bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutrophil Depletion Suppresses Pulmonary Vascular Hyperpermeability and Occurrence of Pulmonary Edema Caused by Hantavirus Infection in C.B-17 SCID Mice
Authors: Koma Takaaki , Yoshimatsu Kumiko , Nagata Noriyo , Sato Yuko , Shimizu Kenta , Yasuda Shumpei P. , Amada Takako , Nishio Sanae , Hasegawa Hideki , Arikawa Jiro 
Published: April 2014

ABSTRACT
Hantavirus infections are characterized by vascular hyperpermeability and neutrophilia. However, the pathogenesis of this disease is poorly understood. Here, we demonstrate for the first time that pulmonary vascular permeability is increased by Hantaan virus infection and results in the development of pulmonary edema in C.B-17 severe combined immunodeficiency (SCID) mice lacking functional T cells and B cells. Increases in neutrophils in the lung and blood were observed when pulmonary edema began to be observed in the infected SCID mice. The occurrence of pulmonary edema was inhibited by neutrophil depletion. Moreover, the pulmonary vascular permeability was also significantly suppressed by neutrophil depletion in the infected mice. Taken together, the results suggest that neutrophils play an important role in pulmonary vascular hyperpermeability and the occurrence of pulmonary edema after hantavirus infection in SCID mice.

IMPORTANCE
Although hantavirus infections are characterized by the occurrence of pulmonary edema, the pathogenic mechanism remains largely unknown. In this study, we demonstrated for the first time
in vivo
that hantavirus infection increases pulmonary vascular permeability and results in the development of pulmonary edema in SCID mice. This novel mouse model for human hantavirus infection will be a valuable tool and will contribute to elucidation of the pathogenetic mechanisms. Although the involvement of neutrophils in the pathogenesis of hantavirus infection has largely been ignored, the results of this study using the mouse model suggest that neutrophils are involved in the vascular hyperpermeability and development of pulmonary edema in hantavirus infection. Further study of the mechanisms could lead to the development of specific treatment for hantavirus infection.
Electrostatic Interactions Drive the Self-Assembly and the Transcription Activity of the Pseudomonas Phage ϕ6 Procapsid
Authors: Sun Xiaoyu , Bamford Dennis H. , Poranen Minna M. 
Published: April 2014

ABSTRACT
Assembly of an empty procapsid is a crucial step in the formation of many complex viruses. Here, we used the self-assembly system of the double-stranded RNA bacteriophage ϕ6 to study the role of electrostatic interactions in a scaffolding-independent procapsid assembly pathway. We demonstrate that ϕ6 procapsid assembly is sensitive to salt at both the nucleation and postnucleation steps. Furthermore, we observed that the salt sensitivity of ϕ6 procapsid-directed transcription is reversible.
Molecular Insights on the Recognition of a Lactococcus lactis Cell Wall Pellicle by the Phage 1358 Receptor Binding Protein
Authors: Farenc Carine , Spinelli Silvia , Vinogradov Evgeny , Tremblay Denise , Blangy Stéphanie , Sadovskaya Irina , Moineau Sylvain , Cambillau Christian 
Published: April 2014

ABSTRACT

The Gram-positive bacterium
Lactococcus lactis
is used for the production of cheeses and other fermented dairy products. Accidental infection of
L. lactis
cells by virulent lactococcal tailed phages is one of the major risks of fermentation failures in industrial dairy factories. Lactococcal phage 1358 possesses a host range limited to a few
L. lactis
strains and strong genomic similarities to
Listeria
phages. We report here the X-ray structures of phage 1358 receptor binding protein (RBP) in complex with monosaccharides. Each monomer of its trimeric RBP is formed of two domains: a “shoulder” domain linking the RBP to the rest of the phage and a jelly roll fold “head/host recognition” domain. This domain harbors a saccharide binding crevice located in the middle of a monomer. Crystal structures identified two sites at the RBP surface, ∼8 Å from each other, one accommodating a GlcNAc monosaccharide and the other accommodating a GlcNAc or a glucose 1-phosphate (Glc1P) monosaccharide. GlcNAc and GlcNAc1P are components of the polysaccharide pellicle that we identified at the cell surface of
L. lactis
SMQ-388, the host of phage 1358. We therefore modeled a galactofuranose (Gal
f
) sugar bridging the two GlcNAc saccharides, suggesting that the trisaccharidic motif GlcNAc-Gal
f
-GlcNAc (or Glc1P) might be common to receptors of genetically distinct lactococcal phages p2, TP091-1, and 1358. Strain specificity might therefore be elicited by steric clashes induced by the remaining components of the pellicle hexasaccharide. Taken together, these results provide a first insight into the molecular mechanism of host receptor recognition by lactococcal phages.

IMPORTANCE
Siphophages infecting the Gram-positive bacterium
Lactococcus lactis
are sources of milk fermentation failures in the dairy industry. We report here the structure of the pellicle polysaccharide from
L. lactis
SMQ-388, the specific host strain of phage 1358. We determined the X-ray structures of the lytic lactococcal phage 1358 receptor binding protein (RBP) in complex with monosaccharides. The positions and nature of monosaccharides bound to the RBP are in agreement with the pellicle structure and suggest a general binding mode of lactococcal phages to their pellicle saccharidic receptor.
Incorporation of Mouse APOBEC3 into Murine Leukemia Virus Virions Decreases the Activity and Fidelity of Reverse Transcriptase
Authors: Boi Stefano , Kolokithas Angelo , Shepard Joyce , Linwood Rebecca , Rosenke Kyle , Van Dis Erik , Malik Frank , Evans Leonard H. 
Published: April 2014

ABSTRACT
APOBEC3 proteins are restriction factors that induce G→A hypermutation in retroviruses during replication as a result of cytidine deamination of minus-strand DNA transcripts. However, the mechanism of APOBEC inhibition of murine leukemia viruses (MuLVs) does not appear to be G→A hypermutation and is unclear. In this report, the incorporation of mA3 in virions resulted in a loss in virion reverse transcriptase (RT) activity and RT fidelity that correlated with the loss of virion-specific infectivity.
Analysis of the ambient conditions in an IL-LLW storage cell in a deep clay repository during the waiting closure period
Authors: Bénet Luc-Vincent , Bouillet Charlaine , Wendling Jacques 
Published: April 2014

Abstract
In the 2009 Andra repository concept, Intermediate Level Long Lived Wastes are stored in several 100-m-long storage cells. Concrete over-packs are stacked in piles before being emplaced by row. The large sections opened in the slab floor to enable emplacement by the conveyor could have a major effect on the temperature distribution in the storage cell. The aim of the study is to assess the ability of the ventilation to regulate temperatures along the cell. We focus on the period before closure, when the ventilation rate is at a minimum. The issue has been addressed by undertaking numerical simulations. A specific modelling approach based on head-loss correlations has been used to calculate the distributions of temperature and air velocity at a decimetre scale along the storage cell. The heat transfer and the air flow problems have been solved on a 3D mesh representing 225 rows of waste packages, the concrete walls and the surrounding rock. Different scenarios have been considered about the air flow rate, the heat release and the closure of the conveyor sections at several locations. Results have been analysed in terms of flow patterns, temperature distributions and thermal gradients in air and in concrete.
Analysis of the long-term hydraulic-gas transient in the central zone of a deep clay repository
Authors: Bénet Luc-Vincent , Tulita Catalin , Pasteau Antoine , Wendling Jacques 
Published: April 2014

Abstract
In the Andra repository concept, a large amount of hydrogen gas will be generated through radiolysis of water and corrosion of metal parts from the infrastructure and the packages containing radioactive waste. The fate of the gas could have a significant impact on the rate of resaturation of the porous media, and needs to be accounted for in order to make accurate predictions of the long-term evolution of the repository. The central zone of the repository consists of a 4.5-km-long network of galleries which connect the storage zones with the surface through three shafts. These shafts, which will be backfilled and sealed after closure, will have a key role in gas and water exchange between the repository and the overlying aquifer. The aim of this work was to describe the evolution in time of both the water and gas flows in the central zone up to the end of the hydraulic-gas transient. The issue was addressed by means of numerical simulations. The simulations produced local predictions of flow rates and pressures, water saturation and amounts of dissolved gas. The results were analysed to determine how water and gas flows combine in the central zone, when the saturation of the seal will be complete, when the free gas will reach the overlying aquifer, and when the saturation of the central zone will be complete.
The Moldanubian Zone in the French Massif Central, Vosges/Schwarzwald and Bohemian Massif revisited: differences and similarities
Authors: Lardeaux J. M. , Schulmann K. , Faure M. , Janoušek V. , Lexa O. , Skrzypek E. , Edel J. B. , Štípská P. 
Published: April 2014

Abstract
In order to portray the main differences and similarities between the Northeastern Variscan segments (French Massif Central (FMC), Vosges, Black Forest and Bohemian Massif (BM)), we review their crustal-scale architectures, the specific rock associations and lithotectonic sequences, as well as the ages of the main magmatic and metamorphic events. This review demonstrates significant differences between the ‘Moldanubian’ domains in the BM and the FMC. On this basis we propose distinguishing between the Eastern and Western Moldanubian zones, while the Vosges/Black Forest Mountains are an intermediate section between the BM and the FMC. The observed differences are the result of, first, the presence in the French segment of an early large-scale accretionary system prior to the main Variscan collision and, second, the duration of Saxothuringian/Armorican subduction, which generated long-lived magmatic arc and back-arc systems in the Bohemian segment, while the magmatic activity in the FMC was comparably short-lived.
Reproducibility of the Optical Biometer OA-1000 (Tomey)
Authors: Goebels Susanne Christiane , Seitz Berthold , Langenbucher Achim 
Published: April 2014

Aim. The OA-1000 (Tomey, Japan) is a new optical biometer, which measures axial length (AL), anterior chamber depth (ACD), and central corneal thickness (CT) utilizing optical interference technology. The aim of this study was to prove the reproducibility which is considered fundamental for other clinical investigations.Methods. 55 healthy volunteers were enrolled in this study. For each measurement of AL, ACD, and CT the biometer is grabbing a sequence of 10 shots and mean value (mean) and standard deviation (SD) are displayed. Five consecutive measurements were performed and average and standard deviation were assessed. Cronbach’sαwas derived as a quality measure for reproducibility.Results. For AL measurement Cronbach’sαwas 1.000, for CT 0.999, and for ACD 0.979, respectively. Mean value for AL was23.36±1.03 mm, for ACD it was3.60±0.687 mm, and for CT it was552.08±29.70 μm, respectively. Standard deviation for AL was0.013±0.022 mm, for ACD0.09±0.11 mm, and for CT2.18±1.75 μm. One correlation was found between mean values for AL and ACD (R = 0.388,P = 0.005); no other correlations were found between mean values or values of standard deviation of AL, ACD, or CT.Conclusion. The OA-1000 shows an excellent reproducibility for measurement of AL, ACD, and CT and can be used in clinical practice.
Associations between Estrogen Receptor–Negative Breast Cancer and Timing of Reproductive Events Differ between African American and European American Women
Authors: Ambrosone Christine B. , Zirpoli Gary R. , Bovbjerg Dana Howard , Shankar Jyoti , Hong Chi-Chen , McCann Susan E. , Ruszczyk Melanie , Khoury Thaer , Yao Song , Ciupak Gregory L. , Jandorf Lina , Pawlish Karen S. , Bandera Elisa V. 
Published: April 2014

Abstract
The effects of reproductive factors on breast cancer risk seem to differ by estrogen receptor (ER) status. Menarche and first live birth (FLB) tend to occur at younger ages in African Americans (AA) than European Americans (EA), and could play a role in breast cancer disparities. In the Women's Circle of Health Study, a case–control study of breast cancer in EA and AA women, in-person interviews were conducted to collect epidemiologic data, including reproductive histories. Data on ER status, abstracted from pathology reports, were available for 814 AA and 538 EA breast cancer cases, and were analyzed with 1015 AA and 715 EA controls, to evaluate associations between subgroups and age at menarche, age at FLB, and the interval between those ages. Among AA women, later age at menarche (≥14 years) was associated with reduced risk of both ER+ and ER− breast cancer, with ORs strongest for ER− disease [OR = 0.57; 95% confidence interval (CI), 0.37–0.88]; associations were weaker and nonsignificant for EA women. There were no significant associations with age at FLB, but AA women with a FLB within 15 years of menarche had increased risk of ER− disease (OR = 2.26; 95% CI, 1.29–3.95), with no significant associations among EAs. In our data, earlier age at menarche and shorter intervals until FLB are associated with ER− breast cancer in AA women; differential distributions by race of these and other reproductive risk factors could contribute to the higher prevalence of ER− breast cancer in AA women. Cancer Epidemiol Biomarkers Prev; 23(6); 1115–20. ©2014 AACR.
Sustained Inhibition of Receptor Tyrosine Kinases and Macrophage Depletion by PLX3397 and Rapamycin as a Potential New Approach for the Treatment of MPNSTs
Authors: Patwardhan Parag P. , Surriga Oliver , Beckman Michael J. , de Stanchina Elisa , Dematteo Ronald P. , Tap William D. , Schwartz Gary K. 
Published: April 2014

Abstract
Purpose: Malignant peripheral nerve sheath tumor (MPNST) is a highly aggressive tumor type that is resistant to chemotherapy and there are no effective therapies. MPNSTs have been shown to have gene amplification for receptor tyrosine kinases (RTK), PDGFR and c-Kit. We tested the c-Kit inhibitor, imatinib, and PLX3397, a selective c-Fms and c-Kit inhibitor, to evaluate their efficacy against MPNST cells in vitro and in vivo.
Experimental Design: We tested the efficacy of imatinib or PLX3397 either alone or in combination with TORC1 inhibitor rapamycin in a cell proliferation assay in vitro and by immunoblotting to determine target inhibition. Immunoblotting and immunohistochemical analysis was further carried out using xenograft samples in vivo.
Results: Our in vitro studies show that imatinib and PLX3397 similarly inhibit cell growth and this can be enhanced with rapamycin with comparable target specificity. However, in vivo studies clearly demonstrate that compared with imatinib, PLX3397 results in sustained blockade of c-Kit, c-Fms, and PDGFRβ, resulting in significant suppression of tumor growth. Moreover, staining for Iba-1, a marker for macrophages, indicates that PLX3397 results in significant depletion of macrophages in the growing tumors. The combination of PLX3397 and rapamycin results in even greater macrophage depletion with continued growth suppression, even when the drug treatment is discontinued.
Conclusions: Taken together, our data strongly suggest that PLX3397 is superior to imatinib in the treatment of MPNSTs, and the combination of PLX3397 with a TORC1 inhibitor could provide a new therapeutic approach for the treatment of this disease. Clin Cancer Res; 20(12); 3146–58. ©2014 AACR.
Markets for Land, Labour and Capital in Late Antique Iraq, AD 200-700
Authors: Rezakhani Khodadad , Morony Michael G. 
Published: April 2014

Abstract
Lack of direct evidence on the functioning of factor markets in Sasanian/Late Antique Iraq makes it difficult to present a clear picture of the production side of economy during this period. However, relying on the Talmudic evidence, as well as what is mentioned in the Mādayān ī Hezār Dādestān (mhd), this article aims to provide an idea of factor markets during the Sasanian period, as well as demonstrating the areas where further evidence and research could render better results and allow us to understand the economy of this region in more depth.
Diabatic Damping of Zonal Index Variations
Authors: Xia Xiaoming , Chang Edmund K. M. 
Published: April 2014

Abstract
Zonal index variations, or north–south shifts of the midlatitude jet, are the dominant mode of zonal wind variability in the Southern Hemisphere. Previous studies have shown that synoptic-time-scale eddy momentum flux provides a positive feedback and acts to increase the persistence and low-frequency variance of the zonal index. However, the impact of diabatic heating due to the precipitation associated with these eddies has not been investigated. In this study, regression analyses have been conducted to demonstrate that a robust precipitation anomaly can be found to accompany the jet and eddy momentum flux anomalies associated with a poleward shift of the jet, with enhanced precipitation on the poleward flank of the jet and reduced precipitation on the equatorward flank. Diabatic heating associated with such a precipitation anomaly is expected to reduce the temperature gradient across the jet anomaly, thus decreasing eddy generation and damping the anomaly. This expectation is confirmed by three sets of mechanistic model experiments, using three different ways to mimic the impact of moist heating in a dry model. Results of this study suggest that diabatic heating provides a negative feedback to zonal index variations, partially offsetting the positive feedback provided by eddy momentum flux. These results could partially explain why zonal index variations have been found to be very persistent in dry mechanistic model experiments since this negative diabatic feedback is absent in dry models. These results suggest that these models may be overly sensitive to climate forcings that produce a jet shift response.
Predictability of Major Stratospheric Sudden Warmings of the Vortex Split Type: Case Study of the 2002 Southern Event and the 2009 and 1989 Northern Events
Authors: Taguchi Masakazu 
Published: April 2014

Abstract
This study investigates the predictability of three major stratospheric sudden warmings (MSSWs) of the vortex split type: the Southern Hemisphere case in September 2002 and two Northern Hemisphere cases in January 2009 and February 1989. The author examines changes in the predictability of the MSSWs with lead time, as well as the connection of the predictability to lower-atmospheric features for pre- and post-MSSW periods. The Japan Meteorological Agency (JMA)’s 1-month ensemble hindcast (HC) experiment data are compared to the Japanese 25-year Reanalysis Project (JRA-25)/JMA Climate Data Assimilation System (JCDAS) data.
For the pre-MSSW period, a strong predictability connection is observed among all three cases. Unsuccessful predictions of the MSSWs are characterized by an underestimation (or lack) of the enhanced wave activity in the lower stratosphere, which is further related to the strength and persistence of the upper-tropospheric ridge and trough. The mean zonal wind profile in the upper troposphere is also important for the 2009 case. These results confirm the role of tropospheric wave forcing of the MSSWs in the context of predictability. The characteristic time scale for successful predictions is approximately 10 days–2 weeks, which roughly corresponds to the time scale of the tropospheric wave forcing. No ensemble member successfully predicts the MSSWs with lead times longer than the time scale.
The predictability connection between the stratospheric and tropospheric anomalies is more subtle for the post-MSSW period. In particular, the HC group initialized about 1 week before the MSSWs tends to reproduce the evolution of the stratosphere after the MSSWs well but not that of the troposphere in some cases.
ENSO Seasonal Synchronization Theory
Authors: Stein Karl , Timmermann Axel , Schneider Niklas , Jin Fei-Fei , Stuecker Malte F. 
Published: April 2014

Abstract
One of the key characteristics of El Niño–Southern Oscillation (ENSO) is its synchronization to the annual cycle, which manifests in the tendency of ENSO events to peak during boreal winter. Current theory offers two possible mechanisms to account the for ENSO synchronization: frequency locking of ENSO to periodic forcing by the annual cycle, or the effect of the seasonally varying background state of the equatorial Pacific on ENSO’s coupled stability. Using a parametric recharge oscillator (PRO) model of ENSO, the authors test which of these scenarios provides a better explanation of the observed ENSO synchronization.
Analytical solutions of the PRO model show that the annual modulation of the growth rate parameter results directly in ENSO’s seasonal variance, amplitude modulation, and 2:1 phase synchronization to the annual cycle. The solutions are shown to be applicable to the long-term behavior of the damped model excited by stochastic noise, which produces synchronization characteristics that agree with the observations and can account for the variety of ENSO synchronization behavior in state-of-the-art coupled general circulation models. The model also predicts spectral peaks at “combination tones” between ENSO and the annual cycle that exist in the observations and many coupled models. In contrast, the nonlinear frequency entrainment scenario predicts the existence of a spectral peak at the biennial frequency corresponding to the observed 2:1 phase synchronization. Such a peak does not exist in the observed ENSO spectrum. Hence, it can be concluded that the seasonal modulation of the coupled stability is responsible for the synchronization of ENSO events to the annual cycle.
Intraseasonal Variability in Coupled GCMs: The Roles of Ocean Feedbacks and Model Physics
Authors: DeMott Charlotte A. , Stan Cristiana , Randall David A. , Branson Mark D. 
Published: April 2014

The interaction of ocean coupling and model physics in the simulation of the intraseasonal oscillation (ISO) is explored with three general circulation models: the Community Atmospheric Model, versions 3 and 4 (CAM3 and CAM4), and the superparameterized CAM3 (SPCAM3). Each is integrated coupled to an ocean model, and as an atmosphere-only model using sea surface temperatures (SSTs) from the coupled SPCAM3, which simulates a realistic ISO. For each model, the ISO is best simulated with coupling. For each SST boundary condition, the ISO is best simulated in SPCAM3.Near-surface vertical gradients of specific humidity, [Formula: see text] (temperature, [Formula: see text]), explain ~20% (50%) of tropical Indian Ocean latent (sensible) heat flux variance, and somewhat less of west Pacific variance. In turn, local SST anomalies explain ~5% (25%) of [Formula: see text] [Formula: see text] variance in coupled simulations, and less in uncoupled simulations. Ergo, latent and sensible heat fluxes are strongly controlled by wind speed fluctuations, which are largest in the coupled simulations, and represent a remote response to coupling. The moisture budget reveals that wind variability in coupled simulations increases east-of-convection midtropospheric moistening via horizontal moisture advection, which influences the direction and duration of ISO propagation.These results motivate a new conceptual model for the role of ocean feedbacks on the ISO. Indian Ocean surface fluxes help developing convection attain a magnitude capable of inducing the circulation anomalies necessary for downstream moistening and propagation. The “processing” of surface fluxes by model physics strongly influences the moistening details, leading to model-dependent responses to coupling.