bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adenovirus Serotype 26 Utilizes CD46 as a Primary Cellular Receptor and Only Transiently Activates T Lymphocytes following Vaccination of Rhesus Monkeys
Authors: Li Hualin , Rhee Elizabeth G. , Masek-Hammerman Katherine , Teigler Jeffrey E. , Abbink Peter , Barouch Dan H. 
Published: July 2012

ABSTRACTThe cellular receptor utilized by adenovirus serotype 26 (Ad26) has remained unclear. Here we show that Ad26 transduction is CD46-dependent and is efficiently blocked by anti-CD46 but not anti-CAR antibodies, demonstrating that Ad26 utilizes CD46 as a primary cellular receptor. Moreover, following Ad26 vaccination of rhesus monkeys, we did not observe sustained activation of peripheral or mucosal vector-specific CD4+T lymphocytes. These data contribute to our understanding of Ad26 as a candidate vaccine vector.
An Effector Phenotype of CD8+T Cells at the Junction Epithelium during Clinical Quiescence of Herpes Simplex Virus 2 Infection
Authors: Peng Tao , Zhu Jia , Phasouk Khamsone , Koelle David M. , Wald Anna , Corey Lawrence 
Published: July 2012

ABSTRACTHerpes simplex virus 2 infection is characterized by cycles of viral quiescence and reactivation. CD8+T cells persist at the site of viral reactivation, at the genital dermal-epidermal junction contiguous to neuronal endings of sensory neurons, for several months after herpes lesion resolution. To evaluate whether these resident CD8+T cells frequently encounter HSV antigen even during times of asymptomatic viral infection, we analyzed the transcriptional output of CD8+T cells captured by laser microdissection from human genital skin biopsy specimens during the clinically quiescent period of 8 weeks after lesion resolution. These CD8+T cells expressed a characteristic set of genes distinct from those of three separate control cell populations, and network and pathway analyses revealed that these T cells significantly upregulated antiviral genes such asGZMB,PRF1,INFG,IL-32, andLTA, carbohydrate and lipid metabolism-related genes such asGLUT-1, and chemotaxis and recruitment genes such asCCL5andCCR1, suggesting a possible feedback mechanism for the recruitment of CD8+T cells to the site of infection. Many of these transcripts are known to have half-lives of <48 h, suggesting that cognate antigen is released frequently into the mucosa and that resident CD8+T cells act as functional effectors in controlling viral spread.
Strain-Specific Role of RNAs in Prion Replication
Authors: Saá Paula , Sferrazza Gian Franco , Ottenberg Gregory , Oelschlegel Anja M. , Dorsey Kerri , Lasmézas Corinne I. 
Published: July 2012

ABSTRACT

Several lines of evidence suggest that various cofactors may be required for prion replication. PrP binds to polyanions, and RNAs were shown to promote the conversion of PrP
C
into PrP
Sc
in vitro
. In the present study, we investigated strain-specific differences in RNA requirement during
in vitro
conversion and the potential role of RNA as a strain-specifying component of infectious prions. We found that RNase treatment impairs PrP
Sc
-converting activity of 9 murine prion strains by protein misfolding cyclic amplification (PMCA) in a strain-specific fashion. While the addition of RNA restored PMCA conversion efficiency, the effect of synthetic polynucleotides or DNA was strain dependent, showing a different promiscuity of prion strains in cofactor utilization. The biological properties of RML propagated by PMCA under RNA-depleted conditions were compared to those of brain-derived and PMCA material generated in the presence of RNA. Inoculation of RNA-depleted RML in
Tga20
mice resulted in an increased incidence of a distinctive disease phenotype characterized by forelimb paresis. However, this abnormal phenotype was not conserved in wild-type mice or upon secondary transmission. Immunohistochemical and cell panel assay analyses of mouse brains did not reveal significant differences between mice injected with the different RML inocula. We conclude that replication under RNA-depleted conditions did not modify RML prion strain properties. Our study cannot, however, exclude small variations of RML properties that would explain the abnormal clinical phenotype observed. We hypothesize that RNA molecules may act as catalysts of prion replication and that variable capacities of distinct prion strains to utilize different cofactors may explain strain-specific dependency upon RNA.
Evolution of the Hepatitis E Virus Polyproline Region: Order from Disorder
Authors: Purdy Michael A. 
Published: July 2012

ABSTRACT
The hepatitis E virus (HEV) polyproline region (PPR) is an intrinsically unstructured region (IDR). This relaxed structure allows IDRs, which are implicated in the regulation of transcription and translation, to bind multiple ligands. Originally the nucleotide variability seen in the HEV PPR was assumed to be due to high rates of insertion and deletion. This study shows that the mutation rate is about the same in the PPR as in the rest of the nonstructural polyprotein. The difference between the PPR and the rest of the polyprotein is due to the higher tolerance of the PPR for substitutions at the first and second codon positions. With this higher promiscuity there is a shift in nucleotide occupation of these codons leading to translation of more cytosine residues: a shift that leads to more proline, alanine, serine, and threonine being encoded rather than histidine, phenylalanine, tryptophan, and tyrosine. This pattern of amino acid usage is typical of proline-rich IDRs. Increased usage of cytosine also leads to >22% of all amino acids in the PPR being prolines. Alignments of PPR sequences from HEV strains representing all genotypes indicate that all zoonotic isolates share an ancestor, and the carboxyl half of the PPR is more tolerant of mutations than the amino half. The evolution of HEV PPR, in contrast with that of the rest of the nonstructural polyprotein, is molded by pressures that lead toward increased proline usage with a corresponding decrease in the usage of aromatic amino acids, favoring formation of IDR structures.
Timing of growth reductions in black spruce stem and branches during the 1970s spruce budworm outbreak1This article is one of a selection of papers from the 7th International Conference on Disturbance Dynamics in Boreal Forests.
Authors: Krause Cornelia , Luszczynski Boris , Morin Hubert , Rossi Sergio , Plourde Pierre-Y. 
Published: July 2012

Spruce budworm ( Choristoneura fumiferana (Clemens)) defoliation is known to regularly produce radial growth decrease in black spruce ( Picea mariana (Mill.) Britton, Sterns & Poggenb.) in the boreal forest of Quebec. Some studies have already shown that the first year of defoliation does not induce growth losses in the stem but could occur in other tree parts. We therefore examined the timing and duration of the growth reduction caused by the last outbreak in black spruce by also considering the branches. More than 79% of branches and 65% of stems exhibited a >40% growth decrease.The reduction was first registered in the upper part of the stem before being detected lower in the stem in 87% of the trees. Probabilities of growth reduction in the upper part of the stem were highest in 1976 and 1977. In the lower stem, the probabilities were highest in 1978. An interesting finding was that in 69% of the studied stands, the probability of growth reduction started earlier (1–2 years) in the branches than in the stem at 1.3 m. Branch analysis should be considered whenever questions arise in regard to the evolution of spruce budworm defoliation as well as the timing of observed growth reduction in black spruce.
Increasing nitrogen availability and soil temperature: effects on xylem phenology and anatomy of mature black spruce1This article is one of a selection of papers from the 7th International Conference on Disturbance Dynamics in Boreal Forests.
Authors: Lupi Carlo , Morin Hubert , Deslauriers Annie , Rossi Sergio , Houle Daniel 
Published: July 2012

Since plant growth in the boreal forest is often considered to be limited by low temperatures and low N availability and these variables are projected to increase due to climate warming and increased anthropogenic activities, it is important to understand whether and to what extent these disturbances may affect the growth of boreal trees. In this study, the hypotheses that wood phenology and anatomy were affected by increased soil temperatures and N depositions have been tested in two mature black spruce ( Picea mariana (Mill.) BSP) stands at different altitudes in Quebec, Canada. For 3 years, soil temperature was increased by 4 °C during the first part of the growing season and precipitations containing three times the current N concentration were added in the field by frequent canopy applications. Soil warming resulted in earlier onsets of xylogenesis and interacted with N addition producing longer durations of xylogenesis for the treated trees. The effect of warming was especially marked in the phenology of roots, while wood production, in terms of number of tracheids, was not affected by the treatment. Xylem anatomy and soil and needle chemistry showed no effect of the treatments, except for an increase of cell wall thickness in earlywood of treated trees. This short-term experiment with black spruce suggested that previous fertilization studies that used large and unrealistic rates of N addition may have overestimated the impact of N depositions on boreal forest productivity.
Recent impact of fire on high-altitude balsam fir forests in south-central Quebec1This article is one of a selection of papers from the 7th International Conference on Disturbance Dynamics in Boreal Forests.
Authors: Couillard Pierre-Luc , Payette Serge , Grondin Pierre 
Published: July 2012

The dynamics of high-altitude balsam fir ( Abies balsamea (L.) Mill.) forests is mainly driven by insect outbreaks and windthrows. However, very little work has been done on the role of fire on the development and maintenance of this ecosystem. In this study, we document the role of fire in the high-altitude balsam fir forests of the Réserve Faunique des Laurentides (RFL), southern Quebec. Sixteen sites were sampled among six different forest types described according to plant composition and fire evidence. At each site, the diameter structure was recorded and stand age was calculated based on tree-ring dating of individual trees and radiocarbon-dated surficial charcoal samples. Fire played a major role in the recent dynamics of high-altitude fir forests in the RFL. Over the last 250 years, nearly 50% of the study area burned during two fire conflagrations, i.e., around 1815 and in 1878. The fires triggered gradual changes in plant composition and forest structure, as shown by a succession of forest types ranging from white birch ( Betula papyrifera Marsh.) to spruce–fir types. Absence of surficial charcoal older than 300 years suggests that high-altitude forests of the RFL area were not subjected to a constant fire regime. It is possible that recent fires were caused by human activity.
Cancer-Associated Fibroblasts Induce Matrix Metalloproteinase–Mediated Cetuximab Resistance in Head and Neck Squamous Cell Carcinoma Cells
Authors: Johansson Ann-Charlotte , Ansell Anna , Jerhammar Fredrik , Lindh Maja Bradic , Grénman Reidar , Munck-Wikland Eva , Östman Arne , Roberg Karin 
Published: July 2012

Abstract
A growing body of evidence suggests that components of the tumor microenvironment, including cancer-associated fibroblasts (CAF), may modulate the treatment sensitivity of tumor cells. Here, we investigated the possible influence of CAFs on the sensitivity of head and neck squamous cell carcinoma (HNSCC) cell lines to cetuximab, an antagonistic epidermal growth factor receptor (EGFR) antibody. Cetuximab treatment caused a reduction in the proliferation rate of HNSCC cell lines, whereas the growth of HNSCC-derived CAF cultures was unaffected. When tumor cells were cocultured with CAFs in a transwell system, the cetuximab-induced growth inhibition was reduced, and a complete protection from growth inhibition was observed in one of the tumor cell lines investigated. Media that had been conditioned by CAFs offered protection from cetuximab treatment in a concentration-dependent manner, suggesting that the resistance to treatment was mediated by CAF-derived soluble factors. The coculture of HNSCC cell lines with CAFs resulted in an elevated expression of matrix metalloproteinase-1 (MMP-1) in both the tumor cells and CAFs. Moreover, the CAF-induced resistance was partly abolished by the presence of an MMP inhibitor. However, CAFs treated with siRNA targeting MMP-1 still protected tumor cells from cetuximab treatment, suggesting that several MMPs may cooperate to facilitate resistance or that the protective effect is mediated by another member of the MMP family. These results identify a novel CAF-dependent modulation of cetuximab sensitivity and suggest that inhibiting MMPs may improve the effects of EGFR-targeted therapy. Mol Cancer Res; 10(9); 1158–68. ©2012 AACR.
Microwave Properties of Ice-Phase Hydrometeors for Radar and Radiometers: Sensitivity to Model Assumptions
Authors: Johnson Benjamin T. , Petty Grant W. , Skofronick-Jackson Gail 
Published: July 2012

AbstractA simplified framework is presented for assessing the qualitative sensitivities of computed microwave properties, satellite brightness temperatures, and radar reflectivities to assumptions concerning the physical properties of ice-phase hydrometeors. Properties considered included the shape parameter μ of a gamma size distribution and the melted-equivalent mass median diameter D0, the particle density, the dielectric mixing formula, and the choice of complex index of refraction for ice. These properties are examined for selected radiometer frequencies of 18.7, 36.5, 89.0, and 150.0 GHz and radar frequencies at 2.8, 13.4, 35.6, and 94.0 GHz—consistent with existing and planned remote sensing instruments. Passive and active microwave observables of ice particles are found to be extremely sensitive to the D0 of the size distribution. Similar large sensitivities are found for variations in the ice volume fraction whenever the geometric mass median diameter exceeds approximately ⅛th of the wavelength. At 94 GHz the two-way path-integrated attenuation is potentially large for dense/compact particles. The distribution parameter μ has a comparatively weak effect on any observable: less than 1–2 K in brightness temperature and a maximum of 2.7 dB (S band only) in the effective radar reflectivity. Reversal of the roles of ice and air in the Maxwell Garnett dielectric mixing formula leads to a substantial change in both microwave brightness temperature (~10 K) and radar reflectivity (approximately 2 dB across all frequencies). The choice of the complex index of refraction of ice can produce a 3%–4% change in the brightness temperature depression.
Climate Warming–Related Strengthening of the Tropical Hydrological Cycle
Authors: Zahn Matthias , Allan Richard P. 
Published: July 2012

Abstract
The authors estimate climate warming–related twenty-first-century changes of moisture transports from the descending into the ascending regions in the tropics. Unlike previous studies that employ time and space averaging, here homogeneous high horizontal and vertical resolution data from an Intergovernmental Panel on Climate Change Fourth Assessment Report (IPCC AR4) climate model are used. This allows for estimating changes in much greater detail (e.g., the estimation of the distribution of ascending and descending regions, changes in the vertical profile, and separating changes of the inward and outward transports). Low-level inward and midlevel outward moisture transports of the convective regions in the tropics are found to increase in a simulated anthropogenically warmed climate as compared to a simulated twentieth-century atmosphere, indicating an intensification of the hydrological cycle. Since an increase of absolute inward transport exceeds the absolute increase of outward transport, the resulting budget is positive, meaning that more water is projected to converge in the moist tropics. The intensification is found mainly to be due to the higher amount of water in the atmosphere, while the contribution of weakening wind counteracts this response marginally. In addition the changing statistical properties of the vertical profile of the moisture transport are investigated and the importance of the substantial outflow of moisture from the moist tropics at midlevels is demonstrated.
Internal Tides and Mixing in a Submarine Canyon with Time-Varying Stratification
Authors: Zhao Zhongxiang , Alford Matthew H. , Lien Ren-Chieh , Gregg Michael C. , Carter Glenn S. 
Published: July 2012

Abstract
The time variability of the energetics and turbulent dissipation of internal tides in the upper Monterey Submarine Canyon (MSC) is examined with three moored profilers and five ADCP moorings spanning February–April 2009. Highly resolved time series of velocity, energy, and energy flux are all dominated by the semidiurnal internal tide and show pronounced spring-neap cycles. However, the onset of springtime upwelling winds significantly alters the stratification during the record, causing the thermocline depth to shoal from about 100 to 40 m. The time-variable stratification must be accounted for because it significantly affects the energy, energy flux, the vertical modal structures, and the energy distribution among the modes. The internal tide changes from a partly horizontally standing wave to a more freely propagating wave when the thermocline shoals, suggesting more reflection from up canyon early in the observational record. Turbulence, computed from Thorpe scales, is greatest in the bottom 50–150 m and shows a spring-neap cycle. Depth-integrated dissipation is 3 times greater toward the end of the record, reaching 60 mW m−2 during the last spring tide. Dissipation near a submarine ridge is strongly tidally modulated, reaching 10−5 W kg−1 (10–15-m overturns) during spring tide and appears to be due to breaking lee waves. However, the phasing of the breaking is also affected by the changing stratification, occurring when isopycnals are deflected downward early in the record and upward toward the end.
Sensitivities of a Squall Line over Central Europe in a Convective-Scale Ensemble
Authors: Hanley K. E. , Kirshbaum D. J. , Roberts N. M. , Leoncini G. 
Published: July 2012

AbstractConvective-scale ensemble simulations with perturbed initial and lateral boundary conditions are performed to investigate the mechanisms and sensitivities of a central European convection event from the Convective and Orographically Induced Precipitation Study (COPS). In this event, a “primary” squall line developed ahead of a decaying mesoscale convective system (MCS) upstream of the Vosges Mountains (France), weakened over the Rhine valley, then regenerated as a “secondary” squall line over the Black Forest Mountains (Germany). All ensemble members captured the squall-line evolution, but most suffered from a delay in the onset of convection and positional errors of 50–150 km over the COPS region. These errors in the secondary initiation were linked to errors in the primary initiation. Detailed analysis revealed a similar primary initiation mechanism in all members: in the ascending branch of a midlevel frontal circulation ahead of the MCS, convection initiated within a mesoscale moisture anomaly embedded within the prefrontal flow. The differences in the skill of the ensemble members were related to subtle differences in their initial upper-level representation of potential vorticity (PV). Members that verified well possessed a stronger PV gradient at the leading edge of an upper-level trough. This led to more rapid cyclogenesis over northern France and the United Kingdom and faster development and propagation of the midlevel front and the prefrontal moisture anomaly. As a consequence, the squall lines in these members developed earlier and closer to the COPS region. This case study provides an example of the subtle mechanisms by which errors on the larger scales may transfer to the convective scale and lead to errors in quantitative precipitation forecasts.
Validation of Noninvasive Body Sensor Network Technology in the Detection of Agitation in Dementia
Authors: Bankole Azziza , Anderson Martha , Smith-Jackson Tonya , Knight Aubrey , Oh Kyunghui , Brantley Jeff , Barth Adam , Lach John 
Published: July 2012

Objective: Agitated behaviors are one of the most frequent reasons that patients with dementia are placed in long-term care settings. This study aims to validate the ability of a custom Body Sensor Network (BSN) to capture the presence of agitation against currently accepted subjective measures, the Cohen-Mansfield Agitation Inventory (CMAI) and the Aggressive Behavior Scale (ABS) and to discriminate between agitation and cognitive decline. Methods: Six patients identified as being at high risk for agitated behaviors were enrolled in this study. The devices were applied at three sites for three hours while behaviors were annotated simultaneously and subsequently repeated twice for each enrolled subject. Results: We found that the BSN was a valid measure of agitation based on construct validity testing and secondary validation using non-parametric ANOVAs. Discussion: The BSN shows promise from these pilot results. Further testing with a larger sample is needed to replicate these results.
APOE Genotype in the Diagnosis of Alzheimer’s Disease in Patients With Cognitive Impairment
Authors: Sun Xiaoyan , Nicholas Joyce , Walker Aljoeson , Wagner Mark T. , Bachman David 
Published: July 2012

Background: Although an association between the apolipoprotein E ( APOE) ∊4 allele and increased risk of Alzheimer’s disease (AD) is established, the utility of APOE genotyping in the clinical diagnosis of AD is still under investigation. Methods: Medical records of 89 patients with cognitive impairment and APOE genotype data underwent a retrospective review. Results: Comparison of age, age at onset, education, Mini-Mental State Examination, months of follow-up, and family history of dementia did not reveal statistical difference among the patients with different APOE genotypes. The APOE ∊4 carriers had a higher percentage of AD diagnoses after a median 16 months follow-up than non- APOE ∊4 carriers. The APOE ∊4 designation had a high sensitivity and high positive predictive value for the diagnosis of AD but a low negative predictive value and specificity. Conclusions: The APOE genotyping may be helpful in diagnosing AD especially in patients presenting with atypical features or early age of onset of dementia.