3,152 results match your criteria modeling yields

Comparative Metabolic Modeling of Multiple Sulfate-reducing Prokaryotes Reveals Versatile Energy Conservation Mechanisms.

Biotechnol Bioeng 2021 Apr 12. Epub 2021 Apr 12.

Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Read More

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Simulation of Wheat Productivity Using a Model Integrated With Proximal and Remotely Controlled Aerial Sensing Information.

Front Plant Sci 2021 24;12:649660. Epub 2021 Mar 24.

Department of Agricultural Science, Gyeongsang National University, Jinju, South Korea.

A crop model incorporating proximal sensing images from a remote-controlled aerial system (RAS) can serve as an enhanced alternative for monitoring field-based geospatial crop productivity. This study aimed to investigate wheat productivity for different cultivars and various nitrogen application regimes and determine the best management practice scenario. We simulated spatiotemporal wheat growth and yield by integrating RAS-based sensing images with a crop-modeling system to achieve the study objective. Read More

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Identifying resting locations of a small elusive forest carnivore using a two-stage model accounting for GPS measurement error and hidden behavioral states.

Mov Ecol 2021 Apr 6;9(1):17. Epub 2021 Apr 6.

US Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, Cook, WA, 98605, USA.

Background: Studies of animal movement using location data are often faced with two challenges. First, time series of animal locations are likely to arise from multiple behavioral states (e.g. Read More

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Slamming the sham: A Bayesian model for adaptive adjustment with noisy control data.

Stat Med 2021 Apr 5. Epub 2021 Apr 5.

Department of Information and Computing Sciences, Utrecht University, Utrecht, Netherlands.

It is not always clear how to adjust for control data in causal inference, balancing the goals of reducing bias and variance. We show how, in a setting with repeated experiments, Bayesian hierarchical modeling yields an adaptive procedure that uses the data to determine how much adjustment to perform. The result is a novel analysis with increased statistical efficiency compared with the default analysis based on difference estimates. Read More

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Reaction pathways in the solid state and the Hubbard U correction.

J Chem Phys 2021 Mar;154(12):124121

School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.

We investigate how the Hubbard U correction influences vacancy defect migration barriers in transition metal oxide semiconductors. We show that, depending on the occupation of the transition metal d orbitals, the Hubbard U correction can cause severe instabilities in the migration barrier energies predicted using generalized gradient approximation density functional theory (GGA DFT). For the d oxide SrTiO, applying a Hubbard correction to the Ti 3d orbitals below 4-5 eV yields a migration barrier of ∼0. Read More

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Magnetoelastic Coupling and Delta-E Effect in Magnetoelectric Torsion Mode Resonators.

Sensors (Basel) 2021 Mar 12;21(6). Epub 2021 Mar 12.

Institute of Materials Science, Faculty of Engineering, Kiel University, 24143 Kiel, Germany.

Magnetoelectric resonators have been studied for the detection of small amplitude and low frequency magnetic fields via the delta-E effect, mainly in fundamental bending or bulk resonance modes. Here, we present an experimental and theoretical investigation of magnetoelectric thin-film cantilevers that can be operated in bending modes (BMs) and torsion modes (TMs) as a magnetic field sensor. A magnetoelastic macrospin model is combined with an electromechanical finite element model and a general description of the delta-E effect of all stiffness tensor components is derived. Read More

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Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors.

Molecules 2021 Mar 30;26(7). Epub 2021 Mar 30.

N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia.

A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to and rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Read More

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Novel (Phenothiazinyl)Vinyl-Pyridinium Dyes and Their Potential Applications as Cellular Staining Agents.

Int J Mol Sci 2021 Mar 15;22(6). Epub 2021 Mar 15.

Research Center on Fundamental and Applied Heterochemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.

We report here the synthesis and structural characterization of novel cationic (phenothiazinyl)vinyl-pyridinium (PVP) dyes, together with optical (absorption/emission) properties and their potential applicability as fluorescent labels. Convective heating, ultrasound irradiation and mechanochemical synthesis were considered as alternative synthetic methodologies proficient for overcoming drawbacks such as long reaction time, nonsatisfactory yields or solvent requirements in the synthesis of novel dye (E)-1-(3-chloropropyl)-4-(2-(10-methyl-10H-phenothiazin-3-yl)vinyl)pyridin-1-ium bromide and its -alkyl-2-methylpyridinium precursor . The geometry of the newly synthesized (E)-4-(2-(7-bromo-10-ethyl-10H-phenothiazin-3-yl)vinyl)-1-methylpyridin-1-ium iodide and (E)-1-methyl-4-(2-(10-methyl-10H-phenothiazin-3-yl)vinyl)pyridin-1-ium tetrafluoroborate was confirmed by single crystal X-ray diffraction. Read More

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Multi-Time Resolution Ensemble LSTMs for Enhanced Feature Extraction in High-Rate Time Series.

Sensors (Basel) 2021 Mar 10;21(6). Epub 2021 Mar 10.

Air Force Research Laboratory, Munitions Directorate, Fuzes Branch, Eglin Air Force Base, FL 32542, USA.

Systems experiencing high-rate dynamic events, termed high-rate systems, typically undergo accelerations of amplitudes higher than 100 g-force in less than 10 ms. Examples include adaptive airbag deployment systems, hypersonic vehicles, and active blast mitigation systems. Given their critical functions, accurate and fast modeling tools are necessary for ensuring the target performance. Read More

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PSMA-D4 Radioligand for Targeted Therapy of Prostate Cancer: Synthesis, Characteristics and Preliminary Assessment of Biological Properties.

Int J Mol Sci 2021 Mar 8;22(5). Epub 2021 Mar 8.

National Centre for Nuclear Research, Radioisotope Centre POLATOM, 05-400 Otwock, Poland.

A new PSMA ligand (PSMA-D4) containing the Glu-CO-Lys pharmacophore connected with a new linker system (L-Trp-4-Amc) and chelator DOTA was developed for radiolabeling with therapeutic radionuclides. Herein we describe the synthesis, radiolabeling, and preliminary biological evaluation of the novel PSMA-D4 ligand. Synthesized PSMA-D4 was characterized using TOF-ESI-MS, NMR, and HPLC methods. Read More

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Optimizing wheat production and reducing environmental impacts through scientist-farmer engagement: Lessons from the North China Plain.

Food Energy Secur 2021 Feb 4;10(1):e255. Epub 2020 Nov 4.

National Academy of Agriculture Green Development Department of Plant Nutrition, College of Resources and Environmental Sciences China Agricultural University Beijing 100193 China.

Producing high economic benefits and high grain yields with limited environmental impacts is crucial for feeding the world's growing population. Yet it remains challenging to improve the performance of one objective without creating unintended consequences for other objectives. This is especially difficult for smallholders navigating a diverse array of environmental and personal demands. Read More

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February 2021

Predicting Reaction Yields via Supervised Learning.

Acc Chem Res 2021 Mar 31. Epub 2021 Mar 31.

Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.

ConspectusNumerous disciplines, such as image recognition and language translation, have been revolutionized by using machine learning (ML) to leverage big data. In organic synthesis, providing accurate chemical reactivity predictions with supervised ML could assist chemists with reaction prediction, optimization, and mechanistic interrogation.To apply supervised ML to chemical reactions, one needs to define the object of prediction (e. Read More

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Effective Automatic Method Selection for Nonlinear Regression Modeling.

Int J Neural Syst 2021 Mar 29:2150020. Epub 2021 Mar 29.

The Czech Academy of Sciences, Institute of Computer Science, Pod Vodárenskou věží 2, 182 07 Prague 8, Czech Republic.

Metalearning, an important part of artificial intelligence, represents a promising approach for the task of automatic selection of appropriate methods or algorithms. This paper is interested in recommending a suitable estimator for nonlinear regression modeling, particularly in recommending either the standard nonlinear least squares estimator or one of such available alternative estimators, which is highly robust with respect to the presence of outliers in the data. The authors hold the opinion that theoretical considerations will never be able to formulate such recommendations for the nonlinear regression context. Read More

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Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.

Annu Rev Biomed Eng 2021 Mar 29. Epub 2021 Mar 29.

Department of Biochemistry, University of Wisconsin-Madison, Madison,Wisconsin 53706, USA; email:

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. Read More

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Non-stationary response of rain-fed spring wheat yield to future climate change in northern latitudes.

Sci Total Environ 2021 Jun 30;772:145474. Epub 2021 Jan 30.

Watershed Science and Modeling Laboratory, Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2R3, Canada. Electronic address:

The non-stationary response of crop growth to changes in hydro-climatic variables makes yield projection uncertain and the design and implementation of adaptation strategies debatable. This study simulated the time-varying behavior of the underlying cause-and-effect mechanisms affecting spring wheat yield (SWY) under various climate change and nitrogen (N) application scenarios in the Red Deer River basin in agricultural lands of the western Canadian Prairies. A calibrated and validated Soil and Water Assessment Tool and Analysis of Variance decomposition methods were utilized to assess the contribution of crop growth parameters, Global Climate Models, Representative Concentration Pathways, and downscaling techniques to the total SWY variance for the 2040-2064 period. Read More

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Understanding solid-state processing of pharmaceutical cocrystals via milling: Role of tablet excipients.

Int J Pharm 2021 Mar 22;601:120514. Epub 2021 Mar 22.

Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland; Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland.

Discovery of novel cocrystal systems and improvement of their physicochemical properties dominates the current literature on cocrystals yet the required end-product formulation is rarely addressed. Drug product manufacturing includes complex API solid state processing steps such as milling, granulation, and tableting. These all require high mechanical stress which can lead to solid-state phase transformations into polymorphs and solvates, or lead to dissociation of cocrystals into their individual components. Read More

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Robust data assimilation with noise: Applications to cardiac dynamics.

Chaos 2021 Jan;31(1):013118

School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.

Reconstructions of excitation patterns in cardiac tissue must contend with uncertainties due to model error, observation error, and hidden state variables. The accuracy of these state reconstructions may be improved by efforts to account for each of these sources of uncertainty, in particular, through the incorporation of uncertainty in model specification and model dynamics. To this end, we introduce stochastic modeling methods in the context of ensemble-based data assimilation and state reconstruction for cardiac dynamics in one- and three-dimensional cardiac systems. Read More

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January 2021

DropConnect is effective in modeling uncertainty of Bayesian deep networks.

Sci Rep 2021 Mar 9;11(1):5458. Epub 2021 Mar 9.

Department of Electrical and Computer Engineering, University of Houston, Houston, TX, 77004, USA.

Deep neural networks (DNNs) have achieved state-of-the-art performance in many important domains, including medical diagnosis, security, and autonomous driving. In domains where safety is highly critical, an erroneous decision can result in serious consequences. While a perfect prediction accuracy is not always achievable, recent work on Bayesian deep networks shows that it is possible to know when DNNs are more likely to make mistakes. Read More

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Dry Deposition of Ozone over Land: Processes, Measurement, and Modeling.

Rev Geophys 2020 Mar;58(1)

Earth System Science Programme, Faculty of Science, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.

Dry deposition of ozone is an important sink of ozone in near surface air. When dry deposition occurs through plant stomata, ozone can injure the plant, altering water and carbon cycling and reducing crop yields. Quantifying both stomatal and nonstomatal uptake accurately is relevant for understanding ozone's impact on human health as an air pollutant and on climate as a potent short-lived greenhouse gas and primary control on the removal of several reactive greenhouse gases and air pollutants. Read More

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Application of soft-computing techniques for statistical modeling and optimization of seed oil extraction using polar and non-polar solvents.

Heliyon 2021 Mar 8;7(3):e06342. Epub 2021 Mar 8.

Department of Chemical Engineering, Alex Ekwueme Federal University, Ndufu-Alike, Abakaliki, Nigeria.

This research presents optimal factor evaluation for maximum seed oil (DESO) extraction by applying central composite design (CCD) based on Box-Behnken (BB) experimental design of response surface methodology (RSM) and Artificial neural network (ANN) on feed forward-back propagation (FFBP) of Levenberg Marquardt (LM) training algorithm. Polar solvents (ethanol and combination of methanol and chloroform (M/C)) and non-polar solvents (n-hexane) were used for the extraction. The RSM optimal predicted oil yields were 45. Read More

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The Discovery of Novel BCR-ABL Tyrosine Kinase Inhibitors Using a Pharmacophore Modeling and Virtual Screening Approach.

Front Cell Dev Biol 2021 4;9:649434. Epub 2021 Mar 4.

College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States.

Chronic myelogenous leukemia (CML) typically results from a reciprocal translocation between chromosomes 9 and 22 to produce the oncogene that when translated, yields the p210 BCR-ABL protein in more than 90% of all CML patients. This protein has constitutive tyrosine kinase activity that activates numerous downstream pathways that ultimately produces uncontrolled myeloid proliferation. Although the use of the BCR-ABL tyrosine kinase inhibitors (TKIs), such as imatinib, nilotinib, dasatinib, bosutinib, and ponatinib have increased the overall survival of CML patients, their use is limited by drug resistance and severe adverse effects. Read More

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Potential benefits of liming to acid soils on climate change mitigation and food security.

Glob Chang Biol 2021 Mar 20. Epub 2021 Mar 20.

State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, PR China.

Globally, about 50% of all arable soils are classified as acidic. As crop and plant growth are significantly hampered under acidic soil conditions, many farmers, but increasingly as well forest managers, apply lime to raise the soil pH. Besides its direct effect on soil pH, liming also affects soil C and nutrient cycles and associated greenhouse gas (GHG) fluxes. Read More

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Bacterial fermentation and isotope labelling optimized for amyloidogenic proteins.

Microb Biotechnol 2021 Mar 19. Epub 2021 Mar 19.

Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, H-1117, Hungary.

We developed a cost sensitive isotope labelling procedure using a fed-batch fermentation method and tested its efficiency producing the N-, C- and N/ C-labelled variants of an amyloidogenic miniprotein (E5: EEEAVRLYIQWLKEGGPSSGRPPPS). E5 is a surface active protein, which forms amyloids in solution. Here, we confirm, using both PM-IRRAS and AFM measurements, that the air-water interface triggers structural rearrangement and promotes the amyloid formation of E5, and thus it is a suitable test protein to work out efficient isotope labelling schemes even for such difficult sequences. Read More

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Improving Pesticide Uptake Modeling into Potatoes: Considering Tuber Growth Dynamics.

J Agric Food Chem 2021 Mar 17;69(12):3607-3616. Epub 2021 Mar 17.

Quantitative Sustainability Assessment, Department of Technology, Management and Economics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.

To explore pesticide uptake from soil into a growing potato, a moving-boundary dynamic model is proposed on the basis of the radical diffusion process of a chemical to a sphere. This model, which considers the logistic growth of the potato tuber, describes two hypothetical processes of chemical diffusion within a growing tuber. The model was tested in an illustrative case study for an application of chlorpyrifos. Read More

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Parameter optimization and uncertainty assessment for rainfall frequency modeling using an adaptive Metropolis-Hastings algorithm.

Water Sci Technol 2021 Mar;83(5):1085-1102

College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China and Center for Marine Environmental and Ecological Modelling, Shanghai Maritime University, Shanghai 201306, China E-mail:

A new parameter optimization and uncertainty assessment procedure using the Bayesian inference with an adaptive Metropolis-Hastings (AM-H) algorithm is presented for extreme rainfall frequency modeling. An efficient Markov chain Monte Carlo sampler is adopted to explore the posterior distribution of parameters and calculate their uncertainty intervals associated with the magnitude of estimated rainfall depth quantiles. Also, the efficiency of AM-H and conventional maximum likelihood estimation (MLE) in parameter estimation and uncertainty quantification are compared. Read More

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In situ synchrotron diffraction and modeling of non-equilibrium solidification of a MnFeCoNiCu alloy.

Sci Rep 2021 Mar 15;11(1):5921. Epub 2021 Mar 15.

Colorado School of Mines, Golden, CO, 80401, USA.

The solidification mechanism and segregation behavior of laser-melted MnFeCoNiCu was firstly investigated via in situ synchrotron x-ray diffraction at millisecond temporal resolution. The transient composition evolution of the random solid solution during sequential solidification of dendritic and interdendritic regions complicates the analysis of synchrotron diffraction data via any single conventional tool, such as Rietveld refinement. Therefore, a novel approach combining a hard-sphere approximation model, thermodynamic simulation, thermal expansion measurement and microstructural characterization was developed to assist in a fundamental understanding of the evolution of local composition, lattice parameter, and dendrite volume fraction corresponding to the diffraction data. Read More

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Neighborhood degree sum-based molecular descriptors of fractal and Cayley tree dendrimers.

Eur Phys J Plus 2021 9;136(3):303. Epub 2021 Mar 9.

Department of Mathematics, National Institute of Technology Durgapur, Durgapur, West Bengal 713209 India.

Topological index is a connection between the chemical structure and the real number that remains invariant under graph isomorphism. In structure-property and structure-activity modeling, topological indices are considered as essential molecular descriptors to predict different physicochemical properties of molecule. Dendrimers are considered to be the most significant, commercially accessible basic components in nanotechnology. Read More

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A new approach for balancing the microbial synthesis of ethyl acetate and other volatile metabolites during aerobic bioreactor cultivations.

Eng Life Sci 2021 Mar 21;21(3-4):137-153. Epub 2020 Dec 21.

Chair of Bioprocess Engineering, Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany.

Ethyl acetate is an organic solvent with many industrial applications, currently produced by energy-intensive chemical processes based on fossil carbon resources. Ethyl acetate can be synthesized from renewable sugars by yeasts like in aerobic processes. However, ethyl acetate is highly volatile and thus stripped from aerated cultivation systems which complicate the quantification of the produced ester. Read More

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Complex wall modeling for hemodynamic simulations of intracranial aneurysms based on histologic images.

Int J Comput Assist Radiol Surg 2021 Mar 14. Epub 2021 Mar 14.

Faculty of Computer Science, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, D-39106, Magdeburg, Germany.

Purpose: For the evaluation and rupture risk assessment of intracranial aneurysms, clinical, morphological and hemodynamic parameters are analyzed. The reliability of intracranial hemodynamic simulations strongly depends on the underlying models. Due to the missing information about the intracranial vessel wall, the patient-specific wall thickness is often neglected as well as the specific physiological and pathological properties of the vessel wall. Read More

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Stochastic Epidemic Models inference and diagnosis with Poisson Random Measure Data Augmentation.

Math Biosci 2021 May 10;335:108583. Epub 2021 Mar 10.

Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209, Sorbonne Université, France; iGLOBE, UMI CNRS 3157, University of Arizona, Tucson, AZ, United States of America.

We present a new Bayesian inference method for compartmental models that takes into account the intrinsic stochasticity of the process. We show how to formulate a SIR-type Markov jump process as the solution of a stochastic differential equation with respect to a Poisson Random Measure (PRM), and how to simulate the process trajectory deterministically from a parameter value and a PRM realization. This forms the basis of our Data Augmented MCMC, which consists of augmenting parameter space with the unobserved PRM value. Read More

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