstrated that fungal pathogens were not associated with the presence of WVD symptoms (3,4). By 2006, other watermelon fields were also affected. Field trials in 2007 and 2008 with insect-proof cages and insecticides suggested a role of whiteflies (Bemisia tabaci) in the transmission of a virus (3,4). Here, we report that watermelon and pumpkin plants were successfully infected in Puerto Rico by mechanical inoculation and through B. tabaci transmission assays, similarly to transmissions previously conducted in Florida with Squash vein yellowing virus (SqVYV) (1). In addition, plants of Cucurbita moschata exhibited vein clearing symptoms typical of SqVYV after mechanical inoculation with extracts from watermelon plants with WVD symptoms. In 2011, eight watermelon samples from plants exhibiting WVD syndrome were collected in Guánica, Santa Isabel, Juana Díaz, and Mayagüez, and two Momordica charantia samples were collected from Mayagüez. RNA was extracted from all 10 original samples, as well as from plants that were used in mechanical and vector transmission assays, using RNeasy Plant Mini Kit (Qiagen, Valencia, California), and all samples were found positive for SqVYV by reverse transcription-PCR, using previously described primers and methods (1,2). In all cases, a single ~1-kb PCR fragment was revealed, and PCR fragments from four samples were selected for direct sequencing. All sequences showed high levels (>99%) of nucleotide identity with SqVYV sequences from Florida (JF897989, JF897985, and JF897984). Sequences of the SqVYV CP gene from Puerto Rico were deposited in GenBank under accession numbers KC713961 to KC713964. To our knowledge, this is the first report of SqVYV in Puerto Rico associated with WVD syndrome in cucurbits, and thus has implications for management of viral diseases of watermelon in the Caribbean. This is also the first detection of SqVYV outside of the continental United States in both watermelon and a wild species, M. charantia (bitter gourd). References: (1) S. Adkins et al. Phytopathology 97:145, 2007. (2) S. Adkins et al. Plant Dis. 92:1119, 2008. (3) C. Estévez de Jensen et al. Phytopathology 98:S52, 2008. (4) L. Polanco-Florián. El marchitamiento súbito de la sandía [Citrullus lanatus (Thumb.) Matsum & Nakai]. M.S. thesis, University of Puerto Rico, Mayagüez, PR, 2009.
Bringing tropical forest biodiversity conservation into financial accounting calculation
Authors: Cuckston Thomas 
Published: June 2013

PurposeThis paper seeks to examine how the biodiversity comprising a tropical forest ecosystem is being protected as a result of having its conservation brought into financial accounting calculations by constructing a greenhouse gas emissions offset product to sell on the voluntary over‐the‐counter carbon markets.Design/methodology/approachThe research examines a single embedded case study of a biodiversity conservation project in Kenya. The resulting discussion builds upon the existing accounting and organisation studies literature regarding the construction of markets.FindingsWhilst the case examined does successfully bring tropical forest biodiversity conservation into the financial accounting calculations of the sellers and buyers of the offset product, via processes of objectification and singularisation, there are considerable accounting obstacles to constructing a calculative mechanism capable of achieving this on a global scale to facilitate financing of the conservation of all the world's remaining tropical forest biodiversity.Originality/valueThe paper contributes to the debate on accounting for biodiversity by examining market construction as a theoretical framework for turning the loss/conservation of biodiversity from an externality into an entity that is taken into account in organisations' calculations of profit and loss.
Biodiversity reporting in Denmark
Authors: van Liempd Dennis , Busch Jacob 
Published: June 2013

PurposeThis paper aims to suggest that companies have ethical reasons to report about biodiversity issues and to investigate whether companies act on these reasons by examining the extent of biodiversity reporting in Denmark.Design/methodology/approachFor the first purpose, desk research was conducted using consequentialist ethics, while for the second purpose, data were gathered from the 2009‐2011 annual reports, CSR‐type reports and homepages of 24 Danish large‐cap companies.FindingsPhilosophically, it is shown that biodiversity preservation and reporting is an ethical issue, even on the assumption that biodiversity does not possess intrinsic value. Empirically, it is shown that Danish companies score poorly overall, both quantitatively and qualitatively, with regards to reporting on biodiversity.Research limitations/implicationsEven though the importance of biodiversity can be justified on different assumptions, biodiversity reporting is under‐researched offering potential for future research on a globally important issue.Practical implicationsJustifying the preservation of biodiversity from an instrumental viewpoint might convince accounting audiences that are sceptical of normative ethical argumentation based on intrinsic value. The relative lack of biodiversity reporting in Denmark shows the need for the State and accounting standard setters to address this issue together with business and other stakeholders.Originality/valueFew studies theorize on why there is a need for environmental reporting. Those that do are based on non‐instrumental considerations. This paper gives philosophical arguments for biodiversity reporting normally outside the scope of accounting. It emphasizes how even those who deny that biodiversity has intrinsic value are morally obliged to account for biodiversity. The argument also provides novel reasons for why thinking about discount rates should be governed by pure preference considerations. Empirically, this is only the second paper examining biodiversity reporting and the first about the Danish context.
Exploring hegemonic change in China: a case of accounting evolution
Authors: Xu Lina , Cortese Corinne , Zhang Eagle 
Published: June 2013

PurposeThis paper aims to provide an understanding of how accounting systems have changed across four distinct periods of hegemonic leadership in China.Design/methodology/approachUsing Gramsci's concept of hegemony, periods of leadership and accounting change throughout Chinese history are examined, including the Confucian tradition, the rise of the socialist system followed by the Cultural Revolution in the Maoist era, and the move towards the socialist‐market system in the Dengist era.FindingsThis paper shows how political leaders in these different time periods effectively achieved leadership by destroying an existing hegemony, creating a new ideology, and implanting this into people's daily lives in order to successfully mobilise their ideological systems. Consistent with changes in leadership, Chinese accounting systems are shown to have responded to hegemonic shifts across these periods.Originality/valueThis paper contributes to understandings of Gramsci's concept of hegemony, explanations of, and motivations for, accounting change, and provides an insight into the evolution of accounting systems throughout time in the context of China.
Investigating the drivers that influence the adoption of differentiated food products
Authors: Loizou Efstratios , Michailidis Anastasios , Chatzitheodoridis Fotios 
Published: June 2013

PurposeOver the last years, food safety, health, environmental and societal issues are a few among many other reasons that force people to adopt new differentiated food products. This interesting shift of the consumption pattern from conventional food products to new differentiated products that incorporate innovative features, consist the main reasoning of the present study. The purpose of this paper is to investigate the drivers that influence the adoption of those differentiated food products and shed new light on consumer's behavior, by modeling and understanding better their attitude.Design/methodology/approachA two‐step cluster analysis was employed to explore the different levels of differentiated products adoption and a categorical regression model was estimated to explain this variation. Data were collected through a survey addressing 500 consumers, carried out in 2009 in a typical Greek urban area.FindingsFrom the three different food product categories (organic, functional and genetically modified) four consumers' profiles were identified which were found to differ in terms of several socioeconomic characteristics. The increased level of disposable income, along with exposure to innovative food products, may well explain such a differential food product adoption.Research limitations/implicationsDue to the small sample, the indefinable number of food products adopters (population) and to specific characteristics of the study area consumers, the results might face generalisability deficiencies.Practical implicationsFrom a practical point of view, to identify the reasons driving consumers to adopt or not new differentiated products with novelties is important generally for society, policy makers, food‐producing companies and related economic sectors.Originality/valueThe contribution of this research is in having examined, the adoption drivers of differentiated food product categories, for which there has been longstanding interest. The food product categories are examined comparatively as a group (organic, functional and genetically modified) and not individually.
Strategic management for product development
Authors: Aho Anne‐Maria , Uden Lorna 
Published: June 2013

PurposeThe purpose of this paper is to shed light on understanding how value creation can be improved by developing dynamic capabilities in product development, in the case of a software engineering process.Design/methodology/approachThe methodology involves a single‐case, longitudinal empirical study by progression of cycles of action research and data collection during a seven‐year period (1 January 2004‐31 November 2010), comprising 55 corporate projects.FindingsThis study will provide significant new information about value creation in multi‐disciplined product development. The study integrates value considerations into the principles and practices of software engineering, implements the aspect of dynamic capabilities in a software engineering process in order to create and sustain competitive advantage. As a result of the study, a model of value creation for software engineering process is created and guidelines are established.Research limitations/implicationsThe contextual features were strongly present during the research process, which means that the model created needs to be tested in other settings by other researchers.Practical implicationsThe results of the study provide management with guidelines for developing and maintaining the importance of value creation in the software engineering process.Originality/valueThe paper presents a new model of value creation for the software engineering process in product development, through which competitive advantage is created and sustained.
Damned if you do, damned if you don't: Texas A&M University Libraries' collection assessment for off‐site storage
Authors: Tabacaru Simona , Pickett Carmelita 
Published: June 2013

PurposeThe purpose of this paper is to discuss the Texas A&M University (TAMU) Libraries’ policies that effectively reduced the size of onsite print collections, with minimal impact on the library user community. The paper also aims to examine some of the challenges encountered during the underlying collection assessment process.Design/methodology/approachInvestment in electronic resources, digital preservation initiatives and local print repositories are reasonable solutions for academic libraries that need to responsibly relocate legacy print collections from their open stacks.FindingsBalancing trust issues with local needs and embracing the opportunities offered by digital archives and local print repositories are key elements for successfully implementing collection management decisions.Originality/valueThis article examines local best practices for downsizing local print collections and recommends strategies applicable to any large academic library for addressing collection assessment challenges.
Managing emotions while managing crises
Authors: Guy Mary E. , Newman Meredith A. , Emel Ganapati N. 
Published: June 2013

PurposeUsing the July 2012 massacre at a midnight showing of a Batman movie as a case study, the paper aims to demonstrate how emotional labor is required of responders and spokespersons and then enumerates the human resource functions that can enhance emotion work skills.Design/methodology/approachUsing the massacre as a case in point, the authors demonstrate how emergency responders are called upon to manage their own emotions as well as those of victims and other constituencies. The authors then discuss human resource functions that can legitimize, enhance, and develop emotion work skills.FindingsThis case demonstrates multiple facets of emotional labor in emergency response. Special attention is paid to the case of public information spokespersons because they are the bridge between the event, the response, and the image of competency that is created in the eyes of the public. Recommendations are enumerated for how the human resource function can facilitate emotion work skills.Practical implicationsThis paper provides practical guidance in how human resource practices can be used to hire, train, and retain first responders who are skilled in performing the emotive aspects of response work.Originality/valueDespite the emotional intensity that accompanies crises, rarely so explicitly discussed is how emotional labor is a required aspect of the work. Also less known is what measures can be implemented to develop emotion work skills.