bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytotoxic T Cell Adoptive Immunotherapy as a Treatment for Nasopharyngeal Carcinoma
Authors: Lutzky Viviana P. , Crooks Pauline , Morrison Leanne , Stevens Natasha , Davis Joanne E. , Corban Monika , Hall David , Panizza Benedict , Coman William B. , Coman Scott , Moss Denis J. 
Published: December 2013

ABSTRACTEpstein-Barr virus (EBV) is associated with nasopharyngeal carcinoma (NPC). We assess the safety and tolerability of adoptive transfer of autologous cytotoxic T lymphocytes (CTLs) specific for the EBV latent membrane protein (LMP) in a patient with recurrent NPC. After infusion, the majority of pulmonary lesions were no longer evident, although the primary tumor did not regress.
Antibodies to Both Terminal and Internal B-Cell Epitopes of Francisella tularensisO-Polysaccharide Produced by Patients with Tularemia
Authors: Lu Zhaohua , Perkins Hillary M. , Sharon Jacqueline 
Published: December 2013

ABSTRACTFrancisella tularensis, the Gram-negative bacterium that causes tularemia, is considered a potential bioterrorism threat due to its low infectivity dose and the high morbidity and mortality from respiratory disease. We previously characterized two mouse monoclonal antibodies (MAbs) specific for theO-polysaccharide (O antigen [OAg]) ofF. tularensislipopolysaccharide (LPS): Ab63, which targets a terminal epitope at the nonreducing end of OAg, and Ab52, which targets a repeating internal OAg epitope. These two MAbs were protective in a mouse model of respiratory tularemia. To determine whether these epitope types are also targeted by humans, we tested the ability of each of 18 blood serum samples from 11 tularemia patients to inhibit the binding of Ab63 or Ab52 toF. tularensisLPS in a competition enzyme-linked immunosorbent assay (ELISA). Although all serum samples had Ab63- and Ab52-inhibitory activities, the ratios of Ab63 to Ab52 inhibitory potencies varied 75-fold. However, the variation was only 2.3-fold for sequential serum samples from the same patient, indicating different distributions of terminal- versus internal-binding antibodies in different individuals. Western blot analysis using class-specific anti-human Ig secondary antibodies showed that both terminal- and internal-binding OAg antibodies were of the IgG, IgM, and IgA isotypes. These results support the use of a mouse model to discover protective B-cell epitopes for tularemia vaccines or prophylactic/therapeutic antibodies, and they present a general strategy for interrogating the antibody responses of patients and vaccinees to microbial carbohydrate epitopes that have been characterized in experimental animals.
Spectrum of Pneumococcal Serotype 11A Variants Results from Incomplete Loss of Capsule
O
-Acetylation
Authors: Calix Juan J. , Brady Allison M. , Du Victor Y. , Saad Jamil S. , Nahm Moon H. 
Published: December 2013

ABSTRACT

Streptococcus pneumoniae
is a significant bacterial pathogen that expresses >90 capsule serotypes. Conventional serotyping methods assume that each serotype is a genetically and antigenically distinct entity; however, recent investigations have revealed pneumococcal isolates that cannot be unambiguously serotyped because they share the properties of more than one serotype. Here, we employed a novel serotyping method and NMR spectroscopy to examine clinical isolates sharing properties of serotypes 11A and 11E. These ambiguous clinical isolates were provisionally named 11A variant (11Av) isolates. Serotype 11A pneumococci characteristically express capsule β-galactose-6-
O
-acetylation (βGal6OAc) mediated by the capsule synthesis gene
wcjE
, while 11E strains contain loss-of-function mutations in
wcjE
and completely lack the expression of βGal6OAc. Although 11Av isolates also contained mutated
wcjE
alleles, 11Av clinical isolates were composed of antigenically homogeneous bacteria expressing reduced amounts of 11A-specific capsule antigen. NMR data confirmed reduced but detectable amounts of βGal6OAc on 11Av capsule polysaccharide. Furthermore, the transformation of strains with
wcjE
alleles from 11Av strains was sufficient to restore partial βGal6OAc in an 11E background. We conclude that, instead of being distinct entities, serotypes 11A and 11E represent two extremes of an antigenic spectrum resulting from variable capsule
O
-acetylation secondary to heterologous
wcjE
mutations. These findings challenge whether all clinically relevant pneumococci can be definitively categorized into distinct serotypes.
Predicting Extensively Drug-Resistant Mycobacterium tuberculosis Phenotypes with Genetic Mutations
Authors: Rodwell Timothy C. , Valafar Faramarz , Douglas James , Qian Lishi , Garfein Richard S. , Chawla Ashu , Torres Jessica , Zadorozhny Victoria , Kim Min Soo , Hoshide Matt , Catanzaro Donald , Jackson Lynn , Lin Grace , Desmond Edward , Rodrigues Camilla , Eisenach Kathy , Victor Thomas C. , Ismail Nazir , Crudu Valeru , Gler Maria Tarcela , Catanzaro Antonino 
Published: December 2013

ABSTRACT

Molecular diagnostic methods based on the detection of mutations conferring drug resistance are promising technologies for rapidly detecting multidrug-/extensively drug-resistant tuberculosis (M/XDR TB), but large studies of mutations as markers of resistance are rare. The Global Consortium for Drug-Resistant TB Diagnostics analyzed 417
Mycobacterium tuberculosis
isolates from multinational sites with a high prevalence of drug resistance to determine the sensitivities and specificities of mutations associated with M/XDR TB to inform the development of rapid diagnostic methods. We collected M/XDR TB isolates from regions of high TB burden in India, Moldova, the Philippines, and South Africa. The isolates underwent standardized phenotypic drug susceptibility testing (DST) to isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN), and capreomycin (CAP) using MGIT 960 and WHO-recommended critical concentrations. Eight genes (
katG
,
inhA
,
rpoB
,
gyrA
,
gyrB
,
rrs
,
eis
, and
tlyA
) were sequenced using Sanger sequencing. Three hundred seventy isolates were INH
r
, 356 were RIF
r
, 292 were MOX
r
/OFX
r
, 230 were AMK
r
, 219 were CAP
r
, and 286 were KAN
r
. Four single nucleotide polymorphisms (SNPs) in
katG
/
inhA
had a combined sensitivity of 96% and specificities of 97 to 100% for the detection of INH
r
. Eleven SNPs in
rpoB
had a combined sensitivity of 98% for RIF
r
. Eight SNPs in
gyrA
codons 88 to 94 had sensitivities of 90% for MOX
r
/OFX
r
. The
rrs
1401/1484 SNPs had 89 to 90% sensitivity for detecting AMK
r
/CAP
r
but 71% sensitivity for KAN
r
. Adding
eis
promoter SNPs increased the sensitivity to 93% for detecting AMK
r
and to 91% for detecting KAN
r
. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90 to 98% sensitivity and almost 100% specificity.
Differential Impact of PD-1 and/or Interleukin-10 Blockade on HIV-1-Specific CD4 T Cell and Antigen-Presenting Cell Functions
Authors: Porichis Filippos , Hart Meghan G. , Zupkosky Jennifer , Barblu Lucie , Kwon Douglas S. , McMullen Ashley , Brennan Thomas , Ahmed Rafi , Freeman Gordon J. , Kavanagh Daniel G. , Kaufmann Daniel E. 
Published: December 2013

ABSTRACT

Antigen persistence in chronic infections and cancer upregulates inhibitory networks, such as the PD-1 and interleukin-10 (IL-10) pathways, that impair immunity and lead to disease progression. These pathways are attractive targets for immunotherapy, as demonstrated by recent clinical trials of PD-1/PD-L1 blockade in cancer patients. However, in HIV-1 infection not all subjects respond to inhibition of either pathway and the mechanistic interactions between these two networks remain to be better defined. Here we demonstrate that
in vitro
blockade of PD-L1 and/or IL-10Rα results in markedly different profiles of HIV-1-specific CD4 T cell restoration. Whereas PD-L1 blockade leads to balanced increase in gamma interferon (IFN-γ), IL-2, and IL-13 secretion, IL-10Rα blockade preferentially restores IFN-γ production. In viremic subjects, combined PD-L1/IL-10Rα blockade results in a striking 10-fold increase in IFN-γ secretion by HIV-1-specific CD4 T cells that is not observed in subjects with spontaneous (elite controllers) or therapy-induced control of viral replication. In contrast to the dramatic increase in IFN-γ production, concurrent blockade has a marginal additive effect on IL-2 production, IL-13 secretion, and HIV-1-specific CD4 T cell proliferation. IFN-γ produced by T
helper
cells upregulates PD-L1, HLA I/II, and IL-12 expression by monocytes. The effect of combined blockade on IFN-γ was dependent on reciprocal reinforcement through IL-12. These studies provide crucial information on the different immunoregulatory qualities of PD-1 and IL-10 in progressive disease and link exhausted virus-specific CD4 T cells and monocytes in the regulation of IFN-γ and IL-12 secretion.

IMPORTANCE
Infection with HIV results in most people in uncontrolled viral replication and progressive weakening of the body defenses. In the absence of antiviral therapy, this process results in clinical disease, or AIDS. An important reason why HIV continues to multiply is that a population of white blood cells called CD4 T cells that targets the virus fails to work properly. At least part of this impairment is under the control of inhibitory mechanisms that can be blocked to improve the function of these CD4 T cells. In this report, we show that blocking one or two of the molecules involved, called PD-1 and IL-10, has different effects on the individual functions of these cells and that one is strongly improved. We investigate how these effects are caused by interactions between CD4 T cells and antigen-presenting cells. These observations can have implications for new therapeutic approaches in HIV infection.
An ITAM in a Nonenveloped Virus Regulates Activation of NF-κB, Induction of Beta Interferon, and Viral Spread
Authors: Stebbing Rachael E. , Irvin Susan C. , Rivera-Serrano Efraín E. , Boehme Karl W. , Ikizler Mine , Yoder Jeffrey A. , Dermody Terence S. , Sherry Barbara 
Published: December 2013

ABSTRACT
Immunoreceptor tyrosine-based activation motifs (ITAMs) are signaling domains located within the cytoplasmic tails of many transmembrane receptors and associated adaptor proteins that mediate immune cell activation. ITAMs also have been identified in the cytoplasmic tails of some enveloped virus glycoproteins. Here, we identified ITAM sequences in three mammalian reovirus proteins: μ2, σ2, and λ2. We demonstrate for the first time that μ2 is phosphorylated, contains a functional ITAM, and activates NF-κB. Specifically, μ2 and μNS recruit the ITAM-signaling intermediate Syk to cytoplasmic viral factories and this recruitment requires the μ2 ITAM. Moreover, both the μ2 ITAM and Syk are required for maximal μ2 activation of NF-κB. A mutant virus lacking the μ2 ITAM activates NF-κB less efficiently and induces lower levels of the downstream antiviral cytokine beta interferon (IFN-β) than does wild-type virus despite similar replication. Notably, the consequences of these μ2 ITAM effects are cell type specific. In fibroblasts where NF-κB is required for reovirus-induced apoptosis, the μ2 ITAM is advantageous for viral spread and enhances viral fitness. Conversely, in cardiac myocytes where the IFN response is critical for antiviral protection and NF-κB is not required for apoptosis, the μ2 ITAM stimulates cellular defense mechanisms and diminishes viral fitness. Together, these results suggest that the cell type-specific effect of the μ2 ITAM on viral spread reflects the cell type-specific effects of NF-κB and IFN-β. This first demonstration of a functional ITAM in a nonenveloped virus presents a new mechanism for viral ITAM-mediated signaling with likely organ-specific consequences in the host.
Human T-Cell Leukemia Virus Type 1 Tax-Deregulated Autophagy Pathway and c-FLIP Expression Contribute to Resistance against Death Receptor-Mediated Apoptosis
Authors: Wang Weimin , Zhou Jiansuo , Shi Juan , Zhang Yaxi , Liu Shilian , Liu Yanxin , Zheng Dexian 
Published: December 2013

ABSTRACT
The human T-cell leukemia virus type 1 (HTLV-1) Tax protein is considered to play a central role in the process that leads to adult T-cell leukemia/lymphoma (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 Tax-expressing cells show resistance to apoptosis induced by Fas ligand (FasL) and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL). The regulation of Tax on the autophagy pathway in HeLa cells and peripheral T cells was recently reported, but the function and underlying molecular mechanism of the Tax-regulated autophagy are not yet well defined. Here, we report that HTLV-1 Tax deregulates the autophagy pathway, which plays a protective role during the death receptor (DR)-mediated apoptosis of human U251 astroglioma cells. The cellular FLICE-inhibitory protein (c-FLIP), which is upregulated by Tax, also contributes to the resistance against DR-mediated apoptosis. Both Tax-induced autophagy and Tax-induced c-FLIP expression require Tax-induced activation of IκB kinases (IKK). Furthermore, Tax-induced c-FLIP expression is regulated through the Tax-IKK-NF-κB signaling pathway, whereas Tax-triggered autophagy depends on the activation of IKK but not the activation of NF-κB. In addition, DR-mediated apoptosis is correlated with the degradation of Tax, which can be facilitated by the inhibitors of autophagy.

IMPORTANCE
Our study reveals that Tax-deregulated autophagy is a protective mechanism for DR-mediated apoptosis. The molecular mechanism of Tax-induced autophagy is also illuminated, which is different from Tax-increased c-FLIP. Tax can be degraded via manipulation of autophagy and TRAIL-induced apoptosis. These results outline a complex regulatory network between and among apoptosis, autophagy, and Tax and also present evidence that autophagy represents a new possible target for therapeutic intervention for the HTVL-1 related diseases.
Phosphorylation of a Herpes Simplex Virus 1 dUTPase by a Viral Protein Kinase, Us3, Dictates Viral Pathogenicity in the Central Nervous System but Not at the Periphery
Authors: Kato Akihisa , Shindo Keiko , Maruzuru Yuhei , Kawaguchi Yasushi 
Published: December 2013

ABSTRACT
Herpes simplex virus 1 (HSV-1) encodes Us3 protein kinase, which is critical for viral pathogenicity in both mouse peripheral sites (e.g., eyes and vaginas) and in the central nervous systems (CNS) of mice after intracranial and peripheral inoculations, respectively. Whereas some Us3 substrates involved in Us3 pathogenicity in peripheral sites have been reported, those involved in Us3 pathogenicity in the CNS remain to be identified. We recently reported that Us3 phosphorylated HSV-1 dUTPase (vdUTPase) at serine 187 (Ser-187) in infected cells, and this phosphorylation promoted viral replication by regulating optimal enzymatic activity of vdUTPase. In the present study, we show that the replacement of vdUTPase Ser-187 by alanine (S187A) significantly reduced viral replication and virulence in the CNS of mice following intracranial inoculation and that the phosphomimetic substitution at vdUTPase Ser-187 in part restored the wild-type viral replication and virulence. Interestingly, the S187A mutation in vdUTPase had no effect on viral replication and pathogenic effects in the eyes and vaginas of mice after ocular and vaginal inoculation, respectively. Similarly, the enzyme-dead mutation in vdUTPase significantly reduced viral replication and virulence in the CNS of mice after intracranial inoculation, whereas the mutation had no effect on viral replication and pathogenic effects in the eyes and vaginas of mice after ocular and vaginal inoculation, respectively. These observations suggested that vdUTPase was one of the Us3 substrates responsible for Us3 pathogenicity in the CNS and that the CNS-specific virulence of HSV-1 involved strict regulation of vdUTPase activity by Us3 phosphorylation.

IMPORTANCE
Herpes simplex virus 1 (HSV-1) encodes a viral protein kinase Us3 which is critical for pathogenicity both in peripheral sites and in the central nervous systems (CNS) of mice following peripheral and intracranial inoculations, respectively. Whereas some Us3 substrates involved in Us3 pathogenicity in peripheral sites have been reported, those involved in Us3 pathogenicity in the CNS remain to be identified. Here, we report that Us3 phosphorylation of viral dUTPase (vdUTPase) at serine 187 (Ser-187), which has been shown to promote the vdUTPase activity, appears to be critical for viral virulence in the CNS but not for pathogenic effects in peripheral sites. Since HSV proteins critical for viral virulence in the CNS are, in almost all cases, also involved in viral pathogenicity at peripheral sites, this phosphorylation event is a unique report of a specific mechanism involved in HSV-1 virulence in the CNS.
Sequences Related to SUMO Interaction Motifs in Herpes Simplex Virus 1 Protein ICP0 Act Cooperatively To Stimulate Virus Infection
Authors: Everett Roger D. , Boutell Chris , Pheasant Kathleen , Cuchet-Lourenço Delphine , Orr Anne 
Published: December 2013

ABSTRACT
Herpes simplex virus type 1 immediate-early protein ICP0 is an E3 ubiquitin ligase of the RING finger class that degrades several cellular proteins during infection. This activity is essential for its functions in stimulating efficient lytic infection and productive reactivation from latency. ICP0 targets a number of proteins that are modified by the small ubiquitin-like SUMO family of proteins, and it includes a number of short sequences that are related to SUMO interaction motifs (SIMs). Therefore, ICP0 has characteristics that are related to those of cellular SUMO-targeted ubiquitin ligase enzymes. Here, we analyze the impact of mutation of a number of SIM-like sequences (SLSs) within ICP0 on HSV-1 replication and gene expression and their requirement for ICP0-mediated degradation of both sumoylated and unmodified promyelocytic leukemia (PML) and other sumoylated cellular proteins. One SLS in the central portion of the ICP0 sequence (SLS4) was found to be absolutely required for targeting cellular sumoylated species in general and sumoylated forms of PML other than those of PML isoform I. Mutation of a group of SLSs in the C-terminal quarter of ICP0 also reduced ICP0-mediated degradation of sumoylated PML in a cooperative manner. Although mutation of individual SLSs caused only modest decreases in viral replication, combined mutation of SLS4 with SLS sequences in the C-terminal quarter of the protein reduced plaque formation efficiency by up to two orders of magnitude. These results provide further evidence that the biological activities of ICP0 are connected with host cell sumoylation events.

IMPORTANCE
Herpes simplex virus type 1 protein ICP0 plays important roles in regulating the initial stages of lytic infection and productive reactivation from latency. ICP0 mediates its effects through inducing the degradation of cellular proteins that have repressive effects on viral gene expression. An increasing number of cellular proteins are known to be sensitive to ICP0-mediated degradation; therefore, it is important to understand how ICP0 selects its substrates for degradation. This study identifies sequence motifs within ICP0 that are involved in targeting cellular proteins that are modified by the SUMO family of ubiquitin-like proteins and describes how mutation of combinations of these motifs causes a 100-fold defect in viral infectivity.
Urine C-peptide creatinine ratio can be used to assess insulin resistance and insulin production in people without diabetes: an observational study
Authors: Oram Richard A , Rawlingson Andrew , Shields Beverley M , Bingham Coralie , Besser Rachel E J , McDonald Tim J , Knight Bridget A , Hattersley Andrew T 
Published: December 2013

ObjectivesThe current assessment of insulin resistance (IR) in epidemiology studies relies on the blood measurement of C-peptide or insulin. A urine C-peptide creatinine ratio (UCPCR) can be posted from home unaided. It is validated against serum measures of the insulin in people with diabetes. We tested whether UCPCR could be a surrogate measure of IR by examining the correlation of UCPCR with serum insulin, C-peptide and HOMA2 (Homeostasis Model Assessment 2)-IR in participants without diabetes and with chronic kidney disease (CKD).DesignObservational study.SettingSingle-centre clinical research facility.Participants37 healthy volunteers and 30 patients with CKD (glomerular filtration rate 15–60) were recruited.Primary and secondary endpointsSerum insulin, C-peptide and glucose at fasting (0), 30, 60, 90 and 120 min were measured during an oral glucose tolerance test (OGTT). Second-void fasting UCPCR and 120 min post-OGTT UCPCR were collected. HOMA2-IR was calculated using fasting insulin and glucose. The associations between UCPCR and serum measures were assessed using Spearman's correlations.ResultsIn healthy volunteers, fasting second-void UCPCR strongly correlated with serum insulin (rs=0.69, p<0.0001), C-peptide (rs=0.73, p<0.0001) and HOMA2-IR (rs=−0.69, p<0.0001). 120 min post-OGTT UCPCR correlated strongly with C-peptide and insulin area under the curve. In patients with CKD, UCPCR did not correlate with serum C-peptide, insulin or HOMA2-IR.ConclusionsIn participants with normal renal function, UCPCR may be a simple, practical method for the assessment of IR in epidemiology studies.
DENSITY MEASUREMENT OF ETHANOL BLENDED FUELS
Authors: MAN JOHN 
Published: December 2013

Density measurements for petro-ethanol blended fuels of various mixture ratios were conducted at temperatures from 5°C to 40°C using an oscillatory densitometer at the National Measurement Institute, Australia (NMIA). The petrol and ethanol fuels used for the preparation of samples of ethanol blends were supplied directly from a local petroleum refinery. Results were within the lower end of 0.06% repeatability and 0.3% reproducibility of the ASTM D4052-2011 method. The volume correction factors (VCF) for petrol and ethanol obtained from the measurement results agreed to within 0.1% and 0.01% of the values calculated as per American Petroleum Institute Standard 2540 Chapter 11.1 and 11.3.3 respectively. Based on a simple volume-mixture model, an equation was derived to calculate the VCF for petrol-ethanol blends. The measured and calculated values of VCF were in agreement within 0.1%. This paper presents the measurement method, results and the development of an equation for calculation of VCF for petro-ethanol blends. Note from Publisher: This article contains the abstract only.