bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management influence on maize–wheat system performance, water productivity and soil biology
Authors: Jat H. S. , Singh Gurbachan , Singh Ranbir , Choudhary M. , Jat M. L. , Gathala M. K. , Sharma D. K. 
Published: September 2015

AbstractCereal cropping productivity in the Indo‐Gangetic Plain (IGP) of India is declining, which may be overcome by diversification, alternate crop establishment methods and mulching. This study was conducted to determine whether no‐till flat (NTF), permanent raised beds (PRB) and nontraditionalex situmulching would improve crop and water productivity, economic profitability and soil biological properties in an irrigated maize (Zea mays)–wheat (Triticum aestivum) system (MWS).NTFsystems produced 10% higher economic net returns compared withPRBs. Non‐traditional mulching (Sesbania, JatrophaandBrassica)increased yields by >10% and net returns by >12% compared with no‐mulch. The water saving inPRBs compared withNTFsystems was 79, 94 and 173 mm/ha in maize, wheat andMWS, respectively.PRBs saved 29.2% of irrigation water and improved theMWSirrigation water productivity (WPI) by 24.5% overNTF. On average, mulching saved 23.8 mm/ha irrigation water over no‐mulch and improvedWPIby 12.0%.PRBs withex situmulching produced wheat and maize equivalent system yields lower thanNTFbut improvedWPIand soil biological properties.JatrophaandSesbaniamulching improved yield, water saving,WPIand system profitability. In limited irrigation and no crop residue availability conditions,Sesbania, JatrophaandBrassicavegetation material have potential applications forex situmulching underPRBs for water saving andNTFfor productivity.
Do Trade Agreements Increase Food Trade?
Authors: Mujahid Irfan , Kalkuhl Matthias 
Published: September 2015

AbstractIn addition to multilateral trade agreements under the World Trade Organization (WTO), the world has seen a remarkable proliferation of regional trade agreements (RTAs) in the last two decades. This study investigates whether these multilateral and regional trade institutions increase food trade and bring the world into a freer flow of food. The gravity model of international trade is used for the empirical analysis. The model is developed in a large panel data setting and attempted to address some potential problems in the estimations including multilateral trade resistances, zero trade values and endogeneity. The results suggest that both the WTO and RTAs have delivered significant positive effects on trade among the participant countries, but not food. Only RTAs are found to have increased food trade among the participant countries. However, although on average the WTO is found to have negative implications on food trade, it facilitates the developing countries more than the developed countries.
An Epidemiologic Investigation of a Case of Acute Hepatitis E
Authors: Sarkar Souvik , Rivera Elenita M. , Engle Ronald E. , Nguyen Hanh T. , Schechterly Cathy A. , Alter Harvey J. , Liang T. Jake , Purcell Robert H. , Hoofnagle Jay H. , Ghany Marc G. 
Published: September 2015

ABSTRACT

Hepatitis E virus (HEV) is considered a zoonotic infection in developed nations. A case of acute hepatitis E in a researcher following a scalpel injury while working on a pig prompted a seroepidemiologic study to identify potential modes of transmission and determine the seroprevalence of HEV among animal handlers at the institute. Sera from personnel (
n
= 64) in two animal facilities and age/sex-matched blood donors (
n
= 63) as controls were tested for IgG anti-HEV and, if positive, for IgM anti-HEV and HEV RNA. Sera and stool from pigs aged 6 to 12 weeks from the breeding farm and older pigs from animal facilities were tested similarly. The median age of personnel was 36 years, 74% were white, 56% were male, and 74% had direct exposure to pigs. The prevalence of anti-HEV was 3.1% among personnel compared to 3.2% among blood donors; none were positive for IgM anti-HEV or HEV RNA. IgG anti-HEV was detected in sera from 10% of pigs aged 6 to 8 weeks, 80% aged 10 weeks, 100% aged 12 weeks, and 76% aged >12 weeks. HEV RNA was detected in stool but not sera from three 12-week-old pigs. Sequencing revealed HEV genotype 3 with ∼10% difference between the patient and pig sequences. Parenteral transmission is a potential mode of acute HEV infection. The low and similar seroprevalence of anti-HEV between the at-risk group and age-matched blood donors suggests low transmission risk with universal precautions among animal handlers.
Clinical Performance of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Method for Detection of Certain
bla
KPC
-Containing Plasmids
Authors: Youn Jung-Ho , Drake Steven K. , Weingarten Rebecca A. , Frank Karen M. , Dekker John P. , Lau Anna F. 
Published: September 2015

ABSTRACT

Rapid detection of
bla
KPC
-containing organisms can significantly impact infection control and clinical practices, as well as therapeutic choices. Current molecular and phenotypic methods to detect these organisms, however, require additional testing beyond routine organism identification. In this study, we evaluated the clinical performance of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) to detect pKpQIL_p019 (p019)—an ∼11,109-Da protein associated with certain
bla
KPC
-containing plasmids that was previously shown to successfully track a clonal outbreak of
bla
KPC
-pKpQIL-
Klebsiella pneumoniae
in a proof-of-principle study (A. F. Lau, H. Wang, R. A. Weingarten, S. K. Drake, A. F. Suffredini, M. K. Garfield, Y. Chen, M. Gucek, J. H. Youn, F. Stock, H. Tso, J. DeLeo, J. J. Cimino, K. M. Frank, and J. P. Dekker, J Clin Microbiol 52:2804–2812, 2014,
http://dx.doi.org/10.1128/JCM.00694-14
). PCR for the
p019
gene was used as the reference method. Here, blind analysis of 140 characterized
Enterobacteriaceae
isolates using two protein extraction methods (plate extraction and tube extraction) and two peak detection methods (manual and automated) showed sensitivities and specificities ranging from 96% to 100% and from 95% to 100%, respectively (2,520 spectra analyzed). Feasible laboratory implementation methods (plate extraction and automated analysis) demonstrated 96% sensitivity and 99% specificity. All p019-positive isolates (
n
= 26) contained
bla
KPC
and were carbapenem resistant. Retrospective analysis of an additional 720 clinical
Enterobacteriaceae
spectra found an ∼11,109-Da signal in nine spectra (1.3%), including seven from p019-containing, carbapenem-resistant isolates (positive predictive value [PPV], 78%). Instrument tuning had a significant effect on assay sensitivity, highlighting important factors that must be considered as MALDI-TOF MS moves into applications beyond microbial identification. Using a large blind clinical data set, we have shown that spectra acquired for routine organism identification can also be analyzed automatically in real time at high throughput, at no additional expense to the laboratory, to enable rapid detection of potentially
bla
KPC
-containing carbapenem-resistant isolates, providing early and clinically actionable results.
Clinical Performance of Check-Direct CPE, a Multiplex PCR for Direct Detection of
bla
KPC
,
bla
NDM
and/or
bla
VIM
, and
bla
OXA-48
from Perirectal Swabs
Authors: Lau Anna F. , Fahle Gary A. , Kemp Margaret A. , Jassem Agatha N. , Dekker John P. , Frank Karen M. 
Published: September 2015

ABSTRACT

We evaluated the clinical performance of Check-Direct CPE for carbapenemase detection directly from 301 perirectal swabs (258 patients) in a nonoutbreak setting. Culture of a PCR-confirmed, carbapenemase-containing organism, or history of colonization with such organism within the previous 2 weeks, was used as the reference standard. Check-Direct CPE demonstrated a sensitivity value, specificity value, positive predictive value (PPV), and negative predictive value (NPV) of 100% (all
bla
KPC
), 88%, 21%, and 100%, respectively. False positives accounted for 79% (
n
= 34) of samples for which a cycle threshold (

C
T

) value was reached. Simulated studies to evaluate specimen pooling as an approach to minimize costs showed no difference in

C
T

values for pooled groups of three or five that each contained a single specimen spiked with ∼1,500 CFU
bla
KPC
Klebsiella pneumoniae
; however, the detection rate dropped to 60% at a seeded concentration of ∼150 CFU. When data were pooled,

C
T

values for
bla
KPC
were higher for heavy-feces-containing than for light-feces-containing liquid-suspended specimens. Furthermore,

C
T

values for liquid-suspended specimens were 4 to 5

C
T

values lower (i.e., represented greater sensitivity) than those seen in direct swab analysis. Culture was equivalent to or better than Check-Direct CPE for 13/15 (87%) isolates tested in a limit-of-detection analysis. Detection of a carbapenemase gene at a

C
T

cutoff value of ≤35 was culture confirmed in 23/24 (96%) of cases; however,

C
T

values of >35 overlapped broadly between culture-positive (
n
= 21) and culture-negative (
n
= 36) specimens. Check-Direct CPE will likely prove most useful in high-prevalence areas or in outbreak settings where rapid carbapenemase detection is critical for infection control management.
Quality Assurance for Antimicrobial Susceptibility Testing of Neisseria gonorrhoeae in Canada, 2003 to 2012
Authors: Sawatzky Pam , Liu Gary , Dillon Jo-Anne R. , Allen Vanessa , Lefebvre Brigitte , Hoang Linda , Tyrrell Greg , Van Caeseele Paul , Levett Paul , Martin Irene 
Published: September 2015

ABSTRACT
Data from the Canadian National Gonococcal Antimicrobial Susceptibility Comparison Program, including results from 25 proficiency panels distributed between 2003 and 2012, were analyzed. The average MIC agreement between the participating laboratories ranged from 85.6% to 98.8% over the 10-year period, with the interpretation agreement ranging from 85.7% to 98.1%.
Doubly Spliced RNA of Hepatitis B Virus Suppresses Viral Transcription via TATA-Binding Protein and Induces Stress Granule Assembly
Authors: Tsai Kuen-Nan , Chong Chin-Liew , Chou Yu-Chi , Huang Chien-Chiao , Wang Yi-Ling , Wang Shao-Win , Chen Mong-Liang , Chen Chun-Hong , Chang Chungming 
Published: September 2015

ABSTRACT

The risk of liver cancer in patients infected with the hepatitis B virus (HBV) and their clinical response to interferon alpha therapy vary based on the HBV genotype. The mechanisms underlying these differences in HBV pathogenesis remain unclear. In HepG2 cells transfected with a mutant HBV
G2335A
expression plasmid that does not transcribe the 2.2-kb doubly spliced RNA (2.2DS-RNA) expressed by wild-type HBV genotype A, the level of HBV pregenomic RNA (pgRNA) was higher than that in cells transfected with an HBV genotype A expression plasmid. By using cotransfection with HBV genotype D and 2.2DS-RNA expression plasmids, we found that a reduction of pgRNA was observed in the cells even in the presence of small amounts of the 2.2DS-RNA plasmid. Moreover, ectopic expression of 2.2DS-RNA in the HBV-producing cell line 1.3ES2 reduced the expression of pgRNA. Further analysis showed that exogenously transcribed 2.2DS-RNA inhibited a reconstituted transcription
in vitro
. In Huh7 cells ectopically expressing 2.2DS-RNA, RNA immunoprecipitation revealed that 2.2DS-RNA interacted with the TATA-binding protein (TBP) and that nucleotides 432 to 832 of 2.2DS-RNA were required for efficient TBP binding. Immunofluorescence experiments showed that 2.2DS-RNA colocalized with cytoplasmic TBP and the stress granule components, G3BP and poly(A)-binding protein 1 (PABP1), in Huh7 cells. In conclusion, our study reveals that 2.2DS-RNA acts as a repressor of HBV transcription through an interaction with TBP that induces stress granule formation. The expression of 2.2DS-RNA may be one of the viral factors involved in viral replication, which may underlie differences in clinical outcomes of liver disease and responses to interferon alpha therapy between patients infected with different HBV genotypes.

IMPORTANCE
Patients infected with certain genotypes of HBV have a lower risk of hepatocellular carcinoma and exhibit a more favorable response to antiviral therapy than patients infected with other HBV genotypes. Using cultured human hepatoma cells as a model of HBV infection, we found that the expression of 2.2DS-RNA caused a decrease in HBV replication. In cultured cells, the ectopic expression of 2.2DS-RNA obviously reduced the intracellular levels of HBV mRNAs. Our analysis of the 2.2DS-RNA-mediated suppression of viral RNA expression showed that 2.2DS-RNA inhibited transcription via binding to the TATA-binding protein and stress granule proteins. Our findings suggest that the 2.2DS-RNA acts as a suppressive noncoding RNA that modulates HBV replication, which may in turn influence the development of chronic hepatitis B.
Signaling Lymphocytic Activation Molecule Family Receptor Homologs in New World Monkey Cytomegaloviruses
Authors: Pérez-Carmona Natàlia , Farré Domènec , Martínez-Vicente Pablo , Terhorst Cox , Engel Pablo , Angulo Ana 
Published: September 2015

ABSTRACT
Throughout evolution, large DNA viruses have been usurping genes from their hosts to equip themselves with proteins that restrain host immune defenses. Signaling lymphocytic activation molecule (SLAM) family (SLAMF) receptors are involved in the regulation of both innate and adaptive immunity, which occurs upon engagement with their ligands via homotypic or heterotypic interactions. Here we report a total of seven SLAMF genes encoded by the genomes of two cytomegalovirus (CMV) species, squirrel monkey CMV (SMCMV) and owl monkey CMV (OMCMV), that infect New World monkeys. Our results indicate that host genes were captured by retrotranscription at different stages of the CMV-host coevolution. The most recent acquisition led to S1 in SMCMV. S1 is a SLAMF6 homolog with an amino acid sequence identity of 97% to SLAMF6 in its ligand-binding N-terminal Ig domain. We demonstrate that S1 is a cell surface glycoprotein capable of binding to host SLAMF6. Furthermore, the OMCMV genome encodes A33, an LY9 (SLAMF3) homolog, and A43, a CD48 (SLAMF2) homolog, two soluble glycoproteins which recognize their respective cellular counterreceptors and thus are likely to be viral SLAMF decoy receptors. In addition, distinct copies of further divergent CD48 homologs were found to be encoded by both CMV genomes. Remarkably, all these molecules display a number of unique features, including cytoplasmic tails lacking characteristic SLAMF signaling motifs. Taken together, our findings indicate a novel immune evasion mechanism in which incorporation of host SLAMF receptors that retain their ligand-binding properties enables viruses to interfere with SLAMF functions and to supply themselves with convenient structural molds for expanding their immunomodulatory repertoires.

IMPORTANCE
The way in which viruses shape their genomes under the continual selective pressure exerted by the host immune system is central for their survival. Here, we report that New World monkey cytomegaloviruses have broadly captured and duplicated immune cell receptors of the signaling lymphocyte activation molecule (SLAM) family during host-virus coevolution. Notably, we demonstrate that several of these viral SLAMs exhibit exceptional preservation of their N-terminal immunoglobulin domains, which results in maintenance of their ligand-binding capacities. At the same time, these molecules present distinctive structural properties which include soluble forms and the absence of typical SLAM signaling motifs in their cytoplasmic domains, likely reflecting the evolutionary adaptation undergone to efficiently interfere with host SLAM family activities. The observation that the genomes of other large DNA viruses might bear SLAM family homologs further underscores the importance of these molecules as a novel class of immune regulators and as convenient scaffolds for viral evolution.
Epstein-Barr Viruses (EBVs) Deficient in EBV-Encoded RNAs Have Higher Levels of Latent Membrane Protein 2 RNA Expression in Lymphoblastoid Cell Lines and Efficiently Establish Persistent Infections in Humanized Mice
Authors: Gregorovic Goran , Boulden Elizabeth A. , Bosshard Rachel , Elgueta Karstegl Claudio , Skalsky Rebecca , Cullen Bryan R. , Gujer Cornelia , Rämer Patrick , Münz Christian , Farrell Paul J. 
Published: September 2015

ABSTRACT
Functions of Epstein-Barr virus (EBV)-encoded RNAs (EBERs) were tested in lymphoblastoid cell lines containing EBER mutants of EBV. Binding of EBER1 to ribosomal protein L22 (RPL22) was confirmed. Deletion of EBER1 or EBER2 correlated with increased levels of cytoplasmic EBV LMP2 RNA and with small effects on specific cellular microRNA (miRNA) levels, but protein levels of LMP1 and LMP2A were not affected. Wild-type EBV and EBER deletion EBV had approximately equal abilities to infect immunodeficient mice reconstituted with a human hematopoietic system.
Structural Basis of the Inhibition of STAT1 Activity by Sendai Virus C Protein
Authors: Oda Kosuke , Matoba Yasuyuki , Irie Takashi , Kawabata Ryoko , Fukushi Masaya , Sugiyama Masanori , Sakaguchi Takemasa 
Published: September 2015

ABSTRACT

Sendai virus (SeV) C protein inhibits the signal transduction pathways of interferon alpha/beta (IFN-α/β) and IFN-γ by binding to the N-terminal domain of STAT1 (STAT1ND), thereby allowing SeV to escape from host innate immunity. Here we determined the crystal structure of STAT1ND associated with the C-terminal half of the C protein (Y3 [amino acids 99 to 204]) at a resolution of 2.0 Å. This showed that two molecules of Y3 symmetrically bind to each niche created between two molecules of the STAT1ND dimer. Molecular modeling suggested that an antiparallel form of the full-length STAT1 dimer can bind only one Y3 molecule and that a parallel form can bind two Y3 molecules. Affinity analysis demonstrated anticooperative binding of two Y3 molecules with the STAT1 dimer, which is consistent with the hypothetical model that the second Y3 molecule can only target the STAT1 dimer in a parallel form. STAT1 with excess amounts of Y3 was prone to inhibit the dephosphorylation at Tyr
701
by a phosphatase. In an electrophoretic mobility shift assay, tyrosine-phosphorylated STAT1 (pY-STAT1) with Y3 associated with the γ-activated sequence, probably as high-molecular-weight complexes (HMWCs), which may account for partial inhibition of a reporter assay from IFN-γ by Y3. Our study suggests that the full-length C protein interferes with the domain arrangement of the STAT1 dimer, leading to the accumulation of pY-STAT1 and the formation of HMWCs. In addition, we discuss the mechanism by which phosphorylation of STAT2 is inhibited in the presence of the C protein after stimulation by IFN-α/β.

IMPORTANCE
Sendai virus, a paramyxovirus that causes respiratory diseases in rodents, possesses the C protein, which inhibits the signal transduction pathways of interferon alpha/beta (IFN-α/β) and IFN-γ by binding to the transcription factor STAT1. In virus-infected cells, phosphorylation of STAT1 at the Tyr
701
residue is potently enhanced, although transcription by STAT1 is inert. Here, we determined the crystal structure of the N-terminal domain of STAT1 associated with the C-terminal half of the C protein. Molecular modeling and experiments suggested that the two C proteins bind to and stabilize the parallel form of the STAT1 dimer, which are likely to be phosphorylated at Tyr
701
, further inducing high-molecular-weight complex formation and inhibition of transcription by IFN-γ. We also discuss the possible mechanism of inhibition of the IFN-α/β pathways by the C protein. This is the first structural report of the C protein, suggesting a mechanism of evasion of the paramyxovirus from innate immunity.
The ns12.9 Accessory Protein of Human Coronavirus OC43 Is a Viroporin Involved in Virion Morphogenesis and Pathogenesis
Authors: Zhang Ronghua , Wang Kai , Ping Xianqiang , Yu Wenjing , Qian Zhikang , Xiong Sidong , Sun Bing 
Published: September 2015

ABSTRACTAn accessory gene between the S and E gene loci is contained in all coronaviruses (CoVs), and its function has been studied in some coronaviruses. This gene locus in human coronavirus OC43 (HCoV-OC43) encodes the ns12.9 accessory protein; however, its function during viral infection remains unknown. Here, we engineered a recombinant mutant virus lacking the ns12.9 protein (HCoV-OC43-Δns12.9) to characterize the contributions of ns12.9 in HCoV-OC43 replication. The ns12.9 accessory protein is a transmembrane protein and forms ion channels in bothXenopusoocytes and yeast through homo-oligomerization, suggesting that ns12.9 is a newly recognized viroporin. HCoV-OC43-Δns12.9 presented at least 10-fold reduction of viral titerin vitroandin vivo. Intriguingly, exogenous ns12.9 and heterologous viroporins with ion channel activity could compensate for the production of HCoV-OC43-Δns12.9, indicating that the ion channel activity of ns12.9 plays a significant role in the production of infectious virions. Systematic dissection of single-cycle replication revealed that ns12.9 protein had no measurable effect on virus entry, subgenomic mRNA (sgmRNA) synthesis, and protein expression. Further characterization revealed that HCoV-OC43-Δns12.9 was less efficient in virion morphogenesis than recombinant wild-type virus (HCoV-OC43-WT). Moreover, reduced viral replication, inflammatory response, and virulence in HCoV-OC43-Δns12.9-infected mice were observed compared to the levels for HCoV-OC43-WT-infected mice. Taken together, our results demonstrated that the ns12.9 accessory protein functions as a viroporin and is involved in virion morphogenesis and the pathogenesis of HCoV-OC43 infection.IMPORTANCEHCoV-OC43 was isolated in the 1960s and is a major agent of the common cold. The functions of HCoV-OC43 structural proteins have been well studied, but few studies have focused on its accessory proteins. In the present study, we demonstrated that the ns12.9 protein is a newly recognized viroporin, and the ns12.9 gene knockout virus (HCoV-OC43-Δns12.9) presents a growth defectin vitroandin vivo. We identified the important functions of the ns12.9 viroporin in virion morphogenesis during HCoV-OC43 infection. Furthermore, mice infected with HCoV-OC43-Δns12.9 exhibited reduced inflammation and virulence accompanied by a lower titer in the brain than that of wild-type-infected mice, suggesting the ns12.9 viroporin influences virus pathogenesis. Therefore, our findings revealed that the ns12.9 viroporin facilitates virion morphogenesis to enhance viral production, and these results provided a deeper understanding of HCoV-OC43 pathogenesis.