Bayesian modelling for matching and alignment of biomolecules

2018 ◽  
Author(s):  
Peter Green ◽  
Kanti Mardia ◽  
Vysaul Nyirongo ◽  
Yann Ruffieux
Keyword(s):  
Shape Analysis ◽  
Three Dimensional ◽  
Statistical Modelling ◽  
Field Analysis ◽  
Dimensional Structure ◽  
Future Research ◽  
Bayesian Modelling ◽  
Bayesian Hierarchical ◽  
Statistical Shape ◽  
Alternative Approaches

This article describes Bayesian modelling for matching and alignment of biomolecules. One particular task where statistical modelling and inference can be useful in scientific understanding of protein structure is that of matching and alignment of two or more proteins. In this regard, statistical shape analysis potentially has something to offer in solving biomolecule matching and alignment problems. The article discusses the use of Bayesian methods for shape analysis to assist with understanding the three-dimensional structure of protein molecules, with a focus on the problem of matching instances of the same structure in the CoMFA (Comparative Molecular Field Analysis) database of steroid molecules. It introduces a Bayesian hierarchical model for pairwise matching and for alignment of multiple configurations before concluding with an overview of some advantages of the Bayesian approach to problems in protein bioinformatics, along with modelling and computation issues, alternative approaches, and directions for future research.

scholarly journals The Flow Field Analysis and Flow Calculation of Ultrasonic Flowmeter Based on the Fluent Software

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Ling Guo ◽  
Yue Sun ◽  
Ling Liu ◽  
Zhixi Shen ◽  
Ruizhen Gao ◽  
...  
Keyword(s):  
Flow Field ◽  
Three Dimensional ◽  
Simulation Method ◽  
Ultrasonic Flowmeter ◽  
Field Analysis ◽  
Dimensional Structure ◽  
Power Correction ◽  
Ideal Condition ◽  
Proposed Model ◽  
Fluent Software

We can build the three-dimensional structure model based on the Gambit software and achieve the distribution of flow field in the pipe and reflux flow condition at the position of transducer in regard to the real position of transducer according to the Fluent software. Under the framework, define the reflux length based on the distance of reflux along the channel and evaluate the effect of reflux on flow field. Then we can correct the power factor with the transmission speed difference method in the ideal condition and obtain the matching expression of power correction factor according to the practice model. In the end, analyze the simulation experience and produce the sample table based on the proposed model. The comparative analysis of test results and simulation results demonstrates the validity and feasibility of the proposed simulation method. The research in this paper will lay a foundation for further study on the optimization of ultrasonic flowmeter, enhance the measurement precision, and extend the application of engineering.

scholarly journals Correlation between the cross-sectional morphology of the mandible and the three-dimensional facial skeletal pattern: A structural equation modeling approach

2018 ◽  
Vol 89 (1) ◽  
pp. 78-86 ◽  
Author(s):  
Mi So Ahn ◽  
Sang Min Shin ◽  
Te-Ju Wu ◽  
Dong Joon Lee ◽  
Ching-Chang Ko ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Shape Analysis ◽  
Structural Equation ◽  
Three Dimensional ◽  
Equation Modeling ◽  
Outer Cortex ◽  
Cross Sectional ◽  
Statistical Shape ◽  
Skeletal Pattern ◽  
The Cross

ABSTRACT Objective: To clarify the relationship between the cross-sectional morphology of the mandible and vertical, transverse, and anteroposterior facial skeletal patterns using statistical shape analysis and structural equation modeling (SEM). Materials and Methods: We used 150 cone beam computed tomography (CBCT) images to obtain three-dimensional (3D) facial landmarks and cross-sectional images of the mandible. The morphology of the inner and outer cortices of the mandible was analyzed using statistical shape analysis, including generalized Procrustes analysis and principal component analysis (PCA). Factor analysis was performed to determine factors pertaining to the skeletal measurements and shape variations for the inner and outer cortices, following which a structural equation model was constructed. Results: Using factor analysis, characteristics of the vertical, transverse, and anteroposterior facial skeletal patterns were determined. PCA of the cross-sectional morphology of the mandible revealed 70% of the cumulative proportion by PC1 and PC2 after generalized Procrustes superimpositions. SEM showed complex relationships between the facial skeletal patterns and variations in the cross-sectional morphology of the mandibular cortices. The influence of the transverse factors on the outer cortex as a latent variable was relatively significant (P = .057). However, the influence of the vertical factors on the outer and inner cortices was not significant. Conclusions: The transverse skeletal pattern is associated with the morphology of the outer cortex of the mandible.

Head shape analysis of National Football League Players

2021 ◽  
pp. 175433712110206
Author(s):  
Gwansik Park ◽  
Lee F Gabler ◽  
Ann M Bailey ◽  
Nathan Z Dau ◽  
Chris Sherwood ◽  
...  
Keyword(s):  
Shape Analysis ◽  
National Football League ◽  
Sagittal Plane ◽  
Three Dimensional ◽  
Principal Component ◽  
Shape Variation ◽  
Head Shape ◽  
Two Factors ◽  
Football Helmets ◽  
Statistical Shape

Understanding the size and shape variations of the head is important to the design of football helmets used to mitigate the risk of head injury. Current guidelines for selecting helmets use only the circumference of the player’s head to determine an appropriate size that may not offer the best fit and protection for every player. The goal of this study was to quantify key measurements of head shape to sufficiently characterize variability among players in the National Football League (NFL), focusing on the shape variation of the cranial region. Statistical shape analysis was performed on three-dimensional head scans of 87 contemporary NFL players to identify key features of head shape variability among the players’ heads. The principal component analysis revealed two factors that explained 87% of the head shape variance: (1) height and length of the head in the sagittal plane and (2) prominent back of the head with an oval shape in the transverse plane versus prominent forehead with a round shape. Four head shape measurements (circumference, length, breadth, and height) were then defined and quantified to describe the first two principal components. This information can facilitate improvements in the design of football helmets.

scholarly journals Tο ψυχοκοινωνικό κλίμα της τάξης: Εννοιολογικό περιεχόμενο, θεωρητικό υπόβαθρο, εργαλεία μέτρησης και επίδραση στα μαθησιακά επιτεύγματα των μαθητών

2015 ◽  
Vol 3 (2) ◽  
pp. 157
Author(s):  
Kyriakos Charalampous ◽  
Constantinos M Kokkinos
Keyword(s):  
Academic Achievement ◽  
Learning Outcomes ◽  
Self Efficacy ◽  
Student Outcomes ◽  
Three Dimensional ◽  
Affective Learning ◽  
Dimensional Structure ◽  
Future Research ◽  
Educational Levels ◽  
The Relationship

The purpose of the present paper was to review the extant research on Classroom Psycho-Social Climate (CPSC), in order to underscore and resolve misconceptions, contradictions, and deficiencies, as well as to critically present two of its most important research accomplishments: (a) the construction of a plethora of valid and reliable research instruments to measure the construct of CPSC in various learning environments and at different educational levels, and (b) the association of CPSC with cognitive and affective learning outcomes. The definitions proposed for CPSC are generally characterized by ambiguity. Yet, most researchers agree that the CPSC represents a multidimensional construct, the defining indicators of which, tend to be statistically confirmed in most studies, while at the same time new ones are added, thus providing the construct with a dynamic status. Various theories have been proposed to conceptualize CPSC, the most acknowledged being that of Lewin’s (1936) Field Theory, Murray’s (1938) Needs-Press model, and Getzel and Thelen’s (1960) Socio-Psychological Theory. Two independent research programs and their enduring theoretical and empirical legacy signaled the new era in CPSC research. Rudolf Moos proposed a three-dimensional structure descriptive of all psycho-social climates regardless of the social context (school classrooms, correctional institutions, military facilities, etc.) (1974), and Herbert Walberg demonstrated that students’ were in position to make valid inferences regarding CPSC (1969). Contemporary CPSC research has revealed some methodological issues which need to be taken into consideration when designing CPSC studies. One of the most remarkable achievements of CPSC research is the development of many valid and widely used research instruments for measuring CPSC in various educational contexts and at different educational levels. These instruments reflect the expansion of CPSC research in terms of the integration of new conceptual dimensions, as well as the widening of the age level of students to whom they are addressed. However, despite the increased production of mixed-methods studies in contemporary CPSC research, the cross-cultural adaptation of CPSC instruments, especially those addressing elementary students, has resulted in ambiguous findings. Moreover, whereas most CPSC instruments are based on Moos’s three-dimensional proposal, empirical findings support different allocation of the subscales in these dimensions than the scale developers. Another significant outcome of CPSC research is the examination of the association of CPSC with students’ cognitive and affective learning outcomes. Indeed, empirical findings support the link between the CPSC and various learning outcomes, such as academic achievement, attitudes, self-efficacy, motivation, self-handicapping, and students’ emotional and cognitive involvement. In addition, contemporary CPSC research has examined different paths through which CPSC affects student outcomes. For example, researchers have shown that self-efficacy and achievement goals mediate the relationship between CPSC and student outcomes, such as academic achievement, emotional involvement, etc. Nonetheless, and despite the extended investigation of the relationship between CPSC and student outcomes, research has failed to present consistent evidence with regards to the effect of specific CPSC indicators on student outcomes. What’s more, in cases where CPSC indicators presented negative associations with student outcomes, the explanations provided were insufficient, whereas follow up investigations did not take place. Of course CPSC research has followed other fruitful directions which are also presented in this review. Practical implications of CPSC research findings and future research directions are also discussed.

Validation of the Spanish Version of the School Engagement Measure (SEM)

2016 ◽  
Vol 19 ◽  
Author(s):  
Estibaliz Ramos-Díaz ◽  
Arantzazu Rodríguez-Fernández ◽  
Lorena Revuelta
Keyword(s):  
School Engagement ◽  
Basque Country ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Emotional Engagement ◽  
Future Research ◽  
Confirmatory Factor ◽  
The Subject ◽  
Language Measures

AbstractThe scientific study of school engagement has recently been the subject of considerable interest in the field of educational psychology, and significant advances have been made in our knowledge of this construct. For instance, there is currently consensus in the scientific community that it is multifaceted, and has three dimensions: behavioral engagement, emotional engagement, and cognitive engagement. However, more advanced statistical analyses are needed to validate Spanish-language measures of school engagement, which this study proposes to do. The sample was comprised of 1,250 adolescents from Basque Country (49% boys, 51% girls) aged 12 to 15 years old (M = 13.72, SD = 1.09). The results of confirmatory factor analysis on the School Engagement Measure (Fredricks, Blumenfeld, Friedel, & Paris, 2005) supported a three-dimensional structure of school engagement (χ2(100) = 676.93, p < .001; GFI = .931; CFI = .906; IFI = .907; SRMR = .058; RMSEA = .068). Reliability indexes were satisfactory, ranging from .83 to .94. Adequate evidence of concurrent validity was found for the variable perceived school performance (p < .01). The results are discussed from an educational perspective, and with an eye to future research.

scholarly journals Measuring musical preferences from listening behavior: Data from one million people and 200,000 songs

2019 ◽  
pp. 030573561986828
Author(s):  
Kai R Fricke ◽  
David M Greenberg ◽  
Peter J Rentfrow ◽  
Philipp Y Herzberg
Keyword(s):  
Positive Emotions ◽  
Ecological Validity ◽  
Three Dimensional ◽  
Self Report ◽  
Behavioral Approach ◽  
Dimensional Structure ◽  
Future Research ◽  
Previous Theory ◽  
Musical Preference ◽  
Musical Preferences

Musical preferences are a fundamental individual difference predicting a multitude of listening behaviors. For decades, researchers have investigated how musical preferences are organized but have been hindered by genre-based and self-report methodologies. Recently, researchers have begun to investigate musical preferences at the feature-level using stimuli, rather than at the genre-level using self-reports. However, these new methods have been experimental and limited in their ecological validity. To address these recent limitations, we use an ecologically valid behavioral approach based on one million people who listened to more than 200,000 songs from streaming services, which is to our knowledge the largest study to date on the structure of musical preferences. Individual musical preference was measured from song playback counts and analyzed using principal components analysis on the psychological and sonic music features. Our results showed that music-feature preferences had a three-dimensional structure confirming previous theory and research. These dimensions are Arousal (level of energy in music), Valence (spectrum of negative to positive emotions), and Depth (intellectual and emotional depth in music). These findings lay firm ground for future research on music-feature preferences and pave the way for social-psychological and neurobiological experiments with music.

scholarly journals Inhibitors of Cyclin-Dependent Kinases: Types and Their Mechanism of Action

2021 ◽  
Vol 22 (6) ◽  
pp. 2806
Author(s):  
Paweł Łukasik ◽  
Irena Baranowska-Bosiacka ◽  
Katarzyna Kulczycka ◽  
Izabela Gutowska
Keyword(s):  
Small Molecule ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Point Of View ◽  
Dimensional Structure ◽  
Future Research ◽  
Atp Binding ◽  
Cdk Inhibitors ◽  
Wide Range

Recent studies on cyclin-dependent kinase (CDK) inhibitors have revealed that small molecule drugs have become very attractive for the treatment of cancer and neurodegenerative disorders. Most CDK inhibitors have been developed to target the ATP binding pocket. However, CDK kinases possess a very similar catalytic domain and three-dimensional structure. These features make it difficult to achieve required selectivity. Therefore, inhibitors which bind outside the ATP binding site present a great interest in the biomedical field, both from the fundamental point of view and for the wide range of their potential applications. This review tries to explain whether the ATP competitive inhibitors are still an option for future research, and highlights alternative approaches to discover more selective and potent small molecule inhibitors.

scholarly journals Virtual reality and annotated radiological data as effective and motivating tools to help Social Sciences students learn neuroanatomy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Margot van Deursen ◽  
Laura Reuvers ◽  
Jacobus Dylan Duits ◽  
Guido de Jong ◽  
Marianne van den Hurk ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Correct Diagnosis ◽  
Three Dimensional ◽  
Task Value ◽  
Dimensional Structure ◽  
Future Research ◽  
Alternative Teaching ◽  
Radiological Data ◽  
Motivation For Learning ◽  
Neurological Patients

AbstractNeuroanatomy as a subject is important to learn, because a good understanding of neuroanatomy supports the establishment of a correct diagnosis in neurological patients. However, rapid changes in curricula reduced time assigned to study (neuro)anatomy. Therefore, it is important to find alternative teaching methods to study the complex three-dimensional structure of the brain. The aim of this manuscript was to explore the effectiveness of Virtual Reality (VR) in comparison with Radiological Data (RaD) as suitable learning methods to build knowledge and increase motivation for learning neuroanatomy. Forty-seven students (mean age of 19.47 ± 0.54 years; 43 females; 4 males) were included; 23 students comprised the VR group. Both methods showed to improve knowledge significantly, the improvement between groups was not different. The RaD group showed to have a significantly higher score on expectancy than students in the VR group. Task value scores regarding finding a task interesting, useful and fun were found to be significantly different in favor of the VR group. Consequently, significant higher Motivation scores were found in the VR group. Motivation and expectancy, however, did not moderate learning results, whereas task value impacted the results in favour of the VR group. This study concludes that VR and RaD are effective and diverting methods to learn neuroanatomy, with VR being more motivating than RaD. Future research should investigate motivation and task value when using VR over a longer period of time.

scholarly journals Automatic generation of objective footprint outlines

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7203 ◽  
Author(s):  
Jens N. Lallensack
Keyword(s):  
Shape Analysis ◽  
A Priori ◽  
Three Dimensional ◽  
Automatic Generation ◽  
Contour Lines ◽  
Statistical Shape ◽  
Angular Measurements ◽  
Three Dimensional Models ◽  
Objective Basis ◽  
Definition Of

The objective definition of footprint margins poses a central problem in ichnology. The transition from the footprint to the surrounding sediment is often continuous, and the footprint wall complex, requiring interpolation, approximation, and a priori assumptions about trackmaker anatomy to arrive at feasible interpretations of footprint shapes. The degree of subjectivity of such interpretations is substantial, and outlines produced by separate researchers can differ greatly. As a consequence, statistical shape analysis, regardless if based on linear and angular measurements or on the shape as a whole, are neither fully repeatable nor objective. Here I present an algorithm implemented in the programming environment R that is able to generate continuous footprint outlines based on three-dimensional models—fully automatically, objectively, and repeatable. The approach, which is based on contour lines extracted from the model, traces the outline at the point where the slope of the track wall is steepest. An option for automatic landmark placement is implemented for tridactyl footprints. A case study was carried out on 13 footprints of a single trackway of a theropod trackmaker from the Lower Cretaceous of Münchehagen, Germany. Analysis of the landmark coordinates returned by the script did reproduce statistical results published in an earlier study that was based on human-made interpretative drawings, demonstrating the applicability of the present method for the objective and quantitative shape analysis of tracks. Although faint anatomical details are not always recorded and features not related to the foot anatomy may be included, the generated outlines tend to correspond with human-made interpretative drawings regarding the overall shape. While not suited as a full replacement of interpretative drawings, these generated outlines may be used as an objective basis for such interpretations.

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