scholarly journals A Sequential Higher Order Latent Structural Model for Hierarchical Attributes in Cognitive Diagnostic Assessments

2019 ◽  
Vol 44 (1) ◽  
pp. 65-83 ◽  
Author(s):  
Peida Zhan ◽  
Wenchao Ma ◽  
Hong Jiao ◽  
Shuliang Ding
Keyword(s):  
Structural Model ◽  
Latent Trait ◽  
Simulated Data ◽  
Hierarchical Structures ◽  
Higher Order ◽  
Order Structure ◽  
Cognitive Diagnosis Models ◽  
Attribute Hierarchy ◽  
Latent Attribute ◽  
Attribute Space

The higher-order structure and attribute hierarchical structure are two popular approaches to defining the latent attribute space in cognitive diagnosis models. However, to our knowledge, it is still impossible to integrate them to accommodate the higher-order latent trait and hierarchical attributes simultaneously. To address this issue, this article proposed a sequential higher-order latent structural model (LSM) by incorporating various hierarchical structures into a higher-order latent structure. The feasibility of the proposed higher-order LSM was examined using simulated data. Results indicated that, in conjunction with the deterministic-inputs, noisy “and” gate model, the sequential higher-order LSM produced considerable improvement in person classification accuracy compared with the conventional higher-order LSM, when a certain attribute hierarchy existed. An empirical example was presented as well to illustrate the application of the proposed LSM.

scholarly journals Using JAGS for Bayesian Cognitive Diagnosis Modeling: A Tutorial

2019 ◽  
Vol 44 (4) ◽  
pp. 473-503 ◽  
Author(s):  
Peida Zhan ◽  
Hong Jiao ◽  
Kaiwen Man ◽  
Lijun Wang
Keyword(s):  
Gibbs Sampler ◽  
Logistic Model ◽  
Structural Model ◽  
Higher Order ◽  
Unified Model ◽  
Cognitive Diagnosis ◽  
Cognitive Diagnosis Models ◽  
Log Linear ◽  
Linear Logistic Model ◽  
Or Gate

In this article, we systematically introduce the just another Gibbs sampler (JAGS) software program to fit common Bayesian cognitive diagnosis models (CDMs) including the deterministic inputs, noisy “and” gate model; the deterministic inputs, noisy “or” gate model; the linear logistic model; the reduced reparameterized unified model; and the log-linear CDM (LCDM). Further, we introduce the unstructured latent structural model and the higher order latent structural model. We also show how to extend these models to consider polytomous attributes, the testlet effect, and longitudinal diagnosis. Finally, we present an empirical example as a tutorial to illustrate how to use JAGS codes in R.

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

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