bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of T1249-Resistant Human Immunodeficiency Virus Type 1 Variants
Authors: Eggink Dirk , Baldwin Christopher E. , Deng Yiqun , Langedijk Johannes P. M. , Lu Min , Sanders Rogier W. , Berkhout Ben 
Published: April 2008

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) entry is an attractive target for therapeutic intervention. Two drugs that inhibit this process have been approved: the fusion inhibitor T20 (enfuvirtide [Fuzeon]) and, more recently, the CCR5 blocker maraviroc (Selzentry). T1249 is a second-generation fusion inhibitor with improved antiviral potency compared to the first-generation peptide T20. We selected T1249-resistant HIV-1 variants in vitro by serial virus passage in the presence of increasing T1249 doses after passage with wild-type and T20-resistant variants. Sequence analysis revealed the acquisition of substitutions within the HR1 region of the gp41 ectodomain. The virus acquired mutations of residue V38 to either E or R in 10 of 19 cultures. Both E and R at position 38 were confirmed to cause resistance to T1249, as well as cross-resistance to T20 and C34, but not to the third-generation fusion inhibitor T2635. We also observed substitutions at residues 79 and 90 (Q79E and K90E), which provide modest resistance to T1249 and, interestingly, T2635. Thus, the gp41 amino acid position implicated in T20 resistance (V38 replaced by A, G, or W) is also responsible for T1249 resistance (V38 replaced by E, R, or K). These results indicate that T20 and T1249 exhibit very similar inhibition modes that call for similar but not identical resistance mutations. All T1249-resistant viruses with changes at position 38 are cross resistant to T20, but not vice versa. Furthermore, substitutions at position 38 do not provide resistance to the third-generation inhibitor T2635, while substitution at positions 79 and 90 do, suggesting different resistance mechanisms.
Oligomerization of ICP4 and Rearrangement of Heat Shock Proteins May Be Important for Herpes Simplex Virus Type 1 Prereplicative Site Formation
Authors: Livingston Christine M. , DeLuca Neal A. , Wilkinson Dianna E. , Weller Sandra K. 
Published: April 2008

ABSTRACT
Herpes simplex virus type 1 (HSV-1) DNA replication occurs in replication compartments that form in the nucleus by an ordered process involving a series of protein scaffold intermediates. Following entry of viral genomes into the nucleus, nucleoprotein complexes containing ICP4 can be detected at a position adjacent to nuclear domain 10 (ND10)-like bodies. ND10s are then disrupted by the viral E3 ubiquitin ligase ICP0. We have previously reported that after the dissociation of ND10-like bodies, ICP8 could be observed in a diffuse staining pattern; however, using more sensitive staining methods, we now report that in addition to diffuse staining, ICP8 can be detected in tiny foci adjacent to ICP4 foci. ICP8 microfoci contain UL9 and components of the helicase-primase complex. HSV infection also results in the reorganization of the heat shock cognate protein 70 (Hsc70) and the 20S proteasome into virus-induced chaperone-enriched (VICE) domains. In this report we show that VICE domains are distinct but adjacent to the ICP4 nucleoprotein complexes and the ICP8 microfoci. In cells infected with an ICP4 mutant virus encoding a mutant protein that cannot oligomerize on DNA, ICP8 microfoci are not detected; however, VICE domains could still be formed. These results suggest that oligomerization of ICP4 on viral DNA may be essential for the formation of ICP8 microfoci but not for the reorganization of host cell chaperones into VICE domains.
Mutations in the Amino Terminus of Foamy Virus Gag Disrupt Morphology and Infectivity but Do Not Target Assembly
Authors: Life Rachel B. , Lee Eun-Gyung , Eastman Scott W. , Linial Maxine L. 
Published: April 2008

ABSTRACT
Foamy viruses (FVs) assemble using pathways distinct from those of orthoretroviruses. FV capsid assembly takes place near the host microtubule-organizing center (MTOC). Assembled capsids then migrate by an unknown mechanism to the trans-Golgi network to colocalize with the FV glycoprotein, Env. Interaction with Env is required for FV capsid egress from cells; the amino terminus of FV Gag contains a cytoplasmic targeting/retention signal that is responsible for targeting assembly to the MTOC. A mutant Gag was constructed by addition of a myristylation (M) signal in an attempt to target assembly to the plasma membrane and potentially overcome the dependence upon Env for budding (S. W. Eastman and M. L. Linial, J. Virol. 75:6857-6864, 2001). Using this and additional mutants, we now show that assembly is not redirected to the plasma membrane. Addition of an M signal leads to gross morphological defects. The aberrant particles still assemble near the MTOC but do not produce infectious virus. Although extracellular Gag can be detected in a pelletable form in the absence of Env, the mutant particles contain very little genomic RNA and are less dense. Our analyses indicate that the amino terminus of Gag contains an Env interaction domain that is critical for bona fide egress of assembled capsids.
Citrus Tristeza Virus
: Survival at the Edge of the Movement Continuum
Authors: Folimonova Svetlana Y. , Folimonov Alexey S. , Tatineni Satyanarayana , Dawson William O. 
Published: April 2008

ABSTRACT

Systemic invasion of plants by viruses is thought to involve two processes: cell-to-cell movement between adjacent cells and long-distance movement that allows the virus to rapidly move through sieve elements and unload at the growing parts of the plant. There is a continuum of proportions of these processes that determines the degrees of systemic infection of different plants by different viruses. We examined the systemic distribution of
Citrus tristeza virus
(CTV) in citrus species with a range of susceptibilities. By using a “pure” culture of CTV from a cDNA clone and green fluorescent protein-labeled virus we show that both cell-to-cell and long-distance movement are unusually limited, and the degree of limitation varies depending on the citrus host. In the more-susceptible hosts CTV infected only a small portion of phloem-associated cells, and moreover, the number of infection sites in less-susceptible citrus species was substantially decreased further, indicating that long-distance movement was reduced in those hosts. Analysis of infection foci in the two most differential citrus species,
Citrus macrophylla
and sour orange, revealed that in the more-susceptible host the infection foci were composed of a cluster of multiple cells, while in the less-susceptible host infection foci were usually single cells, suggesting that essentially no cell-to-cell movement occurred in the latter host. Thus, CTV in sour orange represents a pattern of systemic infection in which the virus appears to function with only the long-distance movement mechanism, yet is able to survive in nature.
Human T-Cell Leukemia Virus Type 1 Tax Attenuates the ATM-Mediated Cellular DNA Damage Response
Authors: Chandhasin Chandtip , Ducu Razvan I. , Berkovich Elijahu , Kastan Michael B. , Marriott Susan J. 
Published: April 2008

ABSTRACT
Genomic instability, a hallmark of leukemic cells, is associated with malfunctioning cellular responses to DNA damage caused by defective cell cycle checkpoints and/or DNA repair. Adult T-cell leukemia, which can result from infection with human T-cell leukemia virus type 1 (HTLV-1), is associated with extensive genomic instability that has been attributed to the viral oncoprotein Tax. How Tax influences cellular responses to DNA damage to mediate genomic instability, however, remains unclear. Therefore, we investigated the effect of Tax on cellular pathways involved in recognition and repair of DNA double-strand breaks. Premature attenuation of ATM kinase activity and reduced association of MDC1 with repair foci were observed in Tax-expressing cells. Following ionizing radiation-induced S-phase checkpoint activation, Tax-expressing cells progressed more rapidly than non-Tax-expressing cells toward DNA replication. These results demonstrate that Tax expression may allow premature DNA replication in the presence of genomic lesions. Attempts to replicate in the presence of these lesions would result in gradual accumulation of mutations, leading to genome instability and cellular transformation.
What happened to smokers’ beliefs about light cigarettes when “light/mild” brand descriptors were banned in the UK? Findings from the International Tobacco Control (ITC) Four Country Survey
Authors: Borland R , Fong G T , Yong H-H , Cummings K M , Hammond D , King B , Siahpush M , McNeill A , Hastings G , O’Connor R J , Elton-Marshall T , Zanna M P 
Published: April 2008

Aim:This paper examines how beliefs of smokers in the UK were affected by the removal of “light” and “mild” brand descriptors, which came into effect on 30 September 2003 for Member States of the European Union (EU).Participants:The data come from the first four waves (2002–2005) of the International Tobacco Control Policy Evaluation (ITC) Four-Country Survey, an annual cohort telephone survey of adult smokers in Canada, USA, UK and Australia (15 450 individual cases).Design:The UK ban on misleading descriptors occurred around the second wave of data collection in the ITC survey, permitting us to compare beliefs about light cigarettes among adult smokers in the UK before and after the ban, with beliefs in the three other ITC countries unaffected by the ban.Results:There was a substantial decline in reported beliefs about the benefits of light cigarettes in the UK following the policy change and an associated public information campaign, but by 2005 (ie, wave 4), these beliefs rebounded slightly and the change in beliefs was no greater than in the USA, where there was no policy change.Conclusions:The findings reveal that high levels of misperceptions about light cigarettes existed among smokers in all four countries before and after the EU ban took effect. We cannot conclude that the policy of removing some aspects of misleading labels has been effective in changing beliefs about light cigarettes. Efforts to correct decades of consumer misperceptions about light cigarettes must extend beyond simply removing “light” and “mild” brand descriptors.
Interactive effects of condensed tannin and cellulose additions on soil respiration
Authors: Madritch Michael D. , Jordan Lisa M. , Lindroth Richard L. 
Published: April 2008

Plant polyphenolics are receiving increased attention for their influences on belowground processes. Tannins are of particular interest because of their predominance in natural systems, their wide variation in both quality and quantity, and their protein-binding abilities. Current theory holds that simple phenolics increase microbial activity by acting as carbon substrates, while larger tannins decrease microbial activity by binding with organic nitrogen such as proteins. Here, we present results from a simple microcosm experiment that demonstrates that the influence of condensed tannins on soil respiration depends on the availability of additional carbon substrates. We purified tannins from trembling aspen ( Populus tremuloides Michx.) and crossed three levels of tannin additions with three levels of cellulose additions in laboratory microcosms. Soil respiration was measured over 36 days. In the absence of cellulose, high amounts of condensed tannins increased cumulative soil respiration. In the presence of abundant cellulose, condensed tannins decreased cumulative soil respiration. The positive and negative effects of purified tannins on soil respiration are time dependent, such that initial respiration is likely tannin induced, while later respiration is cellulose induced and tannin limited.
Growth of epiphytic old forest lichens across climatic and successional gradients
Authors: Gauslaa Y. , Palmqvist K. , Solhaug K. A. , Holien H. , Hilmo O. , Nybakken L. , Myhre L. C. , Ohlson M. 
Published: April 2008

This paper aims to assess the influence of canopy cover on lichen growth in boreal forests along a regional forest gradient. Biomass and area gain, and some acclimation traits, were assessed in the old-forest lichens Lobaria pulmonaria (L.) Hoffm., Pseudocyphellaria crocata (L.) Vain., and Usnea longissima Ach. transplanted 110 days in three successional Norway spruce ( Picea abies (L.) Karst.) forest stands (clearcut, young, and old forest) repeated along a rainfall gradient (continental, suboceanic, and Atlantic zones) in Scandinavia. Lichen growth peaked in Atlantic rainforests with mean dry matter (DM) gain up to 36%–38%. The alectorioid lichen U. longissima showed the widest range of growth responses and no signs of chlorophyll degradation. Its highest DM gain consistently occurred in clearcuts, whereas the DM gain was close to zero in the shadiest young forest. The two foliose lichens L. pulmonaria and P. crocata exhibited maximal growth rates in old forests, but apparently growth was limited by low light even in old forests. Their DM gain was reduced in the most sun-exposed clearcuts due to chlorophyll degradation and was relatively high under closed young canopies, suggesting a better adaptation to shade. The lichen responses show that a high frequency and dominance of young and dense fast-growing forest stands at a landscape level are not compatible with large populations of these old-forest lichens and that a lack of lichens under an industrial forestry regime may not necessarily be determined by low dispersal efficiency only.
Relationships among litterfall, fine-root growth, and soil respiration for five tropical tree species
Authors: Valverde-Barrantes Oscar J. 
Published: April 2008

Although significant advances have been made in understanding terrestrial carbon cycling, there is still a large uncertainty about the variability of carbon (C) fluxes at local scales. Using a carbon mass-balance approach, I investigated the relationships between fine detritus production and soil respiration for five tropical tree species established on 16-year-old plantations. Total fine detritus production ranged from 0.69 to 1.21 kg C·m–2·year–1with significant differences among species but with no correlation between litterfall and fine-root growth. Soil CO2emissions ranged from 1.61 to 2.36 kg C·m–2·year–1with no significant differences among species. Soil respiration increased with fine-root production but not with litterfall, suggesting that soil C emissions may depend more on belowground inputs or that both fine root production and soil respiration are similarly influenced by an external factor. Estimates of root + rhizosphere respiration comprised 52% of total soil respiration on average, and there was no evidence that rhizosphere respiration was associated with fine-root growth rates among species. These results suggest that inherent differences in fine-root production among species, rather than differences in aboveground litterfall, might play a main role explaining local-scale, among-forest variations in soil C emissions.
Forest soil rehabilitation with tillage and wood waste enhances seedling establishment but not height after 8 years
Authors: Bulmer C. , Venner K. , Prescott C. 
Published: April 2008

We evaluated soil conditions of rehabilitated log landings in the Interior Douglas-fir biogeoclimatic zone of British Columbia during the first 3 years after treatment and the growth of lodgepole pine ( Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) on these log landings over 8 years. Rehabilitation treatments included combinations of tillage and the addition of either stockpiled topsoil or one of three organic amendments: hog fuel, sort-yard waste, and a wood waste – biosolids compost. The woody amendments were either applied as a surface mulch or incorporated into the soil after tillage. Tillage and addition of wood waste reduced soil bulk density and increased carbon content. Daytime soil temperatures in summer were lower under a hog fuel mulch than for the other treatments. The plots receiving hog fuel also had higher soil moisture content. One year after treatment, soil mechanical resistance for untreated soils, and those that were simply tilled, exceeded 2500 kPa for much of the growing season. Plots receiving wood waste had lower mechanical resistance. Use of wood waste in rehabilitation improved soil conditions and contributed to improved survival rates for planted lodgepole pine seedlings. Height growth after 8 years was not significantly affected by the treatments.
Genetic relationships of meadow vole (Microtus pennsylvanicus) populations in central Appalachian wetlands
Authors: Francl K. E. , Glenn T. C. , Castleberry S. B. , Ford W. M. 
Published: April 2008

We sequenced and compared variation within a 375-base-pair segment of the mitochondrial DNA control region of 323 meadow voles ( Microtus pennsylvanicus (Ord, 1815)) among 14 populations to determine the influence of past and present landscape connectivity among isolated wetlands in the central Appalachian Mountains. To best explain observed differences among sites, we used genetic and landscape-level (GIS) data to test a null hypothesis (no genetic differences) and three alternate explanations of significant variation owing to founder effects, effective population size, or isolation by distance. Sequencing results revealed 16 distinct haplotypes (1–8 haplotypes/site), with two present in samples from most wetlands, and half of the remaining haplotypes concentrated in specific geographic clusters. Our findings best support the explanation that founder effects have influenced current genetic patterns among sites. These founder effects are likely due to historical land-use activities such as exploitative logging (ca. 1880–1920; creating early successional habitats for voles) and subsequent forest regeneration over the past half century; they were also likely influenced by postglacial colonization patterns. Therefore, current genetic diversity in these populations seems to largely reflect the number and source of voles that successfully colonized these isolated wetlands during the window of opportunity immediately following extensive logging.
Early survival of Punjab urial
Authors: Awan Ghulam Ali , Festa-Bianchet Marco , Gaillard Jean-Michel 
Published: April 2008

There is almost no information on age-specific survival of Asiatic ungulates based on mark–recapture studies. Survival of marked Punjab urial ( Ovis vignei punjabiensis Lydekker, 1913) aged 0–2 years was studied in the Salt Range, Pakistan, in 2001–2005. Male lambs were heavier than females at birth. The relationship between litter size and birth mass varied among years, with a tendency for twins to be lighter than singletons. Birth mass had a positive but nonsignificant relation with survival to 1 year. Neither sex nor litter size affected survival to 1 year, which averaged 55% (95% CI = 41%–68%). There was no sex effect on survival of yearlings, which averaged 88% (95% CI = 4%–100%). Although survival of lambs and yearlings was similar to that reported for other ungulates, apparent survival of 2- and 3-year-olds was very low at only 47%, possibly because of emigration. Early survival in this protected area is adequate to allow population growth, but more data are required on adult survival.
Comments on the Rate of Convergence between Mann and Ishikawa Iterations Applied to Zamfirescu Operators
Authors: Qing Yuan , Rhoades B. E. 
Published: April 2008

AbstractIn the work of Babu and Vara Prasad (2006), the claim is made that Mann iteration converges faster than Ishikawa iteration when applied to Zamfirescu operators. We provide an example to demonstrate that this claim is false.
Las estrategias de aculturación de los inmigrantes: su significado psicológico
Authors: Zlobina Anna , Basabe Nekane , Páez Darío 
Published: April 2008

Este trabajo estudia la asociación entre las estrategias de aculturación de los inmigrantes extranjeros en España y sus valores personales, intentando comprender el significado psicológico de dichas estrategias. Se utilizan los datos de una muestra de 1252 inmigrantes provenientes de distintas regiones del mundo (Brasil = 98, Colombia = 296, Ecuador = 325, Europa del Este = 76, Países Árabes = 365, África Subsahariana = 92) con un tiempo de residencia medio de 4,3 años y una edad media de 32,6 años. Se compara la predominancia de distintos tipos de valores en las cuatro estrategias de aculturación—integración, separación, asimilación y marginalización—en los planos actitudinal y conductual. Los análisis revelan que la estrategia de separación se describiría mejor como una postura de conservación grupal sin promocionar el grupo etnocultural propio en la sociedad de acogida; la integración podría describirse como una estrategia de promoción, y la asimilación aparece claramente como una estrategia de movilidad individual y apertura a la nueva cultura. No se ha podido establecer un perfil motivational o de valores de marginalización, probablemente debido a que el instrumento utilizado no diferencia entre el subtipo “cosmopolita” de esta estrategia y el subtipo que describe el estado de anomia y de exclusión social.
Retrievals of Thick Cloud Optical Depth from the Geoscience Laser Altimeter System (GLAS) by Calibration of Solar Background Signal
Authors: Yang Yuekui , Marshak Alexander , Chiu J. Christine , Wiscombe Warren J. , Palm Stephen P. , Davis Anthony B. , Spangenberg Douglas A. , Nguyen Louis , Spinhirne James D. , Minnis Patrick 
Published: April 2008

Abstract
Laser beams emitted from the Geoscience Laser Altimeter System (GLAS), as well as other spaceborne laser instruments, can only penetrate clouds to a limit of a few optical depths. As a result, only optical depths of thinner clouds (&lt; about 3 for GLAS) are retrieved from the reflected lidar signal. This paper presents a comprehensive study of possible retrievals of optical depth of thick clouds using solar background light and treating GLAS as a solar radiometer. To do so one must first calibrate the reflected solar radiation received by the photon-counting detectors of the GLAS 532-nm channel, the primary channel for atmospheric products. Solar background radiation is regarded as a noise to be subtracted in the retrieval process of the lidar products. However, once calibrated, it becomes a signal that can be used in studying the properties of optically thick clouds. In this paper, three calibration methods are presented: (i) calibration with coincident airborne and GLAS observations, (ii) calibration with coincident Geostationary Operational Environmental Satellite (GOES) and GLAS observations of deep convective clouds, and (iii) calibration from first principles using optical depth of thin water clouds over ocean retrieved by GLAS active remote sensing. Results from the three methods agree well with each other. Cloud optical depth (COD) is retrieved from the calibrated solar background signal using a one-channel retrieval. Comparison with COD retrieved from GOES during GLAS overpasses shows that the average difference between the two retrievals is 24%. As an example, the COD values retrieved from GLAS solar background are illustrated for a marine stratocumulus cloud field that is too thick to be penetrated by the GLAS laser. Based on this study, optical depths for thick clouds will be provided as a supplementary product to the existing operational GLAS cloud products in future GLAS data releases.