Download the Free Unbound MEDLINE PubMed App to your smartphone or tablet.
Available for iPhone, iPad, iPod touch, and Android.
information technology [keywords]
- Design of hybrid radial basis function neural networks (HRBFNNs) realized with the aid of hybridization of fuzzy clustering method (FCM) and polynomial neural networks (PNNs). [JOURNAL ARTICLE]
- Neural Netw 2014 Aug 28.:166-181.
In this study, we propose Hybrid Radial Basis Function Neural Networks (HRBFNNs) realized with the aid of fuzzy clustering method (Fuzzy C-Means, FCM) and polynomial neural networks. Fuzzy clustering used to form information granulation is employed to overcome a possible curse of dimensionality, while the polynomial neural network is utilized to build local models. Furthermore, genetic algorithm (GA) is exploited here to optimize the essential design parameters of the model (including fuzzification coefficient, the number of input polynomial fuzzy neurons (PFNs), and a collection of the specific subset of input PFNs) of the network. To reduce dimensionality of the input space, principal component analysis (PCA) is considered as a sound preprocessing vehicle. The performance of the HRBFNNs is quantified through a series of experiments, in which we use several modeling benchmarks of different levels of complexity (different number of input variables and the number of available data). A comparative analysis reveals that the proposed HRBFNNs exhibit higher accuracy in comparison to the accuracy produced by some models reported previously in the literature.
- Genome of the Avirulent Human-Infective Trypanosome-Trypanosoma rangeli. [JOURNAL ARTICLE]
- PLoS Negl Trop Dis 2014 Sep; 8(9):e3176.
Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.The T. rangeli haploid genome is ∼24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heat-shock proteins.Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets.
- Principle of duality in phospholipids: regulators of membrane morphology and dynamics. [JOURNAL ARTICLE]
- Biochem Soc Trans 2014 Oct 1; 42(5):1335-1342.
To suggest and develop intelligent strategies to comprehend the regulation of organelle formation, a deeper mechanistic interpretation requires more than just the involvement of proteins. Our approaches link the formation of endomembranes with both signalling and membrane physical properties. Hitherto, membrane morphology, local physical structure and signalling have not been well integrated. Our studies derive from a cross-disciplinary approach undertaken to determine the molecular mechanisms of nuclear envelope assembly in echinoderm and mammalian cells. Our findings have led to the demonstration of a direct role for phosphoinositides and their derivatives in nuclear membrane formation. We have shown that phosphoinositides and their derivatives, as well as acting as second messengers, are modulators of membrane morphology, and their modifying enzymes regulate nuclear envelope formation. In addition, we have shown that echinoderm eggs can be exploited as a milieu to directly study the roles of phospholipids in maintaining organelle shape. The use of the echinoderm egg is a significant step forward in obtaining direct information about membrane physical properties in situ rather than using simpler models which do not provide a complete mechanistic insight into the role of phospholipids in membrane dynamics.
- Persistent organic pollutants (POPs) and metals in primiparous women: a comparison from Canada and Mexico. [JOURNAL ARTICLE]
- Sci Total Environ 2014 Sep 15.:302-313.
Under the North American Commission for Environmental Cooperation (CEC) and its Sound Management of Chemicals (SMOC) program, a tri-national human contaminant monitoring initiative was completed to provide baseline exposure information for several environmental contaminants in Canada, Mexico and the United States (U.S). Blood samples were collected from primiparous women in Canada and Mexico, and were analysed for a suite of environmental contaminants including polychlorinated biphenyls (PCBs), dichlorodiphenyldichloroethylene(p,p'-DDE),beta-hexachlorocyclohexane (β-HCH), mercury and lead. A multiple stepwise linear regression analysis was conducted using data from Canadian and Mexican primiparous mothers, adjusting for ethnicity group, age, pre-pregnancy BMI, years at current city and ever-smoking status. Concentrations of p,p'-DDE, β-HCH, and lead were found to be higher among Mexican participants; however, concentrations of most PCBs among Mexican participants were similar to Canadian primiparous women after adjusting for covariates. Concentrations of total mercury were generally higher among Mexican primiparous women although this difference was smaller as age increased. This initial dataset can be used to determine priorities for future activities and to track progress in the management of the selected chemicals, both domestically and on a broader cooperative basis within North America.
- Do Abnormal Serum Lipid Levels Increase the Risk of Chronic Low Back Pain? The Nord-Trøndelag Health Study. [JOURNAL ARTICLE]
- PLoS One 2014; 9(9):e108227.
Cross-sectional studies suggest associations between abnormal lipid levels and prevalence of low back pain (LBP), but it is not known if there is any causal relationship.The objective was to determine, in a population-based prospective cohort study, whether there is any relation between levels of total cholesterol, high density lipoprotein (HDL) cholesterol and triglycerides and the probability of experiencing subsequent chronic (LBP), both among individuals with and without LBP at baseline.Information was collected in the community-based HUNT 2 (1995-1997) and HUNT 3 (2006-2008) surveys of an entire Norwegian county. Participants were 10,151 women and 8731 men aged 30-69 years, not affected by chronic LBP at baseline, and 3902 women and 2666 men with LBP at baseline. Eleven years later the participants indicated whether they currently suffered from chronic LBP.Among women without LBP at baseline, HDL cholesterol levels were inversely associated and triglyceride levels positively associated with the risk of chronic LBP at end of follow-up in analyses adjusted for age only. Adjustment for the baseline factors education, work status, physical activity, smoking, blood pressure and in particular BMI largely removed these associations (RR: 0.96, 95% CI: 0.85-1.07 per mmol/l of HDL cholesterol; RR: 1.16, 95% CI: 0.94-1.42 per unit of lg(triglycerides)). Total cholesterol levels showed no associations. In women with LBP at baseline and men without LBP at baseline weaker relationships were observed. In men with LBP at baseline, an inverse association with HDL cholesterol remained after complete adjustment (RR: 0.83, 95% CI: 0.72-0.95 per mmol/l).Crude associations between lipid levels and risk of subsequent LBP in individuals without current LBP are mainly caused by confounding with body mass. However, an association with low HDL levels may still remain in men who are already affected and possibly experience a higher pain intensity.
- tRNA Modifying Enzymes, NSUN2 and METTL1, Determine Sensitivity to 5-Fluorouracil in HeLa Cells. [JOURNAL ARTICLE]
- PLoS Genet 2014 Sep; 10(9):e1004639.
Nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay (RTD). The tRNA modifying enzymes, NSUN2 and METTL1, are mammalian orthologs of yeast Trm4 and Trm8, which are required for protecting tRNA against RTD. A simultaneous overexpression of NSUN2 and METTL1 is widely observed among human cancers suggesting that targeting of both proteins provides a novel powerful strategy for cancer chemotherapy. Here, we show that combined knockdown of NSUN2 and METTL1 in HeLa cells drastically potentiate sensitivity of cells to 5-fluorouracil (5-FU) whereas heat stress of cells revealed no effects. Since NSUN2 and METTL1 are phosphorylated by Aurora-B and Akt, respectively, and their tRNA modifying activities are suppressed by phosphorylation, overexpression of constitutively dephosphorylated forms of both methyltransferases is able to suppress 5-FU sensitivity. Thus, NSUN2 and METTL1 are implicated in 5-FU sensitivity in HeLa cells. Interfering with methylation of tRNAs might provide a promising rationale to improve 5-FU chemotherapy of cancer.
- Texture coarseness responsive neurons and their mapping in layer 2-3 of the rat barrel cortex in vivo. [JOURNAL ARTICLE]
- Elife 2014.
Texture discrimination is a fundamental function of somatosensory systems, yet the manner by which texture is coded and spatially represented in the barrel cortex are largely unknown. Using in vivo two-photon calcium imaging in the rat barrel cortex during artificial whisking against different surface coarseness or controlled passive whisker vibrations simulating different coarseness, we show that layer 2-3 neurons within barrel boundaries differentially respond to specific texture coarsenesses, while only a minority of neurons responded monotonically with increased or decreased surface coarseness. Neurons with similar preferred texture coarseness were spatially clustered. Multi-contact single unit recordings showed a vertical columnar organization of texture coarseness preference in layer 2-3. These findings indicate that layer 2-3 neurons perform high hierarchical processing of tactile information, with surface coarseness embodied by distinct neuronal subpopulations that are spatially mapped onto the barrel cortex.
- Hemolivia and Hepatozoon: Haemogregarines with Tangled Evolutionary Relationships. [JOURNAL ARTICLE]
- Protist 2014 Jul 2; 165(5):688-700.
The generic name Hemolivia has been used for haemogregarines characterized by morphological and biological features. The few molecular studies, focused on other haemogregarine genera but involving Hemolivia samples, indicated its close relationship to the genus Hepatozoon. Here we analyze molecular data for Hemolivia from a broad geographic area and host spectrum and provide detailed morphological documentation of the included samples. Based on molecular analyses in context of other haemogregarines, we demonstrate that several sequences deposited in GenBank from isolates described as Hepatozoon belong to the Hemolivia cluster. This illustrates the overall difficulty with recognizing Hemolivia and Hepatozoon without sufficient morphological and molecular information. The close proximity of both genera is also reflected in uncertainty about their precise phylogeny when using 18S rDNA. They cluster with almost identical likelihood either as two sister taxa or as monophyletic Hemolivia within paraphyletic Hepatozoon. However, regardless of these difficulties, the results presented here provide a reliable background for the unequivocal placement of new samples into the Hemolivia/ Hepatozoon complex.
- Artifact suppression in electron paramagnetic resonance imaging of (14)N- and (15)N-labeled nitroxyl radicals with asymmetric absorption spectra. [JOURNAL ARTICLE]
- J Magn Reson 2014 Aug 20.:31-37.
This article describes an improved method for suppressing image artifacts in the visualization of (14)N- and (15)N-labeled nitroxyl radicals in a single image scan using electron paramagnetic resonance (EPR). The purpose of this work was to solve the problem of asymmetric EPR absorption spectra in spectral processing. A hybrid function of Gaussian and Lorentzian lineshapes was used to perform spectral line-fitting to successfully separate the two kinds of nitroxyl radicals. This approach can process the asymmetric EPR absorption spectra of the nitroxyl radicals being measured, and can suppress image artifacts due to spectral asymmetry. With this improved visualization method and a 750-MHz continuous-wave EPR imager, a temporal change in the distributions of a two-phase paraffin oil and water/glycerin solution system was visualized using lipophilic and hydrophilic nitroxyl radicals, i.e., 2-(14-carboxytetradecyl)-2-ethyl-4,4-dimethyl-3-oxazolidinyloxy (16-DOXYL stearic acid) and 4-hydroxyl-2,2,6,6-tetramethylpiperidine-d17-1-(15)N-1-oxyl (TEMPOL-d17-(15)N). The results of the two-phase separation experiment verified that reasonable artifact suppression could be achieved by the present method that deals with asymmetric absorption spectra in the EPR imaging of (14)N- and (15)N-labeled nitroxyl radicals.
- Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data. [JOURNAL ARTICLE]
- Nat Commun 2014.:4909.
Accurate determination of genome-wide nucleosome positioning can provide important insights into global gene regulation. Here, we describe the development of an improved nucleosome-positioning algorithm-iNPS-which achieves significantly better performance than the widely used NPS package. By determining nucleosome boundaries more precisely and merging or separating shoulder peaks based on local MNase-seq signals, iNPS can unambiguously detect 60% more nucleosomes. The detected nucleosomes display better nucleosome 'widths' and neighbouring centre-centre distance distributions, giving rise to sharper patterns and better phasing of average nucleosome profiles and higher consistency between independent data subsets. In addition to its unique advantage in classifying nucleosomes by shape to reveal their different biological properties, iNPS also achieves higher significance and lower false positive rates than previously published methods. The application of iNPS to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process.