bluuebunny/crossref_metadata_2025_split huggingface dataset:
Murine MusD Retrotransposon: Structure and Molecular Evolution of an “Intracellularized” Retrovirus
Authors: Ribet David , Harper Francis , Dewannieux Marie , Pierron Gérard , Heidmann Thierry 
Published: December 2006

ABSTRACT

We had previously identified active autonomous copies of the MusD long terminal repeat-retrotransposon family, which have retained transpositional activity. These elements are closely related to betaretroviruses but lack an envelope (
env
) gene. Here we show that these elements encode strictly intracellular virus-like particles that can unambiguously be identified by electron microscopy. We demonstrate intracellular maturation of the particles, with a significant proportion of densely packed cores for wild-type MusD but not for a protease mutant. We show that the molecular origin of this unexpected intracellular localization is solely dependent on the N-terminal part of the Gag protein, which lacks a functional sequence for myristoylation and plasma membrane targeting: replacement of the N-terminal domain of the MusD matrix protein by that of its closest relative—the Mason-Pfizer monkey virus—led to targeting of the MusD Gag to the plasma membrane, with viral particles budding and being released into the cell supernatant. These particles can further be pseudotyped with a heterologous envelope protein and become infectious, thus “reconstituting” a functional retrovirus prone to proviral insertions. Consistent with its retroviral origin, a sequence with a constitutive transport element-like activity can further be identified at the MusD 3′ untranslated region. A molecular scenario is proposed that accounts for the transition, during evolution, from an ancestral infectious betaretrovirus to the strictly intracellular MusD retrotransposon, involving not only the loss of the
env
gene but also an inability to escape the cell—via altered targeting of the Gag protein—resulting de facto in the generation of a very successful “intracellularized” insertional mutagen.
Electron Cryotomography Reveals the Portal in the Herpesvirus Capsid
Authors: Chang Juan T. , Schmid Michael F. , Rixon Frazer J. , Chiu Wah 
Published: December 2006

ABSTRACT
Herpes simplex virus type 1 is a human pathogen responsible for a range of illnesses from cold sores to encephalitis. The icosahedral capsid has a portal at one fivefold vertex which, by analogy to portal-containing phages, is believed to mediate genome entry and exit. We used electron cryotomography to determine the structure of capsids lacking pentons. The portal vertex appears different from pentons, being located partially inside the capsid shell, a position equivalent to that of bacteriophage portals. Such similarity in portal organization supports the idea of the evolutionary relatedness of these viruses.
Persistent Antigen Presentation after Acute Vesicular Stomatitis Virus Infection
Authors: Turner Damian L. , Cauley Linda S. , Khanna Kamal M. , Lefrançois Leo 
Published: December 2006

ABSTRACTLong-term antigen expression is believed to play an important role in modulation of T-cell responses to chronic virus infections. However, recent studies suggest that immune responses may occur late after apparently acute infections. We have now analyzed the CD8 T-cell response to vesicular stomatitis virus (VSV), which is thought to cause to an infection characterized by rapid virus clearance by innate and adaptive immune system components. Unexpectedly, virus-encoded antigen was detectable more than 6 weeks after intranasal VSV infection in both draining and nondraining lymph nodes by adoptively transferred CD8 T cells. Infection withListeria monocytogenesexpressing the same antigen did not result in prolonged antigen presentation. Weeks after VSV infection, discrete T-cell clustering with dendritic cells within the lymph node was observed after transfer of antigen-specific CD8 T cells. Moreover, memory CD8 T cells as defined by phenotype and function were generated from naïve CD8 T cells entering the response late after infection. These findings suggested that protracted antigen presentation after an apparently acute virus infection may contribute to an ongoing antiviral immune response.
Identification of Differentially Activated Cell-Signaling Networks Associated with Pichinde Virus Pathogenesis by Using Systems Kinomics
Authors: Bowick Gavin C. , Fennewald Susan M. , Scott Erin P. , Zhang LiHong , Elsom Barry L. , Aronson Judith F. , Spratt Heidi M. , Luxon Bruce A. , Gorenstein David G. , Herzog Norbert K. 
Published: December 2006

ABSTRACTPhosphorylation plays a key role in regulating many signaling pathways. Although studies investigating the phosphorylated forms of signaling pathways are now commonplace, global analysis of protein phosphorylation and kinase activity has lagged behind genomics and proteomics. We have used a kinomics approach to study the effect of virus infection on host cell signaling in infected guinea pigs. Delineating the host responses which lead to clearance of a pathogen requires the use of a matched, comparative model system. We have used two passage variants of the arenavirus Pichinde, used as a biosafety level 2 model of Lassa fever virus as it produces similar pathologies in guinea pigs and humans, to compare the host cell responses between infections which lead to either a mild, self-limiting infection or lethal disease. Using this model, we can begin to understand the differences in signaling events which give rise to these markedly different outcomes. By contextualizing these data using pathway analysis, we have identified key differences in cellular signaling matrices. By comparing these differentially involved networks, we have identified a number of key signaling “nodes” which show differential phosphorylations between mild and lethal infections. We believe that these nodes provide potential targets for the development of antiviral therapies by acting at the level of the host response rather than by directly targeting viral proteins.
Replication and Propagation of Attenuated Vesicular Stomatitis Virus Vectors In Vivo: Vector Spread Correlates with Induction of Immune Responses and Persistence of Genomic RNA
Authors: Simon Ian D. , Publicover Jean , Rose John K. 
Published: December 2006

ABSTRACT
Live-attenuated vesicular stomatitis virus (VSV) vectors expressing foreign antigens induce potent immune responses and protect against viral diseases in animal models. Highly attenuated (VSV-CT1) or single-cycle VSV (VSVΔG) vectors induce immune responses lower than those generated by attenuated wild-type VSV vectors when given intranasally. We show here that reduced spread of the more highly attenuated or single-cycle vectors to other organs, including lymph nodes, correlates with the reduction in the immune responses. A reverse transcription, real-time PCR assay for VSV genomic RNA (gRNA) sequences showed long-term persistence of gRNA from replicating vectors in lymph nodes, long after viral clearance. Such persistence may be important for induction of potent immune responses by VSV vectors.
Smoking Relapse during the First Year after Treatment for Early-Stage Non–Small-Cell Lung Cancer
Authors: Walker Mark S. , Vidrine Damon J. , Gritz Ellen R. , Larsen Randy J. , Yan Yan , Govindan Ramaswamy , Fisher Edwin B. 
Published: December 2006

AbstractBackground: Non–small-cell lung cancer patients who continue to smoke after cancer diagnosis are more likely to experience disease recurrence, decreased treatment efficacy, and treatment complications. Despite this, many continue to smoke, with estimates ranging from 13% to ∼60%.Methods: Participants were 154 early-stage, non–small-cell lung cancer patients who had smoked within 3 months before surgery. Patients were followed for 12 months after surgery to assess smoking status and duration of continuous abstinence after surgery. Predictors included medical, smoking history, psychosocial, and demographic characteristics.Results: At some point after surgery, 42.9% of patients smoked; at 12 months after surgery, 36.9% were smoking. Sixty percent of patients who lapsed did so during the first 2 months after surgery. Smoking at follow-up was predicted by shorter quit duration before surgery, more intense Appetitive cravings (expectation of pleasure from smoking), lower income, and having a higher level of education. Time until the first smoking lapse was predicted by shorter quit duration before surgery, more intense Appetitive cravings to smoke, and lower income. Among those who lapsed, greater delay before the lapse was associated with abstinence at the 12-month follow-up assessment.Conclusions: Nearly half of non–small-cell lung cancer patients return to smoking after surgery if they have recent smoking histories. Most initial lapses happen within 2 months and occur in response to more recent smoking and more intense cravings. Findings suggest that interventions to prevent relapse should target those who wait until cancer surgery to quit smoking and should be started as soon as possible after treatment. (Cancer Epidemiol Biomarkers Prev 2006;15(12):2370–7)
Intakes of Fruits, Vegetables, Vitamins A, C, and E, and Carotenoids and Risk of Renal Cell Cancer
Authors: Lee Jung Eun , Giovannucci Edward , Smith-Warner Stephanie A. , Spiegelman Donna , Willett Walter C. , Curhan Gary C. 
Published: December 2006

Abstract
Background: Fruits and vegetables rich in antioxidants have been proposed to reduce the risk of renal cell cancer. However, few prospective studies have examined the intakes of fruits, vegetables, and antioxidant vitamins in relation to the risk of renal cell cancer.
Methods: We prospectively examined the associations between the intakes of fruits, vegetables, vitamins A, C, and E, and carotenoids and risk of renal cell cancer in women and men. We followed 88,759 women in the Nurses' Health Study from 1980 to 2000, and 47,828 men in the Health Professionals Follow-up Study from 1986 to 2000. We assessed dietary intake every 2 to 4 years using a validated semiquantitative food frequency questionnaire. The Cox proportional hazards model was used to estimate study-specific multivariate relative risks (RR), which were pooled using a random effects model.
Results: A total of 248 (132 women and 116 men) incident renal cell cancer cases were ascertained during 2,316,525 person-years of follow-up. The consumption of fruits and vegetables was associated with a decreased risk of renal cell cancer in men (multivariate RR, 0.45; 95% CI, 0.25-0.81, for ≥6 servings of fruit and vegetable intake/d versus &lt;3 servings/d; P test for trend = 0.02), but not in women (multivariate RR, 1.17; 95% CI, 0.66-2.07, for the same contrast; P test for trend = 0.25; P test for between-studies heterogeneity = 0.02). Intakes of vitamins A and C from food and carotenoids were inversely associated with the risk of renal cell cancer in men only, but we cannot exclude the possibility that this was due to other factors in fruit and vegetables. No clear association was observed for vitamin E in women or men.
Conclusions: Fruit and vegetable consumption may reduce the risk of renal cell cancer in men. (Cancer Epidemiol Biomarkers Prev 2006;12(24):2445–52)
Cigarette Smoking and Survival after Ovarian Cancer Diagnosis
Authors: Nagle Christina M. , Bain Christopher J. , Webb Penelope M. 
Published: December 2006

Abstract
We have examined the association between cigarette smoking and ovarian cancer survival in 676 women with invasive epithelial ovarian cancer, recruited into a case-control study in the early 1990s. Information about cigarette smoking and other personal and reproductive factors was obtained from a personal interview at the time of diagnosis. Cox proportional hazards models were used to evaluate the association between cigarette smoking and time to ovarian cancer death. Current smokers at diagnosis were more likely to die early than women who had never smoked [adjusted hazard ratio (HR), 1.36; 95% confidence interval (95% CI), 1.01-1.84]. Increased risks of dying were greater among those who had accumulated more pack-years of smoking (HR for 30+ pack-years compared with never smokers, 1.94; 95% CI, 1.41-2.66) and smoked more cigarettes per day (HR, 1.93; 95% CI, 1.37-2.73). All these associations were stronger among women with late-stage disease (HR for current versus never smokers, 1.58; 95% CI, 1.15-2.18). Time since quitting had little effect on survival after adjusting for lifetime smoking exposure. These results validate and extend recent findings and suggest that premorbid cigarette smoking is related to worse outcome in ovarian cancer patients. (Cancer Epidemiol Biomarkers Prev 2006;15(12):2557–60)
Physical Activity and Risk of Colon and Rectal Cancers: The European Prospective Investigation into Cancer and Nutrition
Authors: Friedenreich Christine , Norat Teresa , Steindorf Karen , Boutron-Ruault Marie-Christine , Pischon Tobias , Mazuir Mathieu , Clavel-Chapelon Françoise , Linseisen Jakob , Boeing Heiner , Bergman Manuela , Johnsen Nina Fons , Tjønneland Anne , Overvad Kim , Mendez Michelle , Quirós J. Ramón , Martinez Carmen , Dorronsoro Miren , Navarro Carmen , Gurrea Aurelio Barricarte , Bingham Sheila , Khaw Kay-Tee , Allen Naomi , Key Tim , Trichopoulou Antonia , Trichopoulos Dimitrios , Orfanou Natassa , Krogh Vittorio , Palli Domenico , Tumino Rosario , Panico Salvatore , Vineis Paolo , Bueno-de-Mesquita H. Bas , Peeters Petra H.M. , Monninkhof Evelyn , Berglund Göran , Manjer Jonas , Ferrari Pietro , Slimani Nadia , Kaaks Rudolf , Riboli Elio 
Published: December 2006

AbstractWe investigated several aspects of the role of physical activity in colon and rectal cancer etiology that remain unclear in the European Prospective Investigation into Nutrition and Cancer. This cohort of 413,044 men and women had 1,094 cases of colon and 599 cases of rectal cancer diagnosed during an average of 6.4 years of follow-up. We analyzed baseline data on occupational, household, and recreational activity to examine associations by type of activity, tumor subsite, body mass index (BMI), and energy intake. The multivariate hazard ratio for colon cancer was 0.78 [95% confidence interval (95% CI), 0.59-1.03] among the most active participants when compared with the inactive, with evidence of a dose-response effect (Ptrend = 0.04). For right-sided colon tumors, the risk was 0.65 (95% CI, 0.43-1.00) in the highest quartile of activity with evidence of a linear trend (Ptrend = 0.004). Active participants with a BMI under 25 had a risk of 0.63 (95% CI, 0.39-1.01) for colon cancer compared with the inactive. Finally, an interaction between BMI and activity (Pinteraction = 0.03) was observed for right-sided colon cancers; among moderately active and active participants with a BMI under 25, a risk of 0.38 (95% CI, 0.21-0.68) was found as compared with inactive participants with BMI &gt;30. No comparable decreased risks were observed for rectal cancer for any type of physical activity for any subgroup analyses or interactions considered. We found that physical activity reduced colon cancer risk, specifically for right-sided tumors and for lean participants, but not rectal cancer. (Cancer Epidemiol Biomarkers Prev 2006;15(12):2398–407)
Microphysical and Optical Properties of Atmospheric Ice Crystals at South Pole Station
Authors: Lawson R. Paul , Baker Brad A. , Zmarzly Patrick , O’Connor Darren , Mo Qixu , Gayet Jean-Francois , Shcherbakov Valery 
Published: December 2006

Abstract
In early February 2001 (during the austral summer), over 900 000 digital images of ice crystals were recorded at the South Pole using two ground-based cloud particle imagers (CPIs). Of these, 721 572 crystals &gt;50 μm were classified into crystal habits. When sorted by number, 30% of the crystals were rosette shaped (mixed-habit rosettes, platelike polycrystals, and rosette shapes with side planes), 45% were diamond dust (columns, thick plates, and plates), and 25% were irregular. When sorted by area, rosette shapes comprised 50%, diamond dust 30% and irregular 20%. By mass, the percentages were 57% rosette shapes, 23% diamond dust, and 20% irregular. Particle size distributions as a function of maximum dimension and equivalent radius are compared with previous studies. Particles are generally found to be slightly larger than previous austral wintertime studies. In 2002, a polar nephelometer (PN) that measures scattering phase function was incorporated with one of the CPIs. Correlated measurements between the two instruments showed that 22° and 46° peaks in the phase function were present when diamond dust was recorded by the CPI, but not when rosette shapes were present. Visual observations confirmed the presence of 22° and 46° atmospheric halos in some, but not all, of the diamond dust events. No visual halos were observed when rosette shapes were precipitating. Average PN phase functions are presented for diamond dust and rosette shapes. The diamond dust and rosette-shaped ice crystals appear to be very similar in shape to those observed by CPIs in cirrus clouds. Cloud conditions at the South Pole that were associated with various crystal types are discussed, as are some effects of blowing snow.
A comparative study of the morphology, chemical composition and weathering of rhyolitic and andesitic glass
Authors: Kirkman J. H. , McHardy W. J. 
Published: December 2006

AbstractThe morphology of volcanic glass particles in rhyolitic and andesitic tephra of central North Island and Taranaki areas of New Zealand has been studied by scanning electron microscopy. Electron probe analyses of the glasses are compared with those of the clays to which they weather. Loss of silica characterizes the weathering of both glasses. The rapid rate of weathering of andesitic glass is attributed to its occurrence as fine, soft microlites and extensive substitution of Al for Si in the structure. Rhyolitic glass weathers more slowly because it occurs as hard and brittle particles containing relatively little alumina. It is suggested that the structure, chemical composition and chemical activity of allophane is governed largely by the chemical composition and bonding characteristics of the parent glass.
Quantitative determination of the interlamellar volume in an interstratified mica-smectite soil clay
Authors: Jones A. A. , Greenland D. J. 
Published: December 2006

AbstractTwo well-characterized soils containing substantial amounts of interstratified mica-smectite have been examined by a combination of techniques in an attempt to correlate the characteristics of the interlamellar surfaces with other properties. The techniques used included XRD and chemical analyses, determination of surface area by nitrogen sorption and by desorption of water and ethylene glycol monoethyl ether vapour, and determination of cation exchange capacity. Reasonable agreement was found between the results obtained for the proportion of expanding or smectite-like surfaces, although estimates by XRD, especially when coarser material (> 2/µm) was included, were generally lower than those obtained by the other methods. The mean density of charge on the surfaces of the soil clays appeared to be similar to that of smectite. The decrease in porosity observed for both soils dried by the critical point method was largely accounted for by the decrease in volume associated with the loss of interlamellar water from the smectite-like interlamellar surfaces included within the clay fraction.
Structure de l'espace interlamellaire des vermiculites Ba monocouches
Authors: Alcover J. F. , Gatineau L. 
Published: December 2006

RésuméL'interprétation des diffusions en dehors des taches de Bragg dans une vermiculite saturée par du baryum (d001 = 12·20 Å) permet de préciser l'organisation de l'espace interlamellaire. Le motif élémentaire est constitué par un groupement Ba-6 H2O où le baryum est engagé dans une cavité ditrigonale et les 6 molécules d'eau sont dans le plan médian, l'ensemble forme une pyramide très aplatie de base hexagonale. La répartition de ces motifs est bipériodique avec une maille 2 a,b centrée en projection. Cette organisation se développe dans des domaines identiques, orientés à 120° les uns des autres.
Clay mineral diagenesis in two East African lake sediments
Authors: Singer A. , Stoffers P. 
Published: December 2006

AbstractThe vertical clay mineral distribution pattern in two sediment cores taken from two East African lakes has been studied in detail. In the core from Lake Albert (Mobutu Sese Seko) a clay assemblage consisting principally of smectite with some illite and kaolinite in the uppermost segment of the core changed with depth into first a mixed-layer illite-smectite dominated clay and then at 6·60 m into an iltite dominated clay. Lower in the core there was again a transition towards interlayer mixtures, and in the bottom segment towards smectite. These changes are interpreted as a diagenetic transformation of smectite into illite, effected by saline palaeo-lake water with an unusually high K/Na ratio. Three smectite→illite-smectite→illite transition cycles were recognized in a 56 m deep sediment core from Lake Manyara. The sections in which illite dominated contained silt-sized analcime, while those with interlayer mixtures contained alkaline zeolites. The diagenetic illitization of smectite appeared to parallel the process of analcime formation, the K necessary for illitization being released during K,Na-zeolite→analcime transformation. These occurrences suggest that high temperature and pressure may not constitute absolute prerequisites for the diagenetic illitization of smectite.
The application of electron spin resonance spectroscopy to studies of clay minerals: I. Isomorphous substitutions and external surface properties
Authors: Hall Peter L. 
Published: December 2006

AbstractElectron spin resonance (ESR) spectroscopy has contributed significantly to the identification and characterization of paramagnetic impurities associated with clays. Following a brief discussion of the general principles of the technique, a review is given of the application of ESR to the study of those paramagnetic species (chiefly iron and radiation-induced lattice defects) located either within the aluminosilicate structure or present as an external impurity phase.
Effect of thermal treatment on lanthanide montmorillonites: dehydration
Authors: Mozas T. , Bruque S. , Rodriguez A. 
Published: December 2006

AbstractHydration/dehydration behaviour and the effect of various thermal treatments on montmorillonites saturated with lanthanide ions have been investigated by X-ray diffraction, thermal analysis (DTA, TG, DTG), IR spectroscopy and sorption-desorption of water vapour techniques. Heating at 150°C under 10−5 torr did not eliminate all the interlayer water of the montmorillonite, neither did it affect the CEC. Heating above 160°C caused a reduction in CEC. At 25°C La-montmorillonite takes up a maximum of three water layers in the interlayer space, the water molecules adopting a nonacoordinated distribution around the La3+ cation.
Alteration of imogolite by dry grinding
Authors: Henmi Teruo , Yoshinaga Naganori 
Published: December 2006

AbstractThe effects of dry grinding on the structure, morphology and properties of imogolite have been investigated by means of X-ray powder diffraction analysis, IR, DTA, and measurements of CEC and specific surface area. Imogolite is very susceptible to alteration by grinding compared to layer silicate minerals such as halloysite, kaolinite and montmorillonite. In the earlier stages of grinding, the parallel array of imogolite tubular structure units is markedly disturbed. On further grinding, disruption of Si-O-Al linkages, polymerization of the silica component released and loss of structural OH groups proceed simultaneously, these changes eventually resulting in complete breakdown of the structure. Ground imogolite is reaggregated finally into granular particles of irregular shape. All these changes are associated with a decrease in water holding capacity, CEC and specific surface area.