bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Classification Scheme for Outcome Indicators
Authors: Jennings Bonnie Mowinski , Staggers Nancy , Brosch Laura Ruse 
Published: June 2007

Purpose:To provide a framework for classifying outcome indicators for a more comprehensive view of outcomes and quality.Methods:Review of outcomes literature published since 1974 from medicine, nursing, and health services research to identify indicators. Outcome indicators were clustered inductively.Findings:Three groups of outcome indicators were identified: patient‐focused, provider‐focused, and organization‐focused. Although investigators tend to focus on a select few outcome indicators, such as patient satisfaction, quality of life, and mortality, many indicators exist to measure outcomes.Conclusions:Selecting and integrating a wide array of outcome indicators from the various categories will provide a more balanced view of health care delivery as compared with focusing on a few common indicators or only one category.
Unity and Diversity in Feminist Legal Theory
Authors: Davies Margaret 
Published: June 2007

AbstractFeminist legal theory has undergone some significant changes over the past thirty years. This article provides an introductory overview of feminist legal theory, from liberal and radical feminism through to postmodernism. It outlines some of the major current issues within feminist legal thought, notably debates surrounding culture and religion, the relationship of sex and sexuality scholarship to feminist research, and the position of women within transitional societies.
Cross-Reactive T-Cell Responses to the Nonstructural Regions of Dengue Viruses among Dengue Fever and Dengue Hemorrhagic Fever Patients in Malaysia
Authors: Appanna Ramapraba , Huat Tan Lian , See Lucy Lum Chai , Tan Phoay Lay , Vadivelu Jamuna , Devi Shamala 
Published: June 2007

ABSTRACTDengue virus infections are a major cause of morbidity and mortality in tropical and subtropical areas in the world. Attempts to develop effective vaccines have been hampered by the lack of understanding of the pathogenesis of the disease and the absence of suitable experimental models for dengue viral infection. The magnitude of T-cell responses has been reported to correlate with dengue disease severity. Sixty Malaysian adults with dengue viral infections were investigated for their dengue virus-specific T-cell responses to 32 peptides antigens from the structural and nonstructural regions from a dengue virus isolate. Seventeen different peptides from the C, E, NS2B, NS3, NS4A, NS4B, and NS5 regions were found to evoke significant responses in a gamma interferon enzyme-linked immunospot (ELISPOT) assay of samples from 13 selected patients with dengue fever (DF) and dengue hemorrhagic fever (DHF). NS3 and predominantly NS3422-431were found to be important T-cell targets. The highest peaks of T-cell responses observed were in responses to NS3422-431and NS5563-571in DHF patients. We also found almost a sevenfold increase in T-cell response in three DHF patients compared to three DF patient responses to peptide NS3422-431. A large number of patients' T cells also responded to the NS2B97-106region. The ELISPOT analyses also revealed high frequencies of T cells that recognize both serotype-specific and cross-reactive dengue virus antigens in patients with DHF.
Sensitive Oligonucleotide Ligation Assay for Low-Level Detection of Nevirapine Resistance Mutations in Human Immunodeficiency Virus Type 1 Quasispecies
Authors: Lalonde Matthew S. , Troyer Ryan M. , Syed Aslam R. , Bulime Stanley , Demers Korey , Bajunirwe Francis , Arts Eric J. 
Published: June 2007

ABSTRACTThis study has adapted the oligonucleotide ligation assay (OLA) to probe for low-level nevirapine (NVP) resistance mutations K103N and Y181C in the human immunodeficiency virus type 1 (HIV-1) population of infected mother-infant pairs from Uganda. When NVP is used to prevent perinatal transmission, NVP-resistant HIV-1 clones may be rapidly selected due to a low barrier for mutation and a relatively high level of fitness (compared to that of other drug-resistant HIV-1 clones). Monitoring for even a low frequency of NVP resistance mutations may help predict the success of subsequent treatment or warrant the use of another regimen to prevent transmission in a subsequent pregnancy. The standard OLA was optimized by using nonstandard bases in oligonucleotides to allow promiscuous base pairing and accommodate significant HIV-1 heterogeneity. Radiolabeled as opposed to fluorescently tagged oligonucleotides increased the sensitivity, whereas alteration of the template, oligonucleotides, salt, and thermostable DNA ligase concentrations increased the specificity for the detection of minority codons. This modified OLA is now capable of detecting mutants with the K103N or the Y181C mutation present in an HIV-1 population at a frequency of ∼0.4% and is at least 10- to 30-fold more sensitive than the original protocol. A cohort of 19 Ugandan mothers who received NVP treatment perinatally were sampled 6 weeks postdelivery. Ten of 19 HIV-1 DNA samples extracted from peripheral blood mononuclear cells had a detectable K103N (0.5 to 44%) or Y181C (0.8 to 92.5%) mutation, but only one plasma HIV-1 RNA sample had a viral population with the Y181C mutation. These findings suggest that OLA is a robust, sensitive, and specific method for the detection of low-frequency drug resistance mutations in an intrapatient HIV-1 population.
Development of Real-Time PCR Assays for Genotyping of
Chlamydia trachomatis
Authors: Jalal Hamid , Stephen Hannah , Alexander Sarah , Carne Christopher , Sonnex Christopher 
Published: June 2007

ABSTRACT

We have developed and validated a nested real-time PCR (NRT-PCR) for the genotyping of
Chlamydia trachomatis
and used it specifically for the typing of either eight genovars from D to K or three genovars of lymphogranuloma venereum (LGV). The 11 probes used in the NRT-PCR correctly identified the DNA from D to K and LGV reference strains and did not cross-react with the DNA from 26 strains representing the bacterial pathogens and commensals of the oropharynx, genital tract, and rectum. The NRT-PCR had a 95% probability of detection at four genome copies (confidence interval, three to six copies) of
C. trachomatis
per reaction. One hundred cervical and urethral swab specimens containing
C. trachomatis
DNA from 63 women and 37 men were used to validate the method. The results from the NRT-PCR and the DNA sequencing of amplicons generated from the
omp1
gene showed 100% correlation for these samples. The assay also identified the LGV-II genotype in 24 of 48 rectal swab specimens containing
C. trachomatis
DNA that were obtained from men having sex with men. The Sexually Transmitted Bacteria Reference Laboratory, London, independently confirmed these results using group-specific LGV real-time PCR and restriction fragment length polymorphism analysis. Compared with the NRT-PCR, non-NRT-PCR was found to be less sensitive: it typed
C. trachomatis
DNA in only 80% of the genital samples and 90% of the rectal swab samples. This is the first successful demonstration of the use of real-time PCR for the genotype-specific typing of
C. trachomatis
strains that cause sexually transmitted diseases.
Detection of
Clostridium difficile
Toxin: Comparison of Enzyme Immunoassay Results with Results Obtained by Cytotoxicity Assay
Authors: Musher Daniel M. , Manhas Atisha , Jain Pranav , Nuila Franziska , Waqar Amna , Logan Nancy , Marino Bernard , Graviss Edward A. 
Published: June 2007

ABSTRACT

Several kinds of laboratory techniques are available to detect
Clostridium difficile
toxin in fecal samples. Because questions have been raised about the reliability of immunoassays compared to the accepted standard, cytotoxicity assay, we studied three enzyme immunoassays (EIAs) and one rapid EIA, which demonstrated relatively good sensitivities and specificities compared to cytotoxicity assay.
Desulfovibrio fairfieldensis
Bacteremia Associated with Choledocholithiasis and Endoscopic Retrograde Cholangiopancreatography
Authors: Pimentel Jason D. , Chan Raymond C. 
Published: June 2007

ABSTRACT

Desulfovibrio fairfieldensis
is a gram-negative, curved, motile, anaerobic bacillus.
D. fairfieldensis
has been isolated only from human specimens and is considered a normal resident of the human gastrointestinal tract. We report the second case of
Desulfovibrio
bacteremia associated with choledocholithiasis and review the other reported cases of
D. fairfieldensis
bacteremia.
Streptococcus mutans
Clonal Variation Revealed by Multilocus Sequence Typing
Authors: Nakano Kazuhiko , Lapirattanakul Jinthana , Nomura Ryota , Nemoto Hirotoshi , Alaluusua Satu , Grönroos Lisa , Vaara Martti , Hamada Shigeyuki , Ooshima Takashi , Nakagawa Ichiro 
Published: June 2007

ABSTRACT

Streptococcus mutans
is the major pathogen of dental caries, a biofilm-dependent infectious disease, and occasionally causes infective endocarditis.
S. mutans
strains have been classified into four serotypes (
c
,
e
,
f
, and
k
). However, little is known about the
S. mutans
population, including the clonal relationships among strains of
S. mutans
, in relation to the particular clones that cause systemic diseases. To address this issue, we have developed a multilocus sequence typing (MLST) scheme for
S. mutans
. Eight housekeeping gene fragments were sequenced from each of 102
S. mutans
isolates collected from the four serotypes in Japan and Finland. Between 14 and 23 alleles per locus were identified, allowing us theoretically to distinguish more than 1.2 × 10
10
sequence types. We identified 92 sequence types in these 102 isolates, indicating that
S. mutans
contains a diverse population. Whereas serotype
c
strains were widely distributed in the dendrogram, serotype
e
,
f
, and
k
strains were differentiated into clonal complexes. Therefore, we conclude that the ancestral strain of
S. mutans
was serotype
c
. No geographic specificity was identified. However, the distribution of the collagen-binding protein gene (
cnm
) and direct evidence of mother-to-child transmission were clearly evident. In conclusion, the superior discriminatory capacity of this MLST scheme for
S. mutans
may have important practical implications.
Population-Based Study of Salivary Carriage of Periodontal Pathogens in Adults
Authors: Könönen Eija , Paju Susanna , Pussinen Pirkko J. , Hyvönen Mari , Di Tella Paulo , Suominen-Taipale Liisa , Knuuttila Matti 
Published: June 2007

ABSTRACT

Large, general population-based data on carriage rates of periodontal pathogens hardly exist in the current literature. The objectives of the present study were to examine the salivary detection of
Aggregatibacter
(formerly
Actinobacillus
)
actinomycetemcomitans
,
Campylobacter rectus
,
Porphyromonas gingivalis
,
Prevotella intermedia
,
Tannerella forsythensis
, and
Treponema denticola
in a representative sample of the adult population living in southern Finland and to clarify which determinants are associated with the presence of these pathogens in saliva. 16S rRNA-based PCR methods with species-specific primers were employed to determine the presence of the six target bacteria in stimulated saliva samples, which were available from 1,294 subjects aged ≥30 years. The age group, gender, level of education, marital status, smoking history, number of teeth, and number of teeth with deepened pockets were included in the statistical analysis. In general, the carriage of periodontal pathogens was common, since at least one of the examined pathogens was found in 88.2% of the subjects. In descending order, the total detection rates were 56.9%, 38.2%, 35.4%, 31.3%, 20.0%, and 13.9% for
T. forsythensis
,
T. denticola
,
P. gingivalis
,
C. rectus
,
A. actinomycetemcomitans
, and
P. intermedia
, respectively. Age per se was strongly associated with the carriage of
P. gingivalis
(
P
= 0.000), and the level of education with that of
T. denticola
(
P
= 0.000). There was an association between the number of teeth with deepened pockets and carriage of
P. gingivalis
(
P
= 0.000),
P. intermedia
(
P
= 0.000),
T. denticola
(
P
= 0.000), and
A. actinomycetemcomitans
(
P
= 0.004). The data suggest that distinct species have a different carriage profile, depending on variables such as age, educational level, and periodontal status.
Local Expression of Secondary Lymphoid Tissue Chemokine Delivered by Adeno-Associated Virus within the Tumor Bed Stimulates Strong Anti-Liver Tumor Immunity
Authors: Liang Chun-min , Zhong Cui-ping , Sun Rui-xia , Liu Bin-bin , Huang Cheng , Qin Jie , Zhou Shuang , Shan Junling , Liu Yin-kun , Ye Sheng-long 
Published: June 2007

ABSTRACTDevelopment of an effective antitumor immune response depends on the appropriate interaction of effector and target cells. Thus, the expression of chemokines within the tumor may induce a more potent antitumor immune response. Secondary lymphoid tissue chemokine (SLC) is known to play a critical role in establishing a functional microenvironment in secondary lymphoid tissues. Its capacity to attract dendritic cells (DCs) and colocalize them with T cells makes it a good therapeutic candidate against cancer. In this study, we used SLC as a treatment for tumors established from a murine hepatocellular carcinoma model. SLC was encoded by recombinant adeno-associated virus (rAAV), a system chosen for the low host immunity and high efficiency of transduction, enabling long-term expression of the gene of interest. As a result, rAAV-SLC induced a significant delay of tumor progression, which was paralleled by a profound infiltration of DCs and activated CD4+T cells and CD8+T cells (CD3+CD69+cells) into the tumor site. In addition, rAAV-SLC treatment was also found to reduce tumor growth in nude mice, most likely due to inhibition of neoangiogenesis. In conclusion, local expression of SLC by rAAV represents a promising approach to induce immune-mediated regression of malignant tumors.
Retrograde Axonal Transport: a Major Transmission Route of Enterovirus 71 in Mice
Authors: Chen Che-Szu , Yao Yi-Chuan , Lin Shin-Chao , Lee Yi-Ping , Wang Ya-Fang , Wang Jen-Ren , Liu Ching-Chuan , Lei Huan-Yao , Yu Chun-Keung 
Published: June 2007

ABSTRACT
Inoculation of enterovirus 71 (EV71) by the oral (p.o.), intramuscular (i.m.), or intracranial route resulted in brain infection, flaccid paralysis, pulmonary dysfunction, and death of 7-day-old mice. The lag time of disease progression indicated that neuroinvasion from the inoculation sites was a prerequisite for the development of the clinical signs. Although EV71 p.o. inoculation led to a persistent viremia and a transient increase in blood-brain barrier permeability at the early stage of the infection, only low levels of virus, which led to neither severe infection nor clinical illness, could be detected in the brain, suggesting that hematogenous transport might not represent a major transmission route. In the spinal cord, following both p.o. and hind limb i.m. inoculation, the virus first appeared and increased rapidly in the lower segments, especially at the anterior horn areas, and then spread to the upper segments and brain in the presence of viremia. A reverse pattern, with the virus being first detected in the upper segment, was observed when the virus was i.m. inoculated in the forelimb. Colchicine, a fast axonal transport inhibitor, but not sciatic nerve transection reduced EV71 neuroinvasion in a dose-dependent manner, indicating a neuronal transmission of the virus.
Early Production of Type I Interferon during West Nile Virus Infection: Role for Lymphoid Tissues in IRF3-Independent Interferon Production
Authors: Bourne Nigel , Scholle Frank , Silva Maria Carlan , Rossi Shannan L. , Dewsbury Nathan , Judy Barbara , De Aguiar Juliana B. , Leon Megan A. , Estes D. Mark , Fayzulin Rafik , Mason Peter W. 
Published: June 2007

ABSTRACTInfection of cells with flaviviruses in vitro is reduced by pretreatment with small amounts of type I interferon (IFN-α/β). Similarly, pretreatment of animals with IFN and experiments using mice defective in IFN signaling have indicated a role for IFN in controlling flavivirus disease in vivo. These data, along with findings that flavivirus-infected cells block IFN signaling, suggest that flavivirus infection can trigger an IFN response. To investigate IFN gene induction by the very first cells infected during in vivo infection with the flavivirus West Nile virus (WNV), we infected mice with high-titer preparations of WNV virus-like particles (VLPs), which initiate viral genome replication in cells but fail to spread. These studies demonstrated a brisk production of IFN in vivo, with peak levels of over 1,000 units/ml detected in sera between 8 and 24 h after inoculation by either the intraperitoneal or footpad route. The IFN response was dependent on genome replication, and WNV genomes and WNV antigen-positive cells were readily detected in the popliteal lymph nodes (pLN) of VLP-inoculated mice. High levels of IFN mRNA transcripts and functional IFN were also produced in VLP-inoculated IFN regulatory factor 3 null (IRF3−/−) mice, indicating that IFN production was independent of the IRF3 pathways to IFN gene transcription, consistent with the IFN type produced (predominantly α).
Upregulation of PD-1 Expression on Circulating and Intrahepatic Hepatitis C Virus-Specific CD8+T Cells Associated with Reversible Immune Dysfunction
Authors: Golden-Mason Lucy , Palmer Brent , Klarquist Jared , Mengshol John A. , Castelblanco Nicole , Rosen Hugo R. 
Published: June 2007

ABSTRACTInfection with hepatitis C virus (HCV) is associated with persistence in the majority of individuals. We demonstrate here that the inhibitory molecule programmed death-1 (PD-1) is significantly upregulated on total and HCV-specific CD8+cytotoxic T lymphocytes (CTLs) in the peripheral blood and livers of patients with chronic infection compared to subjects with spontaneous HCV resolution, patients with nonviral liver disease, and normal controls. PD-1 expression on cytomegalovirus-specific CTLs also varies according to HCV status and is highest in patients with chronic infection. HCV-specific CTLs that are PD-1highexpress higher levels of the senescence marker CD57 than PD-1lowCTLs, and CD57 expression is greater in chronic than in resolved infection. In vitro blockade of PD-1 by monoclonal antibodies specific to its ligands (PD-L1 and PD-L2) results in restoration of functional competence (proliferation and gamma interferon and interleukin-2 secretion) of HCV-specific CTLs, including those residing in the liver. This reversal of CTL exhaustion is evident even in individuals who lack HCV-specific CD4+T-cell help. Our data indicate that the PD-1/PD-L pathway is critical in persistent HCV infection in humans and represents a potential novel target for restoring function of exhausted HCV-specific CTLs.
Hepatitis C Virus Nonstructural Protein 5A Modulates the Toll-Like Receptor-MyD88-Dependent Signaling Pathway in Macrophage Cell Lines
Authors: Abe Takayuki , Kaname Yuuki , Hamamoto Itsuki , Tsuda Yoshimi , Wen Xiaoyu , Taguwa Shuhei , Moriishi Kohji , Takeuchi Osamu , Kawai Taro , Kanto Tatsuya , Hayashi Norio , Akira Shizuo , Matsuura Yoshiharu 
Published: June 2007

ABSTRACTHepatitis C virus (HCV) infection induces a wide range of chronic liver injuries; however, the mechanism through which HCV evades the immune surveillance system remains obscure. Blood dendritic cells (DCs) play a pivotal role in the recognition of viral infection and the induction of innate and adaptive immune responses. Several reports suggest that HCV infection induces the dysfunction of DCs in patients with chronic hepatitis C. Toll-like receptor (TLR) has been shown to play various roles in many viral infections; however, the involvement of HCV proteins in the TLR signaling pathway has not yet been precisely elucidated. In this study, we established mouse macrophage cell lines stably expressing HCV proteins and determined the effect of HCV proteins on the TLR signaling pathways. Immune cells expressing NS3, NS3/4A, NS4B, or NS5A were found to inhibit the activation of the TLR2, TLR4, TLR7, and TLR9 signaling pathways. Various genotypes of NS5A bound to MyD88, a major adaptor molecule in TLR, inhibited the recruitment of interleukin-1 receptor-associated kinase 1 to MyD88, and impaired cytokine production in response to TLR ligands. Amino acid residues 240 to 280, previously identified as the interferon sensitivity-determining region (ISDR) in NS5A, interacted with the death domain of MyD88, and the expression of a mutant NS5A lacking the ISDR partially restored cytokine production. These results suggest that the expression of HCV proteins modulates the TLR signaling pathway in immune cells.
Viral Phenotypes and Antibody Responses in Long-Term Survivors Infected with Attenuated Human Immunodeficiency Virus Type 1 Containing Deletions in thenefand Long Terminal Repeat Regions
Authors: Verity Erin E. , Zotos Dimitra , Wilson Kim , Chatfield Catherine , Lawson Victoria A. , Dwyer Dominic E. , Cunningham Anthony , Learmont Jennifer , Dyer Wayne , Sullivan John , Churchill Melissa , Wesselingh Steven L. , Gabuzda Dana , Gorry Paul R. , McPhee Dale A. 
Published: June 2007

ABSTRACTThe Sydney Blood Bank Cohort (SBBC) consists of eight blood transfusion recipients infected withnef-attenuated human immunodeficiency virus type 1 (HIV-1) acquired from a single donor. Here, we show that viral phenotypes and antibody responses differ considerably between individual cohort members, despite the single source of infection. Replication of isolated virus varied from barely detectable to similar to that of the wild-type virus, and virus isolated from five SBBC members showed coreceptor usage signatures unique to each individual. Higher viral loads and stronger neutralizing antibody responses were associated with better-replicating viral strains, and detectable viral replication was essential for the development of strong and sustained humoral immune responses. Despite the presence of strong neutralizing antibodies in a number of SBBC members, disease progression was not prevented, and each cohort member studied displayed a unique outcome of infection withnef-attenuated HIV-1.
Differential Polymerase Activity in Avian and Mammalian Cells Determines Host Range of Influenza Virus
Authors: Gabriel G. , Abram M. , Keiner B. , Wagner R. , Klenk H.-D. , Stech J. 
Published: June 2007

ABSTRACT
As recently shown, mutations in the polymerase genes causing increased polymerase activity in mammalian cells are responsible for the adaptation of the highly pathogenic avian influenza virus SC35 (H7N7) to mice (G. Gabriel et al., Proc. Natl. Acad. Sci. USA 102:18590-18595, 2005). We have now compared mRNA, cRNA, and viral RNA levels of SC35 and its mouse-adapted variant SC35M in avian and mammalian cells. The increase in levels of transcription and replication of SC35M in mammalian cells was linked to a decrease in avian cells. Thus, the efficiency of the viral polymerase is a determinant of both host specificity and pathogenicity.