Supplemental Material - Modified Item-Fit Indices for Dichotomous IRT Models with Missing Data

Supplemental Material for Modified Item-Fit Indices for Dichotomous IRT Models with Missing Data by Xue Zhang, Chun Wang in Applied Psychological Measurement</p

PAG_online_supp_final – Supplemental material for Planning Communities for All Ages

Supplemental material, PAG_online_supp_final for Planning Communities for All Ages by Mildred E. Warner and Xue Zhang in Journal of Planning Education and Research</p

Stereoselective Synthesis Axially Chiral Arylnitriles through Base-Induced Chirality-Relay β‑Carbon Elimination of α‑Hydroxyl Ketoxime Esters

We report herein a point-to-axial chirality transfer reaction of α-hydroxyl oxime esters for the synthesis of axially chiral arylnitriles. The reaction proceeds smoothly through a base-promoted retro-benzoin condensation reaction of α-hydroxyl oxime esters, where the axial chirality is created via the C–C bond cleavage based on a proper distorted conformation of the biaryl structure induced by its stereogenic carbon center

Predicting essential proteins by integrating orthology, gene expressions, and PPI networks

<div><p>Identifying essential proteins is very important for understanding the minimal requirements of cellular life and finding human disease genes as well as potential drug targets. Experimental methods for identifying essential proteins are often costly, time-consuming, and laborious. Many computational methods for such task have been proposed based on the topological properties of protein-protein interaction networks (PINs). However, most of these methods have limited prediction accuracy due to the noisy and incomplete natures of PINs and the fact that protein essentiality may relate to multiple biological factors. In this work, we proposed a new centrality measure, OGN, by integrating orthologous information, gene expressions, and PINs together. OGN determines a protein’s essentiality by capturing its co-clustering and co-expression properties, as well as its conservation in the evolution process. The performance of OGN was tested on the species of <i>Saccharomyces cerevisiae</i>. Compared with several published centrality measures, OGN achieves higher prediction accuracy in both working alone and ensemble.</p></div

The protein interaction network for the top 100 selected proteins by OGN (alpha = 0.3).

<p>The protein interaction network for the top 100 selected proteins by OGN (alpha = 0.3).</p

sj-docx-5-tct-10.1177_15330338231180776 - Supplemental material for A Nomogram Based on the Log Odds of Positive Lymph Nodes Predicts the Prognosis of Patients with Colon Neuroendocrine Tumors After Surgery: A Surveillance, Epidemiology, and End Results Population-Based Study

Supplemental material, sj-docx-5-tct-10.1177_15330338231180776 for A Nomogram Based on the Log Odds of Positive Lymph Nodes Predicts the Prognosis of Patients with Colon Neuroendocrine Tumors After Surgery: A Surveillance, Epidemiology, and End Results Population-Based Study by Xue Zhang, Kui Zhang, Su Li and Aman Xu in Technology in Cancer Research & Treatment</p

Properties of 125 neighbors of YLR295C.

<p>Properties of 125 neighbors of YLR295C.</p

Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics

Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a “preparatory state” at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible α-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a “tic-tac-toe” activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of α/β-hydrolase

Data_Sheet_1_A Short Note on Aberrant Responses Bias in Item Response Theory.docx

Item response models often cannot calculate true individual response probabilities because of the existence of response disturbances (such as guessing and cheating). Many studies on aberrant responses under item response theory (IRT) framework had been conducted. Some of them focused on how to reduce the effect of aberrant responses, and others focused on how to detect aberrant examinees, such as person fit analysis. The purpose of this research was to derive a generalized formula of bias with/without aberrant responses, that showed the effect of both non-aberrant and aberrant response data on the bias of capability estimation mathematically. A new evaluation criterion, named aberrant absolute bias (|ABIAS|), was proposed to detect aberrant examinees. Simulation studies and application to a real dataset were conducted to demonstrate the efficiency and the utility of |ABIAS|.</p

Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics

Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a “preparatory state” at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible α-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a “tic-tac-toe” activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of α/β-hydrolase