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Identification of the mammalian Not gene via a phylogenomic approach

GENE EXPRESSION PATTERNS 2004年第1期5卷 11-22页

作者： Plouhinec, JL Granier, C Le Mentec, C Lawson, KA Sabéran-Djoneidi, D Aghion, J Shi, DL Collignon, J Mazan, S Univ Paris 11 Dev & Evolut Vertebres UMR 8080 F-91405 Orsay France Univ Paris 06 CNRS Dept Dev Biol Inst Jacques Monod F-75251 Paris 05 France Univ Paris 07 CNRS Dept Dev Biol Inst Jacques Monod F-75251 Paris 05 France Netherlands Inst Dev Biol Hubrecht Lab NL-3584 CT Utrecht Netherlands CNRS Grp Biol Expt UMR 7622 F-75005 Paris France

Despite the great morphological diversity of early embryos, the underlying mechanisms of gastrulation are known to be broadly conserved in vertebrates. However, a number of genes characterized as fulfilling an essential function in this process in several model organisms display no clear ortholog in mammalian genomes. We have devised an in silico phylogenomic approach, based on exhaustive similarity searches in vertebrate genomes and subsequent bayesian phylogenetic analyses, to identify such missing genes, presumed to be highly divergent. This approach has been used to identify mammalian orthologs of Not, an homeodomain containing gene previously characterized in Xenopus, chick and zebrafish as playing a critical role in the formation of the notochord. This attempt led to the identification of a highly divergent mammalian Not-related gene in the mouse, human and rat. The results from phylogenetic reconstructions, synteny analyses, expression pattern analyses in wild-type and mutant mouse embryos, and overexpression experiments in Xenopus embryos converge to confirm these genes as representatives of the Not family in mammals. The identification of the mammalian Not gene delivers an important component for the understanding of the genetics underlying notochord formation in mammals and its evolution among vertebrates. The phylogenomic method used to retrieve this gene thus provides a tool, which can complement or validate genome annotations in situations when they are weakly supported. (C) 2004 Elsevier B.V. All rights reserved.

关键词： Not floating head nodal Foxa2 axial mesoderm notochord node phylogenomic bayesian algorithm NKL complex

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Population pharmacokinetic and dynamic analysis of the topoisomerase I inhibitor lurtotecan in phase II studies

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INVESTIGATIONAL NEW DRUGS 2002年第1期20卷 83-93页

作者： Schellens, JHM Heinrich, B Lehnert, M Gore, ME Kaye, SB Dombernowsky, P Paridaens, R van Oosterom, AT Verweij, J Loos, WJ Calvert, H Pavlidis, N Cortes-Funes, H Wanders, J Roelvink, M Sessa, C Selinger, K Wissel, PS Gamucci, T Hanauske, AR Netherlands Canc Inst Dept Med Oncol NL-1066 CX Amsterdam Netherlands Tech Univ Munich Klinikum Rechts Isar D-8000 Munich Germany Kantonsspital St Gallen Klin Innere Med C St Gallen Switzerland Inst Canc Res CRC Ctr Canc Therapeut Surrey England Western Infirm & Associated Hosp Beatson Oncol Ctr Dept Med Oncol Glasgow G11 6NT Lanark Scotland Copenhagen Univ Hosp Herlev Denmark Catholic Univ Louvain Univ Hosp Gasthuisberg B-3000 Louvain Belgium Rotterdam Canc Inst Daniel den Hoed Klin Rotterdam Netherlands Univ Rotterdam Hosp Rotterdam Netherlands Newcastle Gen Hosp Div Oncol Newcastle Upon Tyne NE4 6BE Tyne & Wear England Univ Ioannina Dept Internal Med GR-45110 Ioannina Greece Hosp Univ 12 Octubre Dept Med Oncol Madrid Spain EORTC New Drug Dev Office Amsterdam Netherlands Osped San Giovanni Bellinzona Bellinzona Switzerland Glaxo Wellcome Inc Res Triangle Pk NC 27709 USA Ist Regina Elena I-00161 Rome Italy

Population pharmacokinetic-dynamic analysis was prospectively integrated in a broad phase II program of lurtotecan (GI147211), a novel camptothecin derived topoisomerase I inhibitor, to determine the population pharmacokinetic profile in a larger population, to estimate individual pharmacokinetic parameters and to investigate relationships with clinical outcome. A sparse sampling method was applied during course one, which involved two sampling time-points. A bayesian algorithm was used to estimate individual pharmacokinetic parameters. in particular total plasma clearance (CL) and volume of distribution. In total, samples were collected of 109 (63%) of 173 patients. Pharmacokinetic-dynamic evaluation could be carried out successfully in 85 (78%) of the sampled patients. CL of lurtotecan showed substantial variability (mean 87 28 L/h) and was of the same magnitude as in the phase I studies where full pharmacokinetic curves were used. Residual variability in the population estimate of CL was 9.9%. No significant relationships were observed between exposure parameters and toxicity nor likelihood of tumor response, however the latter relationship may well have been obscured by the heterogeneity of the studied population. Prospective implementation of large scale population pharmacokinetic-dynamic analysis is feasible and important to establish whether interpatient variability in drug exposure is a major determinant of toxicity or activity.

关键词： lurtotecan (GI147211) population analysis pharmacokinetics pharmacodynamics NONMEM bayesian algorithm phase II topoisomerase I

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Green and energy-saving ecological renovation design of buildings based on energy consumption monitoring data

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MULTISCALE AND MULTIDISCIPLINARY MODELING EXPERIMENTS AND DESIGN 2024年第4期7卷 3227-3241页

作者： Li, Li Henan Tech Coll Construct Zhengzhou 450064 Henan Peoples R China

In order to achieve energy conservation and environmental protection of old buildings and reduce energy consumption, the design method of green energy conservation and ecological conversion of buildings based on energy consumption monitoring data is studied. A building energy consumption monitoring structure is designed to collect energy usage data of typical facilities in the area. According to the typical building energy consumption monitoring data, the building energy consumption prediction model is constructed by using the bayesian algorithm to obtain the energy consumption data of all buildings in the region. We set the building energy consumption comparison benchmark, calculated the energy conservation of the green energy-efficient ecological conversion design of housings according to the energy consumption data of all buildings in the region, took the maximisation of energy saving as the objective function, and built the green ecological transformation design model of buildings based on opportunity constraint planning. Different confidence levels are set within the model to reflect the user's tolerance for constraint violations and their choice of diversified comfort intervals. A particle congestion optimisation process is applied to fix the model, and the decision-making results of building green and energy-saving ecological transformation are obtained. The experimental results show that this method can effectively collect the energy consumption data of building energy usage equipment and accurately anticipate the energy usage data of other buildings in the region. Users can exchange economic and diversified energy consumption decisions by losing a certain degree of comfort and adjusting the constraint interval.

关键词： Energy consumption monitoring Green building Energy-saving and ecological transformation bayesian algorithm Energy consumption forecast Opportunity-constrained planning

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Comparison of various methods for simultaneous retrieval of surface emissivities and gas properties in gray participating media

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JOURNAL OF HEAT TRANSFER-TRANSACTIONS OF THE ASME 2006年第8期128卷 829-837页

作者： Deiveegan, M. Balaji, C. Venkateshan, S. P. Indian Inst Technol Dept Mech Engn Heat Transfer & Thermal Power Lab Madras 600036 Tamil Nadu India

An inverse radiation analysis for simultaneous estimation of the radiative properties and the surface emissivities for a participating medium in between infinitely long parallel planes, from the knowledge of the measured temperatures and heat fluxes at the boundaries, is presented. The differential, discrete ordinate method is employed to solve the radiative transfer equation. The present analysis considers three types of simple scattering phase functions. The inverse problem is solved through minimization of a performance function, which is expressed by the sum of squares of residuals between calculated and observed temperatures and heat fluxes at the boundaries. To check the performance and accuracy in retrieval, a comparison is presented between four retrieval methods, viz. Levenberg-Marquardt algorithm, genetic. algorithm, artificial neural network, and the bayesian algorithm. The results of the present analyses indicate that good precision in retrieval could be achieved by using only temperatures and heat fluxes at,the boundaries. The study shows that. the radiative properties of medium and surface emissivities can be retrieved even with noisy data using bayesian retrieval algorithm and artificial neural network. Also, the results demonstrate that genetic algorithms are not efficient but are quite robust. Additionally, it is observed that an increase in the error in measurements significantly deteriorates the retrieval using the Levenberg-Marquardt algorithm.

关键词： inverse radiation problem parameter estimation discrete ordinate method Levenberg-Marquardt algorithm genetic algorithm artificial neural network bayesian algorithm

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Specificity of the wide QRS complex tachycardia algorithms in recipients of cardiac resynchronization therapy

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JOURNAL OF ELECTROCARDIOLOGY 2012年第3期45卷 319-326页

作者： Jastrzebski, Marek Kukla, Piotr Czarnecka, Danuta Kawecka-Jaszcz, Kalina Univ Hosp Dept Cardiol & Hypertens 1 PL-31501 Krakow Poland H Klimontowicz Specialist Hosp Dept Internal Med Gorlice Poland Jagiellonian Univ Dept Cardiol & Hypertens 1 Coll Med Krakow Poland

Background: We assessed the specificity of wide QRS complex tachycardia (WCT) differentiating algorithms in patients with preexistent left bundle branch block (LBBB) and heart failure. Methods: Three hundred fourteen patients with resynchronization devices were retrospectively screened. electrocardiograms with supraventricular LBBB rhythm were used as a surrogate for supraventricular tachycardia QRS morphology. The Pava lead II criterion, ventricular activation velocity ratio (Vi/Vt) ratio in V-2, Vereckei aVR, Brugada, Griffith, and bayesian algorithms were investigated. Results: The WCT algorithms had a lower specificity (33%-69%) in patients with LBBB than in general WCT populations. The Pava lead II criterion and Brugada algorithm had higher specificity than other algorithms (P<.05). Several of the single criteria (absence of an RS complex in V-1 through V-6, initial R wave in aVR, Vi/Vt <1 in V-2) had specificities of 92% to 99%. Conclusions: In patients with heart failure and LBBB, an electrocardiographic diagnosis of ventricular tachycardia should be based on selected, specific criteria rather than on WCT algorithms. (C) 2012 Elsevier Inc. All rights reserved.

关键词： Wide QRS complex tachycardia Brugada algorithm aVR algorithm Griffith algorithm bayesian algorithm

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bayesian active machine learning for Cluster expansion construction

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COMPUTATIONAL MATERIALS SCIENCE 2024年 231卷

作者： Chen, Hantong Samanta, Sayan Zhu, Siya Eckert, Hagen Schroers, Jan Curtarolo, Stefano van de Walle, Axel Brown Univ Sch Engn Providence RI 02912 USA Duke Univ Dept Mech Engn & Mat Sci Durham NC 27708 USA Yale Univ Dept Mech Engn & Mat Sci New Haven CT 06511 USA

The Cluster expansion (CE) is a powerful method for representing the energetics of alloys from a fit to first principles energies. However, many common fitting methods are computationally demanding and do not provide the guarantee that the system's ground states are preserved. This paper demonstrates the use of an efficient implementation of a bayesian algorithm for cluster expansion construction that ensures all the input structural energies are fitted perfectly while reducing computational cost. The method incorporates an active learning scheme that searches for new optimal structures to include in the fit. As performance tests, we calculate the phase diagram of the Fe-Ir system and study the short range order in an equimolar MoNbTaVW system. The new method has been integrated into the Alloy Theoretic Automated Toolkit (ATAT).

关键词： Cluster expansion bayesian algorithm Active learning

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Predicting stimulus-locked single unit spiking from cortical local field potentials

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JOURNAL OF COMPUTATIONAL NEUROSCIENCE 2010年第3期29卷 581-597页

作者： Galindo-Leon, Edgar E. Liu, Robert C. Emory Univ Dept Biol Atlanta GA 30322 USA Georgia State Univ Ctr Behav Neurosci Atlanta GA 30302 USA

The rapidly increasing use of the local field potential (LFP) has motivated research to better understand its relation to the gold standard of neural activity, single unit (SU) spiking. We addressed this in an in vivo, awake, restrained mouse auditory cortical electrophysiology preparation by asking whether the LFP could actually be used to predict stimulus-evoked SU spiking. Implementing a bayesian algorithm to predict the likelihood of spiking on a trial by trial basis from different representations of the despiked LFP signal, we were able to predict, with high quality and fine temporal resolution (2 ms), the time course of a SU's excitatory or inhibitory firing rate response to natural species-specific vocalizations. Our best predictions were achieved by representing the LFP by its wide-band Hilbert phase signal, and approximating the statistical structure of this signal at different time points as independent. Our results show that each SU's action potential has a unique relationship with the LFP that can be reliably used to predict the occurrence of spikes. This "signature" interaction can reflect both pre- and post-spike neural activity that is intrinsic to the local circuit rather than just dictated by the stimulus. Finally, the time course of this "signature" may be most faithful when the full bandwidth of the LFP, rather than specific narrow-band components, is used for representation.

关键词： LFP Spike prediction Auditory cortex Gamma band Theta band Beta band Oscillation bayesian algorithm A1 Evoked potentials Electroencephalography EEG Hilbert transform Single cortical cells Phase Despiking

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Unknown Malicious Code Detection Based on bayesian

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Procedia Engineering 2011年 15卷 3836-3842页

作者： Yingxu Lai Zhenghui Liu College of Computer Science Beijing University of Technology Beijing 100124China Science and Technology Engineering Faculty Beijing Vocational College of Electronic Science Beijing 100029 China

Analyzed bayesian classifier with string, n -gram and API as features, we found that it is very difficult to improve bayesian classifier detection accuracy because selected features are not completely independent. In order to solve this problem, we propose a new improved choose features method which are most representative properties, and show that our method achieve high detection rates, even on completely new, previously unseen malicious executables.

关键词： malicious codes detection bayesian algorithm

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Efficiency of Optimal Joint Detection and Estimation of Image Areas with Spatial Noise

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OPTOELECTRONICS INSTRUMENTATION AND DATA PROCESSING 2013年第3期49卷 221-227页

作者： Trifonov, A. P. Zimovets, K. A. Korchagin, Yu. E. Voronezh State Univ Univ Pl 1 Voronezh 394006 Russia

bayesian and maximum likelihood algorithms are considered. A comparative analysis of their effectiveness is performed. The results are specified for an image in the shape of an ellipse with linearly varying intensity.

关键词： maximum likelihood algorithm bayesian algorithm characteristics of algorithms statistical modeling

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Mutant Altimetric Parameter Estimation Using a Gradient-Based bayesian Method

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IEEE GEOSCIENCE AND REMOTE SENSING LETTERS 2022年 19卷 1页

作者： Liao, Xianghong Zhang, Zenghui Jiang, Ge China Acad Engn Phys Inst Elect Engn Grad Sch Mianyang 621000 Sichuan Peoples R China Shanghai Jiao Tong Univ Shanghai Key Lab Intelligent Sensing & Recognit Shanghai 200000 Peoples R China China Acad Engn Phys Inst Elect Engn Mianyang 621000 Sichuan Peoples R China

This letter proposes an advanced bayesian algorithm for the estimation of mutant altimetric parameters. A sparse prior is introduced to enforce a mutant evolution of the altimetric parameters. A maximum a posterior (MAP) estimator based on an alternating optimization algorithm is carried out to fulfill our proposed hierarchical bayesian model. The proposed bayesian method and the corresponding estimation algorithm are evaluated using both synthetic and real altimetric data associated with a delay/Doppler altimetric model. The experimental results show that the proposed method brings an improvement on mutant parameter estimation and tracking when compared to smooth estimation and other state-of-the-art estimation algorithms.

关键词： bayesian algorithm mutant topography radar altimetry sparse prior

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