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Glycomics & Glycoproteomics in Glycoconjugate journal. Glycoconj J. 2016 May 13; Authors: Kolarich D, Wuhrer M PMID: 27178342 [PubMed - as supplied by publisher]

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/05/14PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Gas chromatography-mass spectrometric method-based urine metabolomic profile of rats with pelvic inflammatory disease. Exp Ther Med. 2016 May;11(5):1653-1660 Authors: Zou W, Wen X, Sheng X, Zheng YI, Xiao Z, Luo J, Chen S, Wang Y, Cheng Z, Xiang D, Nie Y Abstract Pelvic inflammatory disease (PID) can lead to a poor outcome of severe sequelae, and the current methods of clinical diagnosis are not satisfactory. Metabolomics is an effective method for the identification of disease-related metabolite biomarkers to facilitate disease diagnosis. However, to the best of our knowledge, no PID-associated metabolomic study has yet been carried out. The metabolomic changes of rats with PID were investigated in the present study. A PID model was constructed by the multi-pathogenic infection of the upper genital tract in rats. Infiltration of inflammatory cells and elevated expression levels of the cytokines interleukin (IL)-1β and IL-6 in the uterus and fallopian tubes validated the disease model. Gas chromatography-mass spectrometry coupled with derivatization was used to determine the urine metabolomic profile. Principal component analysis and partial least squares-discriminant analysis of the data sets showed a clear separation of metabolic profiles between rats with PID and control rats. Eighteen differentiating metabolites were found, including four amino acids, three fatty acids, nine organic acids, and two sugars, which indicated alterations in sugar metabolism, the citric acid cycle, amino acid metabolism and fatty acid metabolism. These metabolites could be potential biomarkers of PID, and this research may offer a new approach to evaluate the effect of anti-PID drugs in pre-clinical or clinical trials. PMID: 27168785 [PubMed - as supplied by publisher]

Discovery of biomarkers for oxidative stress based on cellular metabolomics. Biomarkers. 2016 May 10;:1-9 Authors: Wang N, Wei J, Liu Y, Pei D, Hu Q, Wang Y, Di D Abstract Oxidative stress has a close relationship with various pathologic physiology phenomena and the potential biomarkers of oxidative stress may provide evidence for clinical diagnosis or disease prevention. Metabolomics was employed to identify the potential biomarkers of oxidative stress. High-performance liquid chromatography-diode array detector, mass spectrometry and partial least squares discriminate analysis were used in this study. The 10, 15 and 13 metabolites were considered to discriminate the model group, vitamin E-treated group and l-glutathione-treated group, respectively. Some of them have been identified, namely, malic acid, vitamin C, reduced glutathione and tryptophan. Identification of other potential biomarkers should be conducted and their physiological significance also needs to be elaborated. PMID: 27168482 [PubMed - as supplied by publisher]

Mitochondrial Transfer by Photothermal Nanoblade Restores Metabolite Profile in Mammalian Cells. Cell Metab. 2016 May 10;23(5):921-929 Authors: Wu TH, Sagullo E, Case D, Zheng X, Li Y, Hong JS, TeSlaa T, Patananan AN, McCaffery JM, Niazi K, Braas D, Koehler CM, Graeber TG, Chiou PY, Teitell MA Abstract mtDNA sequence alterations are challenging to generate but desirable for basic studies and potential correction of mtDNA diseases. Here, we report a new method for transferring isolated mitochondria into somatic mammalian cells using a photothermal nanoblade, which bypasses endocytosis and cell fusion. The nanoblade rescued the pyrimidine auxotroph phenotype and respiration of ρ0 cells that lack mtDNA. Three stable isogenic nanoblade-rescued clones grown in uridine-free medium showed distinct bioenergetics profiles. Rescue lines 1 and 3 reestablished nucleus-encoded anapleurotic and catapleurotic enzyme gene expression patterns and had metabolite profiles similar to the parent cells from which the ρ0 recipient cells were derived. By contrast, rescue line 2 retained a ρ0 cell metabolic phenotype despite growth in uridine-free selection. The known influence of metabolite levels on cellular processes, including epigenome modifications and gene expression, suggests metabolite profiling can help assess the quality and function of mtDNA-modified cells. PMID: 27166949 [PubMed - as supplied by publisher]

Related Articles Improving Assessment of Lipoprotein Profile in Type 1 Diabetes by 1H NMR Spectroscopy. PLoS One. 2015;10(8):e0136348 Authors: Brugnara L, Mallol R, Ribalta J, Vinaixa M, Murillo S, Casserras T, Guardiola M, Vallvé JC, Kalko SG, Correig X, Novials A Abstract Patients with type 1 diabetes (T1D) present increased risk of cardiovascular disease (CVD). The aim of this study is to improve the assessment of lipoprotein profile in patients with T1D by using a robust developed method 1H nuclear magnetic resonance spectroscopy (1H NMR), for further correlation with clinical factors associated to CVD. Thirty patients with T1D and 30 non-diabetes control (CT) subjects, matched for gender, age, body composition (DXA, BMI, waist/hip ratio), regular physical activity levels and cardiorespiratory capacity (VO2peak), were analyzed. Dietary records and routine lipids were assessed. Serum lipoprotein particle subfractions, particle sizes, and cholesterol and triglycerides subfractions were analyzed by 1H NMR. It was evidenced that subjects with T1D presented lower concentrations of small LDL cholesterol, medium VLDL particles, large VLDL triglycerides, and total triglycerides as compared to CT subjects. Women with T1D presented a positive association with HDL size (p<0.005; R = 0.601) and large HDL triglycerides (p<0.005; R = 0.534) and negative (p<0.005; R = -0.586) to small HDL triglycerides. Body fat composition represented an important factor independently of normal BMI, with large LDL particles presenting a positive correlation to total body fat (p<0.005; R = 0.505), and total LDL cholesterol and small LDL cholesterol a positive correlation (p<0.005; R = 0.502 and R = 0.552, respectively) to abdominal fat in T1D subjects; meanwhile, in CT subjects, body fat composition was mainly associated to HDL subclasses. VO2peak was negatively associated (p<0.005; R = -0.520) to large LDL-particles only in the group of patients with T1D. In conclusion, patients with T1D with adequate glycemic control and BMI and without chronic complications presented a more favourable lipoprotein profile as compared to control counterparts. In addition, slight alterations in BMI and/or body fat composition showed to be relevant to provoking alterations in lipoproteins profiles. Finally, body fat composition appears to be a determinant for cardioprotector lipoprotein profile. PMID: 26317989 [PubMed - indexed for MEDLINE]

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/05/11PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Partner choice through concealed floral sugar rewards evolved with the specialization of ant-plant mutualisms. New Phytol. 2016 May 9; Authors: Chomicki G, M Staedler Y, Schönenberger J, Renner SS Abstract Obligate mutualisms require filtering mechanisms to prevent their exploitation by opportunists, but ecological contexts and traits facilitating the evolution of such mechanisms are largely unknown. We investigated the evolution of filtering mechanisms in an epiphytic ant-plant symbiotic system in Fiji involving Rubiaceae and dolichoderine ants, using field experiments, metabolomics, X-ray micro-computed tomography (micro-CT) scanning and phylogenetics. We discovered a novel plant reward consisting of sugary sap concealed in post-anthetic flowers only accessible to Philidris nagasau workers that bite through the thick epidermis. In five of the six species of Rubiaceae obligately inhabited by this ant, the nectar glands functioned for 10 d after a flower's sexual function was over. Sugar metabolomics and field experiments showed that ant foraging tracks sucrose levels, which only drop at the onset of fruit development. Ontogenetic analyses of our focal species and their relatives revealed a 25-fold increase in nectary size and delayed fruit development in the ant-rewarding species, and Bayesian analyses of several traits showed the correlated evolution of sugar rewards and symbiosis specialization. Concealed floral nectar forestalls exploitation by opportunists (generalist ants) and stabilizes these obligate mutualisms. Our study pinpoints the importance of partner choice mechanisms in transitions from facultative to obligate mutualisms. PMID: 27159681 [PubMed - as supplied by publisher]

Related Articles Metabolites in stored platelets associated with platelet recoveries and survivals. Transfusion. 2016 May 9; Authors: Zimring JC, Slichter S, Odem-Davis K, Felcyn JR, Kapp LM, Bell LN, Gunst PR, Corson J, Jones MK, Pellham E, Bailey SL, Fu X Abstract BACKGROUND: Transfusion of platelets (PLTs) is a common therapy in a number of clinical settings. However, it is well understood that there is substantial donor-to-donor variation in how well PLTs store and thus the quality of the products that are transfused. The basis of such variation is poorly understood, and there are limited metrics by which units of PLTs can be assessed for their posttransfusion performance. It has repeatedly been demonstrated that myriad biologic changes take place during PLT storage; however, which of the changes correlate with quality of the stored PLTs and/or are mechanistically involved in PLT function remains undetermined. STUDY DESIGN AND METHODS: The current study tested stored PLTs from 21 normal subjects, combining high-resolution metabolomics of stored PLTs with in vivo PLT recoveries and survivals. Both individual analytes and metabolic pathways that correlate with posttransfusion PLT viability were identified. RESULTS: Caffeine metabolites were associated with poor PLT recovery; caffeine metabolism was not ongoing in the PLT bag and remained at prestorage levels. Acylcarnitines, particular fatty acid metabolites, and oxidized fatty acids were associated with poor PLT survivals. Of the myriad metabolic changes during PLT storage, these are the first reported metabolic findings to begin distinguishing which changes are of functional importance regarding posttransfusion PLT performance. CONCLUSIONS: Together, these findings provide novel mechanistic insights into the functional biology of the PLT storage lesion as well as identifying potential targets for modifying donor environment (e.g., caffeine consumption) and also metrics of quality assessment for stored human PLTs. PMID: 27158944 [PubMed - as supplied by publisher]

Related Articles Metabolic Characterization of Advanced Liver Fibrosis in HCV Patients as Studied by Serum 1H-NMR Spectroscopy. PLoS One. 2016;11(5):e0155094 Authors: Embade N, Mariño Z, Diercks T, Cano A, Lens S, Cabrera D, Navasa M, Falcón-Pérez JM, Caballería J, Castro A, Bosch J, Mato JM, Millet O Abstract Several etiologies result in chronic liver diseases including chronic hepatitis C virus infection (HCV). Despite its high incidence and the severe economic and medical consequences, liver disease is still commonly overlooked due to the lack of efficient non-invasive diagnostic methods. While several techniques have been tested for the detection of fibrosis, the available biomarkers still present severe limitations that preclude their use in clinical diagnostics. Liver diseases have also been the subject of metabolomic analysis. Here, we demonstrate the suitability of 1H NMR spectroscopy for characterizing the metabolism of liver fibrosis induced by HCV. Serum samples from HCV patients without fibrosis or with liver cirrhosis were analyzed by NMR spectroscopy and the results were submitted to multivariate and univariate statistical analysis. PLS-DA test was able to discriminate between advanced fibrotic and non-fibrotic patients and several metabolites were found to be up or downregulated in patients with cirrhosis. The suitability of the most significantly regulated metabolites was validated by ROC analysis. Our study reveals that choline, acetoacetate and low-density lipoproteins are the most informative biomarkers for predicting cirrhosis in HCV patients. Our results demonstrate that statistical analysis of 1H-NMR spectra is able to distinguish between fibrotic and non-fibrotic patients suffering from HCV, representing a novel diagnostic application for NMR spectroscopy. PMID: 27158896 [PubMed - as supplied by publisher]

Related Articles Stable Isotope Resolved Metabolomics Studies in Ex Vivo TIssue Slices. Bio Protoc. 2016 Feb 5;6(3) Authors: Fan TW, Lane AN, Higashi RM Abstract An important component of this methodology is to assess the role of the tumor microenvironment on tumor growth and survival. To tackle this problem, we have adapted the original approach of Warburg (1), by combining thin tissue slices with Stable Isotope Resolved Metabolomics (SIRM) to determine detailed metabolic activity of human tissues. SIRM enables the tracing of metabolic transformations of source molecules such as glucose or glutamine over defined time periods, and is a requirement for detailed pathway tracing and flux analysis. In our approach, we maintain freshly resected tissue slices (both cancerous and non- cancerous from the same organ of the same subject) in cell culture media, and treat with appropriate stable isotope-enriched nutrients, e.g. (13)C6-glucose or (13)C5, (15)N2 -glutamine. These slices are viable for at least 24 h, and make it possible to eliminate systemic influence on the target tissue metabolism while maintaining the original 3D cellular architecture. It is therefore an excellent pre-clinical platform for assessing the effect of therapeutic agents on target tissue metabolism and their therapeutic efficacy on individual patients (2,3). PMID: 27158639 [PubMed - as supplied by publisher]

Related Articles Dying cell recognition shapes the pathophysiology of cell death. Cell Death Differ. 2016 Jun;23(6):913-4 Authors: Kroemer G PMID: 27157319 [PubMed - in process]

Related Articles Commentary: High-resolution magic angle spinning (1)H nuclear magnetic resonance spectroscopy metabolomics of hyperfunctioning parathyroid glands. Surgery. 2016 May 5; Authors: Thompson GB PMID: 27157122 [PubMed - as supplied by publisher]

Related Articles Precision Treatment and Precision Prevention: Integrating "Below and Above the Skin". JAMA Pediatr. 2016 Jan;170(1):9-10 Authors: Gillman MW, Hammond RA PMID: 26595371 [PubMed - indexed for MEDLINE]

Related Articles Biomarkers of Ectopic Fat Deposition: The Next Frontier in Serum Lipidomics. J Clin Endocrinol Metab. 2016 Jan;101(1):176-82 Authors: Perreault L, Starling AP, Glueck D, Brozinick JT, Sanders P, Siddall P, Kuo MS, Dabelea D, Bergman BC Abstract CONTEXT: Strong evidence suggests that ectopic fat rather than fat mass per se drives risk for type 2 diabetes. Nonetheless, biomarkers of ectopic fat have gone unexplored. OBJECTIVE: To determine the utility of serum lipidomics to predict ectopic lipid deposition. DESIGN: Cross-sectional. SETTING: The Clinical Translational Research Center at the University of Colorado Anschutz Medical Campus. PARTICIPANTS: Endurance-trained athletes (n = 15, 41 ± 0.9 y old; body mass index 24 ± 0.6 kg/m(2)) and obese people with or without type 2 diabetes (n = 29, 42 ± 1.4 y old; body mass index 32 ± 2.5 kg/m(2)). INTERVENTION: Blood sampling and skeletal muscle biopsy. MAIN OUTCOME MEASURES: Multivariable models determined the ability of serum lipids to predict intramuscular (im) lipid accumulation of triacylglycerol (TAG), diacylglycerol (DAG), and ceramide (liquid chromatography tandem mass spectroscopy). RESULTS: Among people with obesity, serum ganglioside C22:0 and lactosylceramide C14:0 predicted muscle TAG (overall model R(2) = 0.48), whereas serum DAG C36:1 and free fatty acid (FFA) C18:4 were strong predictors of muscle DAG (overall model R(2) = 0.77), as were serum TAG C58:5, FFA C14:2 and C14:3, phosphotidylcholine C38:1, and cholesterol ester C24:1 to predict muscle ceramide (overall model R(2) = 0.85). Among endurance-trained athletes, serum FFA C14:1 and sphingosine were significant predictors of muscle TAG (overall model R(2) = 0.81), whereas no models could predict intramuscular DAG or ceramide in this group. CONCLUSIONS: Different serum lipids predict intramuscular TAG accumulation in obese people vs athletes. The ability of serum lipidomics to predict intramuscular DAG and ceramide in insulin-resistant humans may prove a new biomarker to determine risk for diabetes. PMID: 26574956 [PubMed - indexed for MEDLINE]

Related Articles Animal Models and "Omics" Technologies for Identification of Novel Biomarkers and Drug Targets to Prevent Heart Failure. Biomed Res Int. 2015;2015:212910 Authors: Hou Y, Adrian-Segarra JM, Richter M, Kubin N, Shin J, Werner I, Walther T, Schönburg M, Pöling J, Warnecke H, Braun T, Kostin S, Kubin T Abstract It is now accepted that heart failure (HF) is a complex multifunctional disease rather than simply a hemodynamic dysfunction. Despite its complexity, stressed cardiomyocytes often follow conserved patterns of structural remodelling in order to adapt, survive, and regenerate. When cardiac adaptations cannot cope with mechanical, ischemic, and metabolic loads efficiently or become chronically activated, as, for example, after infection, then the ongoing structural remodelling and dedifferentiation often lead to compromised pump function and patient death. It is, therefore, of major importance to understand key events in the progression from a compensatory left ventricular (LV) systolic dysfunction to a decompensatory LV systolic dysfunction and HF. To achieve this, various animal models in combination with an "omics" toolbox can be used. These approaches will ultimately lead to the identification of an arsenal of biomarkers and therapeutic targets which have the potential to shape the medicine of the future. PMID: 26236717 [PubMed - indexed for MEDLINE]

Proteomics and metabolomics analyses reveal the cucurbit sieve tube system as a complex metabolic space. Plant J. 2016 May 7; Authors: Hu C, Ham BK, El-Shabrawi HM, Alexander D, Zhang D, Ryals J, Lucas WJ Abstract The plant vascular system, and specifically the phloem plays a pivotal role in allocation of fixed carbon to developing sink organs. Although the processes involved in loading and unloading of sugars and amino acids are well characterized, in contrast, little information is available regarding the nature of other metabolites in the sieve tube system (STS), at specific sites long the pathway. Here, we elucidate spatial features of metabolite composition mapped with phloem enzymes along the cucurbit STS. Phloem sap (PS) was collected from the loading (source), unloading (apical sink region) and shoot-root junction regions of cucumber, watermelon and pumpkin. Our PS analyses revealed significant differences in the metabolic and proteomic profiles, both along the source-to-sink pathway and between the STSs of these three cucurbits. In addition, metabolite profiles established for PS and vascular tissue indicated the presence of distinct compositions, consistent with the operation of the STS as a unique symplasmic domain. In this regard, at various locations along the STS, we could map metabolites and their related enzymes to specific metabolic pathways. These findings are discussed regarding the function of the STS as a unique and highly complex metabolic space within the plant vascular system. This article is protected by copyright. All rights reserved. PMID: 27155400 [PubMed - as supplied by publisher]

Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modelling. Plant J. 2016 May 7; Authors: Comas J, Benfeitas R, Vilaprinyo E, Sorribas A, Solsona F, Farré G, Berman J, Zorrilla U, Capell T, Sandmann G, Zhu C, Christou P, Alves R Abstract Plant Synthetic Biology is still in its infancy. However, Synthetic Biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops, such as rice, potato, or maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strategies to optimize those yields are still lacking. Here, we present a workflow that combines gene expression and quantitative metabolomics with mathematical modeling to identify strategies for increasing production yields of nutritionally important carotenoids in the seed endosperm synthesized through alternative biosynthetic pathways in synthetic lines of white maize, which is normally devoid of carotenoids. Quantitative metabolomics and gene expression data are used to create and fit parameters of mathematical models that are specific for four independent maize lines. Sensitivity analysis and simulation of each model is used to predict which gene activities should be further engineered in order to increase production yields for carotenoid accumulation in each line. Some of these predictions (e.g. increasing Zmlycb/Gllycb will increase accumulated β-carotenes) are valid across the four maize lines and consistent with experimental observations in other systems. Other predictions are line-specific. The workflow is adaptable to any other biological system for which appropriate quantitative information is available. Furthermore, we validate some of the predictions using experimental data from additional synthetic maize lines for which no models were developed. This article is protected by copyright. All rights reserved. PMID: 27155093 [PubMed - as supplied by publisher]

Lysosomal acid lipase regulates VLDL synthesis and insulin sensitivity in mice. Diabetologia. 2016 May 6; Authors: Radović B, Vujić N, Leopold C, Schlager S, Goeritzer M, Patankar JV, Korbelius M, Kolb D, Reindl J, Wegscheider M, Tomin T, Birner-Gruenberger R, Schittmayer M, Groschner L, Magnes C, Diwoky C, Frank S, Steyrer E, Du H, Graier WF, Madl T, Kratky D Abstract AIMS/HYPOTHESIS: Lysosomal acid lipase (LAL) hydrolyses cholesteryl esters and triacylglycerols (TG) within lysosomes to mobilise NEFA and cholesterol. Since LAL-deficient (Lal (-/-) ) mice suffer from progressive loss of adipose tissue and severe accumulation of lipids in hepatic lysosomes, we hypothesised that LAL deficiency triggers alternative energy pathway(s). METHODS: We studied metabolic adaptations in Lal (-/-) mice. RESULTS: Despite loss of adipose tissue, Lal (-/-) mice show enhanced glucose clearance during insulin and glucose tolerance tests and have increased uptake of [(3)H]2-deoxy-D-glucose into skeletal muscle compared with wild-type mice. In agreement, fasted Lal (-/-) mice exhibit reduced glucose and glycogen levels in skeletal muscle. We observed 84% decreased plasma leptin levels and significantly reduced hepatic ATP, glucose, glycogen and glutamine concentrations in fed Lal (-/-) mice. Markedly reduced hepatic acyl-CoA concentrations decrease the expression of peroxisome proliferator-activated receptor α (PPARα) target genes. However, treatment of Lal (-/-) mice with the PPARα agonist fenofibrate further decreased plasma TG (and hepatic glucose and glycogen) concentrations in Lal (-/-) mice. Depletion of hepatic nuclear factor 4α and forkhead box protein a2 in fasted Lal (-/-) mice might be responsible for reduced expression of microsomal TG transfer protein, defective VLDL synthesis and drastically reduced plasma TG levels. CONCLUSIONS/INTERPRETATION: Our findings indicate that neither activation nor inactivation of PPARα per se but rather the availability of hepatic acyl-CoA concentrations regulates VLDL synthesis and subsequent metabolic adaptations in Lal (-/-) mice. We conclude that decreased plasma VLDL production enhances glucose uptake into skeletal muscle to compensate for the lack of energy supply. PMID: 27153842 [PubMed - as supplied by publisher]

Proteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia. J Proteomics. 2016 May 3; Authors: Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N, Chakraborty S Abstract Oxalic acid (OA) plays dual role in fungal pathogenicity in a concentration dependent manner. While at higher concentration it induces programmed cell death leading to fungal invasion, low oxalate build resistance in plant. Although OA has been identified as a virulence determinant for rot disease caused by Sclerotinia sp., our understanding of how oxalate downregulation impart host immunity is limited. We have earlier shown that ectopic expression of oxalate decarboxylase (FvOXDC) specifically degrades OA in tomato (Solanum lycopersicum). To elucidate low oxalate regulated molecular mechanism imparting immunity, a comparative proteomics approach has been applied to E8.2-OXDC tomato fruit displaying fungal resistance. Mass spectrometric analyses identified 92 OXDC-responsive immunity related protein spots (ORIRPs) presumably associated with acid metabolism, defense signaling and endoplasmic reticulum stress. Metabolome study indicated increased abundance of some of the organic acids paralleling the proteomic analysis. Further, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around 14-3-3, translationally controlled tumor protein, annexin and chaperonin. Taken together, our data demonstrate that low oxalate may act as metabolic and immunity determinant through translational reprogramming. BIOLOGICAL SIGNIFICANCE: Although OA plays critical role as fungal elicitor, our understanding of how oxalate downregulation by decarboxylative degradation impart immunity is limited. Our study confirms the impact of oxalate down-regulation on overall cellular physiology and provides new perspectives to study plant immunity. The network representation may facilitate the prioritization of candidate proteins for patho-stress tolerance in crop plant. These findings are of great importance for future work towards functional determination and exploitation of target proteins in crop improvement program. PMID: 27153761 [PubMed - as supplied by publisher]