Automatic, fast and robust characterization of noise distributions for diffusion MRI

Knowledge of the noise distribution in magnitude diffusion MRI images is the centerpiece to quantify uncertainties arising from the acquisition process. The use of parallel imaging methods, the number of receiver coils and imaging filters applied by the scanner, amongst other factors, dictate the resulting signal distribution. Accurate estimation beyond textbook Rician or noncentral chi distributions often requires information about the acquisition process (e.g. coils sensitivity maps or reconstruction coefficients), which is not usually available. We introduce a new method where a change of variable naturally gives rise to a particular form of the gamma distribution for background signals. The first moments and maximum likelihood estimators of this gamma distribution explicitly depend on the number of coils, making it possible to estimate all unknown parameters using only the magnitude data. A rejection step is used to make the method automatic and robust to artifacts. Experiments on synthetic datasets show that the proposed method can reliably estimate both the degrees of freedom and the standard deviation. The worst case errors range from below 2% (spatially uniform noise) to approximately 10% (spatially variable noise). Repeated acquisitions of in vivo datasets show that the estimated parameters are stable and have lower variances than compared methods.Comment: v2: added publisher DOI statement, fixed text typo in appendix A

Variable protection against experimental broiler necrotic enteritis after immunization with the C-terminal fragment of Clostridium perfringens alpha-toxin and a non-toxic NetB variant

This is the final version of the article. Available from the publisher via the DOI in this record.Necrotic enteritis toxin B (NetB) is a pore-forming toxin produced by Clostridium perfringens and has been shown to play a key role in avian necrotic enteritis, a disease causing significant costs to the poultry production industry worldwide. The aim of this work was to determine whether immunization with a non-toxic variant of NetB (NetB W262A) and the C-terminal fragment of C. perfringens alpha-toxin (CPA247-370) would provide protection against experimental necrotic enteritis. Immunized birds with either antigen or a combination of antigens developed serum antibody levels against NetB and CPA. When CPA247-370 and NetB W262A were used in combination as immunogens, an increased protection was observed after oral challenge by individual dosing, but not after in-feed-challenge

Clostridium perfringens Epsilon Toxin Compromises the Blood-Brain Barrier in a Humanized Zebrafish Model

This is the final version. Available on open access from Elsevier vis the DOI in this recordClostridium perfringens epsilon toxin (ETX) is hypothesized to mediate blood-brain barrier (BBB) permeability by binding to the myelin and lymphocyte protein (MAL) on the luminal surface of endothelial cells (ECs). However, the kinetics of this interaction and a general understanding of ETX's behavior in a live organism have yet to be appreciated. Here we investigate ETX binding and BBB breakdown in living Danio rerio (zebrafish). Wild-type zebrafish ECs do not bind ETX. When zebrafish ECs are engineered to express human MAL (hMAL), proETX binding occurs in a time-dependent manner. Injection of activated toxin in hMAL zebrafish initiates BBB leakage, hMAL downregulation, blood vessel stenosis, perivascular edema, and blood stasis. We propose a kinetic model of MAL-dependent ETX binding and neurovascular pathology. By generating a humanized zebrafish BBB model, this study contributes to our understanding of ETX-induced BBB permeability and strengthens the proposal that MAL is the ETX receptor.National Institute of Neurological Disorders and StrokeWilma S. and Laurence A. Tisch Foundatio

TWIST1 Is Expressed in Colorectal Carcinomas and Predicts Patient Survival

TWIST1 is a transcription factor that belongs to the family of basic helix-loop-helix proteins involved in epithelial-to-mesenchymal transition and invasion processes. The TWIST1 protein possesses oncogenic, drug-resistant, angiogenic and invasive properties, and has been related with several human tumors and other pathologies. Colorectal cancer is one of the tumors in which TWIST1 is over-expressed, but its involvement in the clinical outcome of the disease is still unclear. We tested, by RT-PCR, the expression levels of TWIST1 in normal and tumor paired-sample tissues from a series of 151 colorectal cancer patients, in order to investigate its prognostic value as a tumor marker. TWIST1 expression was restricted to tumor tissues (86.1%) and correlated with lymph node metastasis (LNM). Adjusted analysis showed that the expression levels of TWIST1 correlated with overall survival (OS) and disease-free survival (DFS). Importantly, TWIST1 expression levels predicted OS specifically at stages I and II. Moreover, patients with stage II tumors and high TWIST1 levels showed even shorter survival than patients with stage III tumors. These results suggest that TWIST1 expression levels could be a tumor indicator in stage II patients and help select patients at greater risk of poor prognosis who might benefit from adjuvant chemotherapy

Mycosin-1, a subtilisin-like serine protease of Mycobacterium tuberculosis, is cell wall-associated and expressed during infection of macrophages

BACKGROUND: Exported proteases are commonly associated with virulence in bacterial pathogens, yet there is a paucity of information regarding their role in Mycobacterium tuberculosis. There are five genes (mycP1-5) present within the genome of Mycobacterium tuberculosis H37Rv that encode a family of secreted, subtilisin-like serine proteases (the mycosins). The gene mycP1 (encoding mycosin-1) was found to be situated 3700 bp (four ORF's) from the RD1 deletion region in the genome of the attenuated vaccine strain M. bovis BCG (bacille de Calmette et Guérin) and was selected for further analyses due to the absence of expression in this organism. RESULTS: Full-length, 50 kDa mycosin-1 was observed in M. tuberculosis cellular lysates, whereas lower-molecular-weight species were detected in culture filtrates. A similar lower-molecular-weight species was also observed during growth in macrophages. Mycosin-1 was localized to the membrane and cell wall fractions in M. tuberculosis by Western blotting, and to the cell envelope by electron microscopy. Furthermore, M. tuberculosis culture filtrates were shown to contain a proteolytic activity inhibited by mixed serine/cysteine protease inhibitors and activated by Ca(2+), features typical of the subtilisins. CONCLUSIONS: Mycosin-1 is an extracellular protein that is membrane- and cell wall-associated, and is shed into the culture supernatant. The protein is expressed after infection of macrophages and is subjected to proteolytic processing. Although proteolytically active mycosin-1 could not be generated recombinantly, serine protease activity containing features typical of the subtilisins was detected in M. tuberculosis culture filtrates

CHY representations for gauge theory and gravity amplitudes with up to three massive particles

We show that a wide class of tree-level scattering amplitudes involving scalars, gauge bosons, and gravitons, up to three of which may be massive, can be expressed in terms of a Cachazo-He-Yuan representation as a sum over solutions of the scattering equations. These amplitudes, when expressed in terms of the appropriate kinematic invariants, are independent of the masses and therefore identical to the corresponding massless amplitudes.Comment: 20 pages, 1 figure; v2: minor typos corrected, published versio

Vector boson pair production at the LHC

We present phenomenological results for vector boson pair production at the LHC, obtained using the parton-level next-to-leading order program MCFM. We include the implementation of a new process in the code, pp -> \gamma\gamma, and important updates to existing processes. We incorporate fragmentation contributions in order to allow for the experimental isolation of photons in \gamma\gamma, W\gamma, and Z\gamma production and also account for gluon-gluon initial state contributions for all relevant processes. We present results for a variety of phenomenological scenarios, at the current operating energy of \sqrt{s} = 7 TeV and for the ultimate machine goal, \sqrt{s} = 14 TeV. We investigate the impact of our predictions on several important distributions that enter into searches for new physics at the LHC.Comment: 35 pages, 14 figure

Application of Compromise Programming to a semi-detached housing development in order to balance economic and environmental criteria

This is a post-peer-review, pre-copyedit version of an article published in Journal of the Operational Research Society. The definitive publisher-authenticated version: Ruá Aguilar, MJ.; Guadalajara Olmeda, MN. (2012). 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(3):459-468, is available online at: http://www.palgrave-journals.com/jors/journal/v64/n3/full/jors201276a.html.European Energy Performance of Buildings Directives DE promote energy efficiency in buildings. Under these Directives, the European Union States must apply minimum requirements regarding the energy performance of buildings and ensure the certification of their energy performance. The Directives set only the basic principles and requirements, leaving a significant amount of room for the Member States to establish their specific mechanisms, numeric requirements and ways to implement them, taking into account local conditions. With respect to the Spanish case, the search for buildings that are more energy efficient results in a conflict between users¿ economic objectives and society's environmental objectives. In this paper, Compromise Programming is applied to help in the decision-making process. An appropriate distribution of types of dwellings, according to their energy performance and to the climatic zone considered in Spain, will be suggested. Results provide a compromise solution between both objectives.Ruá Aguilar, MJ.; Guadalajara Olmeda, MN. (2012). 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(3):459-468. doi:10.1057/jors.2012.76S459468643Andaloro, A. P. F., 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. doi:10.1016/j.enpol.2010.05.039André, F. J., Cardenete, M. A., & Romero, C. (2008). Using compromise programming for macroeconomic policy making in a general equilibrium framework: theory and application to the Spanish economy. Journal of the Operational Research Society, 59(7), 875-883. doi:10.1057/palgrave.jors.2602415Baja, S., Chapman, D. M., & Dragovich, D. (2006). Spatial based compromise programming for multiple criteria decision making in land use planning. Environmental Modeling & Assessment, 12(3), 171-184. doi:10.1007/s10666-006-9059-1Ballestero, E., & Romero, C. (1991). A theorem connecting utility function optimization and compromise programming. Operations Research Letters, 10(7), 421-427. doi:10.1016/0167-6377(91)90045-qBallestero, E., & Romero, C. (1993). Weighting in compromise programming: A theorem on shadow prices. Operations Research Letters, 13(5), 325-329. doi:10.1016/0167-6377(93)90055-lDavies, H., & Wyatt, D. (2004). Appropriate use of the ISO 15686-1 factor method for durability and service life prediction. Building Research & Information, 32(6), 552-553. doi:10.1080/0961321042000291938Diakaki, C., Grigoroudis, E., Kabelis, N., Kolokotsa, D., Kalaitzakis, K., & Stavrakakis, G. (2010). A multi-objective decision model for the improvement of energy efficiency in buildings. Energy, 35(12), 5483-5496. doi:10.1016/j.energy.2010.05.012Dı́az-Balteiro, L., & Romero, C. (2003). Forest management optimisation models when carbon captured is considered: a goal programming approach. Forest Ecology and Management, 174(1-3), 447-457. doi:10.1016/s0378-1127(02)00075-0Diaz-Balteiro, L., & Rodriguez, L. C. E. (2006). Optimal rotations on Eucalyptus plantations including carbon sequestration—A comparison of results in Brazil and Spain. Forest Ecology and Management, 229(1-3), 247-258. doi:10.1016/j.foreco.2006.04.005Fattahi, P., & Fayyaz, S. (2009). A Compromise Programming Model to Integrated Urban Water Management. Water Resources Management, 24(6), 1211-1227. doi:10.1007/s11269-009-9492-4Hamdy, M., Hasan, A., & Siren, K. (2011). Applying a multi-objective optimization approach for Design of low-emission cost-effective dwellings. Building and Environment, 46(1), 109-123. doi:10.1016/j.buildenv.2010.07.006Johnstone, I. M. (2001). Energy and mass flows of housing: a model and example. Building and Environment, 36(1), 27-41. doi:10.1016/s0360-1323(99)00065-7Johnstone, I. M. (2001). Energy and mass flows of housing: estimating mortality. Building and Environment, 36(1), 43-51. doi:10.1016/s0360-1323(99)00066-9Linares, P., & Romero, C. (2000). A multiple criteria decision making approach for electricity planning in Spain: economic versus environmental objectives. Journal of the Operational Research Society, 51(6), 736-743. doi:10.1057/palgrave.jors.2600944Rey, F. J., Velasco, E., & Varela, F. (2007). Building Energy Analysis (BEA): A methodology to assess building energy labelling. Energy and Buildings, 39(6), 709-716. doi:10.1016/j.enbuild.2006.07.009Rudbeck, C. (2002). Service life of building envelope components: making it operational in economical assessment. Construction and Building Materials, 16(2), 83-89. doi:10.1016/s0950-0618(02)00003-xSan-José, J. T., Losada, R., Cuadrado, J., & Garrucho, I. (2007). Approach to the quantification of the sustainable value in industrial buildings. Building and Environment, 42(11), 3916-3923. doi:10.1016/j.buildenv.2006.11.013Yu, P. L. (1973). A Class of Solutions for Group Decision Problems. Management Science, 19(8), 936-946. doi:10.1287/mnsc.19.8.936Zelany, M. (1974). 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A novel East African monopartite begomovirus-betasatellite complex that infects Vernonia amygdalina

The complete genomes of a monopartite begomovirus (genus Begomovirus, family Geminiviridae) and an associated betasatellite found infecting Vernonia amygdalina Delile (family Compositae) in Uganda were cloned and sequenced. Begomoviruses isolated from two samples showed the highest nucleotide sequence identity (73.1% and 73.2%) to an isolate of the monopartite begomovirus tomato leaf curl Vietnam virus, and betasatellites from the same samples exhibited the highest nucleotide sequence identity (67.1% and 68.2%) to vernonia yellow vein Fujian betasatellite. Following the current taxonomic criteria for begomovirus species demarcation, the isolates sequenced here represent a novel begomovirus species. Based on symptoms observed in the field, we propose the name vernonia crinkle virus (VeCrV) for this novel begomovirus and vernonia crinkle betasatellite (VeCrB) for the associated betasatellite. This is the first report of a monopartite begomovirus-betasatellite complex from Uganda