Unfolding Model Research Articles

Modeling and predicting spring land surface phenology of the deciduous broadleaf forest in northern China

Using normalized difference vegetation index data, we fitted unified forcing and chilling phenology models to start date of the growing season (SOS) during 1982 to 2006 and selected optimum models for each pixel. Then, we validated performances of optimum models in extrapolating SOS dates during 2007 to 2011. Moreover, we reconstructed SOS time series over 1950 to 2005 and predicted decadal mean anomalies of SOS dates over 2006 to 2100 under scenarios of the representative concentration pathway (RCP) 4.5 and 8.5. Finally, we compared structures and parameters of the satellite data-based phenology model with those of the ground-based leaf unfolding model. Results show that the unified forcing model has higher simulation parsimony and efficiency than the unified chilling model at 96.4% of pixels. The external validation confirmed feasibility of the unified forcing model in predicting the SOS date. Across the entire region, predicted SOS dates indicate significant advancements by 0.65–1.79 days per decade. Taking the mean SOS date during 1961 to 1990 as the reference value, the absolute values of decadal mean anomalies of the SOS date represent an overall increase with the time. Consequently, the average SOS date during 2091 to 2100 would be 11.8–20.0 days earlier than the average SOS date during 1961 to 1990. At pixel scales, the absolute values of decadal mean anomalies of the SOS date under the RCP 8.5 scenario display mostly a latitudinal gradient from south to north. Similar distribution ranges of parameter d and e of the ground-based and satellite data-based phenology models demonstrate that the satellite-derived SOS date has consistent response to air temperature with the leaf unfolding date of dominant deciduous trees, which implies that the predicted start of the growing season may to some extent reflect changing tendency of the ground leafing phenology in the 21st century.

Advantages of Artificial Neural Network in Neutron Spectra Unfolding

Advantages of using the artificial neural network method in neutron spectra unfolding are investigated in comparison with the maximum entropy unfolding method. By introducing the information entropy theory, we find that for the spectrum with the information entropy over 3.5, the four-layer feed-forward neural network (11-35-55-60) and the maximum entropy method generally demonstrate the same unfolding performance, while the spectrum with the information entropy lower than 3.5, the artificial neural network unfolding model is recommend due to the fact that the artificial neural network method has a stronger negative correlation between the entropy of the spectra and the mean squares error of the spectra than the maximum entropy method.

A Review of Methods Available to Estimate Solvent-Accessible Surface Areas of Soluble Proteins in the Folded and Unfolded States

Solvent accessible surface area (SASA) of proteins has always been considered as a decisive factor in protein folding and stability studies. It is defined as the surface characterized around a protein by a hypothetical centre of a solvent sphere with the van der Waals contact surface of the molecule. Based on SASA values, amino acid residues of a protein can be classified as buried or exposed. There are various types of SASAs starting from relative solvent accessibility to absolute surface areas. Direct estimation of accurate SASAs of folded proteins experimentally at the atomic level is not possible. However, the SASA of a native protein can be estimated computationally from the atomic coordinates. Similarly, various simulation methods are available to compute the SASA of a protein in its unfolded state. In efforts to estimate the changes in SASA related to the protein folding, a number of the unfolded state models have been proposed. In this review, we have summarized different algorithms and computational tools for SASA estimations. Furthermore, online resources for SASA calculations and representations have also been discussed in detail. This review will be useful for protein chemists and biologists for the accurate measurements of SASA and its subsequent applications for the calculation of various biophysical and thermodynamic properties of proteins.

Large scale conformational transitions in β-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data.

Gramicidin A (gA) is a polypeptide antibiotic, which forms dimeric channels specific for monovalent cations in artificial and biological membranes. It is a polymorphic molecule that adopts a unique variety of helical conformations, including antiparallel double-stranded ↑↓β5.6 or ↑↓β7.2 helices (number of residues per turn) and a single-stranded β6.3 helix (the 'channel form'). The behavior of gA-Cs(+) complex in the micelles of TX-100 was studied in this work. Transfer of the complex into the micelles activates a cascade of sequential conformational transitions monitored by CD and FT-IR spectroscopy: [Formula: see text] At the first step after Cs(+) removal, the RH ↑↓β5.6 helix is formed, which has been discussed so far only hypothetically. Kinetics of the transitions was measured, and the activation parameters were determined. The activation energies of the ↑↓β5.6 → β-helical monomer transition in dioxane and dioxane/water solutions were also measured for comparison. The presence of water raises the transition rate constant ~10(3) times but does not lead to crucial fall of the activation energy. All activation energies were found in the 20-25 kcal/mol range, i.e. much lower than would be expected for unwinding of the double helix (when 28 H-bonds are broken simultaneously). These results can be accounted for in the light of local unfolding (or 'cracking') model for large scale conformational transitions developed by the P. G.Wolynes team [Miyashita O, Onuchic JN, Wolynes PG. Proc. Natl. Acad. Sci. USA 2003; 100: 12570-12575.].

Unfolding study of a trimeric membrane protein AcrB

The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB.

Folding of the RNA Recognition Motif (RRM) Domains of the Amyotrophic Lateral Sclerosis (ALS)-linked Protein TDP-43 Reveals an Intermediate State

Pathological alteration of TDP-43 (TAR DNA-binding protein-43), a protein involved in various RNA-mediated processes, is a hallmark feature of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Fragments of TDP-43, composed of the second RNA recognition motif (RRM2) and the disordered C terminus, have been observed in cytoplasmic inclusions in sporadic amyotrophic lateral sclerosis cases, suggesting that conformational changes involving RRM2 together with the disordered C terminus play a role in aggregation and toxicity. The biophysical data collected by CD and fluorescence spectroscopies reveal a three-state equilibrium unfolding model for RRM2, with a partially folded intermediate state that is not observed in RRM1. Strikingly, a portion of RRM2 beginning at position 208, which mimics a cleavage site observed in patient tissues, increases the population of this intermediate state. Mutually stabilizing interactions between the domains in the tethered RRM1 and RRM2 construct reduce the population of the intermediate state and enhance DNA/RNA binding. Despite the high sequence homology of the two domains, a network of large hydrophobic residues in RRM2 provides a possible explanation for the increased stability of RRM2 compared with RRM1. The cluster analysis suggests that the intermediate state may play a functional role by enhancing access to the nuclear export signal contained within its sequence. The intermediate state may also serve as a molecular hazard linking productive folding and function with pathological misfolding and aggregation that may contribute to disease.

Effect of personality item writing on psychometric properties of ideal-point and likert scales.

The present study was designed to investigate personality item-writing practices and their effect on the psychometric properties of personality items and scales. Personality items were developed based on ideal-point and dominance models, analyzed using the generalized graded unfolding model, and empirically classified as having an ideal-point or dominance form. Results suggested that writing dominance items were slightly easier (more successful) than writing ideal-point items, but this varied slightly by personality dimensions. Of 3 ideal-point item writing tactics, the "neutral" tactic was least successful; success writing "double-barreled" and "average" ideal-point items was comparable to that of dominance items. Three personality scales were then constructed using successful ideal-point and dominance items. Scales constructed using ideal-point items had substantially inferior psychometric properties, including lower score reliability, lower correlations with important criteria, and mixed test information results. However, lower predictive validity of ideal-point scale scores may be due to lower reliability of the scores. Practical and methodological implications were also discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Critical Evaluation of the Two-State Model Describing the Equilibrium Unfolding of the PI3K SH3 Domain by Time-Resolved Fluorescence Resonance Energy Transfer

It appears that equilibrium unfolding transitions of many small proteins can be described as two-state transitions, because the probes commonly used to measure such transitions cannot detect the underlying heterogeneity inherent in protein folding and unfolding reactions. Time-resolved fluorescence or Forster resonance energy transfer (TRFRET) measurements have the potential to uncover such heterogeneity and to test the cooperativity of protein folding reactions. Here, TRFRET measurements have been used to study the equilibrium unfolding of the SH3 domain of PI3 kinase. The single tryptophan residue (W53) was used as the FRET donor, and a covalently attached thionitrobenzoate moiety at either of two sites (C17 and C70) was used as the FRET acceptor. The individual lifetime and amplitude components estimated from fitting the fluorescence decay kinetics to the sum of three or four exponentials were determined over a range of denaturant concentrations. The equilibrium unfolding transitions reported by these components were found to be noncoincident, suggesting the presence of multiple conformations in equilibrium during the course of unfolding. Fluorescence lifetime distributions were also generated by the model-free maximum entropy method of analysis. Different segments of the protein were found to show differences in the expansion of the native state at low denaturant concentrations, suggestive of gradual structural transitions. The unfolded protein was found to swell at increasingly high denaturant concentrations. The evolution of the fluorescence lifetime distributions with increasing denaturant concentration was also found to be incompatible with a two-state equilibrium unfolding model.

A Beta Unfolding Model for Continuous Bounded Responses

An unfolding model for continuous bounded responses is proposed, derived both from ahypothetical interpolation response mechanism and from the hypothesis of two opposite sources of item refusal being collapsed. These two sources of refusal are made explicit in athree-component Dirichlet response model and then collapsed to obtain a(two-component) beta response model. The two natural parameters of the beta are interpreted as acceptance and refusal parameters and expressed as functions of person-item distances on a latent continuum. The potentially bimodal shape of the beta is exploited to model chaotic response choices among ambivalent subjects.

Constructing a Scale of Attitudes toward School Science Using the General Graded Unfolding Model

The present study aimed at constructing an attitude scale toward school science using the generalized graded unfolding model (GGUM). A 47-item scale (24 positive, 23 negative) with 4-point response format was used to measure attitudes toward science among 9th (n=424) and 10th (n=420) grade students in 38 sections distributed randomly over 22 schools in Irbid district. Respondents selected one of four options to represent their level of agreement with each item. The findings support the hypothesis that the data form a single unidimensional unfolding model. Furthermore, the findings showed that the GGUM didn’t fit the data of 7 items, leaving the final scale with 40 items, where accurate estimates of these item parameters were derived and the GGUM was appropriate. Cronbach's alpha for the internal consistency, and the test retest reliability coefficients of the final scale were 0.932 and 0.875, respectively.

Constructing a Scale of Attitudes toward School Science Using the General Graded Unfolding Model

The present study aimed at constructing an attitude scale toward school science using the generalized graded unfolding model (GGUM). A 47-item scale (24 positive, 23 negative) with 4-point response format was used to measure attitudes toward science among 9th (n=424) and 10th (n=420) grade students in 38 sections distributed randomly over 22 schools in Irbid district. Respondents selected one of four options to represent their level of agreement with each item. The findings support the hypothesis that the data form a single unidimensional unfolding model. Furthermore, the findings showed that the GGUM didn’t fit the data of 7 items, leaving the final scale with 40 items, where accurate estimates of these item parameters were derived and the GGUM was appropriate. Cronbach's alpha for the internal consistency, and the test retest reliability coefficients of the final scale were 0.932 and 0.875, respectively.

Constructing a Scale of Attitudes toward School Science Using the General Graded Unfolding Model

The present study aimed at constructing an attitude scale toward school science using the generalized graded unfolding model (GGUM). A 47-item scale (24 positive, 23 negative) with 4-point response format was used to measure attitudes toward science among 9 th (n=424) and 10 th (n=420) grade students in 38 sections distributed randomly over 22 schools in Irbid district. Respondents selected one of four options to represent their level of agreement with each item. The findings support the hypothesis that the data form a single unidimensional unfolding model. Furthermore, the findings showed that the GGUM didn’t fit the data of 7 items, leaving the final scale with 40 items, where accurate estimates of these item parameters were derived and the GGUM was appropriate. Cronbach's alpha for the internal consistency, and the test retest reliability coefficients of the final scale were 0.932 and 0.875, respectively.

Gone Today but here Tomorrow: Extending the Unfolding Model of Turnover to Consider Boomerang Employees

Turnover research typically views voluntary turnover as an end state that severs the employment relationship permanently. However, this perspective overlooks the possibility that an employee who quits may return in the future. Anecdotal and empirical evidence suggest that these “Boomerangs” can be a valuable staffing resource for their organizations. Yet, research regarding this type of employee is largely absent. Thus, we know little about whether the experiences of these temporary leavers differ from those who leave an organization permanently. In this paper, we examined differences between Boomerangs (employees who quit but are later rehired) and “Alumni” (employees who quit but will not return) using both qualitative and quantitative data. In a large sample of professional service employees, we found that Boomerangs and Alumni reported different reasons for having quit, which meant they were more likely to be classified on different paths in the unfolding model of turnover. In addition, survival analyses on the time to turnover suggest that Boomerangs quit earlier than Alumni in their original tenure, paradoxically suggesting that employees who quit earlier may be the very employees who will return in the future. Together, our findings suggest an extension to the unfolding model that considers how the timing of and reasons for turnover impact post‐turnover (return) decisions.

Optimal blank design based on finite element method for blades of large Francis turbines

Metal pressing process that is widely used in industries has advantages over casting process for producing large Francis turbine blades from thick plates. Prior to the pressing process, blank design is firstly performed to determine flat blanks. The traditional trial and error approach is not applicable to blade design for Francis turbines that are not standard due to hydraulic characteristics of power plant sites. The rapid development of computing technology makes it possible to obtain optimal flat blanks by numerical modelling and simulation. In this paper, inverse finite element approach is investigated for blank design and an elasto-plastic model has been built using the well-known commercial software ANSYS. Numerical simulations for blade unfolding models with thick shell elements, solid elements and shell elements have given results with negligible differences. Unfolding tests with simple geometries have been carried out and the numerical results agree well with the analytical solutions. A large and thick shape of a Francis turbine blade for a hydropower plant has been successfully unfolded by inverse FE model. Sensibility analysis shows that the middle surface of the flat blank is independent of blade thickness. For ensuring the machining of the blade after the pressing process, a new contour is obtained by extending the boundary of the flat blank provided by the numerical model. This research may provide a useful tool for optimal blank design of Francis turbine blades.

The Effects of Ethical Leadership and Abusive Supervision on Job Search Behaviors in the Turnover Process

Drawing upon the unfolding model of turnover and the dual-process theory of information processing, we examined the roles which ethical leadership and abusive supervision play in the turnover process. The central conclusion of this study is that ethical leadership influences job satisfaction, which then influences intentions to quit, which then impacts job search behaviors. Conversely, abusive supervision, which is the conceptual opposite of ethical leadership, has a negative influence on job satisfaction with corresponding impacts on intentions to quit and job search behavior. But, unlike ethical leadership, which does not directly lead to job search behavior, abusive supervision can also directly make people so upset that they initiate job search behaviors. Moreover, findings indicate that even low levels of abusive supervision can neutralize high levels of ethical leadership. Implications for research and practice in human resource management are discussed.

The significance of attitudes towards evidence-based practice in information technology use in the health sector: an empirical investigation

The article investigates the relationship between attitudes towards evidence-based practice (EBP) and the use of information and communication technology (ICT) in practice and demonstrates that the poor correlation reported in the literature is a methodological artifact rather than a substantive fact. Results are based on structured surveying of 1015 medical and nursing staff, drawn from 15 Greek hospitals. We used unfolding item response theory models to demonstrate that by placing the statements assessing attitude towards EBP and ICT self-reported use on a single attitude–behaviour continuum, behaviour statements have a systematically different location on the attitude–behaviour continuum from the attitude statements. Based on the latent probabilistic relation among attitudes towards EBP and ICT use, the practical implications of the study are discussed.

The fluorescence detected guanidine hydrochloride equilibrium denaturation of wild-type staphylococcal nuclease does not fit a three-state unfolding model

A three-state equilibrium unfolding of a protein can be difficult to detect if two of the states fail to differ in some easily measurable way. It has been unclear whether staphylococcal nuclease unfolds in a two-state fashion, with only the native and denatured states significantly populated at equilibrium, or in a three-state manner, with a well-populated intermediate. Since equilibrium unfolding experiments are commonly used to determine protein stability and the course of denaturation are followed by changes in the fluorescence which has difficulty in distinguishing various states, this is a potential problem for many proteins. Over the course of twenty years we have performed more than one hundred guanidine hydrochloride equilibrium denaturations of wild-type staphylococcal nuclease; to our knowledge, a number of denaturations unrivaled in any other protein system. A careful examination of the data from these experiments shows no sign of the behavior predicted by a three-state unfolding model. Specifically, a three-state unfolding should introduce a slight, but characteristic, non-linearity to the plot of stability versus denaturant concentration. The average residuals from this large number of repeated experiments do not show the predicted behavior, casting considerable doubt on the likelihood of a three-state unfolding for the wild-type protein. The methods used for analysis here could be applied to other protein systems to distinguish a two-state from a three-state denaturation.

The Random-Threshold Generalized Unfolding Model and Its Application of Computerized Adaptive Testing

The random-threshold generalized unfolding model (RTGUM) was developed by treating the thresholds in the generalized unfolding model as random effects rather than fixed effects to account for the subjective nature of the selection of categories in Likert items. The parameters of the new model can be estimated with the JAGS (Just Another Gibbs Sampler) freeware, which adopts a Bayesian approach for estimation. A series of simulations was conducted to evaluate the parameter recovery of the new model and the consequences of ignoring the randomness in thresholds. The results showed that the parameters of RTGUM were recovered fairly well and that ignoring the randomness in thresholds led to biased estimates. Computerized adaptive testing was also implemented on RTGUM, where the Fisher information criterion was used for item selection and the maximum a posteriori method was used for ability estimation. The simulation study showed that the longer the test length, the smaller the randomness in thresholds, and the more categories in an item, the more precise the ability estimates would be.

Even the best laid plans sometimes go askew: Career self-management processes, career shocks, and the decision to pursue graduate education.

Drawing on career self-management frameworks as well as image theory and the unfolding model of turnover, we developed a model predicting early career employees' decisions to pursue graduate education. Using a sample of 337 alumni from 2 universities, we found that early career individuals with intrinsic career goals, who engaged in career planning, who were less satisfied with their career, or who experienced impactful positive career shocks were more likely to intend to go to graduate school. In contrast, individuals with extrinsic career goals who were highly satisfied with their careers were less likely to intend to go to graduate school. Graduate education intentions, career planning, and the impact of having one's mentor leave the organization positively related to actual applications to graduate school. However, having extrinsic career goals, an impactful sooner than expected raise or promotion (a positive career shock), and a negative organizational change (a negative career shock) negatively related to the likelihood of applying. The career shocks' direct relationship to applications to graduate school, regardless of one's intentions, suggests that "the best laid plans" can sometimes be altered by unplanned events. This study contributes to the literatures on career self-management and graduate education and extends the application of the shock construct from the unfolding model of turnover to other career-related decisions.

The Unfolding Model of Volunteer Motivation

Unlike other theories, the unfolding model of volunteer motivation proposes that the decision to volunteer is both a function of an individual’s situation (i.e., life experiences, social networks, ...