T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules

Theoretical methods for predicting CD8+ T-cell epitopes are an important tool in vaccine design and for enhancing our understanding of the cellular immune system. The most popular methods currently available produce binding affinity predictions across a range of MHC molecules. In comparing results between these MHC molecules, it is common practice to apply a normalization procedure known as rescaling, to correct for possible discrepancies between the allelic predictors. Using two of the most popular prediction software packages, NetCTL and NetMHC, we tested the hypothesis that rescaling removes genuine biological variation from the predicted affinities when comparing predictions across a number of MHC molecules. We found that removing the condition of rescaling improved the prediction software's performance both qualitatively, in terms of ranking epitopes, and quantitatively, in the accuracy of their binding affinity predictions. We suggest that there is biologically significant variation among class 1 MHC molecules and find that retention of this variation leads to significantly more accurate epitope prediction

Establishing optimal quantitative-polymerase chain reaction assays for routine diagnosis and tracking of minimal residual disease in JAK2-V617F-associated myeloproliferative neoplasms: a joint European LeukemiaNet/MPN&MPNr-EuroNet (COST action BM0902) study

Item does not contain fulltextReliable detection of JAK2-V617F is critical for accurate diagnosis of myeloproliferative neoplasms (MPNs); in addition, sensitive mutation-specific assays can be applied to monitor disease response. However, there has been no consistent approach to JAK2-V617F detection, with assays varying markedly in performance, affecting clinical utility. Therefore, we established a network of 12 laboratories from seven countries to systematically evaluate nine different DNA-based quantitative PCR (qPCR) assays, including those in widespread clinical use. Seven quality control rounds involving over 21,500 qPCR reactions were undertaken using centrally distributed cell line dilutions and plasmid controls. The two best-performing assays were tested on normal blood samples (n=100) to evaluate assay specificity, followed by analysis of serial samples from 28 patients transplanted for JAK2-V617F-positive disease. The most sensitive assay, which performed consistently across a range of qPCR platforms, predicted outcome following transplant, with the mutant allele detected a median of 22 weeks (range 6-85 weeks) before relapse. Four of seven patients achieved molecular remission following donor lymphocyte infusion, indicative of a graft vs MPN effect. This study has established a robust, reliable assay for sensitive JAK2-V617F detection, suitable for assessing response in clinical trials, predicting outcome and guiding management of patients undergoing allogeneic transplant

Differential regulation of NF-κB activation and function by topoisomerase II inhibitors

BACKGROUND: While many common chemotherapeutic drugs and other inducers of DNA-damage result in both NF-κB nuclear translocation and DNA-binding, we have previously observed that, depending on the precise stimulus, there is great diversity of the function of NF-κB. In particular, we found that treatment of U-2 OS osteosarcoma cells with the anthracycine daunorubicin or with ultraviolet (UV-C) light resulted in a form of NF-κB that repressed rather than induced NF-κB reporter plasmids and the expression of specific anti-apoptotic genes. Anthracyclines such as daunorubicin can induce DNA-damage though inhibiting topoisomerase II, intercalating with DNA and undergoing redox cycling to produce oxygen free radicals. In this study we have investigated other anthracyclines, doxorubicin and aclarubicin, as well as the anthracenedione mitoxantrone together with the topoisomerase II inhibitor ICRF-193, which all possess differing characteristics, to determine which of these features is specifically required to induce both NF-κB DNA-binding and transcriptional repression in U-2 OS cells. RESULTS: The use of mitoxantrone, which does not undergo redox cycling, and the reducing agent epigallocatechingallate (EGCG) demonstrated that oxygen free radical production is not required for induction of NF-κB DNA-binding and transcriptional repression by these agents and UV-C. In addition, the use of aclarubicin, which does not directly inhibit topoisomerase II and ICRF-193, which inhibits topoisomerase II but does not intercalate into DNA, demonstrated that topoisomerase II inhibition is not sufficient to induce the repressor form of NF-κB. CONCLUSION: Induction of NF-κB DNA-binding and transcriptional repression by topoisomerase II inhibitors was found to correlate with an ability to intercalate into DNA. Although data from our and other laboratories indicates that topoisomerase II inhibition and oxygen free radicals do regulate NF-κB, they are not required for the particular ability of NF-κB to repress rather than activate transcription. Together with our previous data, these results demonstrate that the nature of the NF-κB response is context dependent. In a clinical setting such effects could profoundly influence the response to chemotherapy and suggest that new methods of analyzing NF-κB function could have both diagnostic and prognostic value

Monoclonal antibodies directed to fucoidan preparations from brown algae

Cell walls of the brown algae contain a diverse range of polysaccharides with useful bioactivities. The precise structures of the sulfated fucan/fucoidan group of polysaccharides and their roles in generating cell wall architectures and cell properties are not known in detail. Four rat monoclonal antibodies, BAM1 to BAM4, directed to sulfated fucan preparations, have been generated and used to dissect the heterogeneity of brown algal cell wall polysaccharides. BAM1 and BAM4, respectively, bind to a non-sulfated epitope and a sulfated epitope present in the sulfated fucan preparations. BAM2 and BAM3 identified additional distinct epitopes present in the fucoidan preparations. All four epitopes, not yet fully characterised, occur widely within the major brown algal taxonomic groups and show divergent distribution patterns in tissues. The analysis of cell wall extractions and fluorescence imaging reveal differences in the occurrence of the BAM1 to BAM4 epitopes in various tissues of Fucus vesiculosus. In Ectocarpus subulatus, a species closely related to the brown algal model Ectocarpus siliculosus, the BAM4 sulfated epitope was modulated in relation to salinity levels. This new set of monoclonal antibodies will be useful for the dissection of the highly complex and yet poorly resolved sulfated polysaccharides in the brown algae in relation to their ecological and economic significance

A multidimensional evaluation framework for personal learning environments

Evaluating highly dynamic and heterogeneous Personal Learning Environments (PLEs) is extremely challenging. Components of PLEs are selected and configured by individual users based on their personal preferences, needs, and goals. Moreover, the systems usually evolve over time based on contextual opportunities and constraints. As such dynamic systems have no predefined configurations and user interfaces, traditional evaluation methods often fall short or are even inappropriate. Obviously, a host of factors influence the extent to which a PLE successfully supports a learner to achieve specific learning outcomes. We categorize such factors along four major dimensions: technological, organizational, psycho-pedagogical, and social. Each dimension is informed by relevant theoretical models (e.g., Information System Success Model, Community of Practice, self-regulated learning) and subsumes a set of metrics that can be assessed with a range of approaches. Among others, usability and user experience play an indispensable role in acceptance and diffusion of the innovative technologies exemplified by PLEs. Traditional quantitative and qualitative methods such as questionnaire and interview should be deployed alongside emergent ones such as learning analytics (e.g., context-aware metadata) and narrative-based methods. Crucial for maximal validity of the evaluation is the triangulation of empirical findings with multi-perspective (end-users, developers, and researchers), mixed-method (qualitative, quantitative) data sources. The framework utilizes a cyclic process to integrate findings across cases with a cross-case analysis in order to gain deeper insights into the intriguing questions of how and why PLEs work

Estimating a threshold price for CO2 emissions of buildings to improve their energy performance level. Case study of a new Spanish home

Energy consumption in homes produces CO2. In many countries, building regulations are being set to enable energy efficiency performance levels to be issued. In Spain, there is a regulated procedure to certify the energy performance of buildings according to their CO2 emissions. Consequently, some software tools have been design to simulate buildings and to obtain their energy consumption and CO2 emissions. In this paper the investment, maintenance and energy consumption costs are calculated for different energy performance levels and for various climatic zones, in a single-family home. According to the results, more energy efficient buildings imply higher construction and maintenance costs, which are not compensated by lower energy costs. Therefore, under current conditions, economic criteria do not support the improvement of the energy efficiency of a dwelling. Among the possible measures to promote energy efficiency, a price on CO2 emissions is to be suggested, including the social cost in the analysis. For this purpose, the cost-optimal methodology is used. In different scenarios for the discount rate y energy prices, various prices for CO2 are obtained, depending on the climatic zone and energy performance level.Ruá Aguilar, MJ.; Guadalajara Olmeda, MN. (2015). Estimating a threshold price for CO2 emissions of buildings to improve their energy performance level. Case study of a new Spanish home. Energy Efficiency. 8(2):183-203. doi:10.1007/s12053-014-9286-2S18320382AICIA. (2009). Escala de calificación energética. Edificios de nueva construcción. Madrid: Instituto para la Diversificación y Ahorro de la Energía, Ministerio de Industria, Turismo y Comercio.Al-Homoud, M. S. (2005). Performance characteristics and practical applications of common building thermal insulation materials. Building and Environment, 40(3), 353–360.Amecke, H. (2012). The impact of energy performances certificates: a survey of German home owners. Energy Policy, 46, 4–14.Andaloro, A., Salomone, R., Ioppolo, G., & Andaloro, L. (2010). Energy certification of buildings: a comparative analysis of progress towards implementation in European countries. Energy Policy, 38(10), 5840–5866.Annunziata, E., Frey, M., & Rizzi, F. (2013). Towards nearly zero-energy buildings: the state-of-art of national regulations in Europe. Energy, 57, 125–133. doi: 10.1016/j.energy.2012.11.049 .Audenaert, A., De Boeck, L., & Roelants, K. (2010). Economic analysis of the profitability of energy-saving architectural measures for the achievement of the EPBD-standard. Energy, 35(7), 2965–2971.Bertrán, A. (2009). Las mediciones en las obras adaptadas al CTE (4th ed.). Granada: Editorial Jorge Loring S.I.Brathal, D., & Langemo, M. (2004). Facilities management: a guide for total workplace design and management. Grand Forks: Knight Printing.Brown, D. W. (1996). Facility maintenance: the manager’s practical guide and handbook. New York: AMACOM American Management Association. New York, NY 10019.Concerted Action EPBD (2008). Implementation of the energy performance of buildings directive. Country reports 2008. Brussels: Directorate General for Energy and Transport, European Commission (available at www.epbd.ca.eu and www.buildup.eu ).Concerted Action EPBD (2011). Implementing the energy performance of buildings directive. Country reports 2011. Brussels: European Union (available at www.epbd.ca.eu and www.buildup.eu ).Davies, H., & Wyatt, D. (2004). Appropriate use or method for durability and service life prediction. Building Research and Information, 32(6), 552–553.Dresner, S., & Ekins, P. (2006). Economic instruments to improve UK home energy efficiency without negative social impacts. Fiscal Studies, 27(1), 47–74.Drury, C. (2008). Management and cost accounting, 7th ed. London.Eurostat European Comission, Instituto de Diversificación y Ahorro de Energía (IDAE), Ministerio de Industria, Energía y Turismo (2011). Proyecto SECH-SPAHOUSEC. Análisis del consumo energético del sector residencial en España. Informe Final. Madrid.Fraunhofer Institute for Systems and Innovation Research ISI (Germany) (2012). Financing the energy efficient transformation of the building sector in the EU. Lessons from the ODYSSEE-MURE project.Garrido, N., Almecija, J. C., Folch, C., Martínez, I. (2011). Certificación energética de edificios. Grupo de Estudios de Energía para la Sostenibilidad (CEES). Cátedra Unesco Sostenibilidad, Universitat Politècnica de Catalunya. (Available at: upcommons.upc.edu/e-prints/bitstream/2117/11820/1/GAS Natural_090406.pdf).Gómez, J. M., & Esteban, M. A. (2010). Sostenibilidad en la edificación. Comparación de dos tipologías constructivas. Rendimiento de los recursos. Ingeniería de Edificación Universitat Politècnica de Catalunya. (Available at: upcommons.upc.edu/pfc/bitstream/2099.1/…/1/PFG_Completo.pdf).Gram-Hanssen, K., Bartiaux, F., Michael Jensen, O., & Cantaert, M. (2007). Do homeowners use energy labels? A comparison between Denmark and Belgium. Energy Policy, 35(5), 2879–2888.Institut de Tecnologia de la Construcció de Catalunya (ITEC) (1991a). Manual de uso y conservación de la vivienda. COAAT Principado de Asturias. Simancas Ediciones S.A. Valladolid.Institut de Tecnologia de la Construcció de Catalunya (ITEC). (1991b). Manteniment de l’edifici. Fitxes (1st ed.). Badalona: Gràfiques Pacífic.Institut de Tecnologia de la Construcció de Catalunya (ITEC). (1991c). Manteniment instal.lacions. Fitxes (1st ed.). Badalona: Gràfiques Pacífic.Institut de Tecnologia de la Construcció de Catalunya (ITEC). (1991d). Manteniment urbanització. Fitxes (1st ed.). Badalona: Gràfiques Pacífic.Institut de Tecnologia de la Construcció de Catalunya (ITEC). (1994). L’actualitat i el cost del manteniment en edificis d’habitatge. Guia pràctic (1st ed.). Barcelona: Gama S.L. Servicios editoriales.Institut de Tecnologia de la Construcció de Catalunya (ITEC). (1996). Ús i manteniment de l’habitatge. Quadern de l’usuari (1st ed.). Zaragoza: Gràfiques Cometa.Institut de Tecnologia de la Construcció de Catalunya (ITEC) (1997). La vivienda: Manual de uso y mantenimient, COAAT de Cantabria. 1ª ed.Institut de Tecnologia de la Construcció de Catalunya (ITEC) (1999). La vivienda: Manual de uso y mantenimiento, COAAT Principado de Asturias. 2ª ed. Simancas Edicionas S.A. Valladolid.Instituto de Diversificación y Ahorro de Energía (IDAE), Ministerio de Industria, Turismo y Comercio (MITYC) (2010). Guía Técnica: Condiciones climáticas exteriores de proyecto, (available at: http://www.minetur.gob.es/energia/desarrollo/eficienciaenergetica/rite/reconocidos/reconocidos/condicionesclimaticas.pdf ).Instituto Eduardo Torroja de Ciencias de la Construcción (IETCC) (2010). Catálogo de Elementos Constructivos del Código Técnico, versión CAT-EC-v06.3-MARZO10. Madrid.Jáber-López, J. T., Valencia-Salazar, I., Peñalvo-López, E., Álvarez-Bel, C., Rivera-López, R., Merino-Hernández, E. (2011). Are energy certification tools for buildings effective? A Spanish case study, Proceedings of the 2011 3rd International Youth Conference on Energetics. Leiria, July 7–9.Johnstone, I. M. (2001a). Energy and mass flows of housing: a model and example. Building and Environment, 36, 27–41.Johnstone, I. M. (2001b). Energy and mass flows of housing: estimating mortality. Building and Environment, 36, 43–51.Kaiser, H. H. (2001). The facilities audit. A process for improving facilities conditions. Arlington: Kirby Lithographic. APPA. The Association of Higher Education Facilities Officers.Kjaerbye, V. H. (2008). Does energy label on residential housing cause energy savings? AKF, Danish Institute of Governmental Research.La Roche, P. (2010). Calculating green house emissions for houses: analysis of the performance of several carbon counting tools in different climates. Informes de la Construcción, 62(517), 61–80.Larsen, B. M., & Nebakken, R. (1997). Norwegian emissions of CO2 1987–1994. Environmental and Resource Economics, 9, 275–290.Laustsen, J. (2008). Energy efficiency requirements in building codes, energy efficiency policies for new buildings. Paris: International Energy Agency information paper.Linares, P., & Labandeira, X. (2010). Energy efficiency: economics and policy. Journal of Economic Surveys, 24(3), 573–592.Liska, R. W. (2000). Means facilities maintenance standards. Kingston: R.S. Means Company, Inc. Construction Publishers & Consultants.Majcen, D., Itard, H., & Visscher, H. (2013). Theoretical vs. actual energy consumption of labelled dwellings in the Netherlands: discrepancies and policy implications. Energy Policy, 54, 125–136.Mercader, M. P., Olivares, M., & Ramírez de Arellano, A. (2012). Modelo de cuantificación del consumo energético en edificación. Informes de la Construcción, 62(308), 567–582.Ministry of Development of Spain. Directorate for Architecture, Housing and Planning. Report on cost optimal calculations and comparison with the current and future energy performance requirements of buildings in Spain. Version 1.1, 7th June 2013.Pérez-Lombard, L., Ortiz, J., & González, R. (2009). A review of benmarching, rating and labelling concepts within the framework of building energy certification schemes. Energy and Buildings, 41(3), 272–278.Piper, J. E. (1995). Handbook of facility management: tools and techniques, formulas and tables. Upper Saddle River: Prentice Hall Inc.Popescu, D., Bienert, S., Schützenhofer, C., & Boazu, R. (2012). Impact of energy efficiency measures on the economic value of buildings. Applied Energy, 89(1), 454–463.Ramírez de Arellano, A. (2004). Presupuestación de obras. 3ª ed. Universidad de Sevilla. Secretariado de Publicaciones. Colección Manuales Universitarios, 37.Rodríguez-González, A. B., Vinagre-Díaz, J. J., Caañamo, A. J., & Wilby, M. R. (2011). Energy and buildings, 43(4), 980–987.Ruá, M. J., & Guadalajara, N. (2013). Application of compromise programming to a semi-detached housing development in order to balance economic and environmental criteria. Journal of the Operational Research Society, 64, 459–468.Ruá, M. J., & Guadalajara, N. (2014). Using the building energy rating software for mathematically modelling operation costs in a simulated home. International Journal of Computer Mathematics. doi: 10.1080/00207160.2014.892588 .Ruá, M. J., & López-Mesa, B. (2012). Certificación energética de edificios en España y sus implicaciones económicas. Informes de la Construcción, 64(527), 307–318.Rudbeck, C. (2002). Service life of building envelope components: making it operational in economical assessment. Construction and Building Materials, 16(2), 83–89.Ruiz, M. C., & Romero, E. (2011). Energy saving in the conventional design of a Spanish house using thermal simulation. Energy and Building, 43(11), 3226–3235.Sanstad, A. H., Blumstein, C., & Stoff, S. E. (1995). How high are option values in energy-efficiency investments? Energy Policy, 23(9), 739–743.Sumner, J., Bird, L., Smith, H. (2009). Carbon taxes: a review of experience and policy design consideration. Technical Report NREL/TP-6A2-47312. National Renewable Energy Laboratory. US Department of Energy.Tuominen, P., Forsström, J., & Honkatukia, J. (2013). Economic effects of energy efficiency improvements in the Finnish building stock. Energy Policy, 52, 181–189.Ucar, A., & Balo, F. (2009). Effect of fuel type on the optimum thickness of selected insulation materials for the four different climatic regions of Turkey. Applied Energy, 86(5), 730–736.Universidad Politécnica De Madrid. Departamento de Construcción y Vías Rurales (2009). Evaluación de los costes constructivos y consumos energéticos derivados de la calificación energética de viviendas. Precost&E. Fase1.Uzsilaityte, L., & Martinaitis, V. (2010). Search for optimal solution of public building renovation in terms of life cycle. Journal of Environmental Engineering and Landscape Management, 18(2), 102–110.Verbruggen, A. (2012). Financial appraisal of efficiency investments: why the good may be the worst enemy of the best. Energy Efficiency, 5, 571–582

Macrophages in inflammatory multiple sclerosis lesions have an intermediate activation status

BACKGROUND: Macrophages play a dual role in multiple sclerosis (MS) pathology. They can exert neuroprotective and growth promoting effects but also contribute to tissue damage by production of inflammatory mediators. The effector function of macrophages is determined by the way they are activated. Stimulation of monocyte-derived macrophages in vitro with interferon-γ and lipopolysaccharide results in classically activated (CA/M1) macrophages, and activation with interleukin 4 induces alternatively activated (AA/M2) macrophages. METHODS: For this study, the expression of a panel of typical M1 and M2 markers on human monocyte derived M1 and M2 macrophages was analyzed using flow cytometry. This revealed that CD40 and mannose receptor (MR) were the most distinctive markers for human M1 and M2 macrophages, respectively. Using a panel of M1 and M2 markers we next examined the activation status of macrophages/microglia in MS lesions, normal appearing white matter and healthy control samples. RESULTS: Our data show that M1 markers, including CD40, CD86, CD64 and CD32 were abundantly expressed by microglia in normal appearing white matter and by activated microglia and macrophages throughout active demyelinating MS lesions. M2 markers, such as MR and CD163 were expressed by myelin-laden macrophages in active lesions and perivascular macrophages. Double staining with anti-CD40 and anti-MR revealed that approximately 70% of the CD40-positive macrophages in MS lesions also expressed MR, indicating that the majority of infiltrating macrophages and activated microglial cells display an intermediate activation status. CONCLUSIONS: Our findings show that, although macrophages in active MS lesions predominantly display M1 characteristics, a major subset of macrophages have an intermediate activation status

Pneumocystis murina colonization in immunocompetent surfactant protein A deficient mice following environmental exposure

<p>Abstract</p> <p>Background</p> <p><it>Pneumocystis spp</it>. are opportunistic pathogens that cause pneumonia in immunocompromised humans and animals. <it>Pneumocystis </it>colonization has also been detected in immunocompetent hosts and may exacerbate other pulmonary diseases. Surfactant protein A (SP-A) is an innate host defense molecule and plays a role in the host response to <it>Pneumocystis</it>.</p> <p>Methods</p> <p>To analyze the role of SP-A in protecting the immunocompetent host from <it>Pneumocystis </it>colonization, the susceptibility of immunocompetent mice deficient in SP-A (KO) and wild-type (WT) mice to <it>P. murina </it>colonization was analyzed by reverse-transcriptase quantitative PCR (qPCR) and serum antibodies were measured by enzyme-linked immunosorbent assay (ELISA).</p> <p>Results</p> <p>Detection of <it>P. murina </it>specific serum antibodies in immunocompetent WT and KO mice indicated that the both strains of mice had been exposed to <it>P. murina </it>within the animal facility. However, P. <it>murina </it>mRNA was only detected by qPCR in the lungs of the KO mice. The incidence and level of the mRNA expression peaked at 8–10 weeks and declined to undetectable levels by 16–18 weeks. When the mice were immunosuppressed, <it>P. murina </it>cyst forms were also only detected in KO mice. <it>P. murina </it>mRNA was detected in <it>SCID </it>mice that had been exposed to KO mice, demonstrating that the immunocompetent KO mice are capable of transmitting the infection to immunodeficient mice. The pulmonary cellular response appeared to be responsible for the clearance of the colonization. More CD4+ and CD8+ T-cells were recovered from the lungs of immunocompetent KO mice than from WT mice, and the colonization in KO mice depleted CD4+ cells was not cleared.</p> <p>Conclusion</p> <p>These data support an important role for SP-A in protecting the immunocompetent host from <it>P. murina </it>colonization, and provide a model to study <it>Pneumocystis </it>colonization acquired via environmental exposure in humans. The results also illustrate the difficulties in keeping mice from exposure to <it>P. murina </it>even when housed under barrier conditions.</p