bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantities of infectious virus and viral RNA recovered from sheep and cattle experimentally infected with foot-and-mouth disease virus O UK 2001
Authors: Alexandersen S. , Zhang Z. , Reid S. M. , Hutchings G. H. , Donaldson A. I. 
Published: August 2015

The profiles of virus production and excretion have been established for sheep experimentally infected with the UK 2001 strain of foot-and-mouth disease (FMD) virus by inoculation and by direct and intensive contact. Virus replicated rapidly in the inoculated sheep, from which a peak infectivity of airborne virus of 104·3TCID50per sheep per 24 h was recovered. Around 24 h later, contact-infected sheep excreted airborne virus maximally. Similar amounts of airborne virus were recovered from cattle. The excretion of virus by the sheep under these conditions fell into three phases. First, a highly infectious period of around 7–8 days. Second, a period of 1–3 days soon afterwards when trace amounts of viral RNA were recovered in nasal and rectal swabs. Third, at 4 weeks after exposure, the demonstration, by tests on oesophageal–pharyngeal samples, that 50% of the sheep were carriers. The implications of the results and the variable role that sheep may play in the epidemiology of FMD are discussed.
A study of the vaccinia virus interferon-γ receptor and its contribution to virus virulence
Authors: Symons Julian A. , Tscharke David C. , Price Nicola , Smith Geoffrey L. 
Published: August 2015

Vaccinia virus (VV) strain Western Reserve gene B8R encodes a 43 kDa glycoprotein that is secreted from infected cells early in infection as a homodimer. This protein has amino acid similarity with the extracellular domain of cellular IFN-γ receptor (IFN-γR) and binds and inhibits IFN-γ from a wide range of species. Here we demonstrate that the B8R protein also inhibits equine IFN-γ. The 5′ end of the B8R mRNA has been mapped by primer extension analysis and the contribution of IFN-γRs to VV virulence was studied by the construction of a deletion mutant lacking the B8R gene (vΔB8R) and a revertant virus (vB8R-R) in which the B8R gene was re-inserted into the deletion mutant. A recombinant virus that expressed a soluble form of the mouse IFN-γR was also constructed and studied. The virulence of these viruses was tested in rodent models of infection. In mice, the loss of the VV IFN-γR did not affect virulence compared with WT and revertant viruses, consistent with the low affinity of the VV IFN-γR for mouse IFN-γ. However, expression of the mouse soluble IFN-γR increased virus virulence slightly. In rabbit skin, loss of the VV IFN-γR produced lesions with histological differences compared with WT and revertant viruses. Lastly, the affinity constants of the VV IFN-γR for human and mouse IFN-γ were determined by surface plasmon resonance.
The Epstein–Barr virus ZEBRA protein activates transcription from the early lytic F promoter by binding to a promoter-proximal AP-1-like site
Authors: Zetterberg Henrik , Jansson Ann , Rymo Lars , Chen Fu , Karlsson Ann , Klein Georg , Brodin Bertha 
Published: August 2015

The ZEBRA protein encoded by the Epstein–Barr virus (EBV) genome activates a switch from the latent to the lytic gene expression programme of the virus. ZEBRA, a member of the basic leucine zipper family of DNA-binding proteins, is a transcriptional activator capable of inducing expression from several virus lytic cycle promoters by binding to activator protein 1 (AP-1)-like sites. The Epstein–Barr virus BamHI F promoter, Fp, was for some time believed to initiate EBNA1-specific transcription in EBV-transformed latent cells. More recent data, however, show that Fp is an early lytic promoter and that the dominant EBNA1 gene promoter in latent cells is Qp, located about 200 bp downstream of Fp. In the present investigation we confirm that Fp displays the characteristics of a lytic promoter. Fp is downregulated in latently EBV-infected cells, both in the endogenous virus genome and in reporter plasmids that carry Fp regulatory sequences upstream of position −136 and down to +10 relative to the Fp transcription start site (+1), and is activated on induction of the virus lytic cycle. We show that the repression of Fp in latent stages of infection can be abolished by ZEBRA, and demonstrate that ZEBRA activates Fp through a direct interaction with an AP-1-like site at position −52/−46 in the promoter-proximal Fp region.
Characterization of late gene expression factors lef-9 and lef-8 from Bombyx mori nucleopolyhedrovirus
Authors: Acharya Asha , Gopinathan Karumathil P. 
Published: August 2015

Late gene expression factors, LEF-4, LEF-8, LEF-9 and P47 constitute the primary components of the Autographa californica multinucleocapsid polyhedrovirus (AcMNPV)-encoded RNA polymerase, which initiates transcription from late and very late promoters. Here, characterization of lef-9 and lef-8, which encode their corresponding counterparts, from Bombyx mori NPV is reported. Transcription of lef-9 initiated at two independent sites: from a GCACT sequence located at −38 nt and a CTCTT sequence located at −50 nt, with respect to the +1 ATG of the open reading frame. The 3′ end of the transcript was mapped to a site 17 nt downstream of a canonical polyadenylation signal located 7 nt downstream of the first of the two tandem translational termination codons. Maximum synthesis of LEF-9 was seen from 36 h post-infection (p.i.). The transcription of lef-8 initiated early in infection from a GTGCAAT sequence that differed in the corresponding region from its AcMNPV counterpart (GCGCAGT), with consequent elimination of the consensus early transcription start site motif (underlined). Peak levels of lef-8 transcripts were attained by 24 h p.i. Immunocopurification analyses suggested that there was an association between LEF-8 and LEF-9 in vivo.
Complete nucleotide sequence of the M RNA segment of Andes virus and analysis of the variability of the termini of the virus S, M and L RNA segments
Authors: Padula P. J. , Sanchez A. J. , Edelstein A. , Nichol S. T. 
Published: August 2015

Hantavirus pulmonary syndrome (HPS) has been recognized increasingly as a significant public health problem in South America since Andes virus was first discovered in Argentina. Here, the isolation of Andes virus is reported from an infected rodent captured in Argentina in close vicinity to the place of the first HPS case, AH1. The complete nucleotide sequences of the virus M segment, partial L segment and the termini of the S, M and L segment genome RNAs were determined. The Andes virus M RNA segment is 3671 nt in length and is predicted to encode a glycoprotein precursor 1138 aa in length; it generally resembles the other HPS-associated hantaviruses in its organization. Relative to the G1 glycoprotein of other HPS-associated hantaviruses, an additional potential glycosylation site was found but this is located in the predicted cytoplasmic domain and is therefore unlikely to be glycosylated. In phylogenetic analyses, Andes virus, together with the more related hantaviruses, represented a monophyletic lineage. The S-terminal nucleotides were conserved relative to other New World hantaviruses. The M and L segment RNA termini had short deletions in the region believed to contain the sequence and structural features necessary for initiation of virus RNA replication and transcription. Clinical manifestations of Andes virus infections range from fulminant respiratory disease with high lethality to mild course without sequelae. Andes virus has also been associated with person-to-person transmission. Accumulation of Andes virus genetic data will be essential for understanding the factors that regulate virus replication and transmission and to determine the pathogenesis of HPS.
Glycoprotein B plays a predominant role in mediating herpes simplex virus type 2 attachment and is required for entry and cell-to-cell spread
Authors: Cheshenko Natalia , Herold Betsy C. 
Published: August 2015

Heparan sulfate moieties serve as receptors for initial binding of herpes simplex virus types 1 and 2 (HSV-1 and -2) to cells. Deletion of HSV-1 glycoprotein C (gC-1) but not HSV-2 gC (gC-2) results in virions with reduced specific binding activity (virus particles bound per cell) and specific infectivity (p.f.u. per particle), suggesting that for HSV-1, but not HSV-2, gC plays a major role in mediating virus attachment. To test the hypothesis that glycoprotein B (gB), the other heparin-binding glycoprotein, mediates HSV-2 attachment, HSV-2 viruses deleted in gB-2 alone or deleted in both gB-2 and gC-2 were constructed. These viruses were grown on complementing or non-complementing cells and were compared with parental HSV-2(G) or a gC-2-deleted HSV-2 mutant (with respect to ability to bind and infect cells). At equivalent input concentrations of purified virions, significantly fewer gB-2-deleted virions bound to cells compared to parental HSV-2(G) or virus grown on complementing cells. In addition, viruses deleted in gB-2 were non-infectious. No immediate early proteins were detected in cells infected with gB-2-deleted virus harvested from non-complementing Vero cells, whereas these proteins were readily detected 4 h post-infection in cells infected with virus grown on complementing cells or with parental viruses. Viruses deleted in gB-2 failed to spread cell to cell, as evidenced by the inability to form plaques. Together these studies demonstrate that gB-2 plays a key role in mediating HSV-2 attachment and is required for entry and cell-to-cell spread. This glycoprotein is an important target for development of novel antiviral drugs.
Osmotic regulation of the Streptomyces lividans thiostrepton-inducible promoter, ptipA
Authors: Ali Nasima , Herron Paul R , Evans Meirwyn C , Dyson Paul J 
Published: August 2015

Transcriptional activation of the thiostrepton-inducible promoter,ptipA, inStreptomyces lividansis mediated by TipAL. This transcriptional activator belongs to the MerR/SoxR family that characteristically binds an operator sequence located between the −10 and −35 hexamers normally occupied by RNA polymerase. As for theEscherichia colimerTpromoter, theptipAhexamers are separated by a long 19 bp spacer and hence a topological transition of the DNA is likely to be a requisite for alignment with RNA polymerase. Growth conditions that could facilitate this conformational change were investigated using transcriptional fusions ofptipAwith reporter genes. Adjustment of growth medium osmolarity led to increased and prolonged TipAL-dependent expression, both with and without the inducer, thiostrepton. These effects correlated with increases in negative DNA supercoiling. Moreover, an inability to induce the promoter with thiostrepton in strain TK64 was corrected by increasing the concentration of osmolyte, compensating for an apparent reduced level of negative DNA supercoiling in the strain. Prolonging the time of activation oftipAin the wild-type by manipulating growth conditions revealed that mycelial autolysis could be induced by thiostrepton in 4-d-old cultures.
Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics
Authors: Tao Yong , Hu Zheng , Ling Shaoping , Yeh Shiou-Hwie , Zhai Weiwei , Chen Ke , Li Chunyan , Wang Yu , Wang Kaile , Wang Hurng-Yi , Hungate Eric A. , Onel Kenan , Liu Jiang , Zeng Changqing , Hudson Richard R. , Chen Pei-Jer , Lu Xuemei , Wu Chung-I 
Published: August 2015

AbstractsThe genetic diversity within a single tumor can be extremely large, possibly with mutations at all coding sites (Ling et al. 2015). In this study, we analyzed 12 cases of multiple hepatocellular carcinoma (HCC) tumors by sequencing and genotyping several samples from each case. In 10 cases, tumors are clonally related by a process of cell migration and colonization. They permit a detailed analysis of the evolutionary forces (mutation, migration, drift and natural selection) that influence the genetic diversity both within and between tumors. In 23 inter-tumor comparisons, the descendant tumor usually shows a higher growth rate than the parent tumor. In contrast, neutral diversity dominates within-tumor observations such that adaptively growing clones are rarely found. The apparent adaptive evolution between tumors can be explained by the inherent bias for detecting larger tumors that have a growth advantage. Beyond these tumors are a far larger number of clones which, growing at a neutral rate and too small to see, can nevertheless be verified by molecular means. Given that the estimated genetic diversity is often very large, therapeutic strategies need to take into account the pre-existence of many drug-resistance mutations. Importantly, these mutations are expected to be in the very low frequency range in the primary tumors (and become frequent in the relapses, as is indeed reported (1-3). In conclusion, tumors may often harbor a very large number of mutations in the very low frequency range. This duality provides both a challenge and an opportunity for designing strategies against drug resistance (4-8).One Sentence SummaryThe total genetic diversity across all tumors of a single patient, with large number of low frequency mutations driven by neutral and adaptive forces, presents both a challenge and an opportunity for new cancer therapeutics.
A comparative analysis of network mutation burdens across 21 tumor types augments discovery from cancer genomes
Authors: Horn Heiko , Lawrence Michael S. , Hu Jessica Xin , Worstell Elizabeth , Ilic Nina , Shrestha Yashaswi , Kim Eejung , Kamburov Atanas , Kashani Alireza , Hahn William C. , Boehm Jesse S. , Getz Gad , Lage Kasper 
Published: August 2015

ABSTRACTHeterogeneity across cancer makes it difficult to find driver genes with intermediate (2-20%) and low frequency (<2%) mutations1, and we are potentially missing entire classes of networks (or pathways) of biological and therapeutic value. Here, we quantify the extent to which cancer genes across 21 tumor types have an increased burden of mutations in their immediate gene network derived from functional genomics data. We formalize a classifier that accurately calculates the significance level of a gene’s network mutation burden (NMB) and show it can accurately predict known cancer genes and recently proposed driver genes in the majority of tested tumours. Our approach predicts 62 putative cancer genes, including 35 with clear connection to cancer and 27 genes, which point to new cancer biology. NMB identifies proportionally more (4x) low-frequency mutated genes as putative cancer genes than gene-based tests, and provides molecular clues in patients without established driver mutations. Our quantitative and comparative analysis of pan-cancer networks across 21 tumour types gives new insights into the biological and genetic architecture of cancers and enables additional discovery from existing cancer genomes. The framework we present here should become increasingly useful with more sequencing data in the future.
Inferring social structure and its drivers from refuge use in the desert tortoise, a relatively solitary species
Authors: Sah Pratha , Nussear Kenneth E. , Esque Todd C. , Aiello Christina M. , Hudson Peter J. , Bansal Shweta 
Published: August 2015

AbstractFor several species, refuges (such as burrows, dens, roosts, nests) are an essential resource for protection from predators and extreme environmental conditions. Refuges also serve as focal sites for social interactions including mating, courtship and aggression. Knowledge of refuge use patterns can therefore provide information about social structure, mating and foraging success, as well as the robustness and health of wildlife populations, especially for species considered to be relatively solitary. In this study, we construct networks of burrow use to infer social associations in a threatened wildlife species typically considered solitary - the desert tortoise. We show that tortoise social networks are significantly different than null networks of random associations, and have moderate spatial constraints. We next use statistical models to identify major mechanisms behind individual-level variation in tortoise burrow use, popularity of burrows in desert tortoise habitat and test for stressor-driven changes in refuge use patterns. We show that seasonal variation has a strong impact on tortoise burrow switching behavior. On the other hand, burrow age and topographical condition influence the number of tortoises visiting a burrow in desert tortoise habitat. Of three major population stressors affecting this species (translocation, drought, disease), translocation alters tortoise burrow switching behavior, with translocated animals visiting fewer unique burrows than residents. In a species that is not social, our study highlights the importance of leveraging refuge use behavior to study the presence of and mechanisms behind non-random social structure and individual-level variation. Our analysis of the impact of stressors on refuge-based social structure further emphasizes the potential of this method to detect environmental or anthropogenic disturbances.Significance statement: Adaptive and social behavior that affects fitness is now being increasingly incorporated in the conservation and management of wildlife species. However, direct observations of social interactions in species considered to be solitary are difficult, and therefore integration of behavior in conservation and management decisions in such species has been infrequent. For such species, we propose quantifying refuge use behavior as it can provide insights towards their (hidden) social structure, establish relevant contact patterns of infectious disease spread, and provide early warning signals of population stressors. Our study highlights this approach in a long-lived and threatened species, the desert tortoise. We provide evidence towards the presence of and identify mechanisms behind the social structure in desert tortoises formed by their burrow use preferences. We also show how individuals burrow use behavior responds to the presence of population stressors.
Strengthening donor stewardship one month at a time
Authors: Gardner Betina L. , Rhodus Krista Zabawa 
Published: August 2015

Purpose
– The purpose of this paper is to discuss Eastern Kentucky University (EKU) Libraries’ experience and success in the creation of a fundraising Communications Plan.

Design/methodology/approach
– The paper is based on observational experiences at EKU Libraries over the course of two years, before and after the implementation of a Communications Plan.

Findings
– Feedback from Friends of EKU Libraries advised that donors appreciate communications from EKU Libraries, especially on a monthly basis. As a result of implementing a Communications Plan, donations to EKU Libraries became more consistent throughout the year and increased in number.

Practical implications
– EKU Libraries found that a meaningful Communications Plan can help strengthen the connection between an organization and its donors. As a result, the Plan will be refined annually and utilized for the foreseeable future.

Originality/value
– This paper provides guidance for libraries and other organizations on the creation and implementation of a fundraising Communications Plan, based on the experience of EKU Libraries.
A comparison of mode effects between face-to-face and drop-off contingent valuation surveys
Authors: Ma Hua , Liu Hui , Gong Yazhen , Jin Jianjun , Mao Xianqiang 
Published: August 2015

Purpose
– The purpose of this paper is to examine the practice potential of self-administered drop-off as a survey mode for contingent valuation (CV) studies.

Design/methodology/approach
– This paper conducts an empirical comparison of mode effects of two survey methods for improved ecological services in Beijing. Data were collected from a CV survey, which has two subsamples, one using face-to-face interviews and the other employing self-administered drop-off surveys.

Findings
– There is some evidence of social desirability bias in the face-to-face interviews for the participation question; however, such effects do not carry over to subjects’ responses to the contribution decision. No difference is observed in sample demographics between modes. And satisficing effect is not observed in the drop-off survey in this study.

Research limitations/implications
– More well-controlled mode comparisons are warranted to test the robustness of the results; and collection time effects as well as the use of drop-off surveys for environmental valuation with different levels of complexity and familiarity are worthy of further study.

Practical implications
– The authors find more similarities between drop-off and face-to-face surveys than differences therefore support the practice of self-administered drop-off surveys in CVM for environmental valuation.

Originality/value
– This paper adds to the limited number of well-controlled mode comparisons in the CV surveys, and contributes to a better understanding of self-administered drop-off surveys, a potential low-cost alternative to face-to-face interviews in future CV applications.
Total-factor energy efficiency in China’s sugar manufacturing industry
Authors: Ru Lei , Si Wei 
Published: August 2015

Purpose
– The purpose of this paper is to evaluate the total-factor energy efficiency (TFEE) in China’s sugar manufacturing industry using firm-level data from 2002/2003 to 2012/2013 crushing seasons, and further explore the determinants of TFEE.

Design/methodology/approach
– Modified data envelopment analysis is used to measure the TFEE of each sugar mill during the crushing seasons. Then heteroskedastic fractional probit model is applied to estimate the determinants of TFEE because of the bounded nature of TFEE and heteroskedasticity of unbalanced panel.

Findings
– The results show that throughout the crushing seasons, the average TFEE is 0.57; there are spatial differences of TFEE in Guangxi sugar industry, highest in southern area; the TFEE of foreign-owned sugar mills is larger than that of private-owned and state-owned sugar mills; the larger the enterprise size, the higher the TFEE; private ownership, large size, raw material, safe productivity, total recovery rate as well as technical progress can improve TFEE significantly.

Originality/value
– This paper analyzes TFEE using a rich data set at firm level, allowing the existence of firm heterogeneity, as well as being complementary to the study of energy efficiency in China’s sugar industry. Moreover, ownership structure is involved in the determinants of TFEE, which is rarely done in literature. Lastly, heteroskedastic fractional probit model is employed to recognize the bounded nature of TFEE as well as selection bias of unbalanced panel to study the determinants of TFEE.