bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Lactobacillus gasseri as a Candidate Oral Vaccine Vector
Authors: Stoeker Laura , Nordone Shila , Gunderson Sara , Zhang Lin , Kajikawa Akinobu , LaVoy Alora , Miller Michael , Klaenhammer Todd R. , Dean Gregg A. 
Published: September 2011

ABSTRACTLactobacillusspecies are commensal bacteria that have long been recognized as probiotic microbes and are generally regarded as safe (GRAS) for human consumption. We have investigated the use ofL. gasserias a vaccine vector for oral immunization against mucosal pathogens. Recent research has shown that the immune response to different lactobacilli can vary widely depending on the species or subspecies ofLactobacillusbeing studied. While some lactobacilli seem to induce oral tolerance, others induce an adaptive immune response. This study characterized the systemic and mucosal immune response to wild-type and genetically modifiedL. gasseri. L. gasseriprimarily activates TLR2/6, with additional activation through the TLR2 homodimer. To expand the Toll-like receptor (TLR) activation profile ofL. gasseriand the immunogenicity of the vector, a plasmid containingfliC, the gene encoding bacterial flagellin, was introduced which resulted in the strong activation of TLR5. The treatment of human myeloid dendritic cells with recombinant lactobacilli expressing flagellin triggered phenotypic maturation and the release of proinflammatory cytokines. In contrast, bacterial treatment also resulted in a statistically significant increase in IL-10 production.In vivostudies established that treatment withL. gasseriled to a diversification of B-cell populations in the lamina propria of the murine colon. Furthermore, treatment with genetically modifiedL. gasseriled to a significant decrease in the percentage of FoxP3+colonic lymphocytes. Taken together, these data clarify the interaction ofL. gasseriwith the host immune system and support further investigation of thein vivoimmunogenicity ofL. gasseriexpressing both flagellin and candidate vaccine antigens.
Development of an Automated and Multiplexed Serotyping Assay for Streptococcus pneumoniae
Authors: Yu Jigui , Lin Jisheng , Kim Kyung-Hyo , Benjamin William H. , Nahm Moon H. 
Published: September 2011

ABSTRACT

Streptococcus pneumoniae
expresses more than 90 capsule types, and currently available pneumococcal vaccines are designed to provide serotype-specific protection. Consequently, serotyping of pneumococcal isolates is important for determining the serotypes to be included in pneumococcal vaccines and to monitor their efficacy. Yet serotyping of pneumococcal isolates has remained a significant technical challenge. By multiplexing many assays, we have now developed a simple yet comprehensive serotyping assay system that can not only identify all known pneumococcal serotypes but also subdivide nontypeable (NT) isolates into those with or without the conventional capsule locus. We have developed this assay system to require only six key reagents: two are used in one multiplex inhibition-type immunoassay, and four are required in two multiplex PCR-based assays. The assay system is largely automated by a seamless combination of monoclonal antibody-based and PCR-based multiplex assays using the flow cytometric bead array technology from Luminex. The assay system has been validated with a panel of pneumococci expressing all known pneumococcal serotypes and was found to be easily transferable to another laboratory.
Molecular Detection of Resistance Determinants
Authors: Ledeboer Nathan A. , Hodinka Richard L. 
Published: September 2011

ABSTRACT

The development of new antibiotics and the emergence of novel resistance mechanisms to counteract these drugs create a dynamic and challenging task for the clinical microbiology laboratory. The goal of antimicrobial resistance testing is to provide timely therapeutic options to guide the management of infectious diseases resulting from bacterial infections. Antimicrobial susceptibility has classically been determined using a variety of
in vitro
methods, such as disk diffusion, broth microdilution, and automated instrument-based methods. Using these methods, the reporting of MICs and interpretations can require 24 to 96 h after a pure culture of the suspected pathogen is obtained (6). Unfortunately, results obtained after 48 h are often of little clinical value and are unlikely to alter antimicrobial therapy. The extended turnaround associated with phenotypic antimicrobial resistance testing provides an opportunity for the use of alternative technologies capable of producing more timely results. The first reports in this supplement explore the manner in which the criteria for interpreting MICs are developed and the clinical relevance of antimicrobial susceptibility testing. In this report, we present an alternative to routine susceptibility testing and examine the role of molecular susceptibility testing now and in the future.
Triazole and Echinocandin MIC Distributions with Epidemiological Cutoff Values for Differentiation of Wild-Type Strains from Non-Wild-Type Strains of Six Uncommon Species of
Candida
Authors: Pfaller Michael A. , Castanheira Mariana , Diekema Daniel J. , Messer Shawn A. , Jones Ronald N. 
Published: September 2011

ABSTRACT

When clinical susceptibility breakpoints (CBPs) are absent, establishing wild-type (WT) MIC distributions and epidemiological cutoff values (ECVs) provides a sensitive means for detecting emerging resistance. We determined species-specific ECVs for anidulafungin (ANF), caspofungin (CSF), micafungin (MCF), fluconazole (FLC), posaconazole (PSC), and voriconazole (VRC) for six rarer
Candida
species (819 strains) using isolates obtained from the ARTEMIS Program and the SENTRY Antimicrobial Surveillance Program, all tested by a reference broth microdilution method. The calculated ECVs, expressed in μg/ml (and the percentages of isolates that had MICs less than or equal to the ECVs), for ANF, CSF, MCF, FLC, PSC, and VRC, respectively, were 0.12 (95.2), 0.12 (97.8), 0.12 (100.0), 0.5 (95.7), 0.12 (98.6), and 0.03 (100.0) for
Candida dubliniensis
; 4 (100.0), 2 (96.0), 2 (99.1), 8 (95.0), 0.5 (97.5), and 0.25 (98.0) for
C. guilliermondii
; 0.25 (98.9), 0.03 (98.0), 0.12 (97.5), 1 (99.1), 0.25 (99.1), and 0.015 (100.0) for
C. kefyr
; 2 (100.0), 1 (99.6), 0.5 (96.6), 2 (96.1), 0.25 (98.6), and 0.03 (96.6) for
C. lusitaniae
; and 2 (100.0), 0.5 (100.0), 1 (100.0), 2 (98.0), 0.25 (97.1), and 0.06 (98.0) for
C. orthopsilosis
, but for
C. pelliculosa
, ECVs could be determined only for CSF (0.12 [94.4]), FLC (4 [98.2]), PSC (2 [98.2]), and VRC (0.25 [98.2]). In the absence of species-specific CBP values, these WT MIC distributions and ECVs will be useful for monitoring the emergence of reduced susceptibility to the triazole and echinocandin antifungals.
HIV-1 Coinfection and Morphine Coexposure Severely Dysregulate Hepatitis C Virus-Induced Hepatic Proinflammatory Cytokine Release and Free Radical Production: Increased Pathogenesis Coincides with Uncoordinated Host Defenses
Authors: El-Hage Nazira , Dever Seth M. , Fitting Sylvia , Ahmed Tasrif , Hauser Kurt F. 
Published: September 2011

ABSTRACTCoinfection with human immunodeficiency virus type-1 (HIV-1) and hepatitis C virus (HCV) is a global problem that is more prevalent in injection drug users because they have a higher risk for acquiring both viruses. The roles of inflammatory cytokines and oxidative stress were examined in HIV-1- and HCV-coinfected human hepatic cells. Morphine (the bioactive product of heroin), HIV-1 Tat and the MN strain gp120 (gp120MN) proteins, and X4 HIV-1LAI/IIIBand R5 HIV-1SF162isolates were used to study the mechanisms of disease progression in HCV (JFH1)-infected Huh7.5.1 cell populations. HCV increased tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) release and augmented production of reactive oxygen species (ROS), nitric oxide (NO), and 3-nitrotyrosine (3-NT) in Huh7.5.1 cells. Morphine preferentially affected R5-tropic, but not X4-tropic, HIV-1 interactions with Huh7.5.1 cells. HIV-1 proteins or isolates increased cytokine release in HCV-infected cells, while adding morphine to coinfected cells caused complex imbalances, significantly disrupting cytokine secretion depending on the cytokine, morphine concentration, exposure duration, and particular pathogen involved. Production of ROS, NO, and 3-NT increased significantly in HCV- and HIV-1-coexposed cells while exposure to morphine further increased ROS. The proteasome inhibitor MG132 significantly decreased oxyradicals, cytokine levels, and HCV protein levels. Our findings indicate that hepatic inflammation is increased by combined exposure to HCV and HIV-1, that the ubiquitin-proteasome system and NF-κB contribute to key aspects of the response, and that morphine further exacerbates the disruption of host defenses. The results suggest that opioid abuse and HIV-1 coinfection each further accelerate HCV-mediated liver disease by dysregulating immune defenses.
Replication of the Rotavirus Genome Requires an Active Ubiquitin-Proteasome System
Authors: López Tomás , Silva-Ayala Daniela , López Susana , Arias Carlos F. 
Published: September 2011

ABSTRACT
Here we show that the ubiquitin-proteasome system is required for the efficient replication of rotavirus RRV in MA104 cells. The proteasome inhibitor MG132 decreased the yield of infectious virus under conditions where it severely reduces the synthesis of not only viral but also cellular proteins. Addition of nonessential amino acids to the cell medium restored both viral protein synthesis and cellular protein synthesis, but the production of progeny viruses was still inhibited. In medium supplemented with nonessential amino acids, we showed that MG132 does not affect rotavirus entry but inhibits the replication of the viral genome. It was also shown that it prevents the efficient incorporation into viroplasms of viral polymerase VP1 and the capsid proteins VP2 and VP6, which could explain the inhibitory effect of MG132 on genome replication and infectious virus yield. We also showed that ubiquitination is relevant for rotavirus replication since the yield of rotavirus progeny in cells carrying a temperature-sensitive mutation in the E1 ubiquitin-activating enzyme was reduced at the restrictive temperature. In addition, overexpression of ubiquitin in MG132-treated MA104 cells partially reversed the effect of the inhibitor on virus yield. Altogether, these data suggest that the ubiquitin-proteasome (UP) system has a very complex interaction with the rotavirus life cycle, with both the ubiquitination and proteolytic activities of the system being relevant for virus replication.
Structural Studies of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated with Endosomal Trafficking
Authors: Nam Hyun-Joo , Gurda Brittney L. , McKenna Robert , Potter Mark , Byrne Barry , Salganik Maxim , Muzyczka Nicholas , Agbandje-McKenna Mavis 
Published: September 2011

ABSTRACT
The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated endocytosis, and infection depends on processing in the early to late endosome as well as in the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and green fluorescent protein (GFP) gene-packaged adeno-associated virus serotype 8 (AAV8) have been determined at pH values of 6.0, 5.5, and 4.0 and then at pH 7.5 after incubation at pH 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side chain conformational rearrangements were observed on (i) the interior surface of the capsid under the icosahedral 3-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (ii) the exterior capsid surface close to the icosahedral 2-fold depression. The 3-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH values and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP-VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (i) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (ii) trigger genome uncoating.
Understanding ethnic and other socio-demographic differences in patient experience of primary care: evidence from the English General Practice Patient Survey
Authors: Lyratzopoulos G , Elliott M , Barbiere J M , Henderson A , Staetsky L , Paddison C , Campbell J , Roland M 
Published: September 2011

BackgroundEthnic minorities and some other patient groups consistently report lower scores on patient surveys, but the reasons for this are unclear. This study examined whether low scores of ethnic minority and other socio-demographic groups reflect their concentration in poorly performing primary care practices, and whether any remaining differences are consistent across practices.MethodsUsing data from the 2009 English General Practice Patient Survey (2 163 456 respondents from 8267 general practices) this study examined associations between patient socio-demographic characteristics and 11 measures of patient-reported experience.FindingsSouth Asian and Chinese patients, younger patients, and those in poor health reported a less positive primary care experience than White patients, older patients and those in better health. For doctor communication, about half of the overall difference associated with South Asian patients (ranging from −6 to −9 percentage points) could be explained by their concentration in practices with low scores, but the other half arose because they reported less positive experiences than White patients in the same practices. Practices varied considerably in the direction and extent of ethnic differences. In some practices ethnic minority patients reported better experience than White patients. Differences associated with gender, Black ethnicity and deprivation were small and inconsistent.ConclusionSubstantial ethnic differences in patient experience exist in a national healthcare system providing universal coverage. Improving the experience of patients in low-scoring practices would not only improve the quality of care provided to their White patients but it would also substantially reduce ethnic group differences in patient experience. There were large variations in the experiences reported by ethnic minority patients in different practices: practices with high patient experience scores from ethnic minority patients could be studied as models for quality improvement.
To resuscitate or not to resuscitate: a logistic regression analysis of physician-related variables influencing the decision
Authors: Einav Sharon , Alon Gady , Kaufman Nechama , Braunstein Rony , Carmel Sara , Varon Joseph , Hersch Moshe 
Published: September 2011

ObjectiveTo determine whether variables in physicians' backgrounds influenced their decision to forego resuscitating a patient they did not previously know.MethodsQuestionnaire survey of a convenience sample of 204 physicians working in the departments of internal medicine, anaesthesiology and cardiology in 11 hospitals in Israel.ResultsTwenty per cent of the participants had elected to forego resuscitating a patient they did not previously know without additional consultation. Physicians who had more frequently elected to forego resuscitation had practised medicine for more than 5 years (p=0.013), estimated the number of resuscitations they had performed as being higher (p=0.009), and perceived their experience in resuscitation as sufficient (p=0.001). The variable that predicted the outcome of always performing resuscitation in the logistic regression model was less than 5 years of experience in medicine (OR 0.227, 95% CI 0.065 to 0.793; p=0.02).ConclusionPhysicians' level of experience may affect the probability of a patient's receiving resuscitation, whereas the physicians' personal beliefs and values did not seem to affect this outcome.
Potential climate change impacts on thermal habitats of Pacific salmon (Oncorhynchus spp.) in the North Pacific Ocean and adjacent seas
Authors: Abdul-Aziz Omar I. , Mantua Nathan J. , Myers Katherine W. 
Published: September 2011

We developed spatially explicit representations for seasonal high-seas (open ocean) thermal habitats for six species of Pacific salmon ( Oncorhynchus spp.) and evaluated the effects of natural climate variability and projected changes under three Intergovernmental Panel on Climate Change scenarios of future greenhouse gas emissions. Changes in high-seas habitat due to natural climatic variation in 20th century were small relative to that under anthropogenic climate change scenarios for the middle to late 21st century. Under a multimodel ensemble average of global climate model outputs using A1B (medium) emissions scenario for the entire study area (North Pacific and part of Arctic Ocean), projected winter habitats of sockeye ( Oncorhynchus nerka ) decreased by 38%, and summer habitat decreased by 86% for Chinook ( Oncorhynchus tshawytscha ), 45% for sockeye, 36% for steelhead ( Oncorhynchus mykiss ), 30% for coho ( Oncorhynchus kisutch ), 30% for pink ( Oncorhynchus gorbuscha ), and 29% for chum ( Oncorhynchus keta ) salmon by 2100. Reductions were 25% lower for B1 (lower) emissions and 7% higher for A2 (higher) emissions scenarios. Projected habitat losses were largest in the Gulf of Alaska and western and central subarctic North Pacific. Nearly complete losses of Gulf of Alaska habitat for sockeye in both seasons and Chinook in summer raise important policy issues for North American fishery managers and governments.
STAT3 Is Necessary for Proliferation and Survival in Colon Cancer–Initiating Cells
Authors: Lin Li , Liu Aiguo , Peng Zhengang , Lin Huey-Jen , Li Pui-Kai , Li Chenglong , Lin Jiayuh 
Published: September 2011

Abstract
STAT3 is constitutively activated in colon cancer but its contributions in cancer-initiating cells have not been explored. In this study, we characterized STAT3 in aldehyde dehydrogenase (ALDH)-positive (ALDH+) and CD133-positive (CD133+) subpopulations of human colon tumor cells that exhibited more potent tumor-initiating ability than ALDH−/CD133− cells in tumor xenograft assays in mice. We found that ALDH+/CD133+ cells expressed higher levels of the active phosphorylated form of STAT3 than either ALDH−/CD133− or unfractionated colon cancer cells. STAT3 inhibition by RNA interference–mediated knockdown or small-molecule inhibitors LLL12 or Stattic blocked downstream target gene expression, cell viability, and tumorsphere-forming capacity in cancer-initiating cells. Similarly, treatment of mouse tumor xenografts with STAT3 short hairpin RNA (shRNA), interleukin 6 shRNA, or LLL12 inhibited tumor growth. Our results establish that STAT3 is constitutively activated in colon cancer–initiating cells and that these cells are sensitive to STAT3 inhibition. These findings establish a powerful rationale to develop STAT3 inhibitory strategies for treating advanced colorectal cancers. Cancer Res; 71(23); 7226–37. ©2011 AACR.
Tumor-Associated Macrophages Mediate Immunosuppression in the Renal Cancer Microenvironment by Activating the 15-Lipoxygenase-2 Pathway
Authors: Daurkin Irina , Eruslanov Evgeniy , Stoffs Taryn , Perrin George Q. , Algood Chester , Gilbert Scott M. , Rosser Charles J. , Su Li-Ming , Vieweg Johannes , Kusmartsev Sergei 
Published: September 2011

Abstract
Renal cell carcinoma (RCC), the most common human kidney cancer, is frequently infiltrated with tumor-associated macrophages (TAM) that can promote malignant progression. Here, we show that TAMs isolated from human RCC produce substantial amounts of the proinflammatory chemokine CCL2 and immunosuppressive cytokine IL-10, in addition to enhanced eicosanoid production via an activated 15-lipoxygenase-2 (15-LOX2) pathway. TAMs isolated from RCC tumors had a high 15-LOX2 expression and secreted substantial amounts of 15(S)-hydroxyeicosatetraenoic acid, its major bioactive lipid product. Inhibition of lipoxygenase activity significantly reduced production of CCL2 and IL-10 by RCC TAMs. In addition, TAMs isolated from RCC were capable of inducing in T lymphocytes, the pivotal T regulatory cell transcription factor forkhead box P3 (FOXP3), and the inhibitory cytotoxic T-lymphocyte antigen 4 (CTLA-4) coreceptor. However, this TAM-mediated induction of FOXP3 and CTLA-4 in T cells was independent of lipoxygenase and could not be reversed by inhibiting lipoxygenase activity. Collectively, our results show that TAMs, often present in RCCs, display enhanced 15-LOX2 activity that contributes to RCC-related inflammation, immunosuppression, and malignant progression. Furthermore, we show that TAMs mediate the development of immune tolerance through both 15-LOX2–dependent and 15-LOX2–independent pathways. We propose that manipulating LOX-dependent arachidonic acid metabolism in the tumor microenvironment could offer new strategies to block cancer-related inflammation and immune escape in patients with RCC. Cancer Res; 71(20); 6400–9. ©2011 AACR.
Definition of a FoxA1 Cistrome That Is Crucial for G1 to S-Phase Cell-Cycle Transit in Castration-Resistant Prostate Cancer
Authors: Zhang Chunpeng , Wang Liguo , Wu Dayong , Chen Hongyan , Chen Zhong , Thomas-Ahner Jennifer M. , Zynger Debra L. , Eeckhoute Jérôme , Yu Jindan , Luo Jun , Brown Myles , Clinton Steven K. , Nephew Kenneth P. , Huang Tim H.-M. , Li Wei , Wang Qianben 
Published: September 2011

Abstract
The enhancer pioneer transcription factor FoxA1 is a global mediator of steroid receptor (SR) action in hormone-dependent cancers. In castration-resistant prostate cancer (CRPC), FoxA1 acts as an androgen receptor cofactor to drive G2 to M-phase cell-cycle transit. Here, we describe a mechanistically distinct SR-independent role for FoxA1 in driving G1 to S-phase cell-cycle transit in CRPC. By comparing FoxA1 binding sites in prostate cancer cell genomes, we defined a codependent set of FoxA1-MYBL2 and FoxA1-CREB1 binding sites within the regulatory regions of the Cyclin E2 and E2F1 genes that are critical for CRPC growth. Binding at these sites upregulate the Cyclin E2 and Cyclin A2 genes in CRPC but not in earlier stage androgen-dependent prostate cancer, establishing a stage-specific role for this pathway in CRPC growth. Mechanistic investigations indicated that FoxA1, MYBL2, or CREB1 induction of histone H3 acetylation facilitated nucleosome disruption as the basis for codependent transcriptional activation and G1 to S-phase cell-cycle transit. Our findings establish FoxA1 as a pivotal driver of the cell-cycle in CRPC which promotes G1 to S-phase transit as well as G2 to M-phase transit through two distinct mechanisms. Cancer Res; 71(21); 6738–48. ©2011 AACR.