bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Long Journey in the Development of ISI Rules for CASS Piping
Authors: Chockie Alan , Griesbach Timothy J. 
Published: January 2014

The factors that make cast austenitic stainless steel (CASS) a good candidate for use in primary piping systems have significantly hampered the ability to detect, locate, and size flaws within the material. The difficulties in effectively inspecting CASS piping has been mirrored in the challenges associated with the development of CASS inspection requirements.
Since the early 1970’s the United States Federal Regulations have made the Section XI inservice inspection (ISI) rules of American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code a mandatory requirement for all operating nuclear power plants. Section XI of the ASME Boiler and Pressure Vessel Code requires that the pressure boundary system of all light water reactors be inspected using a volumetric technique. However, the inhomogeneous coarse-grain structure and elastic anisotropy of the CASS material can produce beam skewing and distortion, high background noise, and uncertainty in the propagation velocity of the ultrasound beam.
The difficulties associated with reliability detecting and sizing flaws in CASS material have been well known since the late 1970’s. To date there are no qualified procedures, equipment, or personnel or performance demonstration requirements for the UT examination of CASS pressure-retaining welds. Until Section XI, Appendix VIII qualification requirements are developed licensees will continue to follow the rules of Appendix III for the inspection of CASS material.
In recent years there have been significant advances in the development of Section XI requirements for the inspection of CASS. This paper reviews the long and difficult journey, the changing strategies and approaches, the driving forces, and the anticipated new Code requirements for the inspection of CASS.
Comparison of 2D and 3D gamma analyses
Authors: Pulliam Kiley B. , Huang Jessie Y. , Howell Rebecca M. , Followill David , Bosca Ryan , O’Daniel Jennifer , Kry Stephen F. 
Published: January 2014

Purpose:As clinics begin to use 3D metrics for intensity‐modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans.Methods:Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system‐calculated (“evaluated dose distributions”) and Monte Carlo‐recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose‐difference (5%, 3%, 2%, and 1%) and distance‐to‐agreement (5, 3, 2, and 1 mm) acceptance criteria, low‐dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma.Results:The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low‐dose threshold ranged from 0.9% to 2.1%. Similarly, using a low‐dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D).Conclusions:The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must be noted that clinical 2D versus 3D datasets may have additional differences—for example, if 2D measurements are made with a different dosimeter than 3D measurements. Factors such as inherent dosimeter differences may be an important additional consideration to the extra dimension of available data that was evaluated in this study.
Field of view extension and truncation correction for MR‐based human attenuation correction in simultaneous MR/PET imaging
Authors: Blumhagen Jan O. , Braun Harald , Ladebeck Ralf , Fenchel Matthias , Faul David , Scheffler Klaus , Quick Harald H. 
Published: January 2014

Purpose:In quantitative PET imaging, it is critical to accurately measure and compensate for the attenuation of the photons absorbed in the tissue. While in PET/CT the linear attenuation coefficients can be easily determined from a low‐dose CT‐based transmission scan, in whole‐body MR/PET the computation of the linear attenuation coefficients is based on the MR data. However, a constraint of the MR‐based attenuation correction (AC) is the MR‐inherent field‐of‐view (FoV) limitation due to static magnetic field (B0) inhomogeneities and gradient nonlinearities. Therefore, the MR‐based human AC map may be truncated or geometrically distorted toward the edges of the FoV and, consequently, the PET reconstruction with MR‐based AC may be biased. This is especially of impact laterally where the patient arms rest beside the body and are not fully considered.Methods:A method is proposed to extend the MR FoV by determining an optimal readout gradient field which locally compensates B0 inhomogeneities and gradient nonlinearities. This technique was used to reduce truncation in AC maps of 12 patients, and the impact on the PET quantification was analyzed and compared to truncated data without applying the FoV extension and additionally to an established approach of PET‐based FoV extension.Results:The truncation artifacts in the MR‐based AC maps were successfully reduced in all patients, and the mean body volume was thereby increased by 5.4%. In some cases large patient‐dependent changes in SUV of up to 30% were observed in individual lesions when compared to the standard truncated attenuation map.Conclusions:The proposed technique successfully extends the MR FoV in MR‐based attenuation correction and shows an improvement of PET quantification in whole‐body MR/PET hybrid imaging. In comparison to the PET‐based completion of the truncated body contour, the proposed method is also applicable to specialized PET tracers with little uptake in the arms and might reduce the computation time by obviating the need for iterative calculations of the PET emission data beyond those required for reconstructing images.
Complete Genome Sequence of Border Disease Virus Genotype 3 Strain Gifhorn
Authors: Fahnøe Ulrik , Höper Dirk , Schirrmeier Horst , Beer Martin , Rasmussen Thomas Bruun 
Published: January 2014

ABSTRACTThe complete genome sequence of the genotype 3 border disease virus strain Gifhorn has been determined; this strain was originally isolated from pigs. This represents the consensus sequence for the virus used to produce the bacterial artificial chromosome (BAC) cDNA clone pBeloGif3, which yields a virus that is severely attenuated in cell culture.
Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82
Authors: Tay Martin , Roizman Dan , Cohen Yehuda , Tolker-Nielsen Tim , Givskov Michael , Yang Liang 
Published: January 2014

ABSTRACT

Pseudomonas putida
OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever since, it has been used as a model organism to study the microbial assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft genome sequence of
P. putida
OUS82 and analyze its featured pathways for biodegradation.
Draft Genome Sequence of the
d
-Xylose-Fermenting Yeast
Spathaspora arborariae
UFMG-HM19.1A
T
Authors: Lobo Francisco P. , Gonçalves Davi L. , Alves Sergio L. , Gerber Alexandra L. , de Vasconcelos Ana Tereza R. , Basso Luiz C. , Franco Glória R. , Soares Marco A. , Cadete Raquel M. , Rosa Carlos A. , Stambuk Boris U. 
Published: January 2014

ABSTRACT

The draft genome sequence of the yeast
Spathaspora arborariae
UFMG-HM19.1A
T
(CBS 11463 = NRRL Y-48658) is presented here. The sequenced genome size is 12.7 Mb, consisting of 41 scaffolds containing a total of 5,625 predicted open reading frames, including many genes encoding enzymes and transporters involved in
d
-xylose fermentation.
Evaluation of Two Line Probe Assays for Rapid Detection of Mycobacterium tuberculosis, Tuberculosis (TB) Drug Resistance, and Non-TB Mycobacteria in HIV-Infected Individuals with Suspected TB
Authors: Luetkemeyer Anne F. , Kendall Michelle A. , Wu Xingye , Lourenço Maria Cristina , Jentsch Ute , Swindells Susan , Qasba Sarojini S. , Sanchez Jorge , Havlir Diane V. , Grinsztejn Beatriz , Sanne Ian M. , Firnhaber Cynthia 
Published: January 2014

ABSTRACT

Limited performance data from line probe assays (LPAs), nucleic acid tests used for the rapid diagnosis of tuberculosis (TB), nontuberculosis mycobacteria (NTM), and
Mycobacterium tuberculosis
drug resistance are available for HIV-infected individuals, in whom paucibacillary TB is common. In this study, the strategy of testing sputum with GenoType MTBDRplus (MTBDR-Plus) and GenoType Direct LPA (Direct LPA) was compared to a gold standard of one mycobacterial growth indicator tube (MGIT) liquid culture. HIV-positive (HIV
+
) individuals with suspected TB from southern Africa and South America with <7 days of TB treatment had 1 sputum specimen tested with Direct LPA, MTBDR-Plus LPA, smear microscopy, MGIT, biochemical identification of mycobacterial species, and culture-based drug-susceptibility testing (DST). Of 639 participants, 59.3% were MGIT
M. tuberculosis
culture positive, of which 276 (72.8%) were acid-fast bacillus (AFB) smear positive. MTBDR-Plus had a sensitivity of 81.0% and a specificity of 100%, with sensitivities of 44.1% in AFB smear-negative versus 94.6% in AFB smear-positive specimens. For specimens that were positive for
M. tuberculosis
by MTBDR-Plus, the sensitivity and specificity for rifampin resistance were 91.7% and 96.6%, respectively, and for isoniazid (INH) they were 70.6% and 99.1%. The Direct LPA had a sensitivity of 88.4% and a specificity of 94.6% for
M. tuberculosis
detection, with a sensitivity of 72.5% in smear-negative specimens. Ten of 639 MGIT cultures grew
Mycobacterium avium
complex or
Mycobacterium kansasii
, half of which were detected by Direct LPA. Both LPA assays performed well in specimens from HIV-infected individuals, including in AFB smear-negative specimens, with 72.5% sensitivity for
M. tuberculosis
identification with the Direct LPA and 44.1% sensitivity with MTBDR-Plus. LPAs have a continued role for use in settings where rapid identification of INH resistance and clinically relevant NTM are priorities.
Comparison of Real-Time Reverse Transcriptase PCR Assays for Detection of Swine Hepatitis E Virus in Fecal Samples
Authors: Gerber Priscilla F. , Xiao Chao-Ting , Cao Dianjun , Meng Xiang-Jin , Opriessnig Tanja 
Published: January 2014

ABSTRACT

Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in people in many developing countries and is also endemic in many industrialized countries. Mammalian HEV (mHEV) isolates can be divided into at least four recognized major genotypes. Several nucleic acid amplification techniques have been developed for mHEV detection, with great differences in sensitivity. The aim of this study was to compare the performances of two singleplex real-time reverse transcriptase (RT) PCR assays for broad detection of all four mHEV genotypes (assays A and B) and two duplex real-time RT-PCR assays for detection and differentiation of mHEV genotypes 3 and 4 (assays C and D). RNAs extracted from 28 fecal samples from pigs experimentally inoculated with HEV genotype 3 and 186 fecal samples from commercial pigs with unknown HEV exposure were tested by all four assays. In experimental samples, HEV RNA was detected in 96.4% (assay A), 39.2% (assay B), 14.2% (assay C), and 0% (assay D) of the samples. In field samples with unknown HEV exposure, HEV RNA was detected in 67.2% (assay A), 36.4% (assay B), 1.1% (assay C), and 0.5% (assay D) of the samples. The assays showed overall poor agreement (κ = 0.19 to 0.03), with differences in detection rates between assays (
P
< 0.01). Assays A and B, which broadly detect HEV genotypes 1 to 4, had significantly higher detection rates for HEV RNA than the duplex assays C and D, which were both designed to detect and differentiate between HEV genotypes 3 and 4.
Performance of Sa
Select
, a Chromogenic Medium for Detection of Staphylococci in Clinical Specimens
Authors: Hirvonen Jari J. , Kerttula Anne-Marie , Kaukoranta Suvi-Sirkku 
Published: January 2014

ABSTRACT

In a preliminary study, known staphylococcus (
n
= 86) and other microbial (
n
= 12) isolates were plated on three chromogenic media, Sa
Select
(Bio-Rad, Hercules, CA, USA), CHROMagar
Staph. aureus
(CHROMagar Microbiology, Paris, France), and
S. aureus
ID (bioMérieux, Marcy l'Etoile, France). The sensitivities of all the media to detect
Staphylococcus aureus
after 24 h of incubation were high (100.0%). However, their specificities varied at 93.3% (95% confidence interval [CI], 86.0% to 100.0%) (CHROMagar
Staph. aureus
), 97.8% (95% CI, 93.5% to 100.0%) (
S. aureus
ID), and 100.0% (Sa
Select
). Sa
Select
also showed the highest sensitivity for recovery and differentiation of other staphylococci. As the best performing chromogenic medium, Sa
Select
was then prospectively compared to conventional culture and identification tests for the detection of staphylococci from 2,780 clinical specimens. A total of 1,589 staphylococcal isolates were recovered. Of these, 912 were
S. aureus
and 677 were other staphylococci. The sensitivity and specificity of Sa
Select
to detect
S. aureus
in clinical specimens after 24 h of incubation were 99.6% and 99.9% (95% CI, 99.2% to 100.0% and 99.8% to 100.0%), respectively, whereas the sensitivity and specificity using conventional plates combined with laboratory identification methods were 96.8% and 99.5% (95% CI, 95.7 to 97.9% and 99.2% to 99.8%). For the recovery and preliminary identification of other staphylococci, the sensitivity and specificity of Sa
Select
were 94.4% and 99.9%. Sa
Select
is a well-performing chromogenic medium that significantly improved the detection of staphylococci, especially
S. aureus
, compared to conventional culture (
P
< 0.0001).
Dynamic Imaging of the Hepatitis C Virus NS5A Protein during a Productive Infection
Authors: Eyre Nicholas S. , Fiches Guillaume N. , Aloia Amanda L. , Helbig Karla J. , McCartney Erin M. , McErlean Christopher S. P. , Li Kui , Aggarwal Anupriya , Turville Stuart G. , Beard Michael R. 
Published: January 2014

ABSTRACT
Hepatitis C virus (HCV) NS5A is essential for viral genome replication within cytoplasmic replication complexes and virus assembly at the lipid droplet (LD) surface, although its definitive functions are poorly understood. We developed approaches to investigate NS5A dynamics during a productive infection. We report here that NS5A motility and efficient HCV RNA replication require the microtubule network and the cytoplasmic motor dynein and demonstrate that both motile and relatively static NS5A-positive foci are enriched with host factors VAP-A and Rab5A. Pulse-chase imaging revealed that newly synthesized NS5A foci are small and distinct from aged foci, while further studies using a unique dual fluorescently tagged infectious HCV chimera showed a relatively stable association of NS5A foci with core-capped LDs. These results reveal new details about the dynamics and maturation of NS5A and the nature of potential sites of convergence of HCV replication and assembly pathways.

IMPORTANCE
Hepatitis C virus (HCV) is a major cause of serious liver disease worldwide. An improved understanding of the HCV replication cycle will enable development of novel and improved antiviral strategies. Here we have developed complementary fluorescent labeling and imaging approaches to investigate the localization, traffic and interactions of the HCV NS5A protein in living, virus-producing cells. These studies reveal new details as to the traffic, composition and biogenesis of NS5A foci and the nature of their association with putative sites of virus assembly.
TRAF2 Facilitates Vaccinia Virus Replication by Promoting Rapid Virus Entry
Authors: Haga Ismar R. , Pechenick Jowers Tali , Griffiths Samantha J. , Haas Juergen , Beard Philippa M. 
Published: January 2014

ABSTRACT

Tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) is a pivotal intracellular mediator of signaling pathways downstream of TNFR1 and -2 with known pro- and antiviral effects. We investigated its role in the replication of the prototype poxvirus vaccinia virus (VACV). Loss of TRAF2 expression, either through small interfering RNA treatment of HeLa cells or through genetic knockout in murine embryonic fibroblasts (MEFs), led to significant reductions in VACV growth following low-multiplicity infection. In single-cycle infections, there was delayed production of both early and late VACV proteins as well as accelerated virus-induced alterations to cell morphology, indicating that TRAF2 influences early stages of virus replication. Consistent with an early role, uncoating assays showed normal virus attachment but delayed virus entry in the absence of TRAF2. Although alterations to c-Jun N-terminal kinase (JNK) signaling were apparent in VACV-infected TRAF2
−/−
MEFs, treatment of wild-type cells with a JNK inhibitor did not affect virus entry. Instead, treatment with an inhibitor of endosomal acidification greatly reduced virus entry into TRAF2
−/−
MEFs, suggesting that VACV is reliant on the endosomal route of entry in the absence of TRAF2. Thus, TRAF2 is a proviral factor for VACV that plays a role in promoting efficient viral entry, most likely via the plasma membrane.

IMPORTANCE
Tumor necrosis factor receptor-associated factors (TRAFs) are key facilitators of intracellular signaling with roles in innate and adaptive immunity and stress responses. We have discovered that TRAF2 is a proviral factor in vaccinia virus replication in both HeLa cells and mouse embryonic fibroblasts and that its influence is exercised through promotion of efficient virus entry.
Hepatitis C Virus-Induced Changes in MicroRNA 107 (miRNA-107) and miRNA-449a Modulate CCL2 by Targeting the Interleukin-6 Receptor Complex in Hepatitis
Authors: Sarma Nayan J. , Tiriveedhi Venkataswarup , Crippin Jeffrey S. , Chapman William C. , Mohanakumar Thalachallour 
Published: January 2014

ABSTRACTHepatitis C virus (HCV)-mediated liver diseases are one of the major health issues in the United States and worldwide. HCV infection has been reported to modulate microRNAs (miRNAs) that control various cell surface receptors and gene-regulatory complexes involved in hepatic inflammation and liver diseases. We report here that specific downregulation of miRNA-107 and miRNA-449a following HCV infection in patients with HCV-mediated liver diseases modulates expression of CCL2, an inflammatory chemokine upregulated in patients with chronic liver diseases, by targeting components of the interleukin-6 receptor (IL-6R) complex. Computational analysis for DNA-bound transcription factors in theCCL2promoter identified adjacent binding sites for CCAAT/CEBPα, spleen focus-forming virus, proviral integration oncogene (SPI1/PU.1), and STAT3. We demonstrate that CEBPα, PU.1, and STAT3 interacted with each other physically to cooperatively bind to the promoter and activateCCL2expression. Analysis ofIL-6RandJAK1expression in HCV patients by quantitative PCR showed significant upregulation when there was impaired miRNA-107 and miRNA-449a expression, along with upregulation of PU.1 and STAT3, but not CEBPα. miRNA-449a and miRNA-107 target expression ofIL-6RandJAK1, respectively,in vitroand also inhibit IL-6 signaling and impair STAT3 activation in human hepatocytes. Taken together, our results demonstrate a novel gene-regulatory mechanism in which HCV-induced changes in miRNAs (miRNA-449a and miRNA-107) regulate CCL2 expression by activation of the IL-6-mediated signaling cascade, which we propose will result in HCV-mediated induction of inflammatory responses and fibrosis.IMPORTANCEHepatitis C virus (HCV)-induced hepatitis is a major health concern worldwide. HCV infection results in modulation of noncoding microRNAs affecting major cellular pathways, including inflammatory responses. In this study, we have identified a microRNA-regulated pathway for the chemokine CCL2 in HCV-induced hepatitis. Understanding microRNA-mediated transcriptional-regulatory pathways will result in development of noninvasive biomarkers for better disease prediction and development of effective therapeutics.
Epstein-Barr Virus Latent Membrane Protein 1 Genetic Variability in Peripheral Blood B Cells and Oropharyngeal Fluids
Authors: Renzette Nicholas , Somasundaran Mohan , Brewster Frank , Coderre James , Weiss Eric R. , McManus Margaret , Greenough Thomas , Tabak Barbara , Garber Manuel , Kowalik Timothy F. , Luzuriaga Katherine 
Published: January 2014

ABSTRACTWe report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic compartments by using virus genomes amplified directly from oropharyngeal wash specimens and peripheral blood B cells during acute infection and convalescence. The intrahost nucleotide variability of the founder virus was 0.02% across the region sequences, and diversity increased significantly over time in the oropharyngeal compartment (P= 0.004). The LMP1 region showing the greatest level of variability in both compartments, and over time, was concentrated within the functional carboxyl-terminal activating regions 2 and 3 (CTAR2 and CTAR3). Interestingly, a deletion in a proline-rich repeat region (amino acids 274 to 289) of EBV commonly reported in EBV sequenced from cancer specimens was not observed in acute infectious mononucleosis (AIM) patients. Taken together, these data highlight the diversity in circulating EBV genomes and its potential importance in disease pathogenesis and vaccine design.IMPORTANCEThis study is among the first to leverage an improved high-throughput deep-sequencing methodology to investigate directly from patient samples the degree of diversity in Epstein-Barr virus (EBV) populations and the extent to which viral genome diversity develops over time in the infected host. Significant variability of circulating EBV latent membrane protein 1 (LMP1) gene sequences was observed between cellular and oral wash samples, and this variability increased over time in oral wash samples. The significance of EBV genetic diversity in transmission and disease pathogenesis are discussed.
Antigenic Mapping of the Hemagglutinin of an H9N2 Avian Influenza Virus Reveals Novel Critical Amino Acid Positions in Antigenic Sites
Authors: Wan Zhimin , Ye Jianqiang , Xu Liangliang , Shao Hongxia , Jin Wenjie , Qian Kun , Wan Hongquan , Qin Aijian 
Published: January 2014

ABSTRACT
H9N2 influenza virus is undergoing extensive genetic and antigenic evolution, warranting detailed antigenic mapping of its hemagglutinin (HA). Through examining antibody escape mutants of an Asian avian H9N2 virus, we identified 9 critical amino acid positions in H9 antigenic sites. Five of these positions, 164, 167, 168, 196, and 207, have not been reported previously and, thus, represent novel molecular markers for monitoring the antigenic change of H9N2 virus.