bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting the incremental effects of context on word processing: Evidence from single‐word event‐related brain potentials
Authors: Payne Brennan R. , Lee Chia‐Lin , Federmeier Kara D. 
Published: August 2015

AbstractThe amplitude of the N400—an event‐related potential (ERP) component linked to meaning processing and initial access to semantic memory—is inversely related to the incremental buildup of semantic context over the course of a sentence. We revisited the nature and scope of this incremental context effect, adopting a word‐level linear mixed‐effects modeling approach, with the goal of probing the continuous and incremental effects of semantic and syntactic context on multiple aspects of lexical processing during sentence comprehension (i.e., effects of word frequency and orthographic neighborhood). First, we replicated the classic word‐position effect at the single‐word level: Open‐class words showed reductions in N400 amplitude with increasing word position in semantically congruent sentences only. Importantly, we found that accruing sentence context had separable influences on the effects of frequency and neighborhood on the N400. Word frequency effects were reduced with accumulating semantic context. However, orthographic neighborhood was unaffected by accumulating context, showing robust effects on the N400 across all words, even within congruent sentences. Additionally, we found that N400 amplitudes to closed‐class words were reduced with incrementally constraining syntactic context in sentences that provided only syntactic constraints. Taken together, our findings indicate that modeling word‐level variability in ERPs reveals mechanisms by which different sources of information simultaneously contribute to the unfolding neural dynamics of comprehension.
Antibiotic prescribing practices for patients with fever in the transition from presumptive treatment of malaria to ‘confirm and treat’ in Zambia: a cross‐sectional study
Authors: Ndhlovu Micky , Nkhama Emmy , Miller John M. , Hamer Davidson H. 
Published: August 2015

AbstractObjectivesTo evaluate antibiotic use among patients presenting to primary healthcare facilities with febrile illness in Zambia.MethodsWe analysed data from a 2011 nationwide cross‐sectional health facility survey of routine malaria case management in Zambia. Patient consultation observation and medical record charts were used to calculate the proportion of febrile patients who were prescribed antibiotics, stratified by symptoms, health workers' diagnosis and malaria test results. Logistic regression was used to identify factors affecting antibiotic prescribing behaviour.ResultsOf 872 patients presenting with fever, 651 (74.6%) were tested for malaria. Among those tested, 608 (93.4%) had analysable results; 230 (37.8%) had positive results. Antibiotics were prescribed to 69/230 (30.0%), 247/378 (65.3%) and 132/221 (59.7%) of those who tested positive, negative and those ‘not tested’, respectively. Furthermore, antibiotics were prescribed to 36/59 (61.0%) and 242/322 (75.1%) of those diagnosed with diarrhoea and upper respiratory tract infection (URTI), respectively. Among patients prescribed any antibiotic, concurrent antimalarial prescribing occurred in 66/69 (95.6%), 32/247 (12.9%) and 19/132 (14.4%) for those with positive results, negative results and ‘not tested’, respectively. Respiratory symptoms, diagnosis of URTI, malaria or skin disease and level of health care in the health delivery system were associated with antibiotic prescribing.ConclusionsTesting positive for malaria or receiving a malaria diagnosis was associated with reduced antibiotic prescribing, while testing negative, not being tested or a diagnosis of URTI resulted in higher rates of antibiotic prescribing. There is a need for improving diagnostic capacity for non‐malaria causes of febrile illness at healthcare delivery points and limiting antibiotic use to patients with definite bacterial infections.
miR408 is involved in abiotic stress responses in Arabidopsis
Authors: Ma Chao , Burd Shaul , Lers Amnon 
Published: August 2015

SummaryMicroRNAs (miRNAs) are small RNAs that regulate the expression of target genes post‐transcriptionally; they are known to play major roles in development and responses to abiotic stress. miR408 is a highly conserved miRNA in plants that responds to the availability of copper and targets genes encoding copper‐containing proteins. It was recently recognized to be an important component of the HY5–SPL7 gene network that mediates a coordinated response to light and copper, illustrating its central role in the response of plants to the environment. Expression of miR408 is significantly affected by a variety of developmental and ‏environmental conditions; however, its biological function is ‏unknown. Involvement of miR408 in the abiotic stress response was investigated in Arabidopsis. Expression of miR408, as well as its target genes, was investigated in response to salinity, cold, oxidative stress, drought and osmotic stress. Analyses of transgenic plants with modulated miR408 expression revealed that higher miR408 expression leads to improved tolerance to salinity, cold and oxidative stress, but enhanced sensitivity to drought and osmotic stress. Cellular antioxidant capacity was enhanced in plants with elevated miR408 expression, as manifested by reduced levels of reactive oxygen species and induced expression of genes associated with antioxidative functions, including Cu/Zn superoxide dismutases (CSD1 and CSD2) and glutathione‐S‐transferase (GST‐U25), as well as auxiliary genes: the copper chaperone CCS1 and the redox stress‐associated gene SAP12. Overall, the results demonstrate significant involvement of miR408 in abiotic stress responses, emphasizing the central function of miR408 in plant survival.
Glucosylceramides are critical for cell‐type differentiation and organogenesis, but not for cell viability in Arabidopsis
Authors: Msanne Joseph , Chen Ming , Luttgeharm Kyle D. , Bradley Amanda M. , Mays Elizabeth S. , Paper Janet M. , Boyle Daniel L. , Cahoon Rebecca E. , Schrick Kathrin , Cahoon Edgar B. 
Published: August 2015

SummaryGlucosylceramides (GlcCer), glucose‐conjugated sphingolipids, are major components of the endomembrane system and plasma membrane in most eukaryotic cells. Yet the quantitative significance and cellular functions of GlcCer are not well characterized in plants and other multi‐organ eukaryotes. To address this, we examined Arabidopsis lines that were lacking or deficient in GlcCer by insertional disruption or by RNA interference (RNAi) suppression of the single gene for GlcCer synthase (GCS, At2g19880), the enzyme that catalyzes GlcCer synthesis. Null mutants for GCS (designated ‘gcs‐1’) were viable as seedlings, albeit strongly reduced in size, and failed to develop beyond the seedling stage. Heterozygous plants harboring the insertion allele exhibited reduced transmission through the male gametophyte. Undifferentiated calli generated from gcs‐1 seedlings and lacking GlcCer proliferated in a manner similar to calli from wild‐type plants. However, gcs‐1 calli, in contrast to wild‐type calli, were unable to develop organs on differentiation media. Consistent with a role for GlcCer in organ‐specific cell differentiation, calli from gcs‐1 mutants formed roots and leaves on media supplemented with the glucosylated sphingosine glucopsychosine, which was readily converted to GlcCer independent of GCS. Underlying these phenotypes, gcs‐1 cells had altered Golgi morphology and fewer cisternae per Golgi apparatus relative to wild‐type cells, indicative of protein trafficking defects. Despite seedling lethality in the null mutant, GCS RNAi suppression lines with ≤2% of wild‐type GlcCer levels were viable and fertile. Collectively, these results indicate that GlcCer are essential for cell‐type differentiation and organogenesis, and plant cells produce amounts of GlcCer in excess of that required for normal development.
The role of shear wave elastography in the diagnosis of chronic autoimmune thyroiditis
Authors: Hekimoglu Koray , Donmez Fuldem Yildirim , Arslan Serdar , Ozdemir Adnan , Demir Canan , Yazici Canan 
Published: August 2015

Aims: The aim of this study is to assess the applicability of shear wave elastography (SWE) in the diagnosis of chronic autoimmun thyroiditis (CAT) patients. Material and methods: The study group consisted of 50 patients with first-diagnosed CAT and 40 control subjects (CS). In all patients with CAT and CS, sonoelastographic measurements were made in both thyroid lobes. Optimal cut-off values were chosen to maximize the sum of sensitivity and specificity. Positive predictive value (PPV), negative predictive value (NPV), and accuracy values were also calculated. Results: Quantitative elastographic analysis evaluated by SWE in CAT patients (2.56 ± 0.30 m/s) was significantly higher compared with CS (1.63 ± 0.12 m/s) (p<0.001). The optimal cut-off value was 2.42 m/s. SWE had 77% sensitivity, 71% specificity, 92% PPV, 81% NPV, and 87% accuracy for the presence of CAT. Conclusions: Our data indicate that SWE correctly defines the elasticty of thyroid parenchyma, and this technique may assist in the diagnosis and treatment monitoring of CAT.
Human and Pathogen Factors Associated with Chlamydia trachomatis-Related Infertility in Women
Authors: Menon S. , Timms P. , Allan J. A. , Alexander K. , Rombauts L. , Horner P. , Keltz M. , Hocking J. , Huston W. M. 
Published: August 2015

SUMMARYChlamydia trachomatisis the most common bacterial sexually transmitted pathogen worldwide. Infection can result in serious reproductive pathologies, including pelvic inflammatory disease, ectopic pregnancy, and infertility, in women. However, the processes that result in these reproductive pathologies have not been well defined. Here we review the evidence for the human disease burden of these chlamydial reproductive pathologies. We then review human-based evidence that linksChlamydiawith reproductive pathologies in women. We present data supporting the idea that host, immunological, epidemiological, and pathogen factors may all contribute to the development of infertility. Specifically, we review the existing evidence that host and pathogen genotypes, host hormone status, age of sexual debut, sexual behavior, coinfections, and repeat infections are all likely to be contributory factors in development of infertility. Pathogen factors such as infectious burden, treatment failure, and tissue tropisms or ascension capacity are also potential contributory factors. We present four possible processes of pathology development and how these processes are supported by the published data. We highlight the limitations of the evidence and propose future studies that could improve our understanding of how chlamydial infertility in women occurs and possible future interventions to reduce this disease burden.
Applied Protein and Molecular Techniques for Characterization of B Cell Neoplasms in Horses
Authors: Badial Peres R. , Tallmadge Rebecca L. , Miller Steven , Stokol Tracy , Richards Kristy , Borges Alexandre S. , Felippe M. Julia B. 
Published: August 2015

ABSTRACTMature B cell neoplasms cover a spectrum of diseases involving lymphoid tissues (lymphoma) or blood (leukemia), with an overlap between these two presentations. Previous studies describing equine lymphoid neoplasias have not included analyses of clonality using molecular techniques. The objective of this study was to use molecular techniques to advance the classification of B cell lymphoproliferative diseases in five adult equine patients with a rare condition of monoclonal gammopathy, B cell leukemia, and concurrent lymphadenopathy (lymphoma/leukemia). The B cell neoplasms were phenotypically characterized by gene and cell surface molecule expression, secreted immunoglobulin (Ig) isotype concentrations, Ig heavy-chain variable (IGHV) region domain sequencing, and spectratyping. All five patients had hyperglobulinemia due to IgG1 or IgG4/7 monoclonal gammopathy. Peripheral blood leukocyte immunophenotyping revealed high proportions of IgG1- or IgG4/7-positive cells and relative T cell lymphopenia. Most leukemic cells lacked the surface B cell markers CD19 and CD21.IGHG1orIGHG4/7gene expression was consistent with surface protein expression, and secreted isotype and Ig spectratyping revealed one dominant monoclonal peak. The mRNA expression of the B cell-associated developmental genesEBF1,PAX5, andCD19was high compared to that of the plasma cell-associated markerCD38. Sequence analysis of the IGHV domain of leukemic cells revealed mutated Igs. In conclusion, the protein and molecular techniques used in this study identified neoplastic cells compatible with a developmental transition between B cell and plasma cell stages, and they can be used for the classification of equine B cell lymphoproliferative disease.
Is Shiga Toxin-Negative Escherichia coli O157:H7 Enteropathogenic or Enterohemorrhagic Escherichia coli? Comprehensive Molecular Analysis Using Whole-Genome Sequencing
Authors: Ferdous Mithila , Zhou Kai , Mellmann Alexander , Morabito Stefano , Croughs Peter D. , de Boer Richard F. , Kooistra-Smid Anna M. D. , Rossen John W. A. , Friedrich Alexander W. 
Published: August 2015

ABSTRACT

The ability of
Escherichia coli
O157:H7 to induce cellular damage leading to disease in humans is related to numerous virulence factors, most notably the
stx
gene, encoding Shiga toxin (Stx) and carried by a bacteriophage. Loss of the Stx-encoding bacteriophage may occur during infection or culturing of the strain. Here, we collected
stx
-positive and
stx
-negative variants of
E. coli
O157:H7/NM (nonmotile) isolates from patients with gastrointestinal complaints. Isolates were characterized by whole-genome sequencing (WGS), and their virulence properties and phylogenetic relationship were determined. Because of the presence of the
eae
gene but lack of the
bfpA
gene, the
stx
-negative isolates were considered atypical enteropathogenic
E. coli
(aEPEC). However, they had phenotypic characteristics similar to those of the Shiga toxin-producing
E. coli
(STEC) isolates and belonged to the same sequence type, ST11. Furthermore, EPEC and STEC isolates shared similar virulence genes, the locus of enterocyte effacement region, and plasmids. Core genome phylogenetic analysis using a gene-by-gene typing approach showed that the sorbitol-fermenting (SF)
stx
-negative isolates clustered together with an SF STEC isolate and that one non-sorbitol-fermenting (NSF)
stx
-negative isolate clustered together with NSF STEC isolates. Therefore, these
stx
-negative isolates were thought either to have lost the Stx phage or to be a progenitor of STEC O157:H7/NM. As detection of STEC infections is often based solely on the identification of the presence of
stx
genes, these may be misdiagnosed in routine laboratories. Therefore, an improved diagnostic approach is required to manage identification, strategies for treatment, and prevention of transmission of these potentially pathogenic strains.
Inactivation of the Human Cytomegalovirus
US20
Gene Hampers Productive Viral Replication in Endothelial Cells
Authors: Cavaletto Noemi , Luganini Anna , Gribaudo Giorgio 
Published: August 2015

ABSTRACT

The human cytomegalovirus (HCMV)
US12
gene family includes a group of 10 contiguous genes (
US12
to
US21
) encoding predicted seven-transmembrane-domain (7TMD) proteins that are nonessential for replication within cultured fibroblasts. Nevertheless, inactivation of some
US12
family members affects virus replication in other cell types; e.g., deletion of
US16
or
US18
abrogates virus growth in endothelial and epithelial cells or in human gingival tissue, respectively, suggesting a role for some US12 proteins in HCMV cell tropism. Here, we provide evidence that another member,
US20
, impacts the ability of a clinical strain of HCMV to replicate in endothelial cells. Through the use of recombinant HCMV encoding tagged versions of the US20 protein, we investigated the expression pattern, localization, and topology of the US20-encoded protein (pUS20). We show that pUS20 is expressed as a partially glycosylated 7TMD protein which accumulates late in infection in endoplasmic reticulum-derived peripheral structures localized outside the cytoplasmic virus assembly compartment (cVAC). US20-deficient mutants generated in the TR clinical strain of HCMV exhibited major growth defects in different types of endothelial cells, whereas they replicated normally in fibroblasts and epithelial cells. While the attachment and entry phases in endothelial cells were not significantly affected by the absence of US20 protein, US20-null viruses failed to replicate viral DNA and express representative E and L mRNAs and proteins. Taken together, these results indicate that US20 sustains the HCMV replication cycle at a stage subsequent to entry but prior to E gene expression and viral DNA synthesis in endothelial cells.

IMPORTANCE
Human cytomegalovirus (HCMV) is a major pathogen in newborns and immunocompromised individuals. A hallmark of HCMV pathogenesis is its ability to productively replicate in an exceptionally broad range of target cells, including endothelial cells, which represent a key target for viral dissemination and replication in the host, and to contribute to both viral persistence and associated inflammation and vascular diseases. Replication in endothelial cells depends on the activities of a set of viral proteins that regulate different stages of the HCMV replication cycle in an endothelial cell type-specific manner and thereby act as determinants of viral tropism. Here, we report the requirement of a HCMV protein as a postentry tropism factor in endothelial cells. The identification and characterization of HCMV endotheliotropism-regulating proteins will advance our understanding of the molecular mechanisms of HCMV-related pathogenesis and help lead to the design of new antiviral strategies able to exploit these functions.
Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion
Authors: Stapleford Kenneth A. , Rozen-Gagnon Kathryn , Das Pratyush Kumar , Saul Sirle , Poirier Enzo Z. , Blanc Hervé , Vidalain Pierre-Olivier , Merits Andres , Vignuzzi Marco 
Published: August 2015

ABSTRACT
To date, the majority of work on RNA virus replication fidelity has focused on the viral RNA polymerase, while the potential role of other viral replicase proteins in this process is poorly understood. Previous studies used resistance to broad-spectrum RNA mutagens, such as ribavirin, to identify polymerases with increased fidelity that avoid misincorporation of such base analogues. We identified a novel variant in the alphavirus viral helicase/protease, nonstructural protein 2 (nsP2) that operates in concert with the viral polymerase nsP4 to further alter replication complex fidelity, a functional linkage that was conserved among the alphavirus genus. Purified chikungunya virus nsP2 presented delayed helicase activity of the high-fidelity enzyme, and yet purified replication complexes manifested stronger RNA polymerization kinetics. Because mutagenic nucleoside analogs such as ribavirin also affect intracellular nucleotide pools, we addressed the link between nucleotide depletion and replication fidelity by using purine and pyrimidine biosynthesis inhibitors. High-fidelity viruses were more resistant to these conditions, and viral growth could be rescued by the addition of exogenous nucleosides, suggesting that mutagenesis by base analogues requires nucleotide pool depletion. This study describes a novel function for nsP2, highlighting the role of other components of the replication complex in regulating viral replication fidelity, and suggests that viruses can alter their replication complex fidelity to overcome intracellular nucleotide-depleting conditions.

IMPORTANCE
Previous studies using the RNA mutagen ribavirin to select for drug-resistant variants have highlighted the essential role of the viral RNA-dependent RNA polymerase in regulating replication fidelity. However, the role of other viral replicase components in replication fidelity has not been studied in detail. We identified here an RNA mutagen-resistant variant of the nsP2 helicase/protease that conferred increased fidelity and yet could not operate in the same manner as high-fidelity polymerases. We show that the alphavirus helicase is a key component of the fidelity-regulating machinery. Our data show that the RNA mutagenic activity of compounds such as ribavirin is coupled to and potentiated by nucleotide depletion and that RNA viruses can fine-tune their replication fidelity when faced with an intracellular environment depleted of nucleotides.
Positive Selection in CD8+T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages
Authors: Machkovech Heather M. , Bedford Trevor , Suchard Marc A. , Bloom Jesse D. 
Published: August 2015

ABSTRACTNumerous experimental studies have demonstrated that CD8+T cells contribute to immunity against influenza by limiting viral replication. It is therefore surprising that rigorous statistical tests have failed to find evidence of positive selection in the epitopes targeted by CD8+T cells. Here we use a novel computational approach to test for selection in CD8+T-cell epitopes. We define all epitopes in the nucleoprotein (NP) and matrix protein (M1) with experimentally identified human CD8+T-cell responses and then compare the evolution of these epitopes in parallel lineages of human and swine influenza viruses that have been diverging since roughly 1918. We find a significant enrichment of substitutions that alter human CD8+T-cell epitopes in NP of human versus swine influenza virus, consistent with the idea that these epitopes are under positive selection. Furthermore, we show that epitope-altering substitutions in human influenza virus NP are enriched on the trunk versus the branches of the phylogenetic tree, indicating that viruses that acquire these mutations have a selective advantage. However, even in human influenza virus NP, sites in T-cell epitopes evolve more slowly than do nonepitope sites, presumably because these epitopes are under stronger inherent functional constraint. Overall, our work demonstrates that there is clear selection from CD8+T cells in human influenza virus NP and illustrates how comparative analyses of viral lineages from different hosts can identify positive selection that is otherwise obscured by strong functional constraint.IMPORTANCEThere is a strong interest in correlates of anti-influenza immunity that are protective against diverse virus strains. CD8+T cells provide such broad immunity, since they target conserved viral proteins. An important question is whether T-cell immunity is sufficiently strong to drive influenza virus evolution. Although many studies have shown that T cells limit viral replication in animal models and are associated with decreased symptoms in humans, no studies have proven with statistical significance that influenza virus evolves under positive selection to escape T cells. Here we use comparisons of human and swine influenza viruses to rigorously demonstrate that human influenza virus evolves under pressure to fix mutations in the nucleoprotein that promote escape from T cells. We further show that viruses with these mutations have a selective advantage since they are preferentially located on the “trunk” of the phylogenetic tree. Overall, our results show that CD8+T cells targeting nucleoprotein play an important role in shaping influenza virus evolution.