bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Emergence of Language as an Embodied Collective Cognitive Activity
Authors: Hutchins Edwin , Johnson Christine M. 
Published: June 2009

AbstractTwo decades of attempts to model the emergence of language as a collective cognitive activity have demonstrated a number of principles that might have been part of the historical process that led to language. Several models have demonstrated the emergence of structure in a symbolic medium, but none has demonstrated the emergence of the capacity for symbolic representation. The current shift in cognitive science toward theoretical frameworks based on embodiment is already furnishing computational models with additional mechanisms relevant to the emergence of symbolic language. An analysis of embodied interaction among captive, but not human‐enculturated, bonobo chimpanzees reveals a number of additional features of embodiment that are relevant to the emergence of symbolic language, but that have not yet been explored in computational simulation models; for example, complementarity of action in addition to imitation, iconic in addition to indexical gesture, coordination among multiple sensory and perceptual modalities, and the orchestration of intra‐ and inter‐individual motor coordination. The bonobos provide an evolutionarily plausible intermediate stage in the development of symbolic expression that can inform efforts to model the emergence of symbolic language.
Recombinant
Mycobacterium bovis
BCG Expressing the Chimeric Protein of Antigen 85B and ESAT-6 Enhances the Th1 Cell-Mediated Response
Authors: Xu Ying , Liu Wei , Shen Hongbo , Yan Jingran , Qu Di , Wang Honghai 
Published: June 2009

ABSTRACT

The chimeric protein that relies on the T-cell epitopes of antigen 85B (Ag85B) and the 6-kDa early secreted antigen target (ESAT-6) has been demonstrated to augment the Th1 immune response. In this study, we developed a recombinant
Mycobacterium bovis
BCG (rBCG) strain that secretes the chimeric protein of Ag85B and ESAT-6 (rBCG-A
N
-E-A
C
). Immunization with this rBCG strain induced stronger antigen-specific gamma interferon (IFN-γ) activities, as determined by an enzyme-linked immunospot assay, and higher levels of antigen-specific CD4
+
and CD8
+
T-cell responses than those in the control groups immunized with either rBCG expressing the Ag85B-ESAT-6 fusion protein (rBCG-A-E) or BCG. Likewise, rBCG-A
N
-E-A
C
significantly increased the level of production of the major Th1 cytokines IFN-γ and tumor necrosis factor alpha in splenocyte cultures to levels comparable to those elicited by control BCG. Moreover, the antigen-specific immunoglobulin 2c (IgG2c)/IgG1 ratio for mice immunized with rBCG-A
N
-E-A
C
was also much higher than the ratios for the other immunized groups. Together, these results indicate that this rBCG-A
N
-E-A
C
strain enhances the Th1 cell-mediated response and may serve as a potential vaccine against
M. tuberculosis
.
Disappearance of Vaccine-Type Invasive Pneumococcal Disease and Emergence of Serotype 19A in a Minority Population with a High Prevalence of Human Immunodeficiency Virus and Low Childhood Immunization Rates
Authors: Tasslimi Azadeh , Sison Erica J. , Story Elizabeth , Alland David , Burday Michele , Morrison Susan , Nalmas Sandhya , Smith Stephen , Thomas Pauline A. , Wenger Peter , Sinha Anushua 
Published: June 2009

ABSTRACT
We analyzed the epidemiology of invasive pneumococcal disease (IPD) following introduction of pneumococcal conjugated vaccine in an urban population with a 2% human immunodeficiency virus (HIV) prevalence and history of low childhood immunization rates. We observed near-elimination of vaccine-type IPD. Substantial disease remains due to non-vaccine-type pneumococci, highlighting the need to increase pneumococcal immunization among HIV-infected adults.
Evaluation of
Helicobacter pylori
Immunoglobulin G (IgG), IgA, and IgM Serologic Testing Compared to Stool Antigen Testing
Authors: She Rosemary C. , Wilson Andrew R. , Litwin Christine M. 
Published: June 2009

ABSTRACT

The utility of
Helicobacter pylori
serology was evaluated in 4,722 specimens and compared to stool antigen detection. Immunoglobulin M (IgM) sensitivity (6.8%) was unacceptably low. Key performance differences were observed in IgG specificity, IgA sensitivity, and specificity between adults and children that may warrant differentiating optimal serologic cutoff values by age.
Natural Killer Cell Counts Are Not Different between Patients with Post-Lyme Disease Syndrome and Controls
Authors: Marques Adriana , Brown Margaret R. , Fleisher Thomas A. 
Published: June 2009

ABSTRACTIt has been reported that patients with “chronic Lyme disease” have a decreased number of natural killer cells, as defined by the CD57 marker. We performed immunophenotyping in 9 individuals with post-Lyme disease syndrome, 12 who recovered from Lyme disease, and 9 healthy volunteers. The number of natural killer cells was not significantly different between the groups.
Optimization and Limitations of Use of Cryopreserved Peripheral Blood Mononuclear Cells for Functional and Phenotypic T-Cell Characterization
Authors: Weinberg Adriana , Song Lin-Ye , Wilkening Cynthia , Sevin Anne , Blais Bruce , Louzao Raul , Stein Dana , Defechereux Patricia , Durand Deborah , Riedel Eric , Raftery Nancy , Jesser Renee , Brown Betty , Keller M. Fran , Dickover Ruth , McFarland Elizabeth , Fenton Terence 
Published: June 2009

ABSTRACT

The goals of this study were to optimize processing methods of cryopreserved peripheral blood mononuclear cells (PBMC) for immunological assays, identify acceptance parameters for the use of cryopreserved PBMC for functional and phenotypic assays, and to define limitations of the information obtainable with cryopreserved PBMC. Blood samples from 104 volunteers (49 human immunodeficiency virus-infected and 55 uninfected) were used to assess lymphocyte proliferation in response to tetanus, candida, and pokeweed-mitogen stimulation and to enumerate CD4
+
and CD8
+
T cells and T-cell subpopulations by flow cytometry. We determined that slowly diluting the thawed PBMC significantly improved viable cell recovery, whereas the use of benzonase improved cell recovery only sometimes. Cell storage in liquid nitrogen for up to 15 months did not affect cell viability, recovery, or the results of lymphocyte proliferation assays (LPA) and flow cytometry assays. Storage at −70°C for ≤3 weeks versus storage in liquid nitrogen before shipment on dry ice did not affect cell viability, recovery, or flow cytometric results. Storage at −70°C was associated with slightly higher LPA results with pokeweed-mitogen but not with microbial antigens. Cell viability of 75% was the acceptance parameter for LPA. No other acceptance parameters were found for LPA or flow cytometry assay results for cryopreserved PBMC. Under optimized conditions, LPA and flow cytometry assay results for cryopreserved and fresh PBMC were highly correlated, with the exception of phenotypic assays that used CD45RO or CD62L markers, which seemed labile to freezing and thawing.
T-Cell mRNA Expression in Response toMycobacterium bovisBCG Vaccination andMycobacterium bovisInfection of White-Tailed Deer
Authors: Thacker Tyler C. , Palmer Mitchell V. , Waters W. Ray 
Published: June 2009

ABSTRACTUnderstanding immune responses of white-tailed deer (WTD) to infection withMycobacterium bovisprovides insight into mechanisms of pathogen control and may provide clues to development of effective vaccine strategies. WTD were vaccinated with eitherM. bovisBCG strain Pasteur or BCG strain Danish. Both vaccinees and unvaccinated controls were subsequently inoculated with virulentM. bovisvia the intratonsillar route. Real-time PCR was used to assess T-cell mRNA expression in peripheral blood leukocytes (PBL) from animals following vaccination and infection. Recall T-cell responses were measured by assessing the relative expression of gamma interferon (IFN-γ), T-cell-specific T-box transcription factor (Tbet), interleukin 12p40 (IL-12p40), IL-12p35, IL-23p19, FoxP3, IL-17, and GATA3 in PBL stimulated in vitro with purified protein derivative (PPD) ofM. bovisor a recombinant fusion protein, ESAT6-CFP10. Animals vaccinated with BCG Danish expressed more IFN-γ and Tbet than either BCG Pasteur-vaccinated animals or unvaccinated controls. BCG Pasteur-vaccinated animals expressed more GATA3 than either group. After infection, unvaccinated controls expressed more Tbet and IL-12p40 than vaccinated animals. BCG Pasteur-vaccinated animals expressed more GATA3 than either the unvaccinated controls or the BCG Danish-vaccinated animals after infection. Animals were divided into pathology groups to correlate gene expression with severity of pathology. Animals in the visible lesion group expressed more Tbet and IFN-γ than animals that were culture negative, while Tbet and IFN-γ expression in the culture-positive, no-visible-lesion group was intermediate. GATA3 expression inversely correlated with pathology. Overall, expression of immune response genes correlated more closely with pathology than vaccination treatment.
Inaccuracy of Single-Target Sequencing for Discriminating Species of the
Mycobacterium abscessus
Group
Authors: Macheras Edouard , Roux Anne-Laure , Ripoll Fabienne , Sivadon-Tardy Valérie , Gutierrez Cristina , Gaillard Jean-Louis , Heym Beate 
Published: June 2009

ABSTRACT

We determined nucleotide sequences of
rpoB
,
hsp65
, and
sodA
in 59 clinical isolates (from 58 patients) of the
M
ycobacterium abscessus
group. Identification to the species level, based on three target genes, was concordant for 44 isolates (25
M. abscessus
, 13
Mycobacterium massiliense
, and 6
Mycobacterium bolletii
isolates) and discordant for 15 isolates which had “interspecific composite patterns.” Sequence analysis of five housekeeping genes also showed composite patterns in 8 of these 15 isolates.
emmand C-Repeat Region Molecular Typing of Beta-Hemolytic Streptococci in a Tropical Country: Implications for Vaccine Development
Authors: Steer Andrew C. , Magor Graham , Jenney Adam W. J. , Kado Joseph , Good Michael F. , McMillan David , Batzloff Michael , Carapetis Jonathan R. 
Published: June 2009

ABSTRACTWe designed a study to investigate the molecular epidemiology of group A streptococcal (GAS) and group C and G streptococcal (GCS and GGS) disease in Fiji, a country which is known to have a high burden of streptococcal disease. Molecular typing of the N-terminal portion (emmtyping) of the M protein was performed with 817 isolates (535 GAS and 282 GCS/GGS). We also performed genotyping of the C-repeat region in 769 of these isolates to identify J14 sequence types. The profile ofemmtypes for Fiji was very different from that found for the United States and Europe. There were no dominantemmtypes and a large number of overlapping types among clinical disease states. Commonly found GASemmtypes in industrialized countries, includingemm1,emm12, andemm28, were not found among GAS isolates from Fiji. Over 93% of GAS isolates and over 99% of GCS/GGS isolates that underwent J14 sequence typing contained either J14.0 or J14.1. Our data have implications for GAS vaccine development in developing countries and suggest that a vaccine based upon the conserved region of the M protein may be a feasible option for Fiji and potentially for other tropical developing countries.
Performance of MicroScan WalkAway and Vitek 2 for Detection of Oxacillin Resistance in a Set of Methicillin-Resistant
Staphylococcus aureus
Isolates with Diverse Genetic Backgrounds
Authors: Kaase Martin , Baars Barbara , Friedrich Susanne , Szabados Florian , Gatermann S. G. 
Published: June 2009

ABSTRACT

Of 104 genotypically diverse methicillin-resistant
Staphylococcus aureus
(MRSA) isolates tested with the MicroScan WalkAway (Pos MIC 24 panel) and Vitek 2 (AST-P549 card) systems, 7 and 6 isolates, respectively, showed an oxacillin MIC of ≤2mg/liter. Most of these MRSA isolates were community acquired. However, if the cefoxitin screen of AST-P549 was also considered, MRSA detection failed for only one isolate.
Positive Selection Pressure Introduces Secondary Mutations at Gag Cleavage Sites in Human Immunodeficiency Virus Type 1 Harboring Major Protease Resistance Mutations
Authors: Banke Søren , Lillemark Marie R. , Gerstoft Jan , Obel Niels , Jørgensen Louise B. 
Published: June 2009

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) specifically target the HIV-1 protease enzyme. Mutations in the enzyme can result in PI resistance (termed PI mutations); however, mutations in the HIV-1gagregion, the substrate for the protease enzyme, might also lead to PI resistance. We analyzedgagand pol sequence data from the following 313 HIV-1-infected patients: 160 treatment-naïve patients, 93 patients failing antiretroviral treatment that included a PI (with no major PI mutations), and 60 patients failing antiretroviral treatment that included a PI (with major PI mutations). Additional sequences from 13 patients were included for longitudinal analysis. We assessed positive selection pressure on thegag/protease region using a test for the overall influence of positive selection and a total of five tests to identify positively selected single codons. We found that positive selection pressure was the driving evolutionary force for thegagregion in all three patient groups. An increase in positive selection was observed ingagcleavage site regions p7/p1/p6 only after the acquisition of major PI mutations, suggesting that amino acids ingagcleavage sites under positive selection pressure could function as compensatory mutations for major PI mutations in the protease region. Isolatedgagmutations did not appear to confer PI resistance, but mutations in thegagcleavage sites could substitute for minor PI resistance mutations in the protease region.
The Tight Junction-Associated Protein Occludin Is Required for a Postbinding Step in Hepatitis C Virus Entry and Infection
Authors: Benedicto Ignacio , Molina-Jiménez Francisca , Bartosch Birke , Cosset François-Loïc , Lavillette Dimitri , Prieto Jesús , Moreno-Otero Ricardo , Valenzuela-Fernández Agustín , Aldabe Rafael , López-Cabrera Manuel , Majano Pedro L. 
Published: June 2009

ABSTRACT
The precise mechanisms regulating hepatitis C virus (HCV) entry into hepatic cells remain unknown. However, several cell surface proteins have been identified as entry factors for this virus. Of these molecules, claudin-1, a tight junction (TJ) component, is considered a coreceptor required for HCV entry. Recently, we have demonstrated that HCV envelope glycoproteins (HCVgp) promote structural and functional TJ alterations. Additionally, we have shown that the intracellular interaction between viral E2 glycoprotein and occludin, another TJ-associated protein, could be the cause of the mislocalization of TJ proteins. Herein we demonstrated, by using cell culture-derived HCV particles (HCVcc), that interference of occludin expression markedly reduced HCV infection. Furthermore, our results with HCV pseudotyped particles indicated that occludin, but not other TJ-associated proteins, such as junctional adhesion molecule A or zonula occludens protein 1, was required for HCV entry. Using HCVcc, we demonstrated that occludin did not play an essential role in the initial attachment of HCV to target cells. Surface protein labeling experiments showed that both expression levels and cell surface localization of HCV (co)receptors CD81, scavenger receptor class B type I, and claudin-1 were not affected upon occludin knockdown. In addition, immunofluorescence confocal analysis showed that occludin interference did not affect subcellular distribution of the HCV (co)receptors analyzed. However, HCVgp fusion-associated events were altered after occludin silencing. In summary, we propose that occludin plays an essential role in HCV infection and probably affects late entry events. This observation may provide new insights into HCV infection and related pathogenesis.
Activation of Natural Killer Cells by Newcastle Disease Virus Hemagglutinin-Neuraminidase
Authors: Jarahian Mostafa , Watzl Carsten , Fournier Philippe , Arnold Annette , Djandji Dominik , Zahedi Sarah , Cerwenka Adelheid , Paschen Annette , Schirrmacher Volker , Momburg Frank 
Published: June 2009

ABSTRACTThe avian paramyxovirus Newcastle disease virus (NDV) selectively replicates in tumor cells and is known to stimulate T-cell-, macrophage-, and NK cell-mediated responses. The mechanisms of NK cell activation by NDV are poorly understood so far. We studied the expression of ligand structures for activating NK cell receptors on NDV-infected tumor cells. Upon infection with the nonlytic NDV strain Ulster and the lytic strain MTH-68/H, human carcinoma and melanoma cells showed enhanced expression of ligands for the natural cytotoxicity receptors NKp44 and NKp46, but not NKp30. Ligands for the activating receptor NKG2D were partially downregulated. Soluble NKp44-Fc and NKp46-Fc, but not NKp30-Fc, chimeric proteins bound specifically to NDV-infected tumor cells and to NDV particle-coated plates. Hemagglutinin-neuraminidase (HN) of the virus serves as a ligand structure for NKp44 and NKp46, as indicated by the blockade of binding to NDV-infected cells and viral particles in the presence of anti-HN antibodies and by binding to cells transfected with HN cDNA. Consistent with the recognition of sialic acid moieties by the viral lectin HN, the binding of NKp44-Fc and NKp46-Fc was lost after desialylation. NKp44- and NKp46-CD3ζlacZ-inducible reporter cells were activated by NDV-infected cells. NDV-infected tumor cells stimulated NK cells to produce increased amounts of the effector lymphokines gamma interferon and tumor necrosis factor alpha. Primary NK cells and the NK line NK-92 lysed NDV-infected tumor cells with enhanced efficiency, an effect that was eliminated by the treatment of target cells with the neuraminidase inhibitor Neu5Ac2en. These results suggest that direct activation of NK cells contributes to the antitumor effects of NDV.
Vpu Directs the Degradation of the Human Immunodeficiency Virus Restriction Factor BST-2/Tetherin via a βTrCP-Dependent Mechanism
Authors: Douglas Janet L. , Viswanathan Kasinath , McCarroll Matthew N. , Gustin Jean K. , Früh Klaus , Moses Ashlee V. 
Published: June 2009

ABSTRACT
The primary roles attributed to the human immunodeficiency virus type 1 (HIV-1) Vpu protein are the degradation of the viral receptor CD4 and the enhancement of virion release. With regard to CD4 downregulation, Vpu has been shown to act as an adapter linking CD4 with the ubiquitin-proteasome machinery via interaction with the F-box protein βTrCP. To identify additional cellular βTrCP-dependent Vpu targets, we performed quantitative proteomics analyses using the plasma membrane fraction of HeLa cells expressing either wild-type Vpu or a Vpu mutant (S52N/S56N) that does not bind βTrCP. One cellular protein, BST-2 (CD317), was consistently underrepresented in the membrane proteome of cells expressing wild-type Vpu compared to the proteome of cells expressing the Vpu mutant. To verify the biological relevance of this phenotype for HIV pathogenesis, we showed that in T cells infected with HIV-1, BST-2 downregulation occurred in a Vpu-dependent manner. Recently, BST-2 has been identified as the interferon-inducible cellular factor Tetherin, which restricts HIV virion release in the absence of Vpu. We address here the unresolved mechanism of Vpu-mediated BST-2 downregulation. Our data show that the presence of wild-type Vpu reduced cell surface and total steady-state BST-2 levels, whereas that of the mutant Vpu had no effect. In addition, treatment of cells with the lysosome acidification inhibitor concanamycin A, but not treatment with the proteasome inhibitor MG132, reduced BST-2 downregulation by wild-type Vpu, thereby suggesting that the presence of Vpu leads to the degradation of BST-2 via an endosome-lysosome degradation pathway. The importance of βTrCP in this process was confirmed by demonstrating that in the absence of βTrCP, BST-2 levels were restored despite the presence of Vpu. Taken together, these data support the hypothesis that, in similarity to its role in CD4 degradation, Vpu acts as an adapter molecule linking BST-2 to the cellular ubiquitination machinery via βTrCP. However, in contrast to the proteasome-dependent degradation of CD4, which occurs in the endoplasmic reticulum, Vpu appears to interact with BST-2 in the trans-Golgi network or in early endosomes, leading to lysosomal degradation of BST-2. Via this action, Vpu could counter the tethering function of BST-2, resulting in enhanced HIV-1 virion release. Interestingly, although HIV-2 does not express Vpu, an isolate known to exhibit enhanced viral egress can downregulate surface BST-2 by an as-yet-unknown mechanism that does not appear to involve degradation. Understanding the molecular mechanisms of both Vpu-dependent and -independent mediated antagonism of BST-2 will be critical for therapeutic strategies that exploit this novel viral function.
Heterosexual Transmission of Human Immunodeficiency Virus Type 1 Subtype C: Macrophage Tropism, Alternative Coreceptor Use, and the Molecular Anatomy of CCR5 Utilization
Authors: Isaacman-Beck Jesse , Hermann Emilia A. , Yi Yanjie , Ratcliffe Sarah J. , Mulenga Joseph , Allen Susan , Hunter Eric , Derdeyn Cynthia A. , Collman Ronald G. 
Published: June 2009

ABSTRACT
Human immunodeficiency virus type 1 transmission selects for virus variants with genetic characteristics distinct from those of donor quasispecies, but the biological factors favoring their transmission or establishment in new hosts are poorly understood. We compared primary target cell tropisms and entry coreceptor utilizations of donor and recipient subtype C Envs obtained near the time of acute infection from Zambian heterosexual transmission pairs. Both donor and recipient Envs demonstrated only modest macrophage tropism, and there was no overall difference between groups in macrophage or CD4 T-cell infection efficiency. Several individual pairs showed donor/recipient differences in primary cell infection, but these were not consistent between pairs. Envs had surprisingly broad uses of GPR15, CXCR6, and APJ, but little or no use of CCR2b, CCR3, CCR8, GPR1, and CXCR4. Donors overall used GPR15 better than did recipients. However, while several individual pairs showed donor/recipient differences for GPR15 and/or other coreceptors, the direction of the differences was inconsistent, and several pairs had unique alternative coreceptor patterns that were conserved across the transmission barrier. CCR5/CCR2b chimeras revealed that recipients as a group were more sensitive than were donors to replacement of the CCR5 extracellular loops with corresponding regions of CCR2b, but significant differences in this direction were not consistent within pairs. These data show that sexual transmission does not select for enhanced macrophage tropism, nor for preferential use of any alternative coreceptor. Recipient Envs are somewhat more constrained than are donors in flexibility of CCR5 use, but this pattern is not universal for all pairs, indicating that it is not an absolute requirement.