bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Cell-Based Hepatitis C Virus Infection Assay for Quantitative High-Throughput Screening of Anti-Hepatitis C Virus Compounds
Authors: Hu Zongyi , Lan Keng-Hsin , He Shanshan , Swaroop Manju , Hu Xin , Southall Noel , Zheng Wei , Liang T. Jake 
Published: November 2013

ABSTRACT

Therapy for hepatitis C virus (HCV) infection has advanced with the recent approval of direct-acting antivirals in combination with peginterferon and ribavirin. New antivirals with novel targets are still needed to further improve the treatment of hepatitis C. Previously reported screening methods for HCV inhibitors either are limited to a virus-specific function or apply a screening method at a single dose, which usually leads to high false-positive or -negative rates. We developed a quantitative high-throughput screening (qHTS) assay platform with a cell-based HCV infection system. This highly sensitive assay can be miniaturized to a 1,536-well format for screening of large chemical libraries. All candidates are screened over a 7-concentration dose range to give EC
50
s (compound concentrations at 50% efficacy) and dose-response curves. Using this assay format, we screened a library of pharmacologically active compounds (LOPAC). Based on the profile of dose-dependent curves of HCV inhibition and cytotoxicity, 22 compounds with adequate curves and EC
50
s of <10 μM were selected for validation. In two additional independent assays, 17 of them demonstrated specific inhibition of HCV infection. Ten potential candidates with efficacies of >70% and CC
50
s (compound concentrations at 50% cytotoxicity) of <30 μM from these validated hits were characterized for their target stages in the HCV replication cycle. In this screen, we identified both known and novel hits with diverse structural and functional features targeting various stages of the HCV replication cycle. The pilot screen demonstrates that this assay system is highly robust and effective in identifying novel HCV inhibitors and that it can be readily applied to large-scale screening of small-molecule libraries.
Members of the Conserved DedA Family Are Likely Membrane Transporters and Are Required for Drug Resistance in Escherichia coli
Authors: Kumar Sujeet , Doerrler William T. 
Published: November 2013

ABSTRACT

Bacterial resistance to antibiotics and biocides is an increasing public health problem. Genes encoding integral membrane proteins belonging to the DedA family are present in most bacterial genomes, including
Escherichia coli
. An
E. coli
strain lacking partially redundant DedA family genes
yqjA
and
yghB
(strain BC202) displays temperature sensitivity and cell division defects. These phenotypes can be corrected by overexpression of
mdfA
, an Na
+
-K
+
/H
+
antiporter of the major facilitator superfamily. We show that BC202 is hypersensitive to several biocides and cationic compounds that are known substrates of several multidrug resistance transporters, including MdfA, EmrE, and AcrB. The introduction of deletions of genes encoding these drug transporters into BC202 results in additional sensitivity. Expression of wild-type
yghB
or
yqjA
can restore drug resistance, but this is eliminated upon mutation of two membrane-embedded acidic amino acids (E39 or D51 in either protein). This dependence upon membrane-embedded acidic amino acids is a hallmark of proton-dependent antiporters. Overexpression of
mdfA
in BC202 or artificially restoring proton motive force (PMF) restores wild-type resistance to substrates of MdfA as well as other drug resistance transporters such as EmrE and AcrAB. These results suggest that YqjA and YghB may be membrane transporters required for PMF-dependent drug efflux in
E. coli
.
Impact of Surfactant Protein D, Interleukin-5, and Eosinophilia on Cryptococcosis
Authors: Holmer Stephanie M. , Evans Kathy S. , Asfaw Yohannes G. , Saini Divey , Schell Wiley A. , Ledford Julie G. , Frothingham Richard , Wright Jo Rae , Sempowski Gregory D. , Perfect John R. 
Published: November 2013

ABSTRACTCryptococcus neoformansis an opportunistic fungal pathogen that initiates infection following inhalation. As a result, the pulmonary immune response provides a first line of defense againstC. neoformans. Surfactant protein D (SP-D) is an important regulator of pulmonary immune responses and is typically host protective against bacterial and viral respiratory infections. However, SP-D is not protective againstC. neoformans. This is evidenced by previous work from our laboratory demonstrating that SP-D-deficient mice infected withC. neoformanshave a lower fungal burden and live longer than wild-type (WT) control animals. We hypothesized that SP-D alters susceptibility toC. neoformansby dysregulating the innate pulmonary immune response following infection. Thus, inflammatory cells and cytokines were compared in the bronchoalveolar lavage fluid from WT and SP-D−/−mice afterC. neoformansinfection. Postinfection, mice lacking SP-D have reduced eosinophil infiltration and interleukin-5 (IL-5) in lung lavage fluid. To further explore the interplay of SP-D, eosinophils, and IL-5, mice expressing altered levels of eosinophils and/or IL-5 were infected withC. neoformansto assess the role of these innate immune mediators. IL-5-overexpressing mice have increased pulmonary eosinophilia and are more susceptible toC. neoformansinfection than WT mice. Furthermore, susceptibility of SP-D−/−mice toC. neoformansinfection could be restored to the level of WT mice by increasing IL-5 and eosinophils by crossing the IL-5-overexpressing mice with SP-D−/−mice. Together, these studies support the conclusion that SP-D increases susceptibility toC. neoformansinfection by promotingC. neoformans-driven pulmonary IL-5 and eosinophil infiltration.
Outer Membrane Protein P5 Is Required for Resistance of Nontypeable Haemophilus influenzae to Both the Classical and Alternative Complement Pathways
Authors: Rosadini Charles V. , Ram Sanjay , Akerley Brian J. 
Published: November 2013

ABSTRACT

The complement system is an important first line of defense against the human pathogen
Haemophilus influenzae
. To survive and propagate
in vivo
,
H. influenzae
has evolved mechanisms for subverting this host defense, most of which have been shown to involve outer surface structures, including lipooligosaccharide glycans and outer surface proteins. Bacterial defense against complement acts at multiple steps in the pathway by mechanisms that are not fully understood. Here we identify outer membrane protein P5 as an essential factor in serum resistance of both
H. influenzae
strain Rd and nontypeable
H. influenzae
(NTHi) clinical isolate NT127. P5 was essential for resistance of Rd and NT127 to complement in pooled human serum. Further investigation determined that P5 expression decreased cell surface binding of IgM, a potent activator of the classical pathway of complement, to both Rd and NT127. Additionally, P5 expression was required for NT127 to bind factor H (fH), an important inhibitor of alternative pathway (AP) activation. Collectively, the results obtained in this work highlight the ability of
H. influenzae
to utilize a single protein to perform multiple protective functions for evading host immunity.
Key Role of Toll-Like Receptor 2 in the Inflammatory Response and Major Histocompatibility Complex Class II Downregulation in Brucella abortus-Infected Alveolar Macrophages
Authors: Ferrero Mariana C. , Hielpos M. Soledad , Carvalho Natalia B. , Barrionuevo Paula , Corsetti Patricia P. , Giambartolomei Guillermo H. , Oliveira Sergio C. , Baldi Pablo C. 
Published: November 2013

ABSTRACTAlveolar macrophages (AM) seem to constitute the main cellular target of inhaled brucellae. Here, we show thatBrucella abortusinvades and replicates in murine AM without inducing cytotoxicity.B. abortusinfection induced a statistically significant increase of tumor necrosis factor alpha (TNF-α), CXCL1 or keratinocyte chemoattractant (KC), interleukin-1β (IL-1β), IL-6, and IL-12 in AM from C57BL/6 mice and BALB/c mice, but these responses were generally weaker and/or delayed compared to those elicited in peritoneal macrophages. Studies using knockout mice for TLR2, TLR4, and TLR9 revealed that TNF-α and KC responses were mediated by TLR2 recognition.Brucellainfection reduced in a multiplicity of infection-dependent manner the expression of major histocompatibility complex class II (MHC-II) molecules induced by gamma interferon (IFN-γ) in AM. The same phenomenon was induced by incubation with heat-killedB. abortus(HKBA) or the lipidated form of the 19-kDa outer membrane protein ofBrucella(L-Omp19), and it was shown to be mediated by TLR2 recognition. In contrast, no significant downregulation of MHC-II was induced by either unlipidated Omp19 orBrucellaLPS. In a functional assay, treatment of AM with either L-Omp19 or HKBA reduced the MHC-II-restricted presentation of OVA peptides to specific T cells. One week after intratracheal infection, viableB. abortuswas detected in AM from both wild-type and TLR2 KO mice, but CFU counts were higher in the latter. These results suggest thatB. abortussurvives in AM after inhalatory infection in spite of a certain degree of immune control exerted by the TLR2-mediated inflammatory response. Both the modest nature of the latter and the modulation of MHC-II expression by the bacterium may contribute to such survival.
The Core Promoter of the Capsule Operon of Streptococcus pneumoniae Is Necessary for Colonization and Invasive Disease
Authors: Shainheit Mara G. , Mulé Matthew , Camilli Andrew 
Published: November 2013

ABSTRACT

Streptococcus pneumoniae
is a commensal of the human nasopharynx but can cause invasive diseases, including otitis media, pneumonia, sepsis, and meningitis. The capsular polysaccharide (capsule) is a critical virulence factor required for both asymptomatic colonization and invasive disease, yet the expression level is different in each anatomical site. During colonization, reduced levels of capsule promote binding to the host epithelium and biofilm formation, while during systemic infection, increased capsule is required to evade opsonophagocytosis. How this regulation of capsule expression occurs is incompletely understood. To investigate the contribution of transcriptional regulation on capsule level in the serotype 4 strain TIGR4, we constructed two mutants harboring a constitutive promoter that was either comparably weaker (P

cat

) or stronger (P

tRNAGlu

) than the wild-type (WT) capsule promoter, P

cps

. Mild reductions in
cpsA
and
cpsE
transcript levels in the P

cat

promoter mutant resulted in a 2-fold reduction in total amounts of capsule and in avirulence in murine models of lung and blood infection. Additionally, the P

tRNAGlu

mutant revealed that, despite expressing enhanced levels of
cpsA
and
cpsE
and possessing levels of capsule comparable to those of WT TIGR4, it was still significantly attenuated in all tested
in vivo
niches. Further analysis using chimeric promoter mutants revealed that the WT −10 and −35 boxes are required for optimal nasopharyngeal colonization and virulence. These data support the hypothesis that dynamic transcriptional regulation of the capsule operon is required and that the core promoter region plays a central role in fine-tuning levels of capsule to promote colonization and invasive disease.
Taking up physical activity in later life and healthy ageing: the English longitudinal study of ageing
Authors: Hamer Mark , Lavoie Kim L , Bacon Simon L 
Published: November 2013

BackgroundPhysical activity is associated with improved overall health in those people who survive to older ages, otherwise conceptualised as healthy ageing. Previous studies have examined the effects of mid-life physical activity on healthy ageing, but not the effects of taking up activity later in life. We examined the association between physical activity and healthy ageing over 8 years of follow-up.MethodsParticipants were 3454 initially disease-free men and women (aged 63.7±8.9 years at baseline) from the English Longitudinal Study of Ageing, a prospective study of community dwelling older adults. Self-reported physical activity was assessed at baseline (2002–2003) and through follow-up. Healthy ageing, assessed at 8 years of follow-up (2010-2011), was defined as those participants who survived without developing major chronic disease, depressive symptoms, physical or cognitive impairment.ResultsAt follow-up, 19.3% of the sample was defined as healthy ageing. In comparison with inactive participants, moderate (OR, 2.67, 95% CI 1.95 to 3.64), or vigorous activity (3.53, 2.54 to 4.89) at least once a week was associated with healthy ageing, after adjustment for age, sex, smoking, alcohol, marital status and wealth. Becoming active (multivariate adjusted, 3.37, 1.67 to 6.78) or remaining active (7.68, 4.18 to 14.09) was associated with healthy ageing in comparison with remaining inactive over follow-up.ConclusionsSustained physical activity in older age is associated with improved overall health. Significant health benefits were even seen among participants who became physically active relatively late in life.
Unruptured intracranial aneurysms conservatively followed with serial CT angiography: could morphology and growth predict rupture?
Authors: Mehan William A , Romero Javier M , Hirsch Joshua A , Sabbag David J , Gonzalez Ramon G , Heit Jeremy J , Schaefer Pamela W 
Published: November 2013

Background and purposeDespite several landmark studies, the natural history of unruptured intracranial aneurysms (UIA) remains uncertain. Our aim was to identify or confirm factors predictive of rupture of UIA being observed conservatively with serial CT angiography (CTA) in a North American patient population.MethodsWe performed a retrospective review of patients with UIA being followed with serial CTA studies from 1999 to 2010. The following features for each aneurysm were cataloged from the official radiologic reports and CTA images: maximum diameter, growth between follow-up studies, location, multiplicity, wall calcification, intraluminal thrombus and morphology. Univariate logistic regression analysis of the potential independent risk factors for aneurysm rupture was performed. Statistically significant risk factors from the univariate analysis were then entered into a multivariate logistic regression analysis.Results152 patients with a total of 180 UIA had at least two CTA studies. Six aneurysms in six different patients ruptured during the CTA follow-up period for an overall rupture rate of 3.3% and an annual rupture rate of 0.97%. All ruptured aneurysms were ≥9 mm. In the univariate analysis, the statistically significant predictors of aneurysm rupture were aneurysm size (p=0.003), aneurysm growth (p<0.0001) and aneurysm multilobulation (p=0.001). The risk factors that remained significant following the multivariate analysis were growth (OR 55.9; 95% CI 4.47 to 700.08; p=0.002) and multilobulation (OR 17.4; 95% CI 1.52 to 198.4; p=0.022).ConclusionsAneurysm morphology and interval growth are characteristics predictive of a higher risk of subsequent rupture during conservative CTA follow-up.
Ice Sheets and the Anthropocene
Authors: Wolff Eric W. 
Published: November 2013

Abstract

Ice could play a role in identifying and defining the Anthropocene. The recurrence of northern hemisphere glaciation and the stability of the Greenland Ice Sheet are both potentially vulnerable to human impact on the environment. However, only a very long hiatus in either would be unusual in the context of the Quaternary Period, requiring the definition of a geological boundary. Human influence can clearly be discerned in several ice-core measurements. These include a sharp boundary in radioactivity due to atmospheric nuclear testing; increases, unprecedented at least in the Holocene, in Greenland concentrations of sulphate, nitrate and metals such as lead; the appearance in ice-core air bubbles of previously undetectable compounds such as SF
6
; and the rise, unprecedented in the last 800 ka, in concentrations of carbon dioxide and methane. Some combination of these changes could be used by future generations to clearly identify the onset of a new epoch defined at a particular calendar date. However, it is not yet clear what the character of the fully developed Anthropocene will be, and it might be wise to let future generations decide, with hindsight, when the Anthropocene started, acknowledging only that we are in the transition towards it.
System FC with explicit kind equality
Authors: Weirich Stephanie , Hsu Justin , Eisenberg Richard A. 
Published: November 2013

System FC, the core language of the Glasgow Haskell Compiler, is an explicitly-typed variant of System F with first-class type equality proofs called coercions. This extensible proof system forms the foundation for type system extensions such as type families (type-level functions) and Generalized Algebraic Datatypes (GADTs). Such features, in conjunction with kind polymorphism and datatype promotion, support expressive compile-time reasoning.However, the core language lacks explicit kind equality proofs. As a result, type-level computation does not have access to kind-level functions or promoted GADTs, the type-level analogues to expression-level features that have been so useful. In this paper, we eliminate such discrepancies by introducing kind equalities to System FC. Our approach is based on dependent type systems with heterogeneous equality and the "Type-in-Type" axiom, yet it preserves the metatheoretic properties of FC. In particular, type checking is simple, decidable and syntax directed. We prove the preservation and progress theorems for the extended language.
Common and Complex Notch1 Mutations in Chinese Oral Squamous Cell Carcinoma
Authors: Song Xiaomeng , Xia Ronghui , Li Jiang , Long Zhifeng , Ren Hening , Chen Wantao , Mao Li 
Published: November 2013

Abstract
Purpose: To determine Notch1 mutation status in oral squamous cell carcinoma (OSCC) from Chinese population and its potential clinical implications.
Experimental Design: Surgically resected OSCC tissues from 51 Chinese patients and 13 head and neck squamous cell carcinoma (HNSCC) cell lines were sequenced for mutations in the entire coding regions of Notch1 and TP53 using a next-generation sequencing platform. Sequences of the genes were also determined in corresponding normal tissues from 46 of the 51 patients. Mutations and their association with clinical parameters were analyzed.
Results: Six mutations in Notch1 and 11 mutations in TP53 coding regions were detected in 4 (31%) and 10 (77%) of the 13 HNSCC cell lines, respectively. Forty-two somatic Notch1 mutations, including 7 nonsense mutations and 11 mutations within the domain commonly harboring potential activating mutations in acute lymphoblastic leukemia, were detected in 22 (43%) of the 51 Chinese OSCC tumors. In comparison, 25 somatic TP53 mutations were observed in 21 (41%) of the 51 tumors. Patients whose tumors carried Notch1 mutation had significantly shorter overall and disease-free survivals (P = 0.004 and P = 0.001, respectively, by log-rank test) compared with those whose tumors carried no Notch1 mutation. Multivariate analysis showed that both Notch1 mutation and lymph node metastasis are independent prognostic factors in the patient population (P = 0.001). All 15 patients with both Notch1 mutation and nodal metastasis recurred or metastasized within 2 years after surgery.
Conclusions: Notch1 mutation is common in Chinese OSCC and associates with clinical outcomes. The complexity of the mutation spectrum warrants further investigation of Notch1 in Chinese patients with OSCC. Clin Cancer Res; 20(3); 701–10. ©2013 AACR.
The PDGFRβ–AKT Pathway Contributes to CDDP-Acquired Resistance in Testicular Germ Cell Tumors
Authors: Juliachs M. , Muñoz C. , Moutinho C.A. , Vidal A. , Condom E. , Esteller M. , Graupera M. , Casanovas O. , Germà J.R. , Villanueva A. , Viñals F. 
Published: November 2013

Abstract
Purpose: We examined whether PI3K–AKT or extracellular signal–regulated kinase (ERK) signaling pathways could play a role in the development of cisplatin (CDDP) resistance in testicular germ cell tumor (TGT) cells.
Experimental Design: We compared AKT and ERK activation levels in CDDP-sensitive testicular tumor cells and in their corresponding CDDP-resistant–derived cells. We also analyzed these pathways in orthotopic testicular tumors and human patient samples.
Results: Our results indicated that there was overactivation of AKT in CDDP-resistant cells compared with sensitive cells, but no effect on activated ERK levels. We observed an increase in mRNA and protein levels for platelet-derived growth factor (PDGF) receptor β and PDGF-B ligand. These were responsible for AKT overactivation in CDDP-resistant cells. When PDGFRβ levels were decreased by short hairpin RNA (shRNA) treatment or its activation was blocked by pazopanib, CDDP-resistant cells behaved like sensitive cells. Moreover, CDDP-resistant cells were more sensitive to incubation with PDGFRβ inhibitors such as pazopanib or sunitinib than sensitive cells, a finding consistent with these cells being dependent on this signaling pathway. We also found overexpression of PDGFRβ and pAKT in CDDP-resistant choriocarcinoma orthotopic tumor versus their CDDP-sensitive counterparts. Finally, we found high PDGFRβ levels in human testicular tumors, and overexpression in CDDP-resistant testicular choriocarcinomas compared with the CDDP-sensitive and nontreated tumors.
Conclusions: The PDGFRβ–AKT pathway plays a critical role in the development of CDDP resistance in testicular tumoral cells. Clin Cancer Res; 20(3); 658–67. ©2013 AACR.
Telomere Content and Risk of Second Malignant Neoplasm in Survivors of Childhood Cancer: A Report from the Childhood Cancer Survivor Study
Authors: Gramatges Maria M. , Liu Qi , Yasui Yutaka , Okcu M. Fatih , Neglia Joseph P. , Strong Louise C. , Armstrong Gregory T. , Robison Leslie L. , Bhatia Smita 
Published: November 2013

AbstractPurpose: Shorter constitutional telomere length has been associated with increased cancer incidence. Furthermore, telomere shortening is observed in response to intensive chemotherapy and/or ionizing radiation exposure. We aimed to determine whether less telomere content was associated with treatment-related second malignant neoplasms (SMN) in childhood cancer survivors.Experimental Design: Using a nested case–control design, 147 cancer survivors with breast cancer, thyroid cancer, or sarcoma developing after treatment for childhood cancer (cases) were matched (1:1) with childhood cancer survivors without a SMN (controls). Cases and controls were matched by primary cancer diagnosis, years since diagnosis, age at the time of sample collection, years of follow-up from childhood cancer diagnosis, exposure to specific chemotherapy agents, and to specific radiation fields. We performed conditional logistic regression using telomere content as a continuous variable to estimate ORs with corresponding 95% confidence intervals (CI) for development of SMN. ORs were also estimated for specific SMN types, i.e., breast cancer, thyroid cancer, and sarcoma.Results: There was an inverse relationship between telomere content and SMN, with an adjusted OR of 0.3 per unit change in telomere length to single-copy gene ratio (95% CI, 0.09–1.02; P = 0.05). Patients with thyroid cancer SMN were less likely to have more telomere content (OR, 0.04; 95% CI, 0.00–0.55; P = 0.01), but statistically significant associations could not be demonstrated for breast cancer or sarcoma.Conclusions: A relation between less telomere content and treatment-related thyroid cancer was observed, suggesting that shorter telomeres may contribute to certain SMNs in childhood cancer survivors. Clin Cancer Res; 20(4); 904–11. ©2013 AACR.