bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Highly Conserved Arginine Residues at Positions 76 through 78 of Influenza A Virus Matrix Protein M1 Play an Important Role in Viral Replication by Affecting the Intracellular Localization of M1
Authors: Das Subash C. , Watanabe Shinji , Hatta Masato , Noda Takeshi , Neumann Gabrielle , Ozawa Makoto , Kawaoka Yoshihiro 
Published: November 2011

ABSTRACT
Influenza A virus matrix protein (M1) plays an important role in virus assembly and budding. Besides a well-characterized basic amino acid-rich nuclear localization signal region at positions 101 to 105, M1 contains another basic amino acid stretch at positions 76–78 that is highly conserved among influenza A and B viruses, suggesting the importance of this stretch. To understand the role of these residues in virus replication, we mutated them to either lysine (K), alanine (A), or aspartic acid (D). We could generate viruses possessing either single or combination substitutions with K or single substitution with A at any of these positions, but not those with double substitutions with A or a single substitution with D. Viruses with the single substitution with A exhibited slower growth and had lower nucleoprotein/M1 quantitative ratio in virions compared to the wild-type virus. In cells infected with a virus possessing the single substitution with A at position 77 or 78 (R77A or R78A, respectively), the mutated M1 localized in patches at the cell periphery where nucleoprotein and hemagglutinin colocalized more often than the wild-type did. Transmission electron microscopy showed that virus possessing M1 R77A or R78A, but not the wild-type virus, was present in vesicular structures, indicating a defect in virus assembly and/or budding. The M1 mutations that did not support virus generation exhibited an aberrant M1 intracellular localization and affected protein incorporation into virus-like particles. These results indicate that the basic amino acid stretch of M1 plays a critical role in influenza virus replication.
Codelivery of the Chemokine CCL3 by an Adenovirus-Based Vaccine Improves Protection from Retrovirus Infection
Authors: Lietz Ruth , Bayer Wibke , Ontikatze Teona , Johrden Lena , Tenbusch Matthias , Storcksdieck genannt Bonsmann Michael , Überla Klaus , Dittmer Ulf , Wildner Oliver 
Published: November 2011

ABSTRACTProcessing and presentation of vaccine antigens by professional antigen-presenting cells (APCs) is of great importance for the efficient induction of protective immunity. We analyzed whether the efficacy of an adenovirus-based retroviral vaccine can be enhanced by coadministration of adenovirus-encoded chemokines that attract and stimulate APCs. In the Friend retrovirus (FV) mouse model we coexpressed CCL3, CCL20, CCL21, or CXCL14 from adenoviral vectors, together with FV Gag and Env antigens, and then analyzed immune responses and protection from pathogenic FV infection. Although most tested chemokines did not improve protection against FV challenge, mice that received adenoviral vectors encoding CCL3 together with FV antigens showed significantly better control over viral loads and FV-induced disease than mice immunized with the viral antigens only. Improved protection correlated with enhanced virus-specific CD4+T cell responses and higher neutralizing antibody titers. To apply these results to an HIV vaccine, mice were immunized with adenoviral vectors encoding the HIV antigens Env and Gag-Pol and coadministered vectors encoding CCL3. Again, this combination vaccine induced higher virus-specific antibody titers and CD4+T cell responses than did the HIV antigens alone. These results indicate that coexpression of the chemokine CCL3 by adenovirus-based vectors may be a promising tool to improve antiretroviral vaccination strategies.
Varicella-Zoster Virus Inhibition of the NF-κB Pathway during Infection of Human Dendritic Cells: Role for Open Reading Frame 61 as a Modulator of NF-κB Activity
Authors: Sloan Elizabeth , Henriquez Rodney , Kinchington Paul R. , Slobedman Barry , Abendroth Allison 
Published: November 2011

ABSTRACT
Dendritic cells (DC) are antigen-presenting cells essential for initiating primary immune responses and therefore an ideal target for viral immune evasion. Varicella-zoster virus (VZV) can productively infect immature human DCs and impair their function as immune effectors by inhibiting their maturation, as evidenced by the expression modulation of functionally important cell surface immune molecules CD80, CD86, CD83, and major histocompatibility complex I. The NF-κB pathway largely regulates the expression of these immune molecules, and therefore we sought to determine whether VZV infection of DCs modulates the NF-κB pathway. Nuclear localization of NF-κB p50 and p65 indicates pathway activation; however, immunofluorescence studies revealed cytoplasmic retention of these NF-κB subunits in VZV-infected DCs. Western blotting revealed phosphorylation of the inhibitor of κBα (IκBα) in VZV-infected DCs, indicating that the pathway is active at this point. We conclude that VZV infection of DC inhibits the NF-κB pathway following protein phosphorylation but before the translocation of NF-κB subunits into the nucleus. An NF-κB reporter assay identified VZV open reading frame 61 (ORF61) as an inhibitor of tumor necrosis factor alpha-induced NF-κB reporter activity. Mutational analysis of ORF61 identified the E3 ubiquitin ligase domain as a region required for NF-κB pathway inhibition. In summary, we provide evidence that VZV inhibits the NF-κB signaling pathway in human DCs and that the E3 ubiquitin ligase domain of ORF61 is required to modulate this pathway. Thus, this work identifies a mechanism by which VZV modulates host immune function.
Transmissible Gastroenteritis Coronavirus RNA-Dependent RNA Polymerase and Nonstructural Proteins 2, 3, and 8 Are Incorporated into Viral Particles
Authors: Nogales Aitor , Márquez-Jurado Silvia , Galán Carmen , Enjuanes Luis , Almazán Fernando 
Published: November 2011

ABSTRACT
Coronavirus replication and transcription are processes mediated by a protein complex, with the RNA-dependent RNA polymerase (RdRp) as a main component. Proteomic analysis of highly purified transmissible gastroenteritis virus showed the RdRp to be a component of the viral particles. This finding was confirmed by Western blotting, immunofluorescence, and immunoelectron microscopy analyses. Interestingly, the replicase nonstructural proteins 2, 3, and 8 colocalized with the RdRp in the viral factories and were also incorporated into the virions.
Exercise prescription: a case for standardised reporting
Authors: Slade Susan Carolyn , Keating Jennifer Lyn 
Published: November 2011

BackgroundStructured, regular exercise is recommended to improve health outcomes. Exercise takes many forms and varies in type, intensity, duration and frequency. The authors used the example of exercise for chronic health conditions to examine how exercise programmes are described and summarised in systematic reviews.MethodsTwo independent reviewers conducted a review of exercise reporting practices using the evidence of exercise effects for chronic conditions as the source material. Inclusion criteria: systematic reviews that summarised the effects of exercise programmes for adults with chronic health conditions. Exclusion criteria: reviews of studies of children and adolescent populations, and non-English publications.ResultsSeventy-three reviews were included. Data on sample size, number of included trials, interventions, comparisons, programme characteristics, exercise components, author conclusions and recommendations were extracted. Seventy-one per cent of reviews reported being unable to adequately describe the exercise programmes, because the required information was not reported in included trials. Using key exercise descriptors from the included reviews, the authors developed criteria for reporting to a level that enables replication.ConclusionsAll included reviews recommended better and standardised reporting. Incomplete exercise programme descriptions limit confidence in the accurate replication of effective interventions and limits critical appraisal of interventions when conflicting outcomes are reported. The evaluation and implementation of physical activity and exercise research would be facilitated if exercise programmes are comprehensively described. The authors propose that systematic reviews/meta-analysis and clinical application of the outcomes of exercise therapy research would be enhanced if authors used an exercise reporting grid that includes a detailed description of the programme components.
Parenteral methotrexate for patients with Crohn's disease: how to develop a high-quality and safe self-administration service: Figure 1
Authors: Coltart Iona , Blackmore Laura , Caisley Jane , Harris Adam 
Published: November 2011

Parenteral methotrexate is recommended for patients with Crohn's disease who have failed treatment with thiopurines. There is no good evidence for the use of oral methotrexate, yet patients frequently receive this due to the difficulties associated with prescribing and administering an unlicensed, cytotoxic drug.We present our experience of developing a local service to provide our patients with the option to self-administer parenteral methotrexate in a safe and structured manner at home.
Incidence of severe work-related injuries among young adult workers in Brazil: analysis of compensation data
Authors: Sousa Santana Vilma , Villaveces Andrés , Bangdwala Shrikant L , W Runyan Carol , Albuquerque Oliveira Paulo Rogerio 
Published: November 2011

ObjectivesTo obtain national estimates of the annual cumulative incidence and incidence density of severe non-fatal injuries using compensation benefits data from the Brazilian National Social Security Institute (INSS), and to describe their sociodemographic distribution among workers aged under 25 years.MethodsData are records of health-related compensation benefits from the Ministry of Social Insurance's information system of compensation benefits of the INSS recorded in 2006. Injuries were cases classified under chapter XIX, ICD-10. The assessment of their relation with work was made by INSS's occupational physician experts. The study population comprised young workers aged 16–24 years.Results59 381 workers received compensation benefits for injuries in the study year. Among them 14 491 (24.4%) were work related, 12 501 (86.3%) were male and 1990 were female workers (13.7%). The annual cumulative incidence rate of work-related injuries (ACI–WI) was 2.9×1000 workers, higher among men (4.2×1000) than women (1.0×1000). The incidence density rate (IDR–WI) was 0.7/1000 full-time equivalent (FTE), higher for men (0.97/1000 FTE) than women (0.24/1000 FTE). Both morbidity measures were higher in the younger group (16–19 years), and inversely related to wage, especially for women in the younger group. Logging, extraction, food/beverage and construction industries had higher ACI–WI and IDR–WI for adolescents and young adult workers of both sex groups.ConclusionsThese findings suggest that the Brazilian labour laws limiting young adult workers in hazardous settings need to be expanded, adding occupations in other extractive industries and certain types of work in the food/beverage manufacturing industries. Social inequalities associated with sex need to be examined further with more detailed data.
The microstructural and rheological evolution of shear zones
Authors: Austin Nicholas J. 
Published: November 2011

Abstract
Evidence of localized strain is ubiquitous in deformed lithospheric rocks. Recent advances in laboratory deformation techniques, including the use of torsion experiments, have enabled the coupling of microstructural and rheological evolution to be investigated in experiments run to strains approaching those reached in many natural shear zones. Further, the increased use of electron backscatter diffraction to quantify crystallographic preferred orientation (CPO) has significantly increased understanding of CPO formation and evolution. Combined, these laboratory and field observations support the assertion that a rock's microstructure is strongly linked to its rheology. However, complete quantification of the coupling between microstructure and rheology is complicated by the fact that rocks have inherently complex microstructures. This paper reviews recent work focused on quantifying the rates of microstructural evolution and the attainment of steady state for two key microstructural parameters: grain size and crystallographic preferred orientation. Theoretical considerations, laboratory measurements and field observations suggest that a full description of all relevant microstructural parameters, and the appropriate evolution equations for these parameters, may be needed to link microstructural and rheological evolution and therefore to quantify the bulk rheology of the lithosphere.
Torsion experiments on coarse-grained dunite: implications for microstructural evolution when diffusion creep is suppressed
Authors: Skemer Philip , Sundberg Marshall , Hirth Greg , Cooper Reid 
Published: November 2011

Abstract

Large strain deformation experiments in torsion were conducted on a coarse-grained natural dunite with a pre-existing lattice preferred orientation (LPO). Experiments were conducted at conditions where deformation by diffusion creep is initially negligible. Microstructural evolution was studied as a function of strain. We observe that the pre-existing LPO persists to a shear strain of at least 0.5. At larger strains, this LPO is transformed. Relict deformed grains exhibit LPO with [100] crystallographic axes at high angles to the shear plane. Unlike previous experimental studies, these axes do not readily rotate into the shear plane with increasing strain. Partial dynamic recrystallization occurs in samples deformed to moderate strains (
γ
>0.5). Recrystallized material forms bands that mostly transect grain interiors. The negligible rate of diffusion creep along relict grain boundaries, as well as the limited nature of dynamic recrystallization, may account for the relatively large strains required to observe evolution of microstructures. Our data support hypotheses based on natural samples that microstructures may preserve evidence of complex deformation histories. Relationships between LPO, seismic anisotropy and deformation kinematics may not always be straightforward.
Slip-system and EBSD analysis on compressively deformed fine-grained polycrystalline olivine
Authors: Farla R. J. M. , Gerald J. D. Fitz , Kokkonen H. , Halfpenny A. , Faul U. H. , Jackson I. 
Published: November 2011

Abstract
A slip-system analysis was performed on two synthetic compressively deformed olivine aggregates, derived from experimental solution–gelation (sol–gel) and natural San Carlos precursors to determine how dislocation density relates to Schmid factor for slip in olivine. Individual grain orientations were measured with electron backscatter diffraction. Using decorated dislocations, grain populations were separated into subsets of high versus low dislocation density. Analysis of preferred orientations and distributions of Schmid factors suggests that there is only weak correlation between Schmid factor and dislocation density, slip on (010)[100] in San Carlos grains but (001)[100] in sol–gel material, with multiple slip or stress heterogeneity in both.
Characterization of microstructures and interpretation of flow mechanisms in naturally deformed, fine-grained anhydrite by means of EBSD analysis
Authors: Hildyard Rebecca C. , Prior David J. , Mariani Elisabetta , Faulkner Daniel R. 
Published: November 2011

Abstract

Anhydrite-rich layers within foreland fold and thrust belts are frequently observed to be the weakest horizon of the sequence. Characterizing the microstructure of anhydrite is therefore important for interpreting the larger-scale deformation history of these rocks. Two microstructures from naturally deformed, fine-grained (<15 µm mean grain size) anhydrite samples from the Triassic Evaporites of the Umbria–Marche Apennines, Italy were analysed using electron backscatter diffraction (EBSD). Microstructural observations, misorientation analysis and crystallographic preferred orientation (CPO) determination were carried out on these samples. Both samples have a CPO characterized by alignment of 〈001〉 and distribution of 〈100〉 and 〈010〉 on a great circle normal to this. This anhydrite 〈001〉 ‘fibre texture’ has not been described before. Microstructure A is characterized by a moderate to weak CPO and a weak shape preferred orientation at 55° to 70° from the trace of the 〈001〉 maximum. Low-angle boundaries are revealed by misorientation analysis. A change in grain size from
c
. 10 to
c
. 7 µm corresponds to reduction in strength of CPO and reduction in the number of low-angle grain boundaries. Microstructure B is characterized by a very strong CPO. The orientation of the CPO changes between different microstructural domains. The 〈001〉 maximum is always perpendicular to the trace of a strong grain elongation and high-angle grain boundaries have misorientations close to 〈001〉, suggesting that the CPO is geometrically controlled: anhydrite grains are platy with 〈001〉 short axes. The origin of the CPO is therefore unclear but it need not relate to dislocation creep deformation. Whether or not CPO relates to dislocation creep, both samples have a high number of lower-angle grain boundaries and internal grain distortions with 〈010〉 and 〈001〉 misorientation axes. These are indicative of dislocation activity and the data are best explained by slip on either (100)[010] (dominant) and (001)[100] or a combination of these. Neither of these slip systems has been recognized before. Both microstructures are interpreted to have undergone dynamic recrystallization, and the weakening of the CPO with decreasing grain size in microstructure A is suggested to be indicative of a grain-boundary sliding mechanism becoming active. Comparison with experimental data shows that creep mechanisms involving dislocations at the observed grain sizes require the differential stress magnitudes driving deformation to be greater than
c
. 100 MPa.
Grain growth and the lifetime of diffusion creep deformation
Authors: Pearce Mark A. , Wheeler John 
Published: November 2011

Abstract
Extreme grain-size reduction due to cataclasis, neocrystallization or phase change results in a switch to diffusion creep and dramatic weakening in deforming rocks. Grain growth increases strength until dislocation creep becomes a significant deformation mechanism. We quantify the ‘lifetime’ of diffusion creep by substituting the normal grain growth law into the diffusion creep flow law to calculate the time taken for dislocation creep to become significant. Stress-temperature and strain-rate-temperature space is outlined where diffusion creep may accommodate significant strain: these regions have an upper temperature limit beyond which grain growth is fast enough to move the rock quickly into the dislocation creep field. For plagioclase the limit lies in the amphibolite facies. Rocks in a mantle upwelling experience grain-size reduction during phase changes. Pressure-dependent grain growth limits the deformation that can be accommodated by diffusion creep. This time limit and associated strain limit is independent of starting grain size with a small dependence on upwelling rate and plume width. In both these tectonic environments, second phases are likely to play a role in the maximum achievable grain size due to grain-boundary pinning. Hence we predict the minimum lifetimes of diffusion-creep-dominated deformation following extreme grain-size reduction.
Microstructures in deforming–reactive systems
Authors: Hobbs Bruce E. , Ord Alison 
Published: November 2011

Abstract
The inter-relationships between mineral reactions and deformation are explored with a view to understanding the development of certain mineral foliations and lineations. The following arguments are presented: (i) the processes involved during mineral reactions in deforming metamorphic rocks are described by coupled reaction–diffusion–deformation equations; (ii) these reactions can become unstable producing compositional patterning in both space (metamorphic differentiation) and time (compositional zoning); (iii) the patterns (foliations and mineral lineations) that result from coupled reaction–diffusion–deformation equations are described by surfaces that approximate minimal surfaces (surfaces of zero mean curvature) and an example of such geometry is given; and (iv) the foliations and mineral lineations that form by such processes are controlled by the evolution of the kinematics of the deformation history and not by the finite strain tensor.
Diffusion-creep modelling of fibrous pressure shadows II: influence of inclusion size and interface roughness
Authors: Berton J. R. , Durney D. W. , Wheeler J. 
Published: November 2011

Abstract
This paper extends previous work by us to gain a fuller appreciation of the physical factors that affect polycrystal diffusion-creep simulations of fibrous pressure-shadow growth around a pyrite inclusion. The earlier work dealt with the effect of diffusion ratio or diffusional conductance of the inclusion/matrix interface. The new work also examines the effects of inclusion geometry: a smaller inclusion of similar smoothness to the original, a regularly serrated inclusion the same size as the original and a coarse irregular inclusion of the same size. The results show: (1) significant enhancement of fibrous pressure-shadow growth and change of matrix strain pattern with decreased inclusion size, similar to an increase in diffusion ratio; (2) approach towards a maximum fibrous pressure-shadow growth at high diffusion ratios in the small-pyrite model; (3) little influence of the model serrations; (4) significant sliding on the interface at low diffusion ratios in all of the models; and (5) enhanced sliding in the irregular-pyrite model at low diffusion ratios. The results are qualitatively consistent with diffusion creep of a single grain interacting with a deforming medium. They demonstrate factors that may influence development of the natural structures under similar conditions in rocks.
Rock mechanics constraints on mid-crustal low-viscosity flow beneath Tibet
Authors: Rutter E. H. , Mecklenburgh J. , Brodie K. H. 
Published: November 2011

Abstract
It has been inferred from various types of geophysical data that the Tibetan middle and upper crust is detached from the underlying lower crust and mantle by a weak, mid-crustal zone involving partial melting at about 30–35 km depth. Previous modelling of the flow has used an arbitrary mid-crustal rheology to match the constraints imposed by the overall flow regime. Here we show that extrapolation of experimental rock mechanics data for solid-state flow of a quartz-dominated Tibetan middle and upper crust, plus flow of partially molten synthetic ‘granitoid’, are consistent with the geophysical constraints and provide an experimentally constrained basis for the modelling of crustal rheology involving partially molten rocks.