bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Cellular Proteins That Interact with the Adeno-Associated Virus Rep Protein
Authors: Nash Kevin , Chen Weijun , Salganik Max , Muzyczka Nicholas 
Published: October 2008

ABSTRACT
Adeno-associated virus (AAV) codes for four related nonstructural Rep proteins. AAV both replicates and assembles in the nucleus and requires coinfection with a helper virus, either adenovirus (Ad) or herpesvirus, for a productive infection. Like other more complex DNA viruses, it is believed that AAV interacts or modifies host cell proteins to carry out its infection cycle. To date, relatively little is known about the host proteins that interact with the viral Rep proteins, which are known to be directly involved in DNA replication, control of viral and cellular transcription, splicing, and protein translation. In this study, we used affinity-tagged Rep protein to purify cellular protein complexes that were associated with Rep in cells that had been infected with Ad and AAV. In all, we identified 188 cellular proteins from 16 functional categories, including 14 transcription factors, 6 translation factors, 15 potential splicing proteins, 5 proteins involved in protein degradation, and 13 proteins involved in DNA replication or repair. This dramatically increases the number of potential interactions over the current number of approximately 26. Twelve of the novel proteins found were further tested by coimmunoprecipitation or colocalization using confocal immunomicroscopy. Of these, 10 were confirmed as proteins that formed complexes with Rep, including proteins of the MCM complex (DNA replication), RCN1 (membrane transport), SMC2 (chromatin dynamics), EDD1 (ubiquitin ligase), IRS4 (signal transduction), and FUS (splicing). Computer analysis suggested that 45 and 28 of the 188 proteins could be placed in a pathway of interacting proteins involved in DNA replication and protein synthesis, respectively. Of the proteins involved in DNA replication, all of the previously identified proteins involved in AAV DNA replication were found, except Ad DBP. The only Ad protein found to interact with Rep was the E1b55K protein. In addition, we confirmed that Rep interacts with Ku70/80 helicase. In vitro DNA synthesis assays demonstrated that although Ku helicase activity could substitute for MCM to promote strand displacement synthesis, its presence was not essential. Our study suggests that the interaction of AAV with cellular proteins is much more complex than previously suspected and provides a resource for further studies of the AAV life cycle.
Identification of Sequences in Herpes Simplex Virus Type 1 ICP22 That Influence RNA Polymerase II Modification and Viral Late Gene Expression
Authors: Bastian Thomas W. , Rice Stephen A. 
Published: October 2008

ABSTRACT
Previous studies have shown that the herpes simplex virus type 1 (HSV-1) immediate-early protein ICP22 alters the phosphorylation of the host cell RNA polymerase II (Pol II) during viral infection. In this study, we have engineered several ICP22 plasmid and virus mutants in order to map the ICP22 sequences that are involved in this function. We identify a region in the C-terminal half of ICP22 (residues 240 to 340) that is critical for Pol II modification and further show that the N-terminal half of the protein (residues 1 to 239) is not required. However, immunofluorescence analysis indicates that the N-terminal half of ICP22 is needed for its localization to nuclear body structures. These results demonstrate that ICP22's effects on Pol II do not require that it accumulate in nuclear bodies. As ICP22 is known to enhance viral late gene expression during infection of certain cultured cells, including human embryonic lung (HEL) cells, we used our engineered viral mutants to map this function of ICP22. It was found that mutations in both the N- and C-terminal halves of ICP22 result in similar defects in viral late gene expression and growth in HEL cells, despite having distinctly different effects on Pol II. Thus, our results genetically uncouple ICP22's effects on Pol II from its effects on viral late gene expression. This suggests that these two functions of ICP22 may be due to distinct activities of the protein.
Comparative Analysis of Complete Genome Sequences of Three Avian Coronaviruses Reveals a Novel Group 3c Coronavirus
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Lam Carol S. F. , Lai Kenneth K. Y. , Huang Yi , Lee Paul , Luk Geraldine S. M. , Dyrting Kitman C. , Chan Kwok-Hung , Yuen Kwok-Yung 
Published: October 2008

ABSTRACT

In this territory-wide molecular epidemiology study of coronaviruses (CoVs) in Hong Kong involving 1,541 dead wild birds, three novel CoVs were identified in three different bird families (bulbul CoV HKU11 [BuCoV HKU11], thrush CoV HKU12 [ThCoV HKU12], and munia CoV HKU13 [MuCoV HKU13]). Four complete genomes of the three novel CoVs were sequenced. Their genomes (26,396 to 26,552 bases) represent the smallest known CoV genomes. In phylogenetic trees constructed using chymotrypsin-like protease (3CL
pro
), RNA-dependent RNA polymerase (Pol), helicase, spike, and nucleocapsid proteins, BuCoV HKU11, ThCoV HKU12, and MuCoV HKU13 formed a cluster distantly related to infectious bronchitis virus and turkey CoV (group 3a CoVs). For helicase, spike, and nucleocapsid, they were also clustered with a CoV recently discovered in Asian leopard cats, for which the complete genome sequence was not available. The 3CL
pro
, Pol, helicase, and nucleocapsid of the three CoVs possessed higher amino acid identities to those of group 3a CoVs than to those of group 1 and group 2 CoVs. Unique genomic features distinguishing them from other group 3 CoVs include a distinct transcription regulatory sequence and coding potential for small open reading frames. Based on these results, we propose a novel CoV subgroup, group 3c, to describe this distinct subgroup of CoVs under the group 3 CoVs. Avian CoVs are genetically more diverse than previously thought and may be closely related to some newly identified mammalian CoVs. Further studies would be important to delineate whether the Asian leopard cat CoV was a result of interspecies jumping from birds, a situation analogous to that of bat and civet severe acute respiratory syndrome CoVs.
Effect of latanoprost and timolol on the histopathology of the human conjunctiva
Authors: Terai N , Schlötzer-Schrehardt U , Lampel J , Böhm A G , Rummelt C , Schmidt E , Pillunat L E 
Published: October 2008

Aim:To investigate the effect of timolol and latanoprost on the extracellular matrix organisation, inflammatory infiltration, and expression of matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs) in the human conjunctiva.Methods:Conjunctival biopsies were obtained from the inferior fornix during routine cataract surgery from 20 patients with primary open-angle glaucoma, who had received a monotherapy either with timolol or latanoprost, and from 10 non-glaucomatous patients. Specimens were investigated by light microscopy, immunohistochemistry using antibodies against MMP-1,-3, TIMP-2,-3 and CD 68 antibodies and by quantitative transmission electron microscopy.Results:The number of collagen fibres was significantly decreased in latanoprost-treated conjunctival specimens compared with timolol-treated eyes (p<0.01) but showed no difference to controls. Amorphous material was increased in both treated groups compared with controls (p<0.001) but was less in latanoprost-treated specimens compared with timolol-treated eyes (p<0.001). Optically clear spaces, probably containing glycosaminoglycans, were significantly reduced in both treated groups—with less of a reduction in latanoprost—compared with timolol-treated eyes (p<0.001). A marked upregulation of MMP-1 and MMP-3 and moderately increased staining for TIMP-2 and TIMP-3 was found in epithelial cells and subepithelial stromal cells of latanoprost-treated eyes. A moderate infiltration with macrophages and inflammatory cells was observed in timolol-treated eyes.Conclusions:Latanoprost-treated conjunctival specimens showed a decreased stromal collagen density and a less pronounced inflammatory infiltration. The upregulation of MMP-1 and MMP-3 in latanoprost-treated eyes might explain the reduced extracellular matrix accumulation in the conjunctival stroma. Therefore, latanoprost therapy might have a more favourable effect on the outcome of glaucoma filtering surgery.
Correlation of visual recovery with presence of photoreceptor inner/outer segment junction in optical coherence images after epiretinal membrane surgery
Authors: Mitamura Y , Hirano K , Baba T , Yamamoto S 
Published: October 2008

Aims:To investigate the relationship between the presence of the photoreceptor inner and outer segment (IS/OS) junction and visual acuity after epiretinal membrane (ERM) surgery.Methods:Seventy eyes of 70 consecutive patients who had undergone vitrectomy for idiopathic ERM were examined by optical coherence tomography before and 3 and 6 months after surgery. The IS/OS junction was graded into three grades. The time course of recovery of the IS/OS junction, central foveal thickness (CFT) and best corrected visual acuity (BCVA) during the postoperative period was studied.Results:A normal IS/OS junction was detected in 47.1% of the eyes before surgery and in 65.7% at 3 months and 75.7% at 6 months after. There was a significant correlation between the IS/OS grade and BCVA before and at 3 and 6 months after the operation (p = 0.0001, p<0.0001, p<0.0001, respectively). The preoperative IS/OS junction grade correlated significantly with BCVA at 6 months (p = 0.0239). CFT did not correlate significantly with BCVA at 3 and 6 months.Conclusions:The presence of a normal IS/OS junction was associated with good visual acuity after ERM surgery. A normal IS/OS junction probably indicates morphological and functional recovery of the photoreceptors.
Randomised, double-blind, placebo-controlled clinical trial of a new topical glyceryl trinitrate patch for chronic lateral epicondylosis: Table 1
Authors: Paoloni J A , Murrell G A C , Burch R M , Ang R Y 
Published: October 2008

Objective:This study aimed to determine whether a new glyceryl trinitrate patch preparation is effective in treating chronic lateral epicondylosis.Design:Randomised double-blind controlled clinical trial.Setting:Private practice patients: 154 adult patients with chronic lateral epicondylosis were recruited, with 136 patients completing the trial.Interventions:8 weeks of glyceryl trinitrate patch application (dosages of 72 mg/24 h, 1.44 mg/24 h, and 3.6 mg/24 h), or placebo patch application.Main outcome measures:Subjective global assessment of change in elbow symptoms, patient-rated tennis elbow evaluation, visual analogue pain at rest, visual analogue pain with activity, visual analogue pain intensity, grip strength, and strength testing using the Orthopaedic Research Institute-Tennis Elbow Testing System.Results:At 8 weeks there was a significant decrease in elbow pain with activity in the glyceryl trinitrate 0.72 mg/24 h group compared with placebo (p = 0.04). There were no other significant differences.Conclusions:Continuous 1.25 mg/24 h topical glyceryl trinitrate treatment, when combined with daily exercise rehabilitation, has previously demonstrated efficacy in treating chronic lateral epicondylosis. There was significantly decreased elbow pain with activity at 8 weeks in the glyceryl trinitrate 0.72 mg/24 h group (p = 0.04). This short-term dose-ranging study did not demonstrate a treatment effect of a new topical glyceryl trinitrate patch in dosages of 1.44 mg/24 h or 3.6 mg/24 h, which conflicts with previous studies on topical glyceryl trinitrate treatment.Trial registration number:NCT00447928.
Cost-effectiveness of interventions promoting physical activity
Authors: Müller-Riemenschneider F , Reinhold T , Willich S N 
Published: October 2008

Background:Sedentary and inactive lifestyle continues to increase and is associated with a substantial economic burden in most industrialised countries. To implement effective physical activity interventions on a broad population basis, their cost-effectiveness needs to be evaluated.Objective:To evaluate the cost-effectiveness of physical activity interventions targeted at healthy adults and to identify cost-effective intervention components.Design:Systematic review.Methods and data sources:The search strategy in electronic databases identified relevant literature published until June 2008. We included studies investigating the cost-effectiveness of interventions aiming to promote physical activity behaviour in healthy adults. Two researchers independently assessed publications according to predefined inclusion criteria and with regard to methodological quality. Study characteristics and predefined outcome measures were extracted and costs per participant to become sufficiently active were compared between interventions.Results:Out of 6543 identified publications, eight studies investigating 11 intervention strategies met the inclusion criteria. There was substantial heterogeneity in study quality, intervention strategies and intervention effects. Behavioural interventions were able to promote physical activity, with participants meeting recommended levels of physical activity, for about 800 Euros per year. Environmental interventions and interventions targeted at general practitioners seemed to have the potential to be substantially more cost-effective.Discussion:There was evidence that current physical activity intervention strategies can be a cost-effective means of resource allocation. But, despite the growing literature on physical activity promotion, appropriate cost-effectiveness analyses are rare and the generalisability of presented findings is limited. Further research is warranted to investigate the cost-effectiveness of behavioural and environmental intervention strategies.
Medical students’ attitudes towards abortion: a UK study
Authors: Gleeson R , Forde E , Bates E , Powell S , Eadon-Jones E , Draper H 
Published: October 2008

Background:There is little research into medical students’ or doctors’ attitudes to abortion, yet knowing this is important, as policy makers should be aware of the views held by professionals directly involved in abortion provision and changing views may have practical implications for the provision of abortion in the future.Methods:We surveyed 300 medical students about their views on abortion, their beliefs about the status of the fetus and the rights of the mother, their attitude towards UK law and their willingness to be involved in abortion provision as qualified doctors.Results:62% of medical students were pro-choice, 33% pro-life and 7% undecided. Students’ views correlated with gender, year of study and holding a religious belief. Their beliefs about abortion, the status of the fetus and the rights of women significantly correlated with their attitudes towards the UK law and their willingness to be involved in abortion provision. Students’ willingness to be involved in abortion provision was related to their views on abortion, the extent of participation required, the circumstances of the pregnancy and the stage of pregnancy.Conclusions:The percentage of pro-choice students was lower than that found in research on general practitioners’ attitudes to abortion. It is unclear whether this is because students become more pro-choice as they progress through their medical career or because there is genuinely a change in attitudes to abortion.
Communicating environmental geoscience: introduction
Authors: Liverman Dave , Pereira Christopher P. G. , Marker Brian 
Published: October 2008

Abstract
This collection of papers is aimed primarily at the environmental geoscientist faced with the challenges of communicating important scientific results to those who might benefit from them, whether they are politicians, policy-makers, potential victims of geological disasters, fellow scientists or other members of the public. Environmental geoscience has grown to become one of the most important disciplines of geoscience as a whole, and scientific methods of investigation have become sophisticated and effective at addressing numerous problems that directly affect health and safety. The audience for such research thus is wide, and for such research to be used in the most effective manner requires well-developed communication skills to reach an audience that varies greatly in education and ability to comprehend scientific concepts. The implications of failing to communicate effectively may be severe: geological disasters have had a massive economic and social impact, with major loss of life.
The modelling and visualization of digital geoscientific data as a communication aid to land-use planning in the urban environment: an example from the Thames Gateway
Authors: Royse K. R. , Reeves H. J. , Gibson A. R. 
Published: October 2008

Abstract
The Thames Gateway Development Zone is the biggest urban development project in the UK for over 50 years. Developers and planners need to understand the implications of such large-scale urbanization on the environment. Requirements for sustainable growth within the Thames Gateway region mean that developers are being required to demonstrate that proposals are based on sound scientific information. This has resulted in a growing demand for geo-environmental information to be provided in more accessible, relevant and understandable forms. Advances in the use of geographic information systems (GIS) and 3D modelling software mean that there is now far greater opportunity to develop geo-environmental information products for urban development. New and innovative ways of visualizing and communicating geoscience information have been developed. Using this new technology it is possible to predict not only the types of rocks beneath a site, but also the engineering properties (such as rock strength, shrink–swell characteristics or compressibility), hydrogeological properties (such as permeability, porosity and thickness of the unsaturated zone) and geohazard potential. Geoscientific information can then be imported into standard GIS packages and queried along with other complementary ground investigation data, resulting in the creation of a powerful tool to assist in strategic planning and sustainable development.
Hazard and vulnerability assessment and adaptive planning: mutual and multilateral community–researcher communication, Arctic Canada
Authors: Catto Norm R. , Parewick Kathleen 
Published: October 2008

Abstract
Communities in Arctic Canada are faced with natural geological and environmental hazards. Successful adaptation requires assessment of hazards from a physical science perspective, and appropriate communication with the communities. Transforming a hazard assessment exercise into an effective plan for adaptation requires an intimate cultural understanding. Hazard assessment involving substantial input from all research, administrative, socio-economic and cultural communities will lead to more appropriate and valuable analyses of risk, sensitivity and vulnerability. Residents and communities can contribute greatly to the identification and assessment of natural hazards. Community-driven communication is essential for meaningful risk analysis, adaptive planning and vulnerability assessment. Developing relationships with local media can be extremely beneficial. Using the practices of participatory community planning allows local environmental changes to be assessed and responded to by the people affected. Establishing effective working partnerships is essential for a true vulnerability assessment. The particularly sensitive nature of hazard assessments indicating increasing risk and vulnerability, and the continuing socio-economic changes in some communities, in the work described here, required consideration of the most appropriate methods of communication for each instance. The relationships that have emerged through the course of work in the communities have differed markedly from those originally envisioned, and also exhibit significant differences between communities.
Communicating geoscience to indigenous people: examples from the Solomon Islands
Authors: Petterson M. G. , Tolia D. , Cronin S. J. , Addison R. 
Published: October 2008

Abstract
This paper examines communicating geoscience to indigenous peoples using a communication model that closely follows geological models for pollution issues. Although geoscientists will expend large amounts of energy in understanding a scientific process, relatively little energy is often expended in the analogous communication model. Reasons for this include a narrow focus on pure science, lack of confidence in engaging in communication and negative perceptions of communication ideas. Indigenous peoples are defined as ‘first occupiers’ of regions or nations relatively untouched by the predominant ‘Western–Asian’ technological-oriented culture. Few indigenous peoples are totally ‘untouched’ by the dominant world culture. Four cases studies from the Solomon Islands explore communication strategies relating to land access, a live volcanic event, the setting up of a gold mine, and raising awareness of volcanic hazards. Generic best practice advice offered includes the following: understanding of indigenous culture, customs, values, taboos and political–governance structures; involvement of indigenous people at every level of the communication process; identifying and including all stakeholders; a clear message, method and outcome focus; usage wherever possible of face-to-face communication and pictures as well as words; involvement of the community in practical exercises; a thorough follow-up and evaluation process; and sufficient time to allow the process to be effective.
Framing volcanic risk communication within disaster risk reduction: finding ways for the social and physical sciences to work together
Authors: Barclay Jenni , Haynes Katharine , Mitchell Tom , Solana Carmen , Teeuw Richard , Darnell Amii , Crosweller H. Sian , Cole Paul , Pyle David , Lowe Catherine , Fearnley Carina , Kelman Ilan 
Published: October 2008

Abstract
Sixteen years have passed since the last global volcanic event and more than 25 since a volcanic catastrophe that killed tens of thousands. In this time, volcanology has seen major advances in understanding, modelling and predicting volcanic hazards and, recently, an interest in techniques for reducing and mitigating volcanic risk. This paper provides a synthesis of literature relating to this last aspect, specifically the communication of volcanic risk, with a view to highlighting areas of future research into encouraging risk-reducing behaviour. Evidence suggests that the current ‘multidisciplinary’ approach within physical science needs a broader scope to include sociological knowledge and techniques. Key areas where this approach might be applied are: (1) the understanding of the incentives that make governments and communities act to reduce volcanic risk; (2) improving the communication of volcanic uncertainties in volcanic emergency management and long-term planning and development. To be successful, volcanic risk reduction programmes will need to be placed within the context of other other risk-related phenomena (e.g. other natural hazards, climate change) and aim to develop an all-risks reduction culture. We suggest that the greatest potential for achieving these two aims comes from deliberative inclusive processes and geographic information systems.