1,736 research outputs found

    Finding the "Dark Matter'' in Human and Yeast Protein Network Prediction and Modelling

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    Accurate modelling of biological systems requires a deeper and more complete knowledge about the molecular components and their functional associations than we currently have. Traditionally, new knowledge on protein associations generated by experiments has played a central role in systems modelling, in contrast to generally less trusted bio-computational predictions. However, we will not achieve realistic modelling of complex molecular systems if the current experimental designs lead to biased screenings of real protein networks and leave large, functionally important areas poorly characterised. To assess the likelihood of this, we have built comprehensive network models of the yeast and human proteomes by using a meta-statistical integration of diverse computationally predicted protein association datasets. We have compared these predicted networks against combined experimental datasets from seven biological resources at different level of statistical significance. These eukaryotic predicted networks resemble all the topological and noise features of the experimentally inferred networks in both species, and we also show that this observation is not due to random behaviour. In addition, the topology of the predicted networks contains information on true protein associations, beyond the constitutive first order binary predictions. We also observe that most of the reliable predicted protein associations are experimentally uncharacterised in our models, constituting the hidden or "dark matter'' of networks by analogy to astronomical systems. Some of this dark matter shows enrichment of particular functions and contains key functional elements of protein networks, such as hubs associated with important functional areas like the regulation of Ras protein signal transduction in human cells. Thus, characterising this large and functionally important dark matter, elusive to established experimental designs, may be crucial for modelling biological systems. In any case, these predictions provide a valuable guide to these experimentally elusive regions

    Integration of airborne and ground observations of nitryl chloride in the Seoul metropolitan area and the implications on regional oxidation capacity during KORUS-AQ 2016

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    Nitryl chloride (ClNO2) is a radical reservoir species that releases chlorine radicals upon photolysis. An integrated analysis of the impact of ClNO2 on regional photochemistry in the Seoul metropolitan area (SMA) during the Korea-United States Air Quality Study (KORUS-AQ) 2016 field campaign is presented. Comprehensive multiplatform observations were conducted aboard the NASA DC-8 and at two ground sites (Olympic Park, OP; Taehwa Research Forest, TRF), representing an urbanized area and a forested suburban region, respectively. Positive correlations between daytime Cl2 and ClNO2 were observed at both sites, the slope of which was dependent on O3 levels. The possible mechanisms are explored through box model simulations constrained with observations. The overall diurnal variations in ClNO2 at both sites appeared similar but the nighttime variations were systematically different. For about half of the observation days at the OP site the level of ClNO2 increased at sunset but rapidly decreased at around midnight. On the other hand, high levels were observed throughout the night at the TRF site. Significant levels of ClNO2 were observed at both sites for 4-5 h after sunrise. Airborne observations, box model calculations, and back-trajectory analysis consistently show that these high levels of ClNO2 in the morning are likely from vertical or horizontal transport of air masses from the west. Box model results show that chlorine-radical-initiated chemistry can impact the regional photochemistry by elevating net chemical production rates of ozone by 25% in the morning

    Development of natural fiber-reinforced plastics (NFRP) based on biobased polyethylene and waste fibers from Posidonia oceanica seaweed

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    In the present study the valorization of wastes from Posidonia oceanica (PO) has been carried out in order to obtain a fully biobased composite material in combination with a biobased polyethylene obtained from sugar cane as matrix. Morphological analysis by scanning electron microscopy (SEM) of the fractured surfaces from impact tests has revealed a homogenous distribution of particles of PO, as a consequence, good balanced properties have been obtained for composites with PO contents in the 5-40 wt%. Thermal properties of composites have been studied through differential scanning calorimetry (DSC) and thermogravymetric analysis (TGA); the obtained results show an improvement on the thermal degradation. With regard to thermomechanical properties, dynamic mechanical analysis (DMA) results have shown a much enhanced storage modulus (G) as the Posidonia oceanica content increases. Tensile tests have shown a remarkable increase in stiffness with tensile modulus values about 60% higher for composites with 40 wt% with regard to unfilled material. In a similar way, the flexural modulus is more than twice with regard the unloaded polyethylene. Shore D hardness confirms this improvement on mechanical properties and Charpy impact test shows values very similar to sample without PO, so that the intrinsic high impact energy absorption of HDPE is maintained in HDPE-PO composites. The water uptake test determines that the water absorption percent does not exceed 8%, which is relatively low for a high immersion time (5 months), which guarantees a dimensional stability in lifetime for these composites.Ferrero, B.; Fombuena Borrás, V.; Fenollar Gimeno, OÁ.; Boronat Vitoria, T.; Balart Gimeno, RA. (2015). Development of natural fiber-reinforced plastics (NFRP) based on biobased polyethylene and waste fibers from Posidonia oceanica seaweed. Polymer Composites. 36(8):1378-1385. doi:10.1002/pc.23042S13781385368C. Duarte H. Kirkman Methods for the Measurament of Seagrass Abundant and Depth Distribution: Global Seagrass Research Methods Short, 482 2001Bay, D. (1984). A field study of the growth dynamics and productivity of Posidonia oceanica (L.) delile in Calvi Bay, Corsica. Aquatic Botany, 20(1-2), 43-64. doi:10.1016/0304-3770(84)90026-3Cocozza, C., Parente, A., Zaccone, C., Mininni, C., Santamaria, P., & Miano, T. (2011). Chemical, physical and spectroscopic characterization of Posidonia oceanica (L.) Del. residues and their possible recycle. Biomass and Bioenergy, 35(2), 799-807. doi:10.1016/j.biombioe.2010.10.033Khiari, R., Mhenni, M. F., Belgacem, M. N., & Mauret, E. (2010). Chemical composition and pulping of date palm rachis and Posidonia oceanica – A comparison with other wood and non-wood fibre sources. Bioresource Technology, 101(2), 775-780. doi:10.1016/j.biortech.2009.08.079Guezguez, I., Dridi-Dhaouadi, S., & Mhenni, F. (2009). Sorption of Yellow 59 on Posidonia oceanica, a non-conventional biosorbent: Comparison with activated carbons. Industrial Crops and Products, 29(1), 197-204. doi:10.1016/j.indcrop.2008.05.002Bledzki, A. K., Faruk, O., & Huque, M. (2002). Physico-mechanical studies of wood fiber reinforced composites. Polymer-Plastics Technology and Engineering, 41(3), 435-451. doi:10.1081/ppt-120004361Dányádi, L., Janecska, T., Szabó, Z., Nagy, G., Móczó, J., & Pukánszky, B. (2007). Wood flour filled PP composites: Compatibilization and adhesion. Composites Science and Technology, 67(13), 2838-2846. doi:10.1016/j.compscitech.2007.01.024TabkhPaz, M., Behravesh, A. H., Shahi, P., & Zolfaghari, A. (2013). Procedure effect on the physical and mechanical properties of the extruded wood plastic composites. Polymer Composites, 34(8), 1349-1356. doi:10.1002/pc.22549Yeh, S.-K., & Gupta, R. K. (2010). Nanoclay-reinforced, polypropylene-based wood-plastic composites. Polymer Engineering & Science, 50(10), 2013-2020. doi:10.1002/pen.21729Najafi, S. K., Hamidinia, E., & Tajvidi, M. (2006). Mechanical properties of composites from sawdust and recycled plastics. Journal of Applied Polymer Science, 100(5), 3641-3645. doi:10.1002/app.23159D. Plackett A. Södergård Polylactide-Based Biocomposites in Natural Fibers, Biopolymers, Biocomposites 17 M.M.A.K. Mohanty L.T. Drzal 579 596Ferrero, B., Boronat, T., Moriana, R., Fenollar, O., & Balart, R. (2013). Green composites based on wheat gluten matrix andposidonia oceanicawaste fibers as reinforcements. Polymer Composites, 34(10), 1663-1669. doi:10.1002/pc.22567Sánchez-Jiménez, P. E., Pérez-Maqueda, L. A., Perejón, A., & Criado, J. M. (2012). Nanoclay Nucleation Effect in the Thermal Stabilization of a Polymer Nanocomposite: A Kinetic Mechanism Change. The Journal of Physical Chemistry C, 116(21), 11797-11807. doi:10.1021/jp302466pKhiari, R., Marrakchi, Z., Belgacem, M. N., Mauret, E., & Mhenni, F. (2011). New lignocellulosic fibres-reinforced composite materials: A stepforward in the valorisation of the Posidonia oceanica balls. Composites Science and Technology, 71(16), 1867-1872. doi:10.1016/j.compscitech.2011.08.022Gokce, G., & Haznedaroglu, M. Z. (2008). Evaluation of antidiabetic, antioxidant and vasoprotective effects of Posidonia oceanica extract. Journal of Ethnopharmacology, 115(1), 122-130. doi:10.1016/j.jep.2007.09.016Pan, B., Ning, N., Liu, J., Bai, L., & Fu, Q. (2009). MECHANICAL PROPERTIES OF SMC WHISKER REINFORCED HIGH DENSITY POLYETHYLENE COMPOSITES. Chinese Journal of Polymer Science, 27(02), 267. doi:10.1142/s0256767909003893Fombuena, V., L, S.-N., MD, S., D, J., & R, B. (2012). Study of the Properties of Thermoset Materials Derived from Epoxidized Soybean Oil and Protein Fillers. Journal of the American Oil Chemists’ Society, 90(3), 449-457. doi:10.1007/s11746-012-2171-2Sue, H.-J., Wang, S., & Jane, J.-L. (1997). Morphology and mechanical behaviour of engineering soy plastics. Polymer, 38(20), 5035-5040. doi:10.1016/s0032-3861(97)00048-7Wang, S., Sue, H.-J., & Jane, J. (1996). Effects of Polyhydric Alcohols on the Mechanical Properties of Soy Protein Plastics. Journal of Macromolecular Science, Part A, 33(5), 557-569. doi:10.1080/10601329608010878He, Z., Wang, Y., Bai, H., & Song, B. (2008). TOUGHENING AND STIFFENING EFFECTS OF T-ZnOw WHISKERS ON POLYSTYRENE. Chinese Journal of Polymer Science, 26(03), 285. doi:10.1142/s0256767908002935Tjong, S. ., & Meng, Y. . (1998). Performance of potassium titanate whisker reinforced polyamide-6 composites. Polymer, 39(22), 5461-5466. doi:10.1016/s0032-3861(97)10294-4A. Klyosov Natural and Woodfiber Composites in the Real World, in Progress in Woodfibre-Plastic Composites Conference Proceedings, 2004Ab Ghani, M. H., & Ahmad, S. (2011). The Comparison of Water Absorption Analysis between Counterrotating and Corotating Twin-Screw Extruders with Different Antioxidants Content in Wood Plastic Composites. Advances in Materials Science and Engineering, 2011, 1-4. doi:10.1155/2011/40628

    Cost-effectiveness of financial incentives to promote adherence to depot antipsychotic medication: economic evaluation of a cluster-randomised controlled trial

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    Background: Offering a modest financial incentive to people with psychosis can promote adherence to depot antipsychotic medication, but the cost-effectiveness of this approach has not been examined. Methods: Economic evaluation within a pragmatic cluster-randomised controlled trial. 141 patients under the care of 73 teams (clusters) were randomised to intervention or control; 138 patients with diagnoses of schizophrenia, schizo-affective disorder or bipolar disorder participated. Intervention participants received £15 per depot injection over 12 months, additional to usual acute, mental and community primary health services. The control group received usual health services. Main outcome measures: incremental cost per 20% increase in adherence to depot antipsychotic medication; incremental cost of ‘good’ adherence (defined as taking at least 95% of the prescribed number of depot medications over the intervention period). Findings: Economic and outcome data for baseline and 12-month follow-up were available for 117 participants. The adjusted difference in adherence between groups was 12.2% (73.4% control vs. 85.6% intervention); the adjusted costs difference was £598 (95% CI -£4 533, £5 730). The extra cost per patient to increase adherence to depot medications by 20% was £982 (95% CI -£8 020, £14 000). The extra cost per patient of achieving 'good' adherence was £2 950 (CI -£19 400, £27 800). Probability of cost-effectiveness exceeded 97.5%at willingness-to-pay values of £14 000 for a 20% increase in adherence and £27 800 for good adherence. Interpretation: Offering a modest financial incentive to people with psychosis is cost-effective in promoting adherence to depot antipsychotic medication. Direct healthcare costs (including costs of the financial incentive) are unlikely to be increased by this intervention. Trial Registration: ISRCTN.com 7776928

    Effective Theory Approach to the Spontaneous Breakdown of Lorentz Invariance

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    We generalize the coset construction of Callan, Coleman, Wess and Zumino to theories in which the Lorentz group is spontaneously broken down to one of its subgroups. This allows us to write down the most general low-energy effective Lagrangian in which Lorentz invariance is non-linearly realized, and to explore the consequences of broken Lorentz symmetry without having to make any assumptions about the mechanism that triggers the breaking. We carry out the construction both in flat space, in which the Lorentz group is a global spacetime symmetry, and in a generally covariant theory, in which the Lorentz group can be treated as a local internal symmetry. As an illustration of this formalism, we construct the most general effective field theory in which the rotation group remains unbroken, and show that the latter is just the Einstein-aether theory.Comment: 45 pages, no figures

    Circulating microRNAs Reveal Time Course of Organ Injury in a Porcine Model of Acetaminophen-Induced Acute Liver Failure

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    Acute liver failure is a rare but catastrophic condition which can progress rapidly to multi-organ failure. Studies investigating the onset of individual organ injury such as the liver, kidneys and brain during the evolution of acute liver failure, are lacking. MicroRNAs are short, non-coding strands of RNA that are released into the circulation following tissue injury. In this study, we have characterised the release of both global microRNA and specific microRNA species into the plasma using a porcine model of acetaminophen-induced acute liver failure. Pigs were induced to acute liver failure with oral acetaminophen over 19h±2h and death occurred 13h±3h thereafter. Global microRNA concentrations increased 4h prior to acute liver failure in plasma (P<0.0001) but not in isolated exosomes, and were associated with increasing plasma levels of the damage-associated molecular pattern molecule, genomic DNA (P<0.0001). MiR122 increased around the time of onset of acute liver failure (P<0.0001) and was associated with increasing international normalised ratio (P<0.0001). MiR192 increased 8h after acute liver failure (P<0.0001) and was associated with increasing creatinine (P<0.0001). The increase in miR124-1 occurred concurrent with the pre-terminal increase in intracranial pressure (P<0.0001) and was associated with decreasing cerebral perfusion pressure (P<0.002)

    Contribution of microscopy for understanding the mechanism of action against trypanosomatids

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    Transmission electron microscopy (TEM) has proved to be a useful tool to study the ultrastructural alterations and the target organelles of new antitrypanosomatid drugs. Thus, it has been observed that sesquiterpene lactones induce diverse ultrastructural alterations in both T. cruzi and Leishmania spp., such as cytoplasmic vacuolization, appearance of multilamellar structures, condensation of nuclear DNA, and, in some cases, an important accumulation of lipid vacuoles. This accumulation could be related to apoptotic events. Some of the sesquiterpene lactones (e.g., psilostachyin) have also been demonstrated to cause an intense mitochondrial swelling accompanied by a visible kinetoplast deformation as well as the appearance of multivesicular bodies. This mitochondrial swelling could be related to the generation of oxidative stress and associated to alterations in the ergosterol metabolism. The appearance of multilamellar structures and multiple kinetoplasts and flagella induced by the sesquiterpene lactone psilostachyin C indicates that this compound would act at the parasite cell cycle level, in an intermediate stage between kinetoplast segregation and nuclear division. In turn, the diterpene lactone icetexane has proved to induce the external membrane budding on T. cruzi together with an apparent disorganization of the pericellar cytoskeleton. Thus, ultrastructural TEM studies allow elucidating the possible mechanisms and the subsequent identification of molecular targets for the action of natural compounds on trypanosomatids.Fil: Lozano, Esteban Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Spina Zapata, Renata María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Barrera, Patricia Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Tonn, Carlos Eugenio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Investigaciones en Tecnología Química. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Instituto de Investigaciones en Tecnología Química; ArgentinaFil: Sosa Escudero, Miguel Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentin

    Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer

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    Background: Intra-tumour genetic heterogeneity has been reported in both leukaemias and solid tumours and is implicated in the development of drug resistance in CML and AML. The role of genetic heterogeneity in drug response in solid tumours is unknown. Methods: To investigate intra-tumour genetic heterogeneity and chemoradiation response in advanced cervical cancer, we analysed 10 cases treated on the CTCR-CE01 clinical study. Core biopsies for molecular profiling were taken from four quadrants of the cervix pre-treatment, and weeks 2 and 5 of treatment. Biopsies were scored for cellularity and profiled using Agilent 180k human whole genome CGH arrays. We compared genomic profiles from 69 cores from 10 patients to test for genetic heterogeneity and treatment effects at weeks 0, 2 and 5 of treatment. Results: Three patients had two or more distinct genetic subpopulations pre-treatment. Subpopulations within each tumour showed differential responses to chemoradiotherapy. In two cases, there was selection for a single intrinsically resistant subpopulation that persisted at detectable levels after 5 weeks of chemoradiotherapy. Phylogenetic analysis reconstructed the order in which genomic rearrangements occurred in the carcinogenesis of these tumours and confirmed gain of 3q and loss of 11q as early events in cervical cancer progression. Conclusion: Selection effects from chemoradiotherapy cause dynamic changes in genetic subpopulations in advanced cervical cancers, which may explain disease persistence and subsequent relapse. Significant genetic heterogeneity in advanced cervical cancers may therefore be predictive of poor outcome

    Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum

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    The quest for new antimalarial drugs, especially those with novel modes of action, is essential in the face of emerging drug-resistant parasites. Here we describe a new chemical class of molecules, pyrazoleamides, with potent activity against human malaria parasites and showing remarkably rapid parasite clearance in an in vivo model. Investigations involving pyrazoleamide-resistant parasites, whole-genome sequencing and gene transfers reveal that mutations in two proteins, a calcium-dependent protein kinase (PfCDPK5) and a P-type cation-ATPase (PfATP4), are necessary to impart full resistance to these compounds. A pyrazoleamide compound causes a rapid disruption of Na+ regulation in blood-stage Plasmodium falciparum parasites. Similar effect on Na+ homeostasis was recently reported for spiroindolones, which are antimalarials of a chemical class quite distinct from pyrazoleamides. Our results reveal that disruption of Na+ homeostasis in malaria parasites is a promising mode of antimalarial action mediated by at least two distinct chemical classes
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