bluuebunny/crossref_metadata_2025_split huggingface dataset:
Naturally processed peptides spanning the HPA-1a polymorphism are efficiently generated and displayed from platelet glycoprotein by HLA-DRB3*0101–positive antigen-presenting cells
Authors: Anani Sarab Gholamreza , Moss Michael , Barker Robert N. , Urbaniak Stanislaw J. 
Published: June 2009

AbstractIn neonatal alloimmune thrombocytopenia, almost all human platelet antigen (HPA)–1b1b mothers who produce anti–HPA-1a antibody through carrying an HPA-1a fetus are human histocompatibility leukocyte antigen (HLA)–DRB3*0101 positive. It is predicted that the HPA-1a Leu33 polymorphism forms part of an HLA-DRB3*0101–restricted T-helper epitope, and acts as an anchor residue for binding this class II molecule. However, it is not known whether any corresponding peptides are naturally processed and presented from platelet glycoprotein. In this study, peptides displayed by a homozygous HLA-DRB3*0101 antigen-presenting cell line were identified after pulsing with recombinant HPA-1a (Leu33 plexin-semaphorin-integrin domain). The peptides were eluted from HLA-DR molecules, fractionated by high performance liquid chromatography, and analyzed by tandem mass spectrometry. A “nested set” of naturally presented HPA-1a–derived peptides, each containing the Trp25-Leu33 core epitope, was identified, with the most abundant member being the 16-mer Met22-Arg37. These peptides may provide the basis for novel treatments to tolerize the corresponding T-helper response in women at risk of neonatal alloimmune thrombocytopenia.
Polymorphism and selection of rpoS in pathogenic Escherichia coli
Authors: Dong Tao , Chiang Sarah M , Joyce Charlie , Yu Rosemary , Schellhorn Herb E 
Published: June 2009

Abstract

Background
Though RpoS is important for survival of pathogenic Escherichia coli in natural environments, polymorphism in the rpoS gene is common. However, the causes of this polymorphism and consequential physiological effects on gene expression in pathogenic strains are not fully understood.

Results
In this study, we found that growth on non-preferred carbon sources can efficiently select for loss of RpoS in seven of ten representative verocytotoxin-producing E. coli (VTEC) strains. Mutants (Suc++) forming large colonies on succinate were isolated at a frequency of 10-8 mutants per cell plated. Strain O157:H7 EDL933 yielded mainly mutants (about 90%) that were impaired in catalase expression, suggesting the loss of RpoS function. As expected, inactivating mutations in rpoS sequence were identified in these mutants. Expression of two pathogenicity-related phenotypes, cell adherence and RDAR (r ed d ry a nd r ough) morphotype, were also attenuated, indicating positive control by RpoS. For the other Suc++ mutants (10%) that were catalase positive, no mutation in rpoS was detected.

Conclusion
The selection for loss of RpoS on poor carbon sources is also operant in most pathogenic strains, and thus is likely responsible for the occurrence of rpoS polymorphisms among E. coli isolates.
An integrative multi-platform analysis for discovering biomarkers of osteosarcoma
Authors: Li Guodong , Zhang Wenjuan , Zeng Huazong , Chen Lei , Wang Wenjing , Liu Jilong , Zhang Zhiyu , Cai Zhengdong 
Published: June 2009

Abstract

Background
SELDI-TOF-MS (Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry) has become an attractive approach for cancer biomarker discovery due to its ability to resolve low mass proteins and high-throughput capability. However, the analytes from mass spectrometry are described only by their mass-to-charge ratio (m/z) values without further identification and annotation. To discover potential biomarkers for early diagnosis of osteosarcoma, we designed an integrative workflow combining data sets from both SELDI-TOF-MS and gene microarray analysis.

Methods
After extracting the information for potential biomarkers from SELDI data and microarray analysis, their associations were further inferred by link-test to identify biomarkers that could likely be used for diagnosis. Immuno-blot analysis was then performed to examine whether the expression of the putative biomarkers were indeed altered in serum from patients with osteosarcoma.

Results
Six differentially expressed protein peaks with strong statistical significances were detected by SELDI-TOF-MS. Four of the proteins were up-regulated and two of them were down-regulated. Microarray analysis showed that, compared with an osteoblastic cell line, the expression of 653 genes was changed more than 2 folds in three osteosarcoma cell lines. While expression of 310 genes was increased, expression of the other 343 genes was decreased. The two sets of biomarkers candidates were combined by the link-test statistics, indicating that 13 genes were potential biomarkers for early diagnosis of osteosarcoma. Among these genes, cytochrome c1 (CYC-1) was selected for further experimental validation.

Conclusion
Link-test on datasets from both SELDI-TOF-MS and microarray high-throughput analysis can accelerate the identification of tumor biomarkers. The result confirmed that CYC-1 may be a promising biomarker for early diagnosis of osteosarcoma.
Dysregulation of heat shock protein 27 expression in oral tongue squamous cell carcinoma
Authors: Wang Anxun , Liu Xiqiang , Sheng Shihu , Ye Hui , Peng Tingsheng , Shi Fei , Crowe David L , Zhou Xiaofeng 
Published: June 2009

Abstract

Background
Recent proteomic studies identified Hsp27 as a highly over-expressed protein in oral squamous cell carcinoma (OSCC). Clinical studies that attempted to evaluate the prognostic values of Hsp27 yielded inconsistent results, which may be due to inclusion of OSCC cases from multiple anatomic sites. In this study, to determine the utility of Hsp27 for prognosis, we focused on oral tongue SCC (OTSCC), one of the most aggressive forms of OSCC.

Methods
Archival clinical samples of 15 normal oral tongue mucosa, 31 dysplastic lesions, 80 primary OTSCC, and 32 lymph node metastases were examined for Hsp27 expression by immunohistochemistry (IHC). Statistical analyses were carried out to assess the prognostic value of Hsp27 expression for patients with this disease.

Results
Dysregulation of Hsp27 expression was observed in dysplastic lesions, primary OTSCC, and lymph node metastases, and appears to be associated with disease progression. Statistical analysis revealed that the reduced Hsp27 expression in primary tumor tissue was associated with poor differentiation. Furthermore, the higher expression of Hsp27 was correlated with better overall survival.

Conclusion
Our study confirmed that the dysregulation of Hsp27 expression is a frequent event during the progression of OTSCC. The expression of Hsp27 appears to be an independent prognostic marker for patients with this disease.
Association of parents' alcohol use and family interaction with the initiation of alcohol use by sixth graders: A preliminary study in Taiwan
Authors: Hung Chao-Chia , Yen Lee-Lan , Wu Wen-Chi 
Published: June 2009

Abstract

Background
The family is the main environment where children are socialized and learn individual behavior. Although previous studies have examined predictors of preadolescent first alcohol use, few studies have analyzed factors associated with alcohol use in children in a country with low alcohol consumption. The aim of this study was to investigate the initiation of alcohol use by sixth graders and determine family factors associated with first alcohol use.

Methods
Data used in this study was collected as part of the Child and Adolescent Behaviors in Long-term Evolution (CABLE) project in 2002 (when study participants were in grade 5 and aged 10–11 years) and 2003 (when study participants were in grade 6 and aged 11–12 years). Data from a total of 1,183 participants was analyzed. Main study variables included children's alcohol use: (1) never user (never user in 2002 and 2003), or (2) first-time user (never user in 2002 but ever user in 2003); parents' alcohol use: (1) both parents ever users, (2) mother ever user and father never user, (3) father ever user and mother never user, (4) both parents never users; parental support; and family conflict. Correlates of first alcohol use were identified using logistic regression.

Results
There were 183 students (15.5%) who became first-time users of alcohol in the sixth grade. Having parents who both used alcohol, less parental support, and more family conflict were significant predictors of sixth graders' first alcohol use. Family interaction and parents' drinking were equally important predictors of preteen's first use of alcohol.

Conclusion
Family factors influence children's initiation of alcohol use. It is important to educate parents about the effects of alcohol on children and to emphasize the importance of prevention.
Viscoelastic properties of bovine articular cartilage attached to subchondral bone at high frequencies
Authors: Fulcher Geoffrey R , Hukins David WL , Shepherd Duncan ET 
Published: June 2009

Abstract

Background
Articular cartilage is a viscoelastic material, but its exact behaviour under the full range of physiological loading frequencies is unknown. The objective of this study was to measure the viscoelastic properties of bovine articular cartilage at loading frequencies of up to 92 Hz.

Methods
Intact tibial plateau cartilage, attached to subchondral bone, was investigated by dynamic mechanical analysis (DMA). A sinusoidally varying compressive force of between 16 N and 36 N, at frequencies from 1 Hz to 92 Hz, was applied to the cartilage surface by a flat indenter. The storage modulus, loss modulus and phase angle (between the applied force and the deformation induced) were determined.

Results
The storage modulus, E', increased with increasing frequency, but at higher frequencies it tended towards a constant value. Its dependence on frequency, f, could be represented by, E' = Alog

e
(f) + B where A = 2.5 ± 0.6 MPa and B = 50.1 ± 12.5 MPa (mean ± standard error). The values of the loss modulus (4.8 ± 1.0 MPa mean ± standard deviation) were much less than the values of storage modulus and showed no dependence on frequency. The phase angle was found to be non-zero for all frequencies tested (4.9 ± 0.6°).

Conclusion
Articular cartilage is viscoelastic throughout the full range of frequencies investigated. The behaviour has implications for mechanical damage to articular cartilage and the onset of osteoarthritis. Storage modulus increases with frequency, until the plateau region is reached, and has a higher value than loss modulus. Furthermore, loss modulus does not increase with loading frequency. This means that more energy is stored by the tissue than is dissipated and that this effect is greater at higher frequencies. The main mechanism for this excess energy to be dissipated is by the formation of cracks.
Histopathological and ultrastructural analysis of vestibular endorgans in Meniere's disease reveals basement membrane pathology
Authors: McCall Andrew A , Ishiyama Gail P , Lopez Ivan A , Bhuta Sunita , Vetter Steven , Ishiyama Akira 
Published: June 2009

Abstract

Background
We report the systematic analysis of the ultrastructural and cytological histopathology of vestibular endorgans acquired from labyrinthectomy in Meniere's disease.

Methods
17 subjects with intractable Meniere's disease and ipsilateral non-serviceable hearing presenting to the Neurotology Clinic from 1997 to 2006 who chose ablative labyrinthectomy (average age = 62 years; range 29–83 years) participated. The average duration of symptoms prior to surgery was 7 years (range 1–20 years).

Results
Nearly all vestibular endorgans demonstrated varying degrees of degeneration. A monolayer of epithelial cells occurred significantly more frequently in the horizontal cristae (12/13 = 92%) (p < 0.001), the superior cristae (5/5 = 100%) (p < 0.005), the posterior cristae (2/2) compared with the utricular maculae (4/17 = 24%). Basement membrane (BM) thickening was more common in all of the cristae ampullares (18 out of 20) than the utricular maculae. Although only four saccular maculae were obtained, 3 out of 4 exhibited BM thickening and monolayer degeneration. Monolayer degeneration was highly significantly correlated with the presence of BM thickening (p < 0.001). Other degenerative changes noted equally among the five vestibular endorgans which were not significantly correlated with BM thickening or monolayer degeneration included hair cell vacuolization and stereocilia loss, microvesicles in the supporting cells, and increased stromal intercellular spaces. Transmission electron microscopy demonstrated disorganization of the BM collagen-like fibrils, and normal ultrastructural morphology of the nerve terminals and myelinated fibers. Stromal fibroblasts and endothelial cells of stromal blood vessels demonstrated vacuolization, and stromal perivascular BMs were also thickened.

Conclusion
Systematic histopathological analysis of the vestibular endorgans from Meniere's disease demonstrated neuroepithelial degeneration which was highly correlated with an associated BM thickening. Other findings included hair cell and supporting cell microvessicles, increased intercellular clear spaces in the stroma, and endothelial cell vacuolization and stromal perivascular BM thickening.
Gene and microRNA analysis of neutrophils from patients with polycythemia vera and essential thrombocytosis: down-regulation of micro RNA-1 and -133a
Authors: Slezak Stefanie , Jin Ping , Caruccio Lorraine , Ren Jiaqiang , Bennett Michael , Zia Nausheen , Adams Sharon , Wang Ena , Ascensao Joao , Schechter Geraldine , Stroncek David 
Published: June 2009

Abstract

Background
Since the V617F mutation in JAK2 may not be the initiating event in myeloprofilerative disorders (MPDs) we compared molecular changes in neutrophils from patients with polycythemia vera (PV) and essential thrombocythosis (ET), to neutrophils stimulated by G-CSF administration and to normal unstimulated neutrophils

Methods
A gene expression oligonucleotide microarray with more than 35,000 probes and a microRNA (miR) expression array with 827 probes were used to assess neutrophils from 6 MPD patients; 4 with PV and 2 with ET, 5 healthy subjects and 6 healthy subjects given G-CSF. In addition, neutrophil antigen expression was analyzed by flow cytometry and 64 serum protein levels were analyzed by ELISA.

Results
Gene expression profiles of neutrophils from the MPD patients were similar but distinct from those of healthy subjects, either unstimulated or G-CSF-mobilized. The differentially expressed genes in MPD neutrophils were more likely to be in pathways involved with inflammation while those of G-CSF-mobilized neutrophils were more likely to belong to metabolic pathways. In MPD neutrophils the expression of CCR1 was increased and that of several NF-κB pathway genes were decreased. MicroRNA miR-133a and miR-1 in MPD neutrophils were down-regulated the most. Levels of 11 serum proteins were increased in MPD patients including MMP-10, MMP-13, VCAM, P-selectin, PDGF-BB and a CCR1 ligand, MIP-1α.

Conclusion
These studies showed differential expression of genes particularly involved in inflammatory pathways including the NF-κB pathway and down-regulation of miR-133a and miR-1. These two microRNAs have been previous associated with certain cancers as well as the regulation of hyperthrophy of cardiac and skeletal muscle cells. These changes may contribute to the clinical manifestations of the MPDs.
Isolation and culture of fibroblasts from endoscopic duodenal biopsies of celiac patients
Authors: Roncoroni Leda , Elli Luca , Doneda Luisa , Piodi Luca , Ciulla Michele M , Paliotti Roberta , Bardella Maria Teresa 
Published: June 2009

Abstract

Background
Fibroblasts are actually considered pivotal in inflammation and tissue remodelling process and for these reasons they are involved in the pathogenesis of autoimmune disorders such as celiac disease. Investigations to define the role of fibroblasts in celiac diseases are obstructed by the absence of specific models. Our objective is to isolate and culture primary fibroblasts from endoscopic duodenal biopsies of celiac and non-celiac subjects, to analyze their growth patterns and the morphometric characteristics.

Methods
60 duodenal bioptic specimens from 20 celiac patients and 114 from 38 non-celiac subjects were mechanically chopped and enzymatically digested in order to obtain primary cell cultures. Growth patterns, karyotype (Q-banding analysis), expression of typing proteins (fibroblast surface protein and cytokeratin 20) and morphometric parameters (diameters and their ratio, perimeter, area and perimeter/area ratio at computerised image analysis) were investigated on cultured cells.

Results
Primary cells were successfully cultured in 78% of the collected duodenal biopsies. Cultured cells, expressing the fibroblast surface protein, were negative for cytokeratine 20 and maintained a normal kariotype. Cells grew slowly without differences between the celiac and the non celiac group. Morphometric analysis of celiac fibroblasts revealed significantly increased dimensions, with a preserved diameters ratio, and a reduced perimeter/area ratio.

Conclusion
For the first time this study demonstrates the feasibility of culturing primary fibroblast cell from endoscopic duodenal biopsies in celiac and non-celiac subjects, opening a new window of opportunity in studies intended to establish the role of fibroblasts as a possible partaker in the pathogenesis of the celiac mucosal damage.
Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA
Authors: Friew Yeshitila N , Boyko Vitaly , Hu Wei-Shau , Pathak Vinay K 
Published: June 2009

Abstract

Background
Host restriction factor APOBEC3G (A3G) blocks human immunodeficiency virus type 1 (HIV-1) replication by G-to-A hypermutation, and by inhibiting DNA synthesis and provirus formation. Previous reports have suggested that A3G is a dimer and its virion incorporation is mediated through interactions with viral or nonviral RNAs and/or HIV-1 Gag. We have now employed a bimolecular fluorescence complementation assay (BiFC) to analyze the intracellular A3G-A3G, A3G-RNA, and A3G-Gag interactions in living cells by reconstitution of yellow fluorescent protein (YFP) from its N- or C-terminal fragments.

Results
The results obtained with catalytic domain 1 and 2 (CD1 and CD2) mutants indicate that A3G-A3G and A3G-Gag multimerization is dependent on an intact CD1 domain, which is required for RNA binding. A mutant HIV-1 Gag that exhibits reduced RNA binding also failed to reconstitute BiFC with wild-type A3G, indicating a requirement for both HIV-1 Gag and A3G to bind to RNA for their multimerization. Addition of a non-specific RNA binding peptide (P22) to the N-terminus of a CD1 mutant of A3G restored BiFC and virion incorporation, but failed to inhibit viral replication, indicating that the mutations in CD1 resulted in additional defects that interfere with A3G's antiviral activity.

Conclusion
These studies establish a robust BiFC assay for analysis of intracellular interactions of A3G with other macromolecules. The results indicate that in vivo A3G is a monomer that forms multimers upon binding to RNA. In addition, we observed weak interactions between wild-type A3G molecules and RNA binding-defective mutants of A3G, which could explain previously described protein-protein interactions between purified A3G molecules.
Development of TaqMan® MGB fluorescent real-time PCR assay for the detection of anatid herpesvirus 1
Authors: Guo Yufei , Cheng Anchun , Wang Mingshu , Shen Chanjuan , Jia Renyong , Chen Shun , Zhang Na 
Published: June 2009

Abstract

Background
Anatid herpesvirus 1 (AHV-1) is an alphaherpesvirus associated with latent infection and mortality in ducks and geese and is currently affecting the world-wide waterfowl production severely. Here we describe a fluorescent quantitative real-time PCR (FQ-PCR) method developed for fast measurement of AHV-1 DNA based on TaqMan MGB technology.

Results
The detection limit of the assay was 1 × 101 standard DNA copies, with a sensitivity of 2 logs higher than that of the conventional gel-based PCR assay targeting the same gene. The real-time PCR was reproducible, as shown by satisfactory low intra-assay and inter-assay coefficients of variation.

Conclusion
The high sensitivity, specificity, simplicity and reproducibility of the AHV-1 fluorogenic PCR assay, combined with its wide dynamic range and high throughput, make this method suitable for a broad spectrum of AHV-1 etiologically related application.
Reactive oxygen species regulate urokinase plasminogen activator expression and cell invasion via mitogen-activated protein kinase pathways after treatment with hepatocyte growth factor in stomach cancer cells
Authors: Lee Kyung Hee , Kim Sang Woon , Kim Jae-Ryong 
Published: June 2009

Abstract

Background
Reactive oxygen species (ROS) are closely associated with the intracellular signal cascade, thus strongly implicating involvement in tumor progression. However, the mechanism by which ROS are generated and how ROS target downstream molecules to trigger tumor metastasis is unclear. In this study, we investigated the underlying signal pathways in ROS-induced urokinase plasminogen activator (uPA) expression in the human gastric cancer cells, NUGC-3 and MKN-28.

Methods and Results
Intracellular ROS, as determined using the fluorescent probe, 2'-7' dichlorofluorescein diacetate, decreased after treatment with hepatocyte growth factor (HGF). We confirmed that Rac-1 regulated ROS production after activation of the AKT pathway with HGF. Exogenously added H2O2 promoted the expression of HGF, but not in a dose-dependent manner and also showed negative expression of HGF after co-treatment with H2O2 and HGF. Treatment with NAC, an intracellular free radical scavenger, decreased the enhancement of uPA production and tumor invasion in both cells. We clarified the downstream pathways regulated by ROS after treatment with H2O2, which showed negative control between FRK and p38 kinase activities for uPA regulation.

Conclusion
HGF regulates Rac-1-induced ROS production through the Akt pathway and ROS regulates uPA production and invasion via MAP kinase, which provides novel insight into the mechanisms underlying the progression of gastric cancer.