bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of sugar beet genotype on the Beet necrotic yellow vein virus P25 pathogenicity factor and evidence for a fitness penalty in resistance‐breaking strains
Authors: Bornemann Kathrin , Varrelmann Mark 
Published: January 2013

SummaryBeet necrotic yellow vein virus (BNYVV), vectored by Polymyxa betae, causes rhizomania in sugar beet. For disease control, the cultivation of hybrids carrying Rz1 resistance is crucial, but is compromised by resistance‐breaking (RB) strains with specific mutations in the P25 protein at amino acids 67–70 (tetrad). To obtain evidence for P25 variability from soil‐borne populations, where the virus persists for decades, populations with wild‐type (WT) and RB properties were analysed by P25 deep sequencing. The level of P25 variation in the populations analysed did not correlate with RB properties. Remarkably, one WT population contained P25 with RB mutations at a frequency of 11%. To demonstrate selection by Rz1 and the influence of RB mutations on relative fitness, competition experiments between strains were performed. Following a mixture of strains with four RNAs, a shift in tetrad variants was observed, suggesting that strains did not mix or transreplicate. The plant genotype exerted a clear influence on the frequency of RB tetrads. In Rz1 plants, the RB variants outcompeted the WT variants, and mostly vice versa in susceptible plants, demonstrating a relative fitness penalty of RB mutations. The strong genotype effect supports the hypothesized Rz1 RB strain selection with four RNAs, suggesting that a certain tetrad needs to become dominant in a population to influence its properties. Tetrad selection was not observed when an RB strain, with an additional P26 protein encoded by a fifth RNA, competed with a WT strain, supporting its role as a second BNYVV pathogenicity factor and suggesting the reassortment of both types.
Evaluation of hypercoagulability using soluble fibrin monomer complex in sick newborns
Authors: Takahashi Daijiro , Takahashi Yukihiro , Matsui Miyu , Araki Shunsuke , Kubo Kazuyasu , Sato Hiroshi , Shirahata Akira 
Published: January 2013

AbstractBackgroundSoluble fibrin monomer complex (SFMC) and fibrin monomer (FM) are well known as markers for hypercoagulability, but such measurements have not been investigated in detail for the neonate. To identify the presence of a hypercoagulable state in sick newborns, the behavior of SFMC with special reference to those of other coagulation tests, and the relationships with other parameters of blood coagulation as well as lactate, which is considered to be the gold standard for assessing tissue hypoxia, were studied.MethodsRecords of 216 sick newborns, who had undergone blood coagulation tests, were retrospectively studied based on their medical records.ResultsSFMC had a significant correlation with d‐dimer in infants with birthweight <1500 g, but no correlation was observed with prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen, anti‐thrombin or platelet count. In contrast, in infants with birthweight ≥1500 g, SFMC was correlated with PT, APTT, fibrinogen, and d‐dimer, but no correlation was observed with anti‐thrombin or platelet count. In addition, SFMC was significantly higher in the high lactate group (lactate ≥4 mmol/L), compared with the low lactate group (<4 mmol/L).ConclusionMeasurement of blood SFMC is useful to monitor hypercoagulable state in sick newborns with hypoxia.
Liver Condition Affects Bovine Oocyte Qualities by Changing the Characteristics of Follicular Fluid and Plasma
Authors: Tanaka H , Shibano K , Monji Y , Kuwayama T , Iwata H 
Published: January 2013

ContentsThe liver is an important organ that contributes to milk production in dairy cows. The aim of this study was to examine whether liver conditions affect the characteristics of blood plasma and follicular fluid (FF) and whether supplementing in vitro maturation medium with FF from either cows with damaged livers (DL) or those with healthy livers (HL) affects oocyte developmental competence. Biochemical characteristics of FF were significantly correlated with those in plasma. As such, the characteristics of both plasma and FF were similarly affected by liver conditions in that the concentrations of total protein and inorganic phosphorus were higher for the DL cow group than for the HL cow group, whereas the concentrations of albumin, lactate dehydrogenase and calcium were lower for DL cows than for HL cows. In addition, supplementing the medium with DL‐FF retarded the progression of the nuclear maturation of oocytes collected from the HL cows. On culturing oocytes in maturation medium containing HL‐FF, DL‐FF or foetal calf serum, the highest developmental rate to the blastocyst stage was observed in the HL‐FF group, while the lowest developmental ratio was observed in the DL‐FF group. The growth factor array of the FFs revealed that 10 growth factors were significantly downregulated in the DL‐FF compared with those in HL‐FF. In conclusion, the characteristics of plasma and FF are affected by liver conditions in a similar way. Concentrations of several growth factors were low in DL‐FF, as was the ability of DL‐FF to support oocyte maturation compared with that of HL‐FF.
Topographic Distribution of the Different Cell Types, Connective Tissue and Vascular Tissue/Lumina Within a Functional Bovine Corpus Luteum and its Association with Breed, Type of Fixation Protocol and Stage During the Cycle
Authors: Cools S , Van den Broeck W , De Vliegher S , Piepers S , Hostens M , Opsomer G 
Published: January 2013

ContentsIn the present study, we analysed the effect of fixative, breed, luteal stage and location on the nuclear density, volume density of connective tissue and vascular tissue/lumina within a bovine luteal gland in view of the development of an in vivo sampling technique to longitudinally monitor luteal histophysiology. The inner zone defined as the zone geometrically closest to the centre of the gland shows a significantly lower nuclear density (for all cell types) and a higher volume density of collagen fibres and vessels when compared with the outer zone (p < 0.001). The nuclear density in luteal glands from Holstein‐Friesian cows is not significantly different from that in Belgian Blue cows, nor is it in stage II vs stage III glands. The collagen fibre content was significantly lower in glands of Belgian Blue cows (p = 0.01) and in younger glands (p = 0.003). Hence, it seems that the lower nuclear density in the inner zone was compensated by a higher amount of collagen fibres. As the type of fixative applied has a significant effect on the nuclear density of the different cell types, the present study warrants future research to further optimize the fixation protocol. As a conclusion, we can state that the topographic difference in nuclear distribution for the different cell types in a bovine luteal gland is only significant when comparing the inner vs the outer zone. This implies that if a sample representative for the whole gland has to be taken, for example, when taking an in vivo sample, it is necessary that the biopsy goes through the inner zone and contains the total diameter of the gland.
Risk and Policy Shocks on the US Term Structure
Authors: Weber Enzo , Wolters Jürgen 
Published: January 2013

AbstractWe document two stylized facts of US short‐term and long‐term interest rate data seemingly incompatible with the expectations hypothesis: low contemporaneous cross‐correlation and relatively slow adjustment to long‐run relationships. We explain these features in a small structural model with three types of randomness: While a persistent monetary policy shock implies immediate identical reactions through the term structure, both a transitory policy shock and an autocorrelated risk premium allow for sustained deviations. Indeed, we find important impacts and persistence of risk premia and considerable contribution of transitory policy shocks to short rates. Results of standard expectations hypothesis tests can be rationalized.
A mass conservation‐based optical flow method for cardiac motion correction in 3D‐PET
Authors: Dawood Mohammad , Gigengack Fabian , Jiang Xiaoyi , Schäfers Klaus P. 
Published: January 2013

Purpose:Cardiac positron emission tomography (PET) images usually show two kinds of artifacts: the limited resolution of PET leads to partial volume effects and the motion of the heart induces blurring. These phenomena degrade the PET images and induce errors in the quantification. One method of reducing this problem is to use gated PET data. However, the reduction of information per phase leads to an increase in noise on the reconstructed images. Alternatively, the PET data have to be corrected for motion and partial volume effects.Methods:Optical flow methods have been shown to accurately estimate the motion between PET image frames. These methods assume that the brightness of the objects remains constant between the frames. This condition is not fulfilled in cardiac PET data because the brightness of the cardiac muscle tissue (myocardium) is not accurately resolved due to the partial volume effect. Therefore, the use of a newly developed optical flow method based upon the conservation of mass condition is proposed to correct the cardiac PET data. Mass conservation is applicable to PET images as the total activity in the field of view may be assumed to remain almost constant, if the data are precorrected for radioactive decay. Two variants of the method using the quadratic and the nonquadratic penalization are presented. The methods were evaluated with respect to correlation coefficient, myocardial thickness and the blood pool activity in the left ventricle on phantom data and on 14 patient image volumes.Results:The proposed methods showed that the cardiac motion can be efficiently corrected despite partial volume effects. The correlation coefficient between the image volumes increased from 0.87 to 0.98 on average. The change in myocardial thickness was reduced from 28% to 3%. The variation in blood pool activity was reduced from 80% to 8%. The algorithm needed only about 4 s for execution.Conclusions:A mass preserving optical flow method of cardiac motion correction in 3D PET data has been presented and tested on phantom as well as patient data. The results show that the motion was corrected for all datasets effectively.
Calibrating page sized Gafchromic EBT3 films
Authors: Crijns W. , Maes F. , van der Heide U. A. , Van den Heuvel F. 
Published: January 2013

Purpose:The purpose is the development of a novel calibration method for dosimetry with Gafchromic EBT3 films. The method should be applicable for pretreatment verification of volumetric modulated arc, and intensity modulated radiotherapy. Because the exposed area on film can be large for such treatments, lateral scan errors must be taken into account. The correction for the lateral scan effect is obtained from the calibration data itself.Methods:In this work, the film measurements were modeled using their relative scan values (Transmittance,T). Inside the transmittance domain a linear combination and a parabolic lateral scan correction described the observed transmittance values. The linear combination model, combined a monomer transmittance state (T0) and a polymer transmittance state (T∞) of the film. The dose domain was associated with the observed effects in the transmittance domain through a rational calibration function. On the calibration film only simple static fields were applied and page sized films were used for calibration and measurements (treatment verification). Four different calibration setups were considered and compared with respect to dose estimation accuracy. The first (I) used a calibration table from 32 regions of interest (ROIs) spread on 4 calibration films, the second (II) used 16 ROIs spread on 2 calibration films, the third (III), and fourth (IV) used 8 ROIs spread on a single calibration film. The calibration tables of the setups I, II, and IV contained eight dose levels delivered to different positions on the films, while for setup III only four dose levels were applied. Validation was performed by irradiating film strips with known doses at two different time points over the course of a week. Accuracy of the dose response and the lateral effect correction was estimated using the dose difference and the root mean squared error (RMSE), respectively.Results:A calibration based on two films was the optimal balance between cost effectiveness and dosimetric accuracy. The validation resulted in dose errors of 1%–2% for the two different time points, with a maximal absolute dose error around 0.05 Gy. The lateral correction reduced the RMSE values on the sides of the film to the RMSE values at the center of the film.Conclusions:EBT3 Gafchromic films were calibrated for large field dosimetry with a limited number of page sized films and simple static calibration fields. The transmittance was modeled as a linear combination of two transmittance states, and associated with dose using a rational calibration function. Additionally, the lateral scan effect was resolved in the calibration function itself. This allows the use of page sized films. Only two calibration films were required to estimate both the dose and the lateral response. The calibration films were used over the course of a week, with residual dose errors ⩽2% or ⩽0.05 Gy.
Technical Note: Building a combined cyclotron and MRI facility: Implications for interference
Authors: Hofman Mark B. M. , Kuijer Joost P. A. , de Ridder Jan Willem , Perk Lars R. , Verdaasdonk Rudolf M. 
Published: January 2013

Purpose:With the introduction of hybrid PET/MRI systems, it has become more likely that the cyclotron and MRI systems will be located close to each other. This study considered the interference between a cyclotron and a superconducting MRI system.Methods:Interactions between cyclotrons and MRIs are theoretically considered. The main interference is expected to be the perturbation of the magnetic field in the MRI due to switching on or off the magnetic field of the cyclotron. MR imaging is distorted by a dynamic spatial gradient of an external inplane magnetic field larger than 0.5–0.04μT/m, depending on the specific MR application. From the design of a cyclotron, it is expected that the magnetic fringe field at large distances behaves as a magnetic dipolar field. This allows estimation of the full dipolar field and its spatial gradients from a single measurement. Around an 18 MeV cyclotron (Cyclone, IBA), magnetic field measurements were performed on 5 locations and compared with calculations based upon a dipolar field model.Results:At the measurement locations the estimated and measured values of the magnetic field component and its spatial gradients of the inplane component were compared, and found to agree within a factor 1.1 for the magnetic field and within a factor of 1.5 for the spatial gradients of the field. In the specific case of the 18 MeV cyclotron with a vertical magnetic field and a 3T superconducting whole body MR system, a minimum distance of 20 m has to be considered to prevent interference.Conclusions:This study showed that a dipole model is sufficiently accurate to predict the interference of a cyclotron on a MRI scanner, for site planning purposes. The cyclotron and a whole body MRI system considered in this study need to be placed more than 20 m apart, or magnetic shielding should be utilized.
Recombinant Vaccine Displaying the Loop-Neutralizing Determinant from Protective Antigen Completely Protects Rabbits from Experimental Inhalation Anthrax
Authors: Oscherwitz Jon , Yu Fen , Jacobs Jana L. , Cease Kemp B. 
Published: January 2013

ABSTRACTWe previously showed that a multiple antigenic peptide (MAP) vaccine displaying amino acids (aa) 304 to 319 from the 2β2-2β3 loop of protective antigen was capable of protecting rabbits from an aerosolized spore challenge withBacillus anthracisAmes strain. Antibodies to this sequence, referred to as the loop-neutralizing determinant (LND), are highly potent at neutralizing lethal toxin yet are virtually absent in rabbit and human protective antigen (PA) antiserum. While the MAP vaccine was protective against anthrax, it contains a single heterologous helper T cell epitope which may be suboptimal for stimulating an outbred human population. We therefore engineered a recombinant vaccine (Rec-LND) containing two tandemly repeated copies of the LND fused to maltose binding protein, with enhanced immunogenicity resulting from the p38/P4 helper T cell epitope fromSchistosoma mansoni. Rec-LND was found to be highly immunogenic in four major histocompatibility complex (MHC)-diverse strains of mice. All (7/7) rabbits immunized with Rec-LND developed high-titer antibody, 6 out of 7 developed neutralizing antibody, and all rabbits were protected from an aerosolized spore challenge of 193 50% lethal doses (LD50) of theB. anthracisAmes strain. Survivor serum from Rec-LND-immunized rabbits revealed significantly increased neutralization titers and specific activity compared to prechallenge levels yet lacked PA or lethal factor (LF) antigenemia. Control rabbits immunized with PA, which were also completely protected, appeared sterilely immune, exhibiting significant declines in neutralization titer and specific activity compared to prechallenge levels. We conclude that Rec-LND may represent a prototype anthrax vaccine for use alone or potentially combined with PA-containing vaccines.
Molecular Characterization of Methicillin-Susceptible Staphylococcus aureus Clinical Isolates in the United States, 2004 to 2010
Authors: Miko Benjamin A. , Hafer Cory A. , Lee Caroline J. , Sullivan Sean B. , Hackel Meredith A. M. , Johnson Brian M. , Whittier Susan , Della-Latta Phyllis , Uhlemann Anne-Catrin , Lowy Franklin D. 
Published: January 2013

ABSTRACT

While much is known about the geographic distribution of different clonal types of methicillin-resistant
Staphylococcus aureus
(MRSA), few studies have assessed the molecular epidemiology of methicillin-susceptible
S. aureus
(MSSA), despite its continued clinical importance. In each U.S. Census region, reference laboratories collected successive MSSA isolates from patients with invasive or superficial staphylococcal infections for use in the Tigecycline Evaluation and Surveillance Trial. All isolates from the periods of 2004 to 2005 and 2009 to 2010 underwent antimicrobial susceptibility testing and characterization of their staphylococcal protein A (
spa
) type. Of the 708 isolates analyzed, 274
spa
types were identified and divided into 15 genetic clusters. The most common clones were
spa
t002 (
n
= 63, 8.9%) and t008 (
n
= 56, 7.9%). While the distribution of the predominant
spa
types did not differ by U.S. Census region or time period,
spa
t008 was nearly twice as common in community skin and soft tissue infections than in nosocomial bloodstream infections (11.1% versus 5.6%, respectively;
P
= 0.008). Despite such differences, both community and nosocomial settings had diverse staphylococcal clonal types representing all major
spa
clusters. In contrast to those of MRSA, MSSA infectious isolates show wide genetic diversity without clear geographical or temporal clustering. Notably, the prevalent MSSA strains (
spa
t002 and
spa
t008) are analogous to the predominant MRSA clones, further demonstrating the importance of both lineages.
Prototype Foamy Virus Protease Activity Is Essential for Intraparticle Reverse Transcription Initiation but Not Absolutely Required for Uncoating upon Host Cell Entry
Authors: Hütter Sylvia , Müllers Erik , Stanke Nicole , Reh Juliane , Lindemann Dirk 
Published: January 2013

ABSTRACT
Foamy viruses (FVs) are unique among retroviruses in performing genome reverse transcription (RTr) late in replication, resulting in an infectious DNA genome, and also in their unusual Pol biosynthesis and encapsidation strategy. In addition, FVs display only very limited Gag and Pol processing by the viral protease (PR) during particle morphogenesis and disassembly, both thought to be crucial for viral infectivity. Here, we report the generation of functional prototype FV (PFV) particles from mature or partially processed viral capsid and enzymatic proteins with infectivity levels of up to 20% of the wild type. Analysis of protein and nucleic acid composition, as well as infectivity, of virions generated from different Gag and Pol combinations (including both expression-optimized and authentic PFV open reading frames [ORFs]) revealed that precursor processing of Gag, but not Pol, during particle assembly is essential for production of infectious virions. Surprisingly, when processed Gag (instead of Gag precursor) was provided together with PR-deficient Pol precursor during virus production, infectious, viral DNA-containing particles were obtained, even when different vector or proviral expression systems were used. Although virion infectivity was reduced to 0.5 to 2% relative to that of the respective parental constructs, this finding overturns the current dogma in the FV literature that viral PR activity is absolutely essential at some point during target cell entry. Furthermore, it demonstrates that viral PR-mediated Gag precursor processing during particle assembly initiates intraparticle RTr. Finally, it shows that reverse transcriptase (RT) and integrase are enzymatically active in the Pol precursor within the viral capsid, thus enabling productive host cell infection.
Identification of the N-Terminal Domain of the Influenza Virus PA Responsible for the Suppression of Host Protein Synthesis
Authors: Desmet Emily A. , Bussey Kendra A. , Stone Raychel , Takimoto Toru 
Published: January 2013

ABSTRACT
Cellular protein synthesis is suppressed during influenza virus infection, allowing for preferential production of viral proteins. To explore the impact of polymerase subunits on protein synthesis, we coexpressed enhanced green fluorescent protein (eGFP) or luciferase together with each polymerase component or NS1 of A/California/04/2009 (Cal) and found that PA has a significant impact on the expression of eGFP and luciferase. Comparison of the suppressive activity on coexpressed proteins between various strains revealed that avian virus or avian-origin PAs have much stronger activity than human-origin PAs, such as the one from A/WSN/33 (WSN). Protein synthesis data suggested that reduced expression of coexpressed proteins is not due to PA's reported proteolytic activity. A recombinant WSN containing Cal PA showed enhanced host protein synthesis shutoff and induction of apoptosis. Further characterization of the PA fragment indicated that the N-terminal domain (PANt), which includes the endonuclease active site, is sufficient to suppress cotransfected gene expression. By characterizing various chimeric PANts, we found that multiple regions of PA, mainly the helix α4 and the flexible loop of amino acids 51 to 74, affect the activity. The suppressive effect of PANt cDNA was mainly due to PA-X, which was expressed by ribosomal frameshifting. In both Cal and WSN viruses, PA-X showed a stronger effect than the corresponding PANt, suggesting that the unique C-terminal sequences of PA-X also play a role in suppressing cotransfected gene expression. Our data indicate strain variations in PA gene products, which play a major role in suppression of host protein synthesis.