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        <title>BioMed Central - Latest Articles</title>
        <link>http://www.biomedcentral.com/</link>
        <description>The latest research articles published by BioMed Central</description>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
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                                <rdf:li rdf:resource="http://ccforum.com/content/16/3/311" />
                                <rdf:li rdf:resource="http://www.biomedcentral.com/1472-6882/12/64" />
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                                <rdf:li rdf:resource="http://www.wjso.com/content/10/1/82" />
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        <item rdf:about="http://ccforum.com/content/16/3/311">
        <title>Neurology Emergencies</title>
        <description>None</description>
        <link>http://ccforum.com/content/16/3/311</link>
                <dc:creator>Rajat Dhar</dc:creator>
                <dc:creator>Michael Diringer</dc:creator>
                <dc:source>Critical Care 2012, 16:311</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/cc11318-toc.gif</prism:require>
                <prism:publicationName>Critical Care</prism:publicationName>
        <prism:issn>1364-8535</prism:issn>
        <prism:volume>16</prism:volume>
        <prism:startingPage>311</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>XML</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
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        <item rdf:about="http://www.biomedcentral.com/1472-6882/12/64">
        <title>Baicalin, a natural compound, promotes regulatory T cell differentiation </title>
        <description>Background:
CD4+CD25+Foxp3+ regulatory T (Treg) cells inhibit autoimmunity and protect against tissue injury. The development of these Treg cells is controlled by the regulator protein Foxp3, which can be enhanced by the in vitro activation of Foxp3 in the presence of transforming growth factor-beta. However, little is known about alternative methods, such as the use of natural products, for controlling Foxp3-mediated Treg cell differentiation.MethodHEK 293T cells were transfected with Foxp3 expression plasmid, and then treated with different compounds, Foxp3 mRNA expression was determined by real-time RT-PCR. CD4+CD25-T cells were stimulated with Baicalin, Foxp3 protein expression were analyzed by flow cytometry and confocal microscopy, the regulatory function of T cells stimulated with Baicalin was detected by the carboxyfluorescien succinimidyl ester.
Results:
We demonstrated that Baicalin, a compound isolated from the Chinese herb Huangqin, induced Foxp3 protein expression in cultured T cells, promoted Treg cell differentiation and regulatory activity. Our data also indicated that Baicalin restored Foxp3 expression following its initial interleukin-6-mediated inhibition and induced Foxp3 expression in vitro.
Conclusions:
These data suggest that Baicalin may promote Treg cell differentiation and regulatory activity and may serve as a promising natural immunosuppressive compound for treating autoimmune inflammatory diseases.</description>
        <link>http://www.biomedcentral.com/1472-6882/12/64</link>
                <dc:creator>ji yang</dc:creator>
                <dc:creator>xue yang</dc:creator>
                <dc:creator>ming li</dc:creator>
                <dc:source>BMC Complementary and Alternative Medicine 2012, 12:64</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1472-6882-12-64-toc.gif</prism:require>
                <prism:publicationName>BMC Complementary and Alternative Medicine</prism:publicationName>
        <prism:issn>1472-6882</prism:issn>
        <prism:volume>12</prism:volume>
        <prism:startingPage>64</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1471-2407/12/178">
        <title>Circulating tumour cells escape from EpCAM-based detection due to epithelial-to-mesenchymal transition</title>
        <description>Background:
Circulating tumour cells (CTCs) have shown prognostic relevance in metastatic breast, prostate, colon and pancreatic cancer. For further development of CTCs as a biomarker, we compared the performance of different protocols for CTC detection in murine breast cancer xenograft models (MDA-MB-231, MDA-MB-468 and KPL-4). Blood samples were taken from tumour bearing animals (20 to 200 mm2) and analysed for CTCs using 1. an epithelial marker based enrichment method (AdnaTest), 2. an antibody independent technique, targeting human gene transcripts (qualitative PCR), and 3. an antibody-independent approach, targeting human DNA-sequences (quantitative PCR). Further, gene expression changes associated with epithelial-to-mesenchymal transition (EMT) were determined with an EMT-specific PCR assay.
Methods:
We used the commercially available Adna Test, RT-PCR on human housekeeping genes and a PCR on AluJ sequences to detect CTCs in xenografts models. Phenotypic changes in CTCs were tested with the commercially available &quot;Human Epithelial to Mesenchymal Transition RT-Profiler PCR Array&quot;.
Results:
Although the AdnaTest detects as few as 1 tumour cell in 1 ml of mouse blood spiking experiments, no CTCs were detectable with this approach in vivo despite visible metastasis formation. The presence of CTCs could, however, be demonstrated by PCR targeting human transcripts or DNA-sequences - without epithelial pre-enrichment. The failure of CTC detection by the AdnaTest resulted from downregulation of EpCAM, whereas mesenchymal markers like Twist and EGFR were upregulated on CTCs. Such a change in the expression profile during metastatic spread of tumour cells has already been reported and was linked to a biological program termed epithelial-mesenchymal transition (EMT).
Conclusions:
The use of EpCAM-based enrichment techniques leads to  the failure to detect CTC populations that have undergone EMT. Our findings may explain clinical results where low CTC numbers have been reported even in patients with late metastatic cancers. These results are a starting point for the identification of new markers for detection or capture of CTCs, including the mesenchymal-like subpopulations.</description>
        <link>http://www.biomedcentral.com/1471-2407/12/178</link>
                <dc:creator>Tobias M Gorges</dc:creator>
                <dc:creator>Ingeborg Tinhofer</dc:creator>
                <dc:creator>Michael Drosch</dc:creator>
                <dc:creator>Lars Roese</dc:creator>
                <dc:creator>Thomas M Zollner</dc:creator>
                <dc:creator>Thomas Krahn</dc:creator>
                <dc:creator>Oliver von Ahsen</dc:creator>
                <dc:source>BMC Cancer 2012, 12:178</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1471-2407-12-178-toc.gif</prism:require>
                <prism:publicationName>BMC Cancer</prism:publicationName>
        <prism:issn>1471-2407</prism:issn>
        <prism:volume>12</prism:volume>
        <prism:startingPage>178</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1472-6882/12/63">
        <title>Hypoglycemic and antilipidemic properties of kombucha tea in alloxan-induced diabetic rats</title>
        <description>Background:
Diabetes has become a serious health problem and a major risk factor associated with troublesome health complications, such as metabolism disorders and liver-kidney dysfunctions. The inadequacies associated with conventional medicines have led to a determined search for alternative natural therapeutic agents. The present study aimed to investigate and compare the hypoglycemic and antilipidemic effects of kombucha and black tea, two natural drinks commonly consumed around the world, in surviving diabetic rats.
Methods:
Alloxan diabetic rats were orally supplied with kombucha and black tea at a dose of 5 mL/kg body weight per day for 30 days, fasted overnight, and sacrificed on the 31st day of the experiment. Their bloods were collected and submitted to various biochemical measurements, including blood glucose, cholesterol, triglcerides, urea, creatinine, transaminases, transpeptidase, lipase, and amylase activities. Their pancreases were isolated and processed to measure lipase and alpha-amylase activities and to perform histological analysis.
Results:
The findings revealed that, compared to black tea, kombucha tea was a better inhibitor of alpha-amylase and lipase activities in the plasma and pancreas and a better suppressor of increased blood glucose levels. Interestingly, kombucha was noted to induce a marked delay in the absorption of LDL-cholesterol and triglycerides and a significant increase in HDL-cholesterol.  Histological analyses also showed that it exerted an ameliorative action on the pancreases and efficiently protected the liver-kidney functions of diabetic rats, evidenced by significant decreases in aspartate transaminase, alanine transaminase, and gamma-glytamyl transpeptidase activities in the plasma, as well as in the creatinine and urea contents.
Conclusions:
The findings revealed that kombucha tea administration induced attractive curative effects on diabetic rats, particularly in terms of liver-kidney functions. Kombucha tea can, therefore, be considered as a potential strong candidate for future application as a functional supplement for the treatment and prevention of diabetes.</description>
        <link>http://www.biomedcentral.com/1472-6882/12/63</link>
                <dc:creator>Ahmed Aloulou</dc:creator>
                <dc:creator>Khaled Hamden</dc:creator>
                <dc:creator>Dhouha Elloumi</dc:creator>
                <dc:creator>Madiha Bou Ali</dc:creator>
                <dc:creator>Khaoula Hargafi</dc:creator>
                <dc:creator>Bassem Jaouadi</dc:creator>
                <dc:creator>Fatma Ayadi</dc:creator>
                <dc:creator>Abdelfettah El Feki</dc:creator>
                <dc:creator>Emna Ammar</dc:creator>
                <dc:source>BMC Complementary and Alternative Medicine 2012, 12:63</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
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                <prism:publicationName>BMC Complementary and Alternative Medicine</prism:publicationName>
        <prism:issn>1472-6882</prism:issn>
        <prism:volume>12</prism:volume>
        <prism:startingPage>63</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1471-2474/13/72">
        <title>Biomechanical comparison of unilateral and bilateral pedicle screws fixation for transforaminal lumbar interbody fusion after decompressive 
surgery -- a finite element analysis</title>
        <description>Background:
Little is known about the biomechanical effectiveness of transforaminal lumbar interbody fusion (TLIF) cages in different positioning and various posterior implants used afterdecompressive surgery. The use of the various implants will induce the kinematic and mechanical changes in range of motion (ROM) and stresses at the surgical and adjacent segments. Unilateral pedicle screw with or without supplementary facet screw fixation in the minimally invasive TLIF procedure has not been ascertained to provide adequate stability without the need to expose on the contralateral side. This study used finite element (FE) models to investigate biomechanical differences in ROM and stress on the neighboring structures after TLIF cages insertion in conjunction with posterior fixation.
Methods:
A validated finite-element (FE) model of L1-S1 was established to implant three types of cages (TLIF with a single moon-shaped cage in the anterior or middle portion of vertebral bodies, and TLIF with a left diagonally placed ogival-shaped cage) from the left L4-5 levelafter unilateral decompressive surgery. Further, the effects of unilateral versus bilateral pedicle screw fixation (UPSF vs. BPSF) in each TLIF cage model was compared to analyze parameters, including stresses and ROM on the neighboring annulus, cage-vertebral interface and pedicle screws.
Results:
All the TLIF cages positioned with BPSF showed similar ROM (&lt;5 %) at surgical and adjacent levels, except TLIF with an anterior cage in flexion (61 % lower) and TLIF with a left diagonal cage in left lateral bending (33 % lower) at surgical level. On the other hand, the TLIF cage models with left UPSF showed varying changes of ROM and annulus stress in extension, right lateral bending and right axial rotation at surgical level. In particular, the TLIF model with a diagonal cage, UPSF, and contralateral facet screw fixation stabilize segmental motion of the surgical level mostly in extension and contralaterally axial rotation. Prominent stress shielded to the contralateral annulus, cage-vertebral interface, and pediclescrew at surgical level. A supplementary facet screw fixation shared stresses around the neighboring tissues and revealed similar ROM and stress patterns to those models with BPSF.
Conclusions:
TLIF surgery is not favored for asymmetrical positioning of a diagonal cage and UPSF used in contralateral axial rotation or lateral bending. Supplementation of a contralateral facetscrew is recommended for the TLIF construct.</description>
        <link>http://www.biomedcentral.com/1471-2474/13/72</link>
                <dc:creator>Shih-Hao Chen</dc:creator>
                <dc:creator>Shang-Chih Lin</dc:creator>
                <dc:creator>Wen-Chi Tsai</dc:creator>
                <dc:creator>Chih-Wei Wang</dc:creator>
                <dc:creator>Shih-Heng Chao</dc:creator>
                <dc:source>BMC Musculoskeletal Disorders 2012, 13:72</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1471-2474-13-72-toc.gif</prism:require>
                <prism:publicationName>BMC Musculoskeletal Disorders</prism:publicationName>
        <prism:issn>1471-2474</prism:issn>
        <prism:volume>13</prism:volume>
        <prism:startingPage>72</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.aacijournal.com/content/8/1/5">
        <title>Skin prick testing with extensively heated milk or egg products helps predict the outcome of an oral food challenge: a retrospective analysis</title>
        <description>Background:
Cow&apos;s milk and hen&apos;s egg are the most frequently encountered food allergens in the pediatric population. Skin prick testing (SPT) with commercial extracts followed by an oral food challenge (OFC) are routinely performed in the diagnostic investigation of these children. Recent evidence suggests that milk-allergic and/or egg-allergic individuals can often tolerate extensively heated (EH) forms of these foods. This study evaluated the predictive value of a negative SPT with EH milk or egg in determining whether a child would tolerate an OFC to the EH food product.
Methods:
Charts from a single allergy clinic were reviewed for any patient with a negative SPT to EH milk or egg, prepared in the form of a muffin. Data collected included age, sex, symptoms of food allergy, co-morbidities and the success of the OFC to the muffin.
Results:
Fifty-eight patients had negative SPTs to the EH milk or egg in a muffin and underwent OFC to the appropriate EH food in the outpatient clinic. Fifty-five of these patients tolerated the OFC. The negative predictive value for the SPT with the EH food product was 94.8%.
Conclusions:
SPT with EH milk or egg products was predictive of a successful OFC to the same food. Larger prospective studies are required to substantiate these findings.</description>
        <link>http://www.aacijournal.com/content/8/1/5</link>
                <dc:creator>Zein Faraj</dc:creator>
                <dc:creator>Harold L Kim</dc:creator>
                <dc:source>Allergy, Asthma &amp; Clinical Immunology 2012, 8:5</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1710-1492-8-5-toc.gif</prism:require>
                <prism:publicationName>Allergy, Asthma &amp; Clinical Immunology</prism:publicationName>
        <prism:issn>1710-1492</prism:issn>
        <prism:volume>8</prism:volume>
        <prism:startingPage>5</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.wjso.com/content/10/1/82">
        <title>Whole body diffusion for metastatic disease
assessment in neuroendocrine carcinomas:
comparison with OctreoScan(R) in two cases</title>
        <description>Neuroendocrine tumor (NET) patients must be adequately staged in order to improve amultidisciplinary approach and optimal management for metastatic disease. Currentlyavailable imaging studies include somatostatin receptor scintigraphy, like OctreoScan(R),computed tomography (CT), scans and magnetic resonance imaging (MRI), which analyzevascular concentration and intravenous contrast enhancement for anatomic tumorlocalization. However, these techniques require high degree of expertise for interpretationand are limited by their availability, cost, reproducibility, and follow-up imagingcomparisons. NETs significantly reduce water diffusion as compared to normal tissue.Diffusion-weighted imaging (DWI) in MRI has an advantageous contrast difference: thetumor is represented with high signal over a black normal surrounding background. Thewhole-body diffusion (WBD) technique has been suggested to be a useful test for detectingmetastasis from various anatomic sites. In this article we report the use of DWI in MRI andWBD in two cases of metastatic pulmonary NET staging in comparison with OctreoScan(R) inorder to illustrate the potential advantage of DWI and WBD in staging NETs.</description>
        <link>http://www.wjso.com/content/10/1/82</link>
                <dc:creator>Rachel Jorge D Cossetti</dc:creator>
                <dc:creator>Regis Otaviano França Bezerra</dc:creator>
                <dc:creator>Brenda Gumz</dc:creator>
                <dc:creator>Adriana Telles</dc:creator>
                <dc:creator>Frederico P Costa</dc:creator>
                <dc:source>World Journal of Surgical Oncology 2012, 10:82</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1477-7819-10-82-toc.gif</prism:require>
                <prism:publicationName>World Journal of Surgical Oncology</prism:publicationName>
        <prism:issn>1477-7819</prism:issn>
        <prism:volume>10</prism:volume>
        <prism:startingPage>82</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1471-2458/12/355">
        <title>Correction: A participatory parent-focused intervention promoting physical activity in preschools: Design of a cluster-randomized trial</title>
        <description>At the time of writing our study design paper1, the study&apos;s recruitment and randomization process was ongoing with numbers of schools in both study arms still changing. We finally were able to recruit more eligible preschools than initially thought. Therefore the numbers in figure 1 have changed (see new attached figure 1).Of finally 46 eligible preschools applying for participation in the state-sponsored PA programme, we recruited 39 (86%) preschools and a total of 826 (80% of eligible) children. Nineteen and 20 preschools (with 441 and 385 children with informed consent) were randomly assigned to the intervention and control group, respectively, after stratification for aggregate SES1 and geographical location. One preschool per arm left the study before baseline, leaving 433 children in 18 intervention and 376 children in 19 control preschools for analysis.In the ethical approval, we announced a minimal number (based upon sample size calculations): 280 per arm=560 total, but had permission from the ethics committee to recruit additional participants in preschools.The increase in preschool and participant numbers might enable us to grasp smaller clinical differences than originally planned. However, consideration of the revised figure with respect to participant flow does not result in any qualitative change of the conclusions of our previous report.We regret any inconvenience that this inaccuracy due to the publication of preliminary numbers of eligible and recruited preschools might have caused.</description>
        <link>http://www.biomedcentral.com/1471-2458/12/355</link>
                <dc:creator>Freia De Bock</dc:creator>
                <dc:creator>Joachim Fischer</dc:creator>
                <dc:creator>Kristina Hoffmann</dc:creator>
                <dc:creator>Herbert Renz-Polster</dc:creator>
                <dc:source>BMC Public Health 2012, 12:355</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1471-2458-12-355-toc.gif</prism:require>
                <prism:publicationName>BMC Public Health</prism:publicationName>
        <prism:issn>1471-2458</prism:issn>
        <prism:volume>12</prism:volume>
        <prism:startingPage>355</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1471-2407/12/179">
        <title>Impaired degradation followed by enhanced recycling of epidermal growth factor receptor caused by hypo-phosphorylation of tyrosine 1045 in RBE cells</title>
        <description>Background:
Since cholangiocarcinoma has a poor prognosis, several epidermal growth factor receptor (EGFR)-targeted therapies with antibody or small molecule inhibitor treatment have been proposed. However, their effect remains limited. The present study sought to understand the molecular genetic characteristics of cholangiocarcinoma related to EGFR, with emphasis on its degradation and recycling.
Methods:
We evaluated EGFR expression and colocalization by immunoblotting and immunofluorescence, cell surface EGFR expression by fluorescence-activated cell sorting (FACS), and EGFR ubiquitination and protein binding by immunoprecipitation in the human cholangiocarcinoma RBE and immortalized cholangiocyte MMNK-1 cell lines. Monensin treatment and Rab11a depletion by siRNA were adopted for inhibition of EGFR recycling.
Results:
Upon stimulation with EGF, ligand-induced EGFR degradation was impaired and the expression of phospho-tyrosine 1068 and phospho-p44/42 MAPK was sustained in RBE cells as compared with MMNK-1 cells. In RBE cells, the process of EGFR sorting for lysosomal degradation was blocked at the early endosome stage, and non-degradated EGFR was recycled to the cell surface. A disrupted association between EGFR and the E3 ubiquitin ligase c-Cbl, as well as hypo-phosphorylation of EGFR at tyrosine 1045 (Tyr1045), were also observed in RBE cells.
Conclusion:
In RBE cells, up-regulation of EGFR Tyr1045 phosphorylation is a potentially useful molecular alteration in EGFR-targeted therapy. The combination of molecular-targeted therapy determined by the characteristics of individual EGFR phosphorylation events and EGFR recycling inhibition show promise in future treatments of cholangiocarcinoma.</description>
        <link>http://www.biomedcentral.com/1471-2407/12/179</link>
                <dc:creator>Anping Gui</dc:creator>
                <dc:creator>Akira Kobayashi</dc:creator>
                <dc:creator>Hiroaki Motoyama</dc:creator>
                <dc:creator>Masato Kitazawa</dc:creator>
                <dc:creator>Michiko Takeoka</dc:creator>
                <dc:creator>Shinichi Miyagawa</dc:creator>
                <dc:source>BMC Cancer 2012, 12:179</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
        <dc:identifier>${item.identifier}</dc:identifier>
                                <prism:require>/content/figures/1471-2407-12-179-toc.gif</prism:require>
                <prism:publicationName>BMC Cancer</prism:publicationName>
        <prism:issn>1471-2407</prism:issn>
        <prism:volume>12</prism:volume>
        <prism:startingPage>179</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
                <prism:versionidentifier>PDF</prism:versionidentifier>
                <cc:license rdf:resource="http://creativecommons.org/licenses/by/2.0/" />
    </item>
        <item rdf:about="http://www.biomedcentral.com/1471-2105/13/99">
        <title>MetaMapp: mapping and visualizing metabolomic
data by integrating information from biochemical
pathways and chemical and mass spectral similarity</title>
        <description>Background:
Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome-reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites.
Results:
We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development.
Conclusion:
MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu.</description>
        <link>http://www.biomedcentral.com/1471-2105/13/99</link>
                <dc:creator>Dinesh K Barupal</dc:creator>
                <dc:creator>Pradeep K Haldiya</dc:creator>
                <dc:creator>Gert Wohlgemuth</dc:creator>
                <dc:creator>Tobias Kind</dc:creator>
                <dc:creator>Shanker L Kothari</dc:creator>
                <dc:creator>Kent E Pinkerton</dc:creator>
                <dc:creator>Oliver Fiehn</dc:creator>
                <dc:source>BMC Bioinformatics 2012, 13:99</dc:source>
        <dc:date>2012-05-16T00:00:00Z</dc:date>
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                <prism:publicationName>BMC Bioinformatics</prism:publicationName>
        <prism:issn>1471-2105</prism:issn>
        <prism:volume>13</prism:volume>
        <prism:startingPage>99</prism:startingPage>
        <prism:publicationDate>2012-05-16T00:00:00Z</prism:publicationDate>
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