bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifactor dimensionality reduction analysis of MTHFR, PAI-1, ACE, PON1, and eNOS gene polymorphisms in patients with early onset coronary artery disease
Authors: Agirbasli M , Guney AI , Ozturhan HS , Agirbasli D , Ulucan K , Sevinc D , Kirac D , Ryckman KK , Williams SM 
Published: February 2011

Background: Association studies in the Turkish population have investigated the single locus effects of different gene polymorphisms on coronary artery disease (CAD). CAD is a complex polygenic disease that involves complex interactions among multiple genetic and environmental conditions. Design: We evaluated associations of five candidate genetic polymorphisms (methylene tetrahydrofolate reductase C677T, plasminogen activator inhibitor 4G/5G, endothelial nitric oxide synthase (eNOS) 3–27 base pair repeat, insertion, or deletion of a 287 bp Alu repeat sequence polymorhism of angiotensin I converting enzyme, and paraoxonase Gln192Arg PON1 polymorphisms) with the presence and extent of early onset CAD. Methods: DNA was isolated and amplified from 90 consecutive patients with angiographically proven early onset CAD (ages 41 ± 5 for men, 49 ± 7 for women) and also from 90 control subjects with no significant coronary obstruction angiographically (ages 42 ± 5 for men, 48 ± 6 for women). Multifactor dimensionality reduction (MDR) analysis was performed to identify a model of CAD based on both genetic and conventional risk factors. Results: MDR analysis detected a significant model with four genes (prediction success ∼ 61%, p = 0.03). When the total number of the conventional risk factors is analysed with the candidate polymorphisms, a different model is identified that includes three of the four genes from the above model and achieves a similar prediction of CAD as the gene only model. Conclusion: These data indicate that gene–gene and gene–environmental risk interactions form significant models in predicting early onset CAD.
Nasal nitric oxide and nitric oxide synthase expression in primary ciliary dyskinesia
Authors: Pifferi M. , Bush A. , Maggi F. , Michelucci A. , Ricci V. , Conidi M.E. , Cangiotti A.M. , Bodini A. , Simi P. , Macchia P. , Boner A.L. 
Published: February 2011

No study has evaluated the correlation between different expression of nitric oxide synthase (NOS) isoforms in nasal epithelial cells and nasal NO (nNO) level in primary ciliary dyskinesia (PCD).Gene expression of endothelial (NOS3) and inducible NOS (NOS2) and their correlation with nNO level, ciliary function and morphology were studied in patients with PCD or secondary ciliary dyskinesia (SCD). NOS3 gene polymorphisms were studied in blood leukocytes.A total of 212 subjects were studied (48 with PCD, 161 with SCD and three normal subjects). nNO level correlated with mean ciliary beat frequency (p = 0.044; r = 0.174). The lower the nNO level the higher was the percentage of immotile cilia (p<0.001; r = -0.375). A significant positive correlation between NOS2 gene expression and nNO levels was demonstrated in all children (p = 0.001; r = 0.428), and this correlation was confirmed in patients with PCD (p = 0.019; r = 0.484). NOS2 gene expression was lower in PCD than in SCD (p = 0.04). The NOS3 isoform correlated with missing central microtubules (p = 0.048; r = 0.447). nNO levels were higher in PCD subjects with the NOS3 thymidine 894 mutation, and this was associated with a higher ciliary beat frequency (p = 0.045).These results demonstrate a relationship between nNO level, NOS mRNA expression and ciliary beat frequency.
All-trans retinoic acid results in irregular repair of septa and fails to inhibit proinflammatory macrophages
Authors: Seifart C. , Muyal J.P. , Plagens A. , Yildirim A.Ö. , Kohse K. , Grau V. , Sandu S. , Reinke C. , Tschernig T. , Vogelmeier C. , Fehrenbach H. 
Published: February 2011

All-trans retinoic acid (ATRA) is controversially discussed in emphysema therapy. We re-evaluated ATRA in the elastase model and hypothesised that beneficial effects should be reflected by increased alveolar surface area, elastin expression and downregulation of inflammatory mediators and matrix metalloproteinases (MMPs).Emphysema was induced by porcine pancreatic elastaseversussaline in Sprague–Dawley rats. On days 26–37, rats received daily intraperitoneal injections with ATRA (500 μg·kg−1body weight)versusolive oil. Lungs were removed at day 38. Rat alveolar epithelial L2 cells were incubated with/without elastase followed by ATRA- or vehicle-treatment, respectively.ATRA only partially ameliorated structural defects. Alveolar walls exhibited irregular architecture: increased arithmetic mean thickness, reduction in surface coverage by alveolar epithelial cells type II. ATRA only partially restored reduced soluble elastin. It tended to increase the ratio of ED1+:ED2+macrophages. Bronchoalveolar lavage (BAL) cells exhibited a proinflammatory state and high expression of interleukin-1β, cytokine-induced neutrophil chemoattractant-1, tumour necrosis factor-α, nuclear factor-κB, MMP-2, MMP-9, MMP-12, tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 in emphysema, with ATRA exerting only few effects. MMP-7 was highly induced by ATRA in healthy but not in emphysematous lungs. ATRA reduced both MMP-2 and TIMP-1 activity in BAL fluid of emphysematous lungs.ATRA-therapy may bear the risk of unwanted side-effects on alveolar septal architecture in emphysematous lungs.
Effects of EpCAM overexpression on human breast cancer cell lines
Authors: Gostner Johanna M , Fong Dominic , Wrulich Oliver A , Lehne Florian , Zitt Marion , Hermann Martin , Krobitsch Sylvia , Martowicz Agnieszka , Gastl Guenther , Spizzo Gilbert 
Published: February 2011

Abstract

Background
Recently, EpCAM has attracted major interest as a target for antibody- and vaccine-based cancer immunotherapies. In breast cancer, the EpCAM antigen is overexpressed in 30-40% of all cases and this increased expression correlates with poor prognosis. The use of EpCAM-specific monoclonal antibodies is a promising treatment approach in these patients.

Methods
In order to explore molecular changes following EpCAM overexpression, we investigated changes of the transcriptome upon EpCAM gene expression in commercially available human breast cancer cells lines Hs578T and MDA-MB-231. To assess cell proliferation, a tetrazolium salt based assay was performed. A TCF/LEF Reporter Kit was used to measure the transcriptional activity of the Wnt/β-catenin pathway. To evaluate the accumulation of β-catenin in the nucleus, a subcellular fractionation assay was performed.

Results
For the first time we could show that expression profiling data of EpCAM transfected cell lines Hs578TEpCAM and MDA-MB-231EpCAM indicate an association of EpCAM overexpression with the downregulation of the Wnt signaling inhibitors SFRP1 and TCF7L2. Confirmation of increased Wnt signaling was provided by a TCF/LEF reporter kit and by the finding of the nuclear accumulation of ß-catenin for MDA-MB-231EpCAM but not Hs578TEpCAM cells. In Hs578T cells, an increase of proliferation and chemosensitivity to Docetaxel was associated with EpCAM overexpression.

Conclusions
These data show a cell type dependent modification of Wnt signaling components after EpCAM overexpression in breast cancer cell lines, which results in marginal functional changes. Further investigations on the interaction of EpCAM with SFRP1 and TCF7L2 and on additional factors, which may be causal for changes upon EpCAM overexpression, will help to characterize unique molecular properties of EpCAM-positive breast cancer cells.
GaInNAs-based Hellish-vertical cavity semiconductor optical amplifier for 1.3 μm operation
Authors: Chaqmaqchee Faten Adel Ismail , Mazzucato Simone , Oduncuoglu Murat , Balkan Naci , Sun Yun , Gunes Mustafa , Hugues Maxime , Hopkinson Mark 
Published: February 2011

AbstractHot electron light emission and lasing in semiconductor heterostructure (Hellish) devices are surface emitters the operation of which is based on the longitudinal injection of electrons and holes in the active region. These devices can be designed to be used as vertical cavity surface emitting laser or, as in this study, as a vertical cavity semiconductor optical amplifier (VCSOA). This study investigates the prospects for a Hellish VCSOA based on GaInNAs/GaAs material for operation in the 1.3-μm wavelength range. Hellish VCSOAs have increased functionality, and use undoped distributed Bragg reflectors; and this coupled with direct injection into the active region is expected to yield improvements in the gain and bandwidth. The design of the Hellish VCSOA is based on the transfer matrix method and the optical field distribution within the structure, where the determination of the position of quantum wells is crucial. A full assessment of Hellish VCSOAs has been performed in a device with eleven layers of Ga0.35In0.65N0.02As0.08/GaAs quantum wells (QWs) in the active region. It was characterised through I-V, L-V and by spectral photoluminescence, electroluminescence and electro-photoluminescence as a function of temperature and applied bias. Cavity resonance and gain peak curves have been calculated at different temperatures. Good agreement between experimental and theoretical results has been obtained.
Tuning the electronic properties of boron nitride nanotube by mechanical uni-axial deformation: a DFT study
Authors: Ju Shin-Pon , Wang Yao-Chun , Lien Ting-Wei 
Published: February 2011

AbstractThe effect of uni-axial strain on the electronic properties of (8,0) zigzag and (5,5) armchair boron nitride nanotubes (BNNT) is addressed by density functional theory calculation. The stress-strain profiles indicate that these two BNNTS of differing types display very similar mechanical properties, but there are variations in HOMO-LUMO gaps at different strains, indicating that the electronic properties of BNNTs not only depend on uni-axial strain, but on BNNT type. The variations in nanotube geometries, partial density of states of B and N atoms, B and N charges are also discussed for (8,0) and (5,5) BNNTs at different strains.
Kinetics of Si and Ge nanowires growth through electron beam evaporation
Authors: Artoni Pietro , Pecora Emanuele Francesco , Irrera Alessia , Priolo Francesco 
Published: February 2011

AbstractSi and Ge have the same crystalline structure, and although Si-Au and Ge-Au binary alloys are thermodynamically similar (same phase diagram, with the eutectic temperature of about 360°C), in this study, it is proved that Si and Ge nanowires (NWs) growth by electron beam evaporation occurs in very different temperature ranges and fluence regimes. In particular, it is demonstrated that Ge growth occurs just above the eutectic temperature, while Si NWs growth occurs at temperature higher than the eutectic temperature, at about 450°C. Moreover, Si NWs growth requires a higher evaporated fluence before the NWs become to be visible. These differences arise in the different kinetics behaviors of these systems. The authors investigate the microscopic growth mechanisms elucidating the contribution of the adatoms diffusion as a function of the evaporated atoms direct impingement, demonstrating that adatoms play a key role in physical vapor deposition (PVD) NWs growth. The concept of incubation fluence, which is necessary for an interpretation of NWs growth in PVD growth conditions, is highlighted.
Memory properties and charge effect study in Si nanocrystals by scanning capacitance microscopy and spectroscopy
Authors: Lin Zhen , Bremond Georges , Bassani Franck 
Published: February 2011

AbstractIn this letter, isolated Si nanocrystal has been formed by dewetting process with a thin silicon dioxide layer on top. Scanning capacitance microscopy and spectroscopy were used to study the memory properties and charge effect in the Si nanocrystal in ambient temperature. The retention time of trapped charges injected by different direct current (DC) bias were evaluated and compared. By ramp process, strong hysteresis window was observed. The DC spectra curve shift direction and distance was observed differently for quantitative measurements. Holes or electrons can be separately injected into these Si-ncs and the capacitance changes caused by these trapped charges can be easily detected by scanning capacitance microscopy/spectroscopy at the nanometer scale. This study is very useful for nanocrystal charge trap memory application.
A cylindrical core-shell-like TiO2 nanotube array anode for flexible fiber-type dye-sensitized solar cells
Authors: Yu Jiefeng , Wang Dan , Huang Yining , Fan Xing , Tang Xin , Gao Cong , Li Jianlong , Zou Dechun , Wu Kai 
Published: February 2011

AbstractA versatile anodization method was reported to anodize Ti wires into cylindrical core-shell-like and thermally crystallized TiO2 nanotube (TNT) arrays that can be directly used as the photoanodes for semi- and all-solid fiber-type dye-sensitized solar cells (F-DSSC). Both F-DSSCs showed higher power conversion efficiencies than or competitive to those of previously reported counterparts fabricated by depositing TiO2 particles onto flexible substrates. The substantial enhancement is presumably attributed to the reduction of grain boundaries and defects in the prepared TNT anodes, which may suppress the recombination of the generated electrons and holes, and accordingly lead to more efficient carrier-transfer channels.
Animal model integration to AutDB, a genetic database for autism
Authors: Kumar Ajay , Wadhawan Rachna , Swanwick Catherine Croft , Kollu Ravi , Basu Saumyendra N , Banerjee-Basu Sharmila 
Published: February 2011

Abstract

Background
In the post-genomic era, multi-faceted research on complex disorders such as autism has generated diverse types of molecular information related to its pathogenesis. The rapid accumulation of putative candidate genes/loci for Autism Spectrum Disorders (ASD) and ASD-related animal models poses a major challenge for systematic analysis of their content. We previously created the Autism Database (AutDB) to provide a publicly available web portal for ongoing collection, manual annotation, and visualization of genes linked to ASD. Here, we describe the design, development, and integration of a new module within AutDB for ongoing collection and comprehensive cataloguing of ASD-related animal models.

Description
As with the original AutDB, all data is extracted from published, peer-reviewed scientific literature. Animal models are annotated with a new standardized vocabulary of phenotypic terms developed by our researchers which is designed to reflect the diverse clinical manifestations of ASD. The new Animal Model module is seamlessly integrated to AutDB for dissemination of diverse information related to ASD. Animal model entries within the new module are linked to corresponding candidate genes in the original "Human Gene" module of the resource, thereby allowing for cross-modal navigation between gene models and human gene studies. Although the current release of the Animal Model module is restricted to mouse models, it was designed with an expandable framework which can easily incorporate additional species and non-genetic etiological models of autism in the future.

Conclusions
Importantly, this modular ASD database provides a platform from which data mining, bioinformatics, and/or computational biology strategies may be adopted to develop predictive disease models that may offer further insights into the molecular underpinnings of this disorder. It also serves as a general model for disease-driven databases curating phenotypic characteristics of corresponding animal models.
The innate immune response to coxsackievirus B3 predicts progression to cardiovascular disease and heart failure in male mice
Authors: Onyimba Jennifer A , Coronado Michael J , Garton Amanda E , Kim Joseph B , Bucek Adriana , Bedja Djahida , Gabrielson Kathleen L , Guilarte Tomas R , Fairweather DeLisa 
Published: February 2011

Abstract

Background
Men are at an increased risk of dying from heart failure caused by inflammatory heart diseases such as atherosclerosis, myocarditis and dilated cardiomyopathy (DCM). We previously showed that macrophages in the spleen are phenotypically distinct in male compared to female mice at 12 h after infection. This innate immune profile mirrors and predicts the cardiac immune response during acute myocarditis.

Methods
In order to study sex differences in the innate immune response, five male and female BALB/c mice were infected intraperitoneally with coxsackievirus B3 (CVB3) or phosphate buffered saline and their spleens were harvested 12 h later for microarray analysis. Gene expression was determined using an Affymetrix Mouse Gene 1.0 ST Array. Significant gene changes were verified by quantitative real-time polymerase chain reaction or ELISA.

Results
During the innate immune response to CVB3 infection, infected males had higher splenic expression of genes which are important in regulating the influx of cholesterol into macrophages, such as phospholipase A2 (PLA2) and the macrophage scavenger receptor compared to the infected females. We also observed a higher expression in infected males compared to infected females of squalene synthase, an enzyme used to generate cholesterol within cells, and Cyp2e1, an enzyme important in metabolizing cholesterol and steroids. Infected males also had decreased levels of the translocator protein 18 kDa (TSPO), which binds PLA2 and is the rate-limiting step for steroidogenesis, as well as decreased expression of the androgen receptor (AR), which indicates receptor activation. Gene differences were not due to increased viral replication, which was unaltered between sexes.

Conclusions
We found that, compared to females, male mice had a greater splenic expression of genes which are important for cholesterol metabolism and activation of the AR at 12 h after infection. Activation of the AR has been linked to increased cardiac hypertrophy, atherosclerosis, myocarditis/DCM and heart failure in male mice and humans.
Real-time ultrasound-guided percutaneous dilatational tracheostomy: a feasibility study
Authors: Rajajee Venkatakrishna , Fletcher Jeffrey J , Rochlen Lauryn R , Jacobs Teresa L 
Published: February 2011

Abstract
Introduction
Ultrasound (US) performed prior to percutaneous tracheostomy (PT) may be useful in avoiding injury to pretracheal vascular structures and in avoiding high placement of the tube. Bedside real-time US guidance with visualization of needle path is routinely utilized for other procedures such as central venous catheterization, and may enhance the safety and accuracy of PT without causing airway occlusion or hypercarbia. Our objective was to demonstrate that PT performed under real-time US guidance with visualization of needle path during tracheal puncture is feasible, including in patients with features that increase the technical difficulty of PT.

Methods
Mechanically ventilated patients with acute brain injury requiring tracheostomy underwent US guided PT. The orotracheal tube was withdrawn using direct laryngoscopy. The trachea was punctured under real-time US guidance (with visualization of the needle path) while using the acoustic shadows of the cricoid and the tracheal rings to identify the level of puncture. After guidewire passage the site and level of entry was verified using the bronchoscope, which was then withdrawn. Following dilatation and tube placement, placement in the airway was confirmed using auscultation and the "lung sliding" sign on US. Bronchoscopy and chest X-ray were then performed to identify any complications.

Results
Thirteen patients successfully underwent US guided PT. Three patients were morbidly obese, two were in cervical spine precautions and one had a previous tracheostomy. In all 13 patients bronchoscopy confirmed that guidewire entry was through the anterior wall and between the first and fifth tracheal rings. There was no case of tube misplacement, pneumothorax, posterior wall injury, significant bleeding or other complication during the procedure.

Conclusions
Percutaneous tracheostomy performed under real-time ultrasound guidance is feasible and appears accurate and safe, including in patients with morbid obesity and cervical spine precautions. Larger studies are required to further define the safety and relative benefits of this technique.

Trial registration
UMIN Clinical Trials Registry, UMIN000005023.
Postcards in Persia: randomised controlled trial to reduce suicidal behaviours 12 months after hospital-treated self-poisoning
Authors: Hassanian-Moghaddam Hossein , Sarjami Saeedeh , Kolahi Ali-Asghar , Carter Gregory L. 
Published: February 2011

BackgroundHospital-treated self-poisoning is common, with limited effective interventions for reducing subsequent suicidal behaviour.AimsTo test the efficacy of a postcard intervention to reduce suicidal behaviour.MethodRandomised controlled trial of individuals who self-poisoned (n = 2300), the intervention consisted of nine postcards sent over 12 months versus usual treatment. Outcomes assessed at 12 months (n = 2113) were suicidal ideation, suicide attempts and self-cutting (proportion and event rates).ResultsThere was a significant reduction in any suicidal ideation (relative risk reduction (RRR) = 0.31, 95% CI 0.22–0.38), any suicide attempt (RRR = 0.42, 95% CI 0.11–0.63) and number of attempts (incidence rate ratios (IRR) = 0.64, 95% CI 0.42–0.97). There was no significant reduction in any self-cutting (RRR = 0.14, 95% CI −-0.29 to 0.42) or self-cutting events (IRR = 1.03 95% CI 0.76–1.39).ConclusionsA postcard intervention reduced suicidal ideation and suicide attempts in a non-Western population. Sustained, brief contact by mail may reduce suicidal ideation and suicide attempts in individuals who self-poison.
Development and validation of an arterial blood gas analysis interpretation algorithm for application in clinical laboratory services
Authors: Park Sang Hyuk , An Dongheui , Chang You Jin , Kim Hyun Jung , Kim Kyung Min , Koo Tai Yeon , Kim Sollip , Lee Woochang , Yang Won Seok , Hong Sang-Bum , Chun Sail , Min Won-Ki 
Published: February 2011

Background Arterial blood gas analysis (ABGA) is a useful test that estimates the acid–base status of patients. However, numerically reported test results make rapid interpretation difficult. To overcome this problem, we have developed an algorithm that automatically interprets ABGA results, and assessed the validity of this algorithm for applications in clinical laboratory services. Methods The algorithm was developed based on well-established guidelines using three test results (pH, PaCO2 and [HCO3−]) as variables. Ninety-nine ABGA test results were analysed by the algorithm. The algorithm's interpretations and the interpretations of two representative web-based ABGA interpretation programs were compared with those of two experienced clinicians. Results The concordance rates between the interpretations of each of the two clinicians and the algorithm were 91.9% and 97.0%, respectively. The web-based programs could not issue definitive interpretations in 15.2% and 25.3% of cases, respectively, but the algorithm issued definitive interpretations in all cases. Of the 10 cases that invoked disagreement among interpretations by the algorithm and the two clinicians, half were interpreted as compensated acid–base disorders by the algorithm but were assessed as normal by at least one of the two clinicians. In no case did the algorithm indicate a normal condition that the clinicians assessed as an abnormal condition. Conclusions The interpretations of the algorithm showed a higher concordance rate with those of experienced clinicians than did two web-based programs. The algorithm sensitively detected acid–base disorders. The algorithm may be adopted by the clinical laboratory services to provide rapid and definitive interpretations of test results.