bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus
Authors: Gomez Pol , Hackett Tillie L , Moore Margo M , Knight Darryl A , Tebbutt Scott J 
Published: June 2010

AbstractBackgroundAspergillus fumigatus (A. fumigatus)is a ubiquitous fungus which reproduces asexually by releasing abundant airborne conidia (spores), which are easily respirable. In allergic and immunocompromised individualsA. fumigatuscan cause a wide spectrum of diseases, including allergic bronchopulmonary aspergillosis, aspergilloma and invasive aspergillosis. Previous studies have demonstrated thatA. fumigatusconidia are internalized by macrophages and lung epithelial cells; however the exact transcriptional responses of airway epithelial cells to conidia are currently unknown. Thus, the aim of this study was to determine the transcriptomic response of the human bronchial epithelial cell line (16HBE14o-) following interaction withA. fumigatusconidia. We used fluorescence-activated cell sorting (FACS) to separate 16HBE14o- cells having bound and/or internalizedA. fumigatusconidia expressing green fluorescent protein from cells without spores. Total RNA was then isolated and the transcriptome of 16HBE14o- cells was evaluated using Agilent Whole Human Genome microarrays.ResultsImmunofluorescent staining and nystatin protection assays demonstrated that 16HBE14o- cells internalized 30-50% of bound conidia within six hrs of co-incubation. After FAC-sorting of the same cell culture to separate cells associated with conidia from those without conidia, genome-wide analysis revealed a set of 889 genes showing differential expression in cells with conidia. Specifically, these 16HBE14o- cells had increased levels of transcripts from genes associated with repair and inflammatory processes (e.g., matrix metalloproteinases, chemokines, and glutathione S-transferase). In addition, the differentially expressed genes were significantly enriched for Gene Ontology terms including: chromatin assembly, G-protein-coupled receptor binding, chemokine activity, and glutathione metabolic process (up-regulated); cell cycle phase, mitosis, and intracellular organelle (down-regulated).ConclusionsWe demonstrate a methodology using FACs for analyzing the transcriptome of infected and uninfected cells from the same cell population that will provide a framework for future characterization of the specific interactions between pathogens such asA. fumigatuswith human cells derived from individuals with or without underlying disease susceptibility.
In vitro and in vivo comparison of the anti-staphylococcal efficacy of generic products and the innovator of oxacillin
Authors: Rodriguez Carlos A , Agudelo Maria , Zuluaga Andres F , Vesga Omar 
Published: June 2010

AbstractBackgroundOxacillin continues to be an important agent in the treatment of staphylococcal infections; many generic products are available and the only requirement for their approval is demonstration of pharmaceutical equivalence. We tested the assumption that pharmaceutical equivalence predicts therapeutic equivalence by comparing 11 generics with the innovator product in terms of concentration of the active pharmaceutical ingredient (API), minimal inhibitory (MIC) and bactericidal concentrations (MBC), and antibacterial efficacy in the neutropenic mouse thigh infection model.MethodsThe API in each product was measured by a validated microbiological assay and compared by slope (potency) and intercept (concentration) analysis of linear regressions. MIC and MBC were determined by broth microdilution according to Clinical and Laboratory Standard Institute (CLSI) guidelines. For in vivo efficacy, neutropenic ICR mice were inoculated with a clinical strain ofStaphylococcus aureus. The animals had 4.14 ± 0.18 log10CFU/thigh when treatment started. Groups of 10 mice per product received a total dose ranging from 2.93 to 750 mg/kg per day administered q1h. Sigmoidal dose-response curves were generated by nonlinear regression fitted to Hill equation to compute maximum effect (Emax), slope (N), and the effective dose reaching 50% of the Emax(ED50). Based on these results, bacteriostatic dose (BD) and dose needed to kill the first log of bacteria (1LKD) were also determined.Results4 generic products failed pharmaceutical equivalence due to significant differences in potency; however, all products were undistinguishable from the innovator in terms of MIC and MBC. Independently of their status with respect to pharmaceutical equivalence or in vitro activity, all generics failed therapeutic equivalence in vivo, displaying significantly lower Emaxand requiring greater BD and 1LKD, or fitting to a non-sigmoidal model.ConclusionsPharmaceutical or in vitro equivalence did not entail therapeutic equivalence for oxacillin generic products, indicating that criteria for approval deserve review to include evaluation of in vivo efficacy.
Depression diagnoses following the identification of bipolar disorder: costly incongruent diagnoses
Authors: Stensland Michael D , Schultz Jennifer F , Frytak Jennifer R 
Published: June 2010

Abstract

Background
Previous research has documented that the symptoms of bipolar disorder are often mistaken for unipolar depression prior to a patient's first bipolar diagnosis. The assumption has been that once a patient receives a bipolar diagnosis they will no longer be given a misdiagnosis of depression. The objectives of this study were 1) to assess the rate of subsequent unipolar depression diagnosis in individuals with a history of bipolar disorder and 2) to assess the increased cost associated with this potential misdiagnosis.

Methods
This study utilized a retrospective cohort design using administrative claims data from 2002 and 2003. Patient inclusion criteria for the study were 1) at least 2 bipolar diagnoses in 2002, 2) continuous enrollment during 2002 and 2003, 3) a pharmacy benefit, and 4) age 18 to 64. Patients with at least 2 unipolar depression diagnoses in 2003 were categorized as having an incongruent diagnosis of unipolar depression. We used propensity scoring to control for selection bias. Utilization was evaluated using negative binomial models. We evaluated cost differences between patient cohorts using generalized linear models.

Results
Of the 7981 patients who met all inclusion criteria for the analysis, 17.5% (1400) had an incongruent depression diagnosis (IDD). After controlling for background differences, individuals who received an IDD had higher rates of inpatient and outpatient psychiatric utilization and cost, on average, an additional $1641 per year compared to individuals without an IDD.

Conclusions
A strikingly high proportion of bipolar patients are given the differential diagnosis of unipolar depression after being identified as having bipolar disorder. Individuals with an IDD had increased acute psychiatric care services, suggesting higher levels of relapses, and were at risk for inappropriate treatment, as antidepressant therapy without a concomitant mood-stabilizing medication is contraindicated in bipolar disorder. Further prospective research is needed to validate the findings from this retrospective administrative claims-based analysis.
Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration
Authors: Nelson Rex T , Avraham Shulamit , Shoemaker Randy C , May Gregory D , Ware Doreen , Gessler Damian DG 
Published: June 2010

Abstract

Background
Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services.

Methods
We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info.

Results
A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST).

Conclusions
The need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high priority data from local, independent, idiosyncratic data schemas to common shared concepts as implemented in web-accessible ontologies. These mappings are then amenable for use in semantic web services. Our implementation of approximately two dozen services means that biological data at three large information resources (Gramene, SoyBase, and LIS) is available for programmatic access, semantic searching, and enhanced interaction between the separate missions of these resources.
Anterior gradient-2 plays a critical role in breast cancer cell growth and survival by modulating cyclin D1, estrogen receptor-α and survivin
Authors: Vanderlaag Kathryn E , Hudak Susan , Bald Laura , Fayadat-Dilman Laurence , Sathe Manjiri , Grein Jeff , Janatpour Mary J 
Published: June 2010

Abstract
Introduction
Anterior-gradient 2 (AGR2) is an estrogen-responsive secreted protein. Its upregulation has been well documented in a number of cancers, particularly breast cancer, for which mixed data exist on the prognostic implications of AGR2 expression. Although emerging evidence indicates that AGR2 is associated with poor prognosis, its function and impact on cancer-relevant pathways have not been elucidated in breast cancer.

Methods
To investigate the biologic role of AGR2 in breast cancer, AGR2 was transiently knocked down, by using siRNA, in T47 D and ZR-75-1 (estrogen receptor-α (ER)-positive) and MDA-MB-231 and SK-BR-3 (ER-negative) human breast cancer cell lines. The impact of silencing AGR2 was evaluated in both anchorage-dependent and anchorage-independent growth (soft agar, spheroid) assays. Cell-cycle profiles in ER-positive cell lines were determined with BrdU incorporation, and cell death was measured with Annexin V, JC-1, and F7-26 staining. After transiently silencing AGR2 or stimulating with recombinant AGR2, modulation of key regulators of growth and survival pathways was assessed with Western blot. Combination studies of AGR2 knockdown with the antiestrogens tamoxifen and fulvestrant were carried out and assessed at the level of anchorage-dependent growth inhibition and target modulation (cyclin D1, ER).

Results
AGR2 knockdown inhibited growth in anchorage-dependent and anchorage-independent assays, with a more-pronounced effect in ER-positive cell lines. Cyclin D1 levels and BrdU incorporation were reduced with AGR2 knockdown. Conversely, cyclin D1 was induced with recombinant AGR2. AGR2 knockdown induced cell death in ZR-75-1 and T47 D cells, and also downregulated survivin and c-Myc. Evidence of AGR2-ER crosstalk was demonstrated by a reduction of ER at the protein level after transiently silencing AGR2. AGR2 knockdown in combination with fulvestrant or tamoxifen did not preclude the efficacy of the antiestrogens, but enhanced it. In addition, p-Src, implicated in tamoxifen resistance, was downregulated with AGR2 knockdown.

Conclusions
Transiently silencing AGR2 in ER-positive breast cancer cell lines inhibited cell growth and cell-cycle progression and induced cell death. Breast cancer drivers (ER and cyclin D1) as well as cancer-signaling nodes (pSrc, c-Myc, and survivin) were demonstrated to be downstream of AGR2. Collectively, the data presented support the utility of anti-AGR2 therapy in ER-positive breast cancers because of its impact on cancer-relevant pathways.
3D Digital Imaging Correlation: Applications to Tire Testing
Authors: Moser Russ A. , Sube H. James , Turner John L. , Zakelj Paul 
Published: June 2010

Abstract
Three-dimensional digital imaging correlation (DIC) techniques are a viable method for measuring surface displacements and strains on tires. DIC provides the capability to measure the full-field noncontact tire surface deformation and strain state, which supports multiple objectives: validation of tire models based on finite element (FE) predictions, setting targets for improving FE predictions and providing insight into the tire deformation state under static and dynamic conditions. A method for verifying the accuracy of the DIC measurement process is presented whereby a thin, rectangular test sample of rubber material is subjected to a combination of strains and rigid body motions of known amounts. Once the measurement technique is proven accurate with a simple specimen, the focus shifts to the objectives explained above. Tire surface strains will be discussed for purposes of validating model predictions of sidewall and belt edge strains. Several types of specimen geometries will be reviewed and their effect on material properties will be presented. Also, the DIC technique can provide insight into complex physical problems that may otherwise be very difficult to measure. Some examples presented here include tire sidewall standing waves at high speeds and strains near tread lugs of agricultural tires. The DIC measurement method is an accurate, noncontacting full field technique for measuring in-plane surface displacements and strains of the magnitudes encountered in tire analysis. This technique serves many functions and has become a valuable tool for both tire testing and development.
Aspiration Technique Improves Reliability of Endoscopically Directed Middle Meatal Cultures in Pediatric Rhinosinusitis
Authors: Hsin Chung-Han , Chen Tsai-Hsin , Su Mao-Chang , Jiang Rong-San , Liu Chia-Ming 
Published: June 2010

Background Most studies demonstrated that the results of endoscopically directed middle meatal cultures (EDMMC) compare favorable with those of maxillary sinus taps in adults rhinosinusitis. Studies comparing results of EDMMC and antral puncture cultures in pediatric rhinosinusitis, however, revealed a decreased correlation. Sampling by suction aspiration was considered likely to improve the reliability of culture. Objective The aim of this study was to compare the microbiology results obtained by EDMMC using swabs or suction aspiration with the results of maxillary sinus taps in pediatric rhinosinusitis. Methods Thirty-one children with chronic rhinosinusitis were enrolled. Patients enrolled in 2007 (group A), underwent EDMMC using a swab, whereas those enrolled in 2008 (group B) underwent EDMMC using suction aspiration. Results obtained by EDMMC were compared with those of maxillary sinus taps. Results In group A, 29 paired cultures were obtained from 15 patients. In group B, 30 paired cultures were obtained from 16 patients. In group A, EDMMC by swab demonstrated a sensitivity of 52%, a specificity of 100%, and a correlation of 66%. In group B, EDMMC by suction aspiration provided a sensitivity of 86%, a specificity of 100%, and a correlation of 87%. The difference in density of growth between EDMMC with swab and maxillary sinus tap was not significant, but the difference between EDMMC with aspiration and maxillary sinus tap was significant. Conclusion Aspiration technique can significantly enhance the reliability of endoscopy cultures in children with rhinosinusitis, probably by increasing the amount of specimen obtained.
Evaluation of Inverted Papilloma and Squamous Cell Carcinoma by Nasal Contact Endoscopy
Authors: Prado Flavio A.P. , Weber Raimar , Romano Fabrizio R. , Voegels Richard L. 
Published: June 2010

Background Contact endoscopy (CE) was initially described as a method used in the analysis of uterine and vocal folds histology. The first nasal cavity CE studies achieved promising results regarding its use for the differentiation between benign and malignant lesions, considering that biopsy might cause some complications, especially bleeding. This study described and compared the findings of CE on inverted papilloma and nasosinusal squamous cell carcinoma (SCC) and tested the effectiveness of this exam as a noninvasive method for in vivo differentiation between these tumors. Methods The patients included in this study were divided into group A, patients diagnosed with inverted papilloma, and group B, patients diagnosed with SCC. CE results were compared among themselves. CE images were presented to examiners not experienced with the method. Results Twenty-two patients were examined, 13 in group A and 9 in group B. The main relevant differences in CE findings between those two groups were corkscrew vessels, presence of mitoses, keratinization and nuclear pleomorphism in carcinoma, and vacuolated cells in papilloma. The examiners were capable of defining the diagnosis of these nasal tumors only based on CE images. Conclusion CE may be a useful noninvasive exam to be used in the in vivo diagnosis of inverted papilloma and nasosinusal SCC, which may enable better preoperative planning.
Role of Adenylate Kinase Type 7 Expression on Cilia Motility: Possible Link in Primary Ciliary Dyskinesia
Authors: Milara Javier , Armengot Miguel , Mata Manuel , Morcillo Esteban J. , Cortijo Julio 
Published: June 2010

Background Adenylate kinase 7 (AK7) mediates the reaction 2ADP ↔ ATP + AMP, providing energy for the beating of cilia. A study recently showed that AK7 expression may be correlated with the primary ciliary dyskinesia (PCD) phenotype in mice. In this study, we characterized AK7 expression in vitro in an air–liquid interface (ALI) model and in middle nasal turbinate biopsy specimens from a cohort of patients with PCD to elucidate whether AK7 expression is correlated with ciliary malfunction. Methods AK7 expression was measured by real-time reverse-transcription polymerase chain reaction and Western blotting. In vitro differentiated nasal human epithelial cell siRNA experiments were performed to investigate the effect of AK7 expression on ciliary beat frequency (CBF). Ciliary motility and ultrastructure were evaluated in a cohort of 29 patients with PCD (PCD, n = 17; Kartagener's syndrome, n = 12) and 26 healthy control donors. Results AK7 expression was mainly located on the apical surface of differentiated nasal ALI cells, and targeted suppression of the AK7 gene decreased CBF by 41%. AK7 expression was diminished significantly in patients with PCD (0.54 ± 0.1-fold; p < 0.05) compared with healthy controls (1.1 ± 0.08-fold). Furthermore, AK7 expression was correlated with CBF in patients with PCD (r = 0.5; p = 0.009). Conclusion AK7 expression was correlated with CBF in vitro and in nasal biopsy specimens from patients with PCD, which may have contributed to the ciliary malfunction observed in our patients with PCD.
Expression of a Disintegrin and Metalloproteinase 33 Protein in Nasal Polyposis: An Immunohistochemical Study
Authors: Erbek Selim S. , Erinanc Hilal , Erbek Seyra , Topal Ozgul , Kiyici Halil 
Published: June 2010

Background A disintegrin and metalloproteinase (ADAM)-33 is a member of matrix metalloproteinases. This protein takes a role in angiogenesis and airway remodeling in asthma. Because histopathological findings of airway remodeling in asthma and nasal polyposis (NP) are similar, the aim of this study was to evaluate the ADAM-33 expression in NP. Methods Immunohistochemical staining of specimens of 47 patients with NP and 8 patients with concha bullosa was performed to detect the expression of ADAM-33. Paraffin blocks were used to identify the expression of ADAM-33 polyclonal antibodies. Immunostaining of epithelial cells, stroma, mesenchymal cells of vessels, and inflammatory cells were analyzed by using light microscopy. Results Immunopositivity scores in epithelial cells in NP (median, 2; range, 1–3) were significantly higher than those of controls (median, 1.5; range, 1–2; p < 0.001). ADAM–33 staining was increased in the mesenchymal cells of vessels of nasal polyps (median, 2; range, 1–3) compared with control tissues (median, 1.5; range, 1–2; p = 0.006). Although the staining scores of fibroblasts in nasal polyp specimens were also high (median, 3; range 1–3), there was no statistical significance when compared with controls (median 2; range, 1–3; p = 0.228). ADAM–33 immunostaining was not related with the presence of allergies, asthma, and aspirin intolerance (p > 0.05). Moreover, no relationship was found between increased expression of ADAM–33 and the stages of polyp or computerized tomography scores (p > 0.05). Conclusion This study suggests that the increased expression of ADAM-33 protein may have a role in the pathogenesis of NP.
Unfolding the landscape drawing method of Rakuchū Rakugai Zu screen paintings in a GIS environment
Authors: Tsukamoto Akihiro 
Published: June 2010

In this paper, I propose a new methodology for analysing landscape drawing methods using a GIS. The subject of my analysis is the genre of Japanese screen paintings known as rakuchū rakugai zu, created between the 16th and 18th centuries. Rakuchū rakugai zu provide bird's-eye views of the then-capital city of Kyoto, including buildings, natural features, and human activities. The methodology introduced here uses GIS spatial analysis functions to scan the painting surface onto a survey coordinate grid based on the relative positions of landmarks in the painting. The analytic sequence is as follows: (1) derive coordinate values for landmarks both on the painting and on a survey coordinate grid; (2) generate a link table from these two point-data sets; (3) use the projective transformation and rubber sheeting techniques to project the painting surface onto the survey coordinate grid; and (4) project the areas of the rubber sheet-derived polygons onto the painting. This process gives visual representation to differences between real space and the depicted space. Results show that rakuchū rakugai zu painted in the seventeenth century and later distorted real space more than those painted in the sixteenth century, indicating a decrease in adherence to conventional perspective-based painting.