bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of High-Resolution Typing Methods for Chlamydia trachomatis in Samples from Heterosexual Couples
Authors: Bom Reinier J. M. , Christerson Linus , Schim van der Loeff Maarten F. , Coutinho Roel A. , Herrmann Björn , Bruisten Sylvia M. 
Published: June 2011

ABSTRACT

We aimed to compare conventional
ompA
typing of
Chlamydia trachomatis
with multilocus sequence typing (MLST) and multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). Previously used MLST and MLVA systems were compared to modified versions that used shorter target regions and nested PCR. Heterosexual couples were selected from among persons with urogenital
C. trachomatis
infections visiting the sexually transmitted infection outpatient clinic in Amsterdam, The Netherlands. We identified 30 couples with a total of 65
C. trachomatis
-positive samples on which MLST and MLVA for eight target regions were performed. All regions were successfully sequenced in 52 samples, resulting in a complete profile for 18 couples and 12 individuals. Nine
ompA
genovars from D to K, with two variants of genovar G, were found. The numbers of sequence type and MLVA type profiles were 20 for MLST and 21 for MLVA, and a combination of MLST and MLVA yielded 28 profiles, with discriminatory indexes (
D
) ranging from 0.95 to 0.99. Partners in 17 couples shared identical profiles, while partners in 1 couple had completely different profiles. Three persons had infections at multiple anatomical locations, and within each of these three individuals, all profiles were identical. The discriminatory capacity of all MLST and MLVA methods is much higher than that of
ompA
genotyping (
D
= 0.78). No genotype variation was found within the samples of the same person or from heterosexual couples with a putative single transmission. This shows that the chlamydial genome in clinical specimens has an appropriate polymorphism to enable epidemiological cluster analysis using MLST and MLVA.
Development of a Highly Sensitive Genus-Specific Quantitative Reverse Transcriptase Real-Time PCR Assay for Detection and Quantitation of Plasmodium by Amplifying RNA and DNA of the 18S rRNA Genes
Authors: Kamau Edwin , Tolbert LaDonna S. , Kortepeter Luke , Pratt Michael , Nyakoe Nancy , Muringo Linda , Ogutu Bernard , Waitumbi John N. , Ockenhouse Christian F. 
Published: June 2011

ABSTRACT

A highly sensitive genus-specific quantitative reverse transcriptase real-time PCR (qRT-PCR) assay for detection of
Plasmodium
has been developed. The assay amplifies total nucleic acids (RNA and DNA) of the 18S rRNA genes with a limit of detection of 0.002 parasite/μl using cultured synchronized ring stage 3D7 parasites. Parasite densities as low as 0.000362 parasite/μl were detected when analyzing clinical samples. Analysis of clinical samples showed that detection of 18S rRNA genes from total nucleic acids increased the analytical sensitivity of the assay by more than 1 log unit compared to DNA only. When clinical samples with no parasites present by microscopy were analyzed by qRT-PCR, 90% (117 of 130) were positive for the presence of
Plasmodium
nucleic acids. Quantification of clinical samples by qRT-PCR using total nucleic acid versus DNA was compared to microscopy. There was a significantly greater correlation of parasite density to microscopy when DNA alone was used than with total nucleic acid. We conclude that analysis of total nucleic acids by qRT-PCR is a suitable assay for detection of low parasite levels in patients with early-stage malaria and/or submicroscopic infections and could greatly benefit malaria diagnosis, intervention trials, and malaria control and elimination efforts.
Early Detection of Colonization by VIM-1-Producing Klebsiella pneumoniae and NDM-1-Producing Escherichia coli in Two Children Returning to France
Authors: Birgy André , Doit Catherine , Mariani-Kurkdjian Patricia , Genel Nathalie , Faye Albert , Arlet Guillaume , Bingen Edouard 
Published: June 2011

ABSTRACT

Rapid identification of metallo-β-lactamase-producing Gram-negative species is crucial for the timely implementation of infection control measures. We describe two pediatric cases in which colonization by VIM-1- and New Delhi metallo-beta-lactamase 1-producing
Enterobacteriaceae
was rapidly detected by phenotypic and genotypic methods. Phenotypic methods can be useful for routine detection of carbapenemase production.
Comparison of Serial Hepatitis C Virus Detection in Samples Submitted through Serology for Reflex Confirmation versus Samples Directly Submitted for Quantitation
Authors: Gale Howard B. , Dufour D. Robert , Qazi Nazia N. , Kan Virginia L. 
Published: June 2011

ABSTRACT
Using real-time technology, we reliably identified chronic hepatitis C virus (HCV) infection and quantified virus from reflex samples originally submitted for serologic testing. There was no need to process specimens obtained directly for quantitation separately. Whether the initial source is a reflex sample or one obtained directly, a repeat HCV RNA test is needed before starting treatment.
Molecular Detection and Identification of Mycobacterium tuberculosis Complex and Four Clinically Important Nontuberculous Mycobacterial Species in Smear-Negative Clinical Samples by the GenoType Mycobacteria Direct Test
Authors: Bicmen Can , Gunduz Ayriz T. , Coskun Meral , Senol Gunes , Cirak A. Kadri , Ozsoz Ayse 
Published: June 2011

ABSTRACT

Although the sensitivity and specificity of nucleic acid amplification assays are high with smear-positive samples, the sensitivity with smear-negative and extrapulmonary samples for the diagnosis of tuberculosis in suspicious tuberculosis cases still remains to be investigated. This study evaluates the performance of the GenoType Mycobacteria Direct (GTMD) test for rapid molecular detection and identification of the
Mycobacterium tuberculosis
complex and four clinically important nontuberculous mycobacteria (
M. avium
,
M. intracellulare
,
M. kansasii
, and
M. malmoense
) in smear-negative samples. A total of 1,570 samples (1,103 bronchial aspiration, 127 sputum, and 340 extrapulmonary samples) were analyzed. When we evaluated the performance criteria in combination with a positive culture result and/or the clinical outcome of the patients, the overall sensitivity, specificity, and positive and negative predictive values were found to be 62.4, 99.5, 95.9, and 93.9%, respectively, whereas they were 63.2, 99.4, 95.7, and 92.8%, respectively, for pulmonary samples and 52.9, 100, 100, and 97.6%, respectively, for extrapulmonary samples. Among the culture-positive samples which had
Mycobacterium
species detectable by the GTMD test, three samples were identified to be
M. intracellulare
and one sample was identified to be
M. avium.
However, five
M. intracellulare
samples and an
M. kansasii
sample could not be identified by the molecular test and were found to be negative. The GTMD test has been a reliable, practical, and easy tool for rapid diagnosis of smear-negative pulmonary and extrapulmonary tuberculosis so that effective precautions may be taken and appropriate treatment may be initiated. However, the low sensitivity level should be considered in the differentiation of suspected tuberculosis and some other clinical condition until the culture result is found to be negative and a true picture of the clinical outcome is obtained.
Nonvirion Protein of Novirhabdovirus Suppresses Apoptosis at the Early Stage of Virus Infection
Authors: Ammayappan Arun , Vakharia Vikram N. 
Published: June 2011

ABSTRACT

Viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV) are members of the genus
Novirhabdovirus
within the
Rhabdoviridae
family, which can cause severe hemorrhagic disease in fresh- and saltwater fish worldwide. These viruses carry an additional nonvirion (NV) gene, which codes for the nonstructural NV protein that has been implicated to play a role in viral pathogenesis. To determine the precise biological function of this NV gene and its gene product, we generated NV-deficient and NV knockout recombinant VHSVs, using reverse genetics. Comparisons of the replication kinetics and markers for virus-induced apoptosis indicated that the NV-deficient and NV knockout mutant viruses induce apoptosis earlier in cell culture than the wild-type recombinant VHSV. These results suggest that the NV protein has an antiapoptotic function at the early stage of virus infection. Furthermore, we created a chimeric VHSV, in which the NV gene of VHSV was replaced by the IHNV NV gene, which was capable of suppressing apoptosis in cell culture. These results show that the NV protein of other members of
Novirhabdovirus
can restore the NV protein function. In this study, we also investigated the kinetics of VHSV replication during a single round of viral replication and examined the mechanism of VHSV-induced apoptosis. Our results show that VHSV infection induced caspases 3, 8 and 9 in cell culture.
Polymorphism in Human APOBEC3H Affects a Phenotype Dominant for Subcellular Localization and Antiviral Activity
Authors: Li Melody M. H. , Emerman Michael 
Published: June 2011

ABSTRACT

The APOBEC3 family of cytidine deaminases is part of the innate host defense targeted toward retroviruses and retroelements.
APOBEC3H
is the most distantly related member of the family and carries functional polymorphisms in current human populations. Haplotype II of
APOBEC3H
, which is more commonly found in individuals of African descent, encodes a protein with the highest antiviral activity in cells, whereas the other haplotypes encode proteins with weak or no antiviral activity. Here, we show that the different human
APOBEC3H
haplotypes exhibit differential subcellular localizations, as the haplotype I protein is mostly found in the nucleus and the haplotype II protein is mostly localized to the cytoplasm. The determinant responsible for this phenotype maps to a single amino acid that is also important for APOBEC3H protein stability. Furthermore, we show that the cytoplasmic localization is dominant over nuclear localization, by using fusion proteins of APOBEC3H. Our data support a model in which the APOBEC3H protein encoded by haplotype II is actively retained in the cytoplasm by interacting with specific host factors, whereas the less active protein encoded by haplotype I is allowed to enter the nucleus by a passive mechanism. Together, cytoplasmic localization and its link with protein stability correlate with the ability of APOBEC3H to inhibit HIV replication, providing a mechanistic basis for the differential antiviral activities of different APOBEC3H haplotypes.
Herpes Simplex Virus 1 Glycoprotein B and US3 Collaborate To Inhibit CD1d Antigen Presentation and NKT Cell Function
Authors: Rao Ping , Pham Hong Thanh , Kulkarni Arpita , Yang Yang , Liu Xueqiao , Knipe David M. , Cresswell Peter , Yuan Weiming 
Published: June 2011

ABSTRACT

Herpes simplex viruses (HSVs) are prevalent human pathogens that establish latency in human neuronal cells and efficiently evade the immune system. It has been a major medical challenge to eradicate them and, despite intensive efforts, an effective vaccine is not available. We previously showed that upon infection of antigen-presenting cells, HSV type 1 (HSV-1) rapidly and efficiently downregulates the major histocompatibility complex class I-like antigen-presenting molecule, CD1d, and potently inhibits its recognition by CD1d-restricted natural killer T (NKT) cells. It suppresses CD1d expression primarily by inhibiting its recycling to the cell surface after endocytosis. We identify here the viral glycoprotein B (gB) as the predominant CD1d-interacting protein. gB initiates the interaction with CD1d in the endoplasmic reticulum and stably associates with it throughout CD1d trafficking. However, an additional HSV-1 component, the serine-threonine kinase US3, is required for optimal CD1d downregulation. US3 expression in infected cells leads to gB enrichment in the
trans
-Golgi network (TGN) and enhances the relocalization of both gB and CD1d to this compartment, suggesting that following internalization CD1d is translocated from the endocytic pathway to the TGN by its association with gB. Importantly, both US3 and gB are required for efficient inhibition of CD1d antigen presentation and NKT cell activation. In summary, our results suggest that HSV-1 uses gB and US3 to rapidly inhibit NKT cell function in the initial antiviral response.
Lymphoid aggregates may contribute to the migration and epithelial commitment of bone marrow-derived cells in colonic mucosa
Authors: Valcz Gábor , Krenács Tibor , Sipos Ferenc , Patai Árpád V , Wichmann Barnabás , Leiszter Katalin , Tóth Kinga , Balogh Zsófia , Csizmadia Annamária , Hagymási Krisztina , Masszi Tamás , Molnár Béla , Tulassay Zsolt 
Published: June 2011

AimsColonic inflammation is followed by regeneration supported by bone marrow-derived cells (BMDCs) including multipotent cells. They migrate to the colonic epithelial layer and may transdifferentiate into epithelial-like cells or keep their stem cell characteristics and produce progenies. The aim was to study the role of lymphoid aggregates in the migration and transition of BMDCs in both healthy colons and non-specific colitis (NSC).MethodsSamples of normal colon (n=5) and NSC (n=5) from female patients who were initially transplanted with male bone marrow were studied. After detecting XY chromosomes using fluorescent in situ hybridisation, tissue sections were digitalised, the coverslips were eliminated and the samples were double stained for CD45 and cytokeratin with immunofluorescence. Then CDX2 expression, as a sign of intestinal epithelial commitment of Musashi-1+ stromal BMDCs, was also tested with both immunoperoxidase and parallel immunofluorescence stainings. The slides were digitalised again and analysed simultaneously.ResultsA significant increase in intraepithelial CD45–BMDCs was found in regions adjacent to lymphoid aggregates (median: 1.01) compared with healthy epithelial regions (median: 0.0175) or NSC (median: 0.04) samples. The stromal Musashi-1+ cells were positive for CDX2 as well, as a sign of epithelial differentiation. The CDX2+ cells bearing the Y chromosome proved the epithelial commitment of several stromal BMDCs.ConclusionElevated number of intraepithelial CD45−BMDCs at lymphoid aggregates suggests that BMDCs play a role in epithelial regeneration and that lymphoid aggregates serve as their migration route.
mTOR–RAPTOR and 14-3-3σ immunohistochemical expression in high grade prostatic intraepithelial neoplasia and prostatic adenocarcinomas: a tissue microarray study
Authors: Evren Sevan , Dermen Arthur , Lockwood Gina , Fleshner Neil , Sweet Joan 
Published: June 2011

BackgroundThe mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase which associates with regulatory-associated protein of TOR (RAPTOR), forming the mTORC1 complex, which is necessary for activation of the mTOR pathway. 14-3-3σ belongs to a family of proteins known to regulate the mTOR–RAPTOR interaction and signalling of this cascade. The mTOR pathway is a key regulator of protein synthesis and growth and is up-regulated in many cancers. The correlation of mTOR, RAPTOR and 14-3-3σ in high grade prostatic intraepithelial neoplasia (HGPIN) and prostate cancer has not previously been investigated.AimsTo examine the immunohistochemical expression of phosphorylated mTOR (p-mTOR), RAPTOR and 14-3-3σ in HGPIN and prostatic adenocarcinoma (PCa) using tissue microarrays.Methods and resultsThere were contrasting immunohistochemical patterns of expression for mTOR and 14-3-3σ in HGPIN and PCa. Cochran–Armitage analysis demonstrated decreasing p-mTOR and increasing 14-3-3σ expression, progressing from PIN through GL6 and GL7 to high grade PCa. In cores with coexistent staining for 14-3-3σ and p-mTOR, the expression of each marker was restricted to different geographical areas of an individual core.ConclusionThe inverse correlation of p-mTOR and 14-3-3σ expression supports the role of 14-3-3σ as an inhibitor of p-mTOR activity in the prostate. The extent of 14-3-3σ and mTOR expression in an individual patient with prostate cancer would determine how effective the use of mTOR inhibitors would be as potential therapeutic agents.
Sporadic Burkitt lymphoma in southern China: 12 years' experience in a single institution in Guangzhou
Authors: Ye Ziyin , Xiao Yanhua , Shi Huijuan , Ke Zunfu , Liu Yongdong , Liang Yingjie , Han Anjia 
Published: June 2011

AimTo analyse the clinicopathological features of sporadic Burkitt lymphoma (sBL).MethodsIn a review of 1682 cases of non-Hodgkin lymphoma diagnosed in the First Affiliated Hospital and Zhongshan School of Medicine, from 1998 to 2010, 20 cases (1.2%) of sBL were identified. Histopathological examination, immunohistochemistry and in situ hybridisation were used to analyse the clinicopathological features of these cases.ResultsOf the 20 cases of sBL, 18 patients were male and two were female. The mean age was 18 years (range 2–67 years). Extranodal presentation was more common than nodal presentation (55% vs 15%). Histopathologically, 18 cases (90%) showed monotonous medium-sized tumour cells, and two cases showed cells that were slightly pleomorphic in nuclear size and shape. Immunophenotypically, MUM1 was positive in three of 17 cases (17.6%). EBER expression was shown in five of 17 cases (29.4%), and all EBER-positive sBLs were Bcl-6+/MUM1−.ConclusionsBL is rare and mainly affects male children, with predominantly extranodal presentation. MUM1 expression was found in some sBLs. EBER expression was found in 29.4% of sBLs from southern China, an area with a well-known high incidence of nasopharyngeal carcinoma, which is closely associated with Epstein–Barr virus infection.
Enhanced Metastasis Suppression by Targeting TRAIL Receptor 2 in a Murine Model of Triple-Negative Breast Cancer
Authors: Malin Dmitry , Chen Feng , Schiller Carol , Koblinski Jennifer , Cryns Vincent L. 
Published: June 2011

Abstract
Purpose: Metastatic breast cancer is a deadly disease which requires new therapeutic strategies. Endogenous TNF-related apoptosis-inducing ligand (TRAIL) functions as a metastasis suppressor by activating proapoptotic TRAIL receptors (TRAIL-R1/DR4 and/or TRAIL-R2/DR5) in transformed cells, making it an attractive pathway for antimetastatic therapies. However, it is unclear whether TRAIL-R1 or TRAIL-R2 is a better therapeutic target in metastatic breast cancer.
Experimental Design: Several metastatic, triple (estrogen receptor, progesterone receptor, and HER2)-negative cancer cell lines were treated with human agonistic monoclonal antibodies targeting TRAIL-R1 (mapatumumab) or TRAIL-R2 (lexatumumab). The effects on cell viability, apoptosis, and caspase-8 activation were determined. An orthotopic model of triple-negative breast cancer in which fluorescently labeled breast cancer cells metastasize from the mammary gland to lymph nodes and lung was utilized to evaluate the effects of mapatumumab, lexatumumab, or doxorubicin on primary and metastatic tumor burden in vivo.
Results: Lexatumumab was more effective than mapatumumab in activating caspase-8, inducing apoptosis and inhibiting long-term survival of metastatic cancer cells, which expressed both TRAIL-R1 and TRAIL-R2. Human mammary epithelial cells transformed by oncogenic Ras were more sensitive to lexatumumab than nontransformed cells. Lexatumumab inhibited lymph node and lung metastases more robustly than mapatumumab in an orthotopic model of triple-negative breast cancer; both agents inhibited mammary tumor growth. In addition, lexatumumab was more effective than doxorubicin at suppressing metastases at doses of doxorubicin that were associated with toxicity, even though doxorubicin reduced primary tumor burden more robustly than lexatumumab.
Conclusion: Targeting TRAIL-R2 receptor may be an effective therapeutic strategy for metastatic breast cancer. Clin Cancer Res; 17(15); 5005–15. ©2011 AACR.
Enhanced Antitumor Effects by Chemical Modified IGb3 Analogues
Authors: Zhou Zhixia , Zhang Cai , Xia Chengfeng , Chen Wenlan , Zhu Huawei , Shang Pingping , Ma Fang , Wang Peng George , Zhang Jian , Xu Wenfang , Tian Zhigang 
Published: June 2011

AbstractCertain glycolipid antigens for natural killer T (NKT) cells can direct the overall cytokine balance of the immune response. However, the molecular mechanism of Th1- or Th2-biased cytokine secretion by NKT cells is still unknown. Previously, we synthesized isoglobotrihexosylceramide (iGb3) analogues by introducing a hydroxyl group at C4 on the ceramide portion of iGb3 to produce 4-HO-iGb3 or to further deoxylation on the terminal galactose to produce 4‴-dh-iGb3. Both modified iGb3, especially 4‴-dh-iGb3, stimulated more IFN-γ production by hepatic NKT cells, and thus elicited preferential Th1 responses. Here, we found that 4‴-dh-iGb3–loaded bone marrow–derived dendritic cells (DC) could significantly inhibit growth of subcutaneous melanoma and suppress lung metastasis in C57BL/6 mice compared with unmodified iGb3-loaded DCs. In investigating the mechanisms of this improved activity, we found that 4‴-dh-iGb3 stimulation increased STAT1 signaling by NKT cells, whereas the phosphorylation of Th2 type cytokine–associated transcription factor STAT6 signaling was not affected. Analysis of the structures of iGb3 and 4‴-dh-iGb3 revealed that 4‴-dh-iGb3 provides greater stability and affinity between glycolipid and CD1d or NKT TCR complex than iGb3. Thus, 4‴-dh-iGb3 can improve the antitumor effects of a DC-based vaccine possibly by stabilizing the CD1d/glycolipid/TCR complex and stimulating IFN-γ signaling of NKT cells. Furthermore, chemical modification of iGb3 can elicit Th1-biased responses by NKT cells, and 4‴-dh-iGb3 combined with a DC vaccine may serve as a potent new NKT-based therapy against tumors and infectious diseases. Mol Cancer Ther; 10(8); 1375–84. ©2011 AACR.
The in vitro effect of the new antithrombotic drug candidate ALX-0081 on blood samples of patients undergoing percutaneous coronary intervention
Authors: Loon Janine E. van , Jaegere Peter P. T de , Vliet Huub H. D. M van , Maat Moniek P. M de , de Groot Philip G. , Simoons Maarten L. , Leebeek Frank W. G. 
Published: June 2011

SummaryCompound ALX-0081 is a bivalent humanised Nanobody® that binds the A1-domain of von Willebrand factor (VWF) with high affinity. Consequently, it can block the interaction between VWF and its platelet-receptor- glycoprotein Ib, which leads inevitably to formation of arterial thrombi. It was the objective of this study to assess the in vitro effects of ALX-0081 on platelet adhesion and aggregation in coronary artery disease (CAD) patients to determine the optimal concentration of ALX-0081 and the effect of co-medication. We included nine CAD patients, who were scheduled for elective percutaneous coronary intervention (PCI), and 11 healthy volunteers. At admission all patients received aspirin, clopidogrel and heparin. Blood was drawn 24 hours (h) before and 1 h after start of the PCI procedure and was subsequently spiked with different concentrations of ALX-0081 or buffer. The efficacy of ALX-0081 was assessed by in vitro experiments: flow chamber experiments, ristocetin-induced platelet aggregation (RIPA), and the platelet function analyser (PFA-100TM). VWF levels in CAD patients were significantly higher than in healthy controls. During PCI VWF levels did not rise. In all in vitro experiments, ALX-0081 led to complete inhibition of platelet adhesion and aggregation. However, the required effective concentration was higher in patients than in controls and was related to plasma VWF levels. In conclusion, ALX-0081 is able to completely inhibit in vitro platelet adhesion and aggregation in CAD patients scheduled for elective PCI. The efficacy of ALX-0081 is not influenced by PCI or co-medication. However, due to higher VWF levels in CAD patients a higher effective concentration of ALX-0081 was required than in healthy individuals.