bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of Classical Swine Fever Virus with Enhanced Pathogenicity Reveals Synergistic Virulence Determinants in E2 and NS4B
Authors: Tamura Tomokazu , Sakoda Yoshihiro , Yoshino Fumi , Nomura Takushi , Yamamoto Naoki , Sato Yuka , Okamatsu Masatoshi , Ruggli Nicolas , Kida Hiroshi 
Published: June 2012

ABSTRACT

Classical swine fever virus (CSFV) is the causative agent of classical swine fever (CSF), a highly contagious disease of pigs. There are numerous CSFV strains that differ in virulence, resulting in clinical disease with different degrees of severity. Low-virulent and moderately virulent isolates cause a mild and often chronic disease, while highly virulent isolates cause an acute and mostly lethal hemorrhagic fever. The live attenuated vaccine strain GPE
−
was produced by multiple passages of the virulent ALD strain in cells of swine, bovine, and guinea pig origin. With the aim of identifying the determinants responsible for the attenuation, the GPE
−
vaccine virus was readapted to pigs by serial passages of infected tonsil homogenates until prolonged viremia and typical signs of CSF were observed. The GPE
−
/P-11 virus isolated from the tonsils after the 11th passage
in vivo
had acquired 3 amino acid substitutions in E2 (T830A) and NS4B (V2475A and A2563V) compared with the virus before passages. Experimental infection of pigs with the mutants reconstructed by reverse genetics confirmed that these amino acid substitutions were responsible for the acquisition of pathogenicity. Studies
in vitro
indicated that the substitution in E2 influenced virus spreading and that the changes in NS4B enhanced the viral RNA replication. In conclusion, the present study identified residues in E2 and NS4B of CSFV that can act synergistically to influence virus replication efficiency
in vitro
and pathogenicity in pigs.
Hepatitis C Virus Upregulates Beclin1 for Induction of Autophagy and Activates mTOR Signaling
Authors: Shrivastava Shubham , Bhanja Chowdhury Joydip , Steele Robert , Ray Ranjit , Ray Ratna B. 
Published: June 2012

ABSTRACT

Hepatitis C virus (HCV) induces autophagosome formation in infected human hepatocytes. We have previously reported that HCV exploits autophagic machinery in favor of virus growth and survival in host cells (S. Shrivastava et al., Hepatology
53:
406–414, 2011); however, the mechanisms for autophagy induction is poorly understood. In the present study, we observed that HCV infection transcriptionally upregulates Beclin1, which forms complex with Vps34, the class III phosphatidylinositol 3-kinase, as a first step for autophagy initiation. Although Bcl-2 has an anti-autophagy effect by its association with Beclin1 in nutrient-deprived cells, our studies revealed that HCV-mediated autophagy occurs independent of Beclin1–Bcl-2 dissociation. Mammalian target of rapamycin (mTOR) is a positive regulator of cell growth and is recognized as an inhibitor of autophagy induction. Our results demonstrated that HCV infection enhances phospho-mTOR expression and its downstream target 4EBP1 activation, suggesting that mTOR is not a negative regulator of HCV-induced autophagy. On the other hand, HCV infection in autophagy-impaired cells reduced phospho-mTOR, mTOR, and phospho-4EBP1 expression. Together, these results suggested that HCV induces autophagy by upregulating Beclin1 and activates mTOR signaling pathway, which in turn may promote hepatocyte growth.
Interleukin-1R Signaling Is Essential for Induction of Proapoptotic CD8 T Cells, Viral Clearance, and Pathology during Lymphocytic Choriomeningitis Virus Infection in Mice
Authors: Joeckel Lars T. , Wallich Reinhard , Metkar Sunil S. , Froelich Christopher J. , Simon Markus M. , Borner Christoph 
Published: June 2012

ABSTRACTThe T cell granule exocytosis pathway is essential to control hepatotropic lymphocytic choriomeningitis virus strain WE (LCMV-WE) but also contributes to the observed pathology in mice. Although effective antiviral T cell immunity and development of viral hepatitis are strictly dependent on perforin and granzymes, the molecular basis underlying induction of functionally competent virus-immune T cells, including participation of the innate immune system, is far from being resolved. We demonstrate here that LCMV-immune T cells of interleukin-1 receptor (IL-1R)-deficient mice readily express transcripts for perforin and granzymes but only translate perforin, resulting in the lack of proapoptotic potentialin vitro. LCMV is not cleared in IL-1R-deficient mice, and yet the infected mice develop neither splenomegaly nor hepatitis. These results demonstrate that IL-1R signaling is central to the induction of proapoptotic CD8 T cell immunity, including viral clearance and associated tissue injuries in LCMV infection.
Structural Properties of the C Terminus of Vesicular Stomatitis Virus N Protein Dictate N-RNA Complex Assembly, Encapsidation, and RNA Synthesis
Authors: Heinrich Bianca S. , Morin Benjamin , Rahmeh Amal A. , Whelan Sean P. J. 
Published: June 2012

ABSTRACT

The vesicular stomatitis virus (VSV) nucleoprotein (N) associates tightly with the viral genomic RNA. This N-RNA complex constitutes the template for the RNA-dependent RNA polymerase L, which engages the nucleocapsid via its phosphoprotein cofactor P. While N and P proteins play important roles in regulating viral gene expression, the molecular basis of this regulation remains incompletely understood. Here we show that mutations in the extreme C terminus of N cause defects in viral gene expression. To determine the underlying cause of such defects, we examined the effects of the mutations separately on encapsidation and RNA synthesis. Expression of N together with P in
Escherichia coli
results predominantly in the formation of decameric N-RNA rings. In contrast, nucleocapsid complexes containing the substitution N
Y415A
or N
K417A
were more loosely coiled, as revealed by electron microscopy (EM). In addition, the N
EF419/420AA
mutant was unable to encapsidate RNA. To further characterize these mutants, we engineered an infectious cDNA clone of VSV and employed N-RNA templates from those viruses to reconstitute RNA synthesis
in vitro
. The transcription assays revealed specific defects in polymerase utilization of the template that result in overall decreased RNA quantities, including reduced amounts of leader RNA. Passage of the recombinant viruses in cell culture led to the accumulation of compensatory second-site mutations in close proximity to the original mutations, underscoring the critical role of structural features within the C terminus in regulating N function.
Cytotoxic T-Lymphocyte Escape Mutations Identified by HLA Association Favor Those Which Escape and Revert Rapidly
Authors: Fryer Helen R. , Frater John , Duda Anna , Palmer Duncan , Phillips Rodney E. , McLean Angela R. 
Published: June 2012

ABSTRACT
Identifying human immunodeficiency virus (HIV) immune escape mutations has implications for understanding the impact of host immunity on pathogen evolution and guiding the choice of vaccine antigens. One means of identifying cytotoxic-T-lymphocyte (CTL) escape mutations is to search for statistical associations between mutations and host human leukocyte antigen (HLA) class I alleles at the population level. The impact of evolutionary rates on the strength of such associations is not well defined. Here, we address this topic using a mathematical model of within-host evolution and between-host transmission of CTL escape mutants that predicts the prevalence of escape mutants at the population level. We ask how the rates at which an escape mutation emerges in a host who bears the restricting HLA and reverts when transmitted to a host who does not bear the HLA affect the strength of an association. We consider the impact of these factors when using a standard statistical method to test for an association and when using an adaptation of that method that corrects for phylogenetic relationships. We show that with both methods, the average sample size required to identify an escape mutation is smaller if the mutation escapes and reverts quickly. Thus, escape mutations identified as HLA associated systematically favor those that escape and revert rapidly. We also present expressions that can be used to infer escape and reversion rates from cross-sectional escape prevalence data.
A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance
Authors: Eyre David W , Golubchik Tanya , Gordon N Claire , Bowden Rory , Piazza Paolo , Batty Elizabeth M , Ip Camilla L C , Wilson Daniel J , Didelot Xavier , O'Connor Lily , Lay Rochelle , Buck David , Kearns Angela M , Shaw Angela , Paul John , Wilcox Mark H , Donnelly Peter J , Peto Tim E A , Walker A Sarah , Crook Derrick W 
Published: June 2012

ObjectivesTo investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management.DesignThe authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistantStaphylococcus aureus(MRSA) andClostridium difficile.SettingIsolates were obtained from potential outbreaks associated with three UK hospitals.ParticipantsIsolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters ofC difficile. Additionally, allC difficileisolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years.Main outcome measureWhole-genome genetic relatedness of the isolates within each epidemiological cluster.ResultsTwenty-six MRSA and 15 C difficileisolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the samespa-type were genetically distinct (≥21 SNVs). In bothC difficileclusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing inC difficilesurveillance provided early outbreak detection and identified previously undetected probable community transmission.ConclusionsThis benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice.
Do chestnut, northern red, and white oak germinant seedlings respond similarly to light treatments? II. Gas exchange and chlorophyll responses
Authors: Rebbeck Joanne , Scherzer Amy , Gottschalk Kurt 
Published: June 2012

Understanding differences in physiological and growth strategies in low-light environments among upland oak species may help managers address the challenges of oaks’ poor regeneration. Gas exchange and chlorophyll content were measured for northern red oak ( Quercus rubra L.), chestnut oak ( Quercus prinus L.), and white oak ( Quercus alba L.) germinants grown at 25%, 18%, and 6% of full sun in one of two native forest soil mixes for two summers. Northern red and chestnut oak photosynthesis at saturating light (Amax, mass) increased by 23%–36% as light levels increased from 6% to 25% of full sun, while white oak Amax, massdeclined by 20% and plateaued at 18% of full sun. White oak light compensation point is representative of deep shade (7.2 µmol·m–2·s–1), while northern red and chestnut oak averaged 17.8 µmol·m–2·s–1. Total chlorophyll content increased as light levels decreased for all species. Of the three species, the slow-growing white oak seedlings appeared to be more efficient in utilizing light than northern red or chestnut oak seedlings. This suggests no additional benefits to increasing light above that typically found in a light shelterwood cut; however, it is crucial to control faster-growing competing vegetation.
An assessment of seedling damage by wild house mice (Mus musculus) and wild deer mice (Peromyscus spp.)
Authors: Witmer Gary W. , Snow Nathan P. , Moulton Rachael S. , Swartz Jenna L. 
Published: June 2012

Although it is known that voles will damage seedlings, we do not know the extent to which deer mice (Peromyscus spp.) and house mice (Mus musculus Linnaeus, 1758) damage seedlings. Knowing this information can assist resource managers in better targeting problem species and implementing appropriate management actions. We planted and monitored ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) and narrow-leaf cottonwood (Populus angustifolia E. James) seedlings in metal stock tanks occupied by deer mice or house mice to assess the potential for damage by these rodents. Both species damaged leaves and stems of cottonwood seedlings, but house mice did more damage. House mouse damage resulted in mortality of over half of the cottonwood seedlings, whereas deer mice caused a much lower level of seedling mortality. Only slight damage was done by either species to pine seedlings. Neither species damaged the roots of seedlings, despite the extensive burrowing by house mice. Although voles are often considered to be the primary rodent species causing seedling damage, we have shown that deer mice and especially house mice could also cause substantial damage to deciduous seedlings. However, our work suggests that rodent control to prevent damage to conifer seedlings might not be warranted in general unless there are extenuating circumstances and the species causing the damage are identified to assist with targeting control methods more precisely.
Relationships between growth, quality, and stocking within managed old-growth northern hardwoods
Authors: Gronewold Chris , D’Amato Anthony W. , Palik Brian J. 
Published: June 2012

An understanding of long-term growth dynamics is central to the development of sustainable uneven-aged silvicultural systems for northern hardwood forests in eastern North America. Of particular importance are quantitative assessments of the relationships between stocking control and long-term growth and quality development. This study examined these relationships in a long-term silviculture experiment established in northern hardwood stands in the Upper Peninsula of Michigan, USA. Stands were old growth at the onset of the experiment and were maintained at three residual stocking levels (11.5, 16.1, and 20.7 m2·ha–1) over a 57-year period. Several aspects of long-term stocking control were evaluated, including the effects of residual stocking on tree quality development and the relationships between stand stocking and individual tree growth and stand-level production. Results suggest that residual stocking had little impact on quality development, likely due to the initial old-growth condition of the stands examined. In contrast, our results indicate that a range of stand densities will maintain acceptable rates of stand-level production in selection systems and that growth can be shifted between diameter classes depending on desired future stand conditions.
Cure Models as a Useful Statistical Tool for Analyzing Survival
Authors: Othus Megan , Barlogie Bart , LeBlanc Michael L. , Crowley John J. 
Published: June 2012

AbstractCure models are a popular topic within statistical literature but are not as widely known in the clinical literature. Many patients with cancer can be long-term survivors of their disease, and cure models can be a useful tool to analyze and describe cancer survival data. The goal of this article is to review what a cure model is, explain when cure models can be used, and use cure models to describe multiple myeloma survival trends. Multiple myeloma is generally considered an incurable disease, and this article shows that by using cure models, rather than the standard Cox proportional hazards model, we can evaluate whether there is evidence that therapies at the University of Arkansas for Medical Sciences induce a proportion of patients to be long-term survivors. Clin Cancer Res; 18(14); 3731–6. ©2012 AACR.
Functional Analysis of the ATM-p53-p21 Pathway in the LRF CLL4 Trial: Blockade at the Level of p21 Is Associated with Short Response Duration
Authors: Lin Ke , Adamson Janet , Johnson Gillian G. , Carter Anthony , Oates Melanie , Wade Rachel , Richards Sue , Gonzalez David , Matutes Estella , Dearden Claire , Oscier David G. , Catovsky Daniel , Pettitt Andrew R. 
Published: June 2012

Abstract
Purpose: This study sought to establish whether functional analysis of the ATM-p53-p21 pathway adds to the information provided by currently available prognostic factors in patients with chronic lymphocytic leukemia (CLL) requiring frontline chemotherapy.
Experimental Design: Cryopreserved blood mononuclear cells from 278 patients entering the LRF CLL4 trial comparing chlorambucil, fludarabine, and fludarabine plus cyclophosphamide were analyzed for ATM-p53-p21 pathway defects using an ex vivo functional assay that uses ionizing radiation to activate ATM and flow cytometry to measure upregulation of p53 and p21 proteins. Clinical endpoints were compared between groups of patients defined by their pathway status.
Results: ATM-p53-p21 pathway defects of four different types (A, B, C, and D) were identified in 194 of 278 (70%) samples. The type A defect (high constitutive p53 expression combined with impaired p21 upregulation) and the type C defect (impaired p21 upregulation despite an intact p53 response) were each associated with short progression-free survival. The type A defect was associated with chemoresistance, whereas the type C defect was associated with early relapse. As expected, the type A defect was strongly associated with TP53 deletion/mutation. In contrast, the type C defect was not associated with any of the other prognostic factors examined, including TP53/ATM deletion, TP53 mutation, and IGHV mutational status. Detection of the type C defect added to the prognostic information provided by TP53/ATM deletion, TP53 mutation, and IGHV status.
Conclusion: Our findings implicate blockade of the ATM-p53-p21 pathway at the level of p21 as a hitherto unrecognized determinant of early disease recurrence following successful cytoreduction. Clin Cancer Res; 18(15); 4191–200. ©2012 AACR.
Progenitor-like Traits Contribute to Patient Survival and Prognosis in Oligodendroglial Tumors
Authors: Ng Felicia Soo-Lee , Toh Tan Boon , Ting Esther Hui-Ling , Koh Geraldene Rong-Hui , Sandanaraj Edwin , Phong Mark , Wong Swee Seong , Leong Siew Hong , Kon Oi Lian , Tucker-Kellogg Greg , Ng Wai Hoe , Ng Ivan , Tang Carol , Ang Beng Ti 
Published: June 2012

Abstract
Purpose: Patient-derived glioma-propagating cells (GPC) contain karyotypic and gene expression profiles that are found in the primary tumor. However, their clinical relevance is unclear. We ask whether GPCs contribute to disease progression and survival outcome in patients with glioma by analyzing gene expression profiles.
Experimental Design: We tapped into public sources of GPC gene expression data and derived a gene signature distinguishing oligodendroglial from glioblastoma multiforme (GBM) GPCs. By adapting a method in glioma biology, the Connectivity Map, we interrogated its strength of association in public clinical databases. We validated the top-ranking signaling pathways Wnt, Notch, and TGFβ, in GPCs and primary tumor specimens.
Results: We observed that patients with better prognosis correlated with oligodendroglial GPC features and lower tumor grade, and this was independent of the current clinical indicator, 1p/19q status. Patients with better prognosis had proneural tumors whereas the poorly surviving cohort had mesenchymal tumors. In addition, oligodendroglial GPCs were more sensitive to Wnt and Notch inhibition whereas GBM GPCs responded to TGFβR1 inhibition.
Conclusions: We provide evidence that GPCs are clinically relevant. In addition, the more favorable prognosis of oligodendroglial tumors over GBM could be recapitulated transcriptomically at the GPC level, underscoring the relevance of this cellular model. Our gene signature detects molecular heterogeneity in oligodendroglial tumors that cannot be accounted for by the 1p/19q status alone, indicating that stem-like traits contribute to clinical status. Collectively, these data highlight the limitation of morphology-based histologic analyses in tumor classification, consequently impacting on treatment decisions. Clin Cancer Res; 18(15); 4122–35. ©2012 AACR.
Performance of p16/Ki-67 Immunostaining to Detect Cervical Cancer Precursors in a Colposcopy Referral Population
Authors: Wentzensen Nicolas , Schwartz Lauren , Zuna Rosemary E. , Smith Katie , Mathews Cara , Gold Michael A. , Allen R. Andy , Zhang Roy , Dunn S. Terence , Walker Joan L. , Schiffman Mark 
Published: June 2012

Abstract
Purpose: Cytology-based screening has limited sensitivity to detect prevalent cervical precancers. Human papilloma virus (HPV) DNA testing is highly sensitive and provides a high, long-term reassurance of low risk of cervical cancer. However, the specificity of HPV DNA testing is limited, requiring additional, more disease-specific markers for efficient screening approaches.
Experimental Design: Liquid-based cytology samples were collected from 625 women referred to colposcopy. A slide was stained using the CINtec plus cytology assay. Pap cytology and HPV genotyping were conducted from the same vial. Clinical performance characteristics were calculated for all women, stratified by age, and for women referred with a low-grade squamous intraepithelial lesion (LSIL) Pap.
Results: p16/Ki-67 positivity increased with histologic severity, from 26.8% in normal histology, 46.5% in CIN1, 82.8% in CIN2 to 92.8% in CIN3. Among women with CIN3, p16/Ki-67 positivity increased from 77.8% for women younger than 30 years without HPV16 to 100% for women 30 years and older with HPV16. The sensitivity and specificity to detect CIN3+ were 93.2% and 46.1%, respectively, and increased to 97.2% and 60.0% among women 30 years and older. In women with high-risk (HR)-HPV–positive atypical squamous cells of undetermined significance (ASC-US) and LSIL, sensitivity and specificity for detection of CIN3 were 90.6% and 48.6%, respectively.
Conclusions: p16/Ki-67 testing could reduce referral to colposcopy by almost half while detecting the most severe cases of CIN3. The high sensitivity of p16/Ki-67 with significantly improved specificity compared with HPV testing makes p16/Ki-67 a viable option for LSIL triage. Further studies are required to evaluate p16/Ki-67 as triage marker in HPV-based screening strategies. Clin Cancer Res; 18(15); 4154–62. ©2012 AACR.