Highly efficient model updating for structural condition assessment of large-scale bridges.

DOT National Transportation Integrated Search

2015-02-01

For eciently updating models of large-scale structures, the response surface (RS) method based on radial basis : functions (RBFs) is proposed to model the input-output relationship of structures. The key issues for applying : the proposed method a...

The Command and Control of Communications in Joint and Combined Operations

DTIC Science & Technology

1994-06-03

war. The Joint Task Force structure is used as the model for command and control relationships . The first part of the thesis assesses the current...Joint Task Force structure is used as the model for conmand and control relationships . The first part of the thesis assesses the current doctrine and...Message Switch Connectivity . . . . . . . 59 10. C4 Architecture Requirements . . . . . . 81 11. Functional Relationships . . . . . . 84 vi LIST OF

Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

PubMed

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. © 2016 The International Union of Biochemistry and Molecular Biology.

Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

ERIC Educational Resources Information Center

Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

2010-01-01

The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

Theoretical relationship between vibration transmissibility and driving-point response functions of the human body.

PubMed

Dong, Ren G; Welcome, Daniel E; McDowell, Thomas W; Wu, John Z

2013-11-25

The relationship between the vibration transmissibility and driving-point response functions (DPRFs) of the human body is important for understanding vibration exposures of the system and for developing valid models. This study identified their theoretical relationship and demonstrated that the sum of the DPRFs can be expressed as a linear combination of the transmissibility functions of the individual mass elements distributed throughout the system. The relationship is verified using several human vibration models. This study also clarified the requirements for reliably quantifying transmissibility values used as references for calibrating the system models. As an example application, this study used the developed theory to perform a preliminary analysis of the method for calibrating models using both vibration transmissibility and DPRFs. The results of the analysis show that the combined method can theoretically result in a unique and valid solution of the model parameters, at least for linear systems. However, the validation of the method itself does not guarantee the validation of the calibrated model, because the validation of the calibration also depends on the model structure and the reliability and appropriate representation of the reference functions. The basic theory developed in this study is also applicable to the vibration analyses of other structures.

Structure-function relationship of skeletal muscle provides inspiration for design of new artificial muscle

NASA Astrophysics Data System (ADS)

Gao, Yingxin; Zhang, Chi

2015-03-01

A variety of actuator technologies have been developed to mimic biological skeletal muscle that generates force in a controlled manner. Force generation process of skeletal muscle involves complicated biophysical and biochemical mechanisms; therefore, it is impossible to replace biological muscle. In biological skeletal muscle tissue, the force generation of a muscle depends not only on the force generation capacity of the muscle fiber, but also on many other important factors, including muscle fiber type, motor unit recruitment, architecture, structure and morphology of skeletal muscle, all of which have significant impact on the force generation of the whole muscle or force transmission from muscle fibers to the tendon. Such factors have often been overlooked, but can be incorporated in artificial muscle design, especially with the discovery of new smart materials and the development of innovative fabrication and manufacturing technologies. A better understanding of the physiology and structure-function relationship of skeletal muscle will therefore benefit the artificial muscle design. In this paper, factors that affect muscle force generation are reviewed. Mathematical models used to model the structure-function relationship of skeletal muscle are reviewed and discussed. We hope the review will provide inspiration for the design of a new generation of artificial muscle by incorporating the structure-function relationship of skeletal muscle into the design of artificial muscle.

Highlighting the Structure-Function Relationship of the Brain with the Ising Model and Graph Theory

PubMed Central

Das, T. K.; Abeyasinghe, P. M.; Crone, J. S.; Sosnowski, A.; Laureys, S.; Owen, A. M.; Soddu, A.

2014-01-01

With the advent of neuroimaging techniques, it becomes feasible to explore the structure-function relationships in the brain. When the brain is not involved in any cognitive task or stimulated by any external output, it preserves important activities which follow well-defined spatial distribution patterns. Understanding the self-organization of the brain from its anatomical structure, it has been recently suggested to model the observed functional pattern from the structure of white matter fiber bundles. Different models which study synchronization (e.g., the Kuramoto model) or global dynamics (e.g., the Ising model) have shown success in capturing fundamental properties of the brain. In particular, these models can explain the competition between modularity and specialization and the need for integration in the brain. Graphing the functional and structural brain organization supports the model and can also highlight the strategy used to process and organize large amount of information traveling between the different modules. How the flow of information can be prevented or partially destroyed in pathological states, like in severe brain injured patients with disorders of consciousness or by pharmacological induction like in anaesthesia, will also help us to better understand how global or integrated behavior can emerge from local and modular interactions. PMID:25276772

Optimization of the time series NDVI-rainfall relationship using linear mixed-effects modeling for the anti-desertification area in the Beijing and Tianjin sandstorm source region

NASA Astrophysics Data System (ADS)

Wang, Jin; Sun, Tao; Fu, Anmin; Xu, Hao; Wang, Xinjie

2018-05-01

Degradation in drylands is a critically important global issue that threatens ecosystem and environmental in many ways. Researchers have tried to use remote sensing data and meteorological data to perform residual trend analysis and identify human-induced vegetation changes. However, complex interactions between vegetation and climate, soil units and topography have not yet been considered. Data used in the study included annual accumulated Moderate Resolution Imaging Spectroradiometer (MODIS) 250 m normalized difference vegetation index (NDVI) from 2002 to 2013, accumulated rainfall from September to August, digital elevation model (DEM) and soil units. This paper presents linear mixed-effect (LME) modeling methods for the NDVI-rainfall relationship. We developed linear mixed-effects models that considered the random effects of sample points nested in soil units for nested two-level modeling and single-level modeling of soil units and sample points, respectively. Additionally, three functions, including the exponential function (exp), the power function (power), and the constant plus power function (CPP), were tested to remove heterogeneity, and an additional three correlation structures, including the first-order autoregressive structure [AR(1)], a combination of first-order autoregressive and moving average structures [ARMA(1,1)] and the compound symmetry structure (CS), were used to address the spatiotemporal correlations. It was concluded that the nested two-level model considering both heteroscedasticity with (CPP) and spatiotemporal correlation with [ARMA(1,1)] showed the best performance (AMR = 0.1881, RMSE = 0.2576, adj- R 2 = 0.9593). Variations between soil units and sample points that may have an effect on the NDVI-rainfall relationship should be included in model structures, and linear mixed-effects modeling achieves this in an effective and accurate way.

Joint two-dimensional inversion of magnetotelluric and gravity data using correspondence maps

NASA Astrophysics Data System (ADS)

Carrillo, Jonathan; Gallardo, Luis A.

2018-05-01

An accurate characterization of subsurface targets relies on the interpretation of multiple geophysical properties and their relationships. There are mainly two links to jointly invert different geophysical parameters: structural and petrophysical relationships. Structural approaches aim at minimizing topological differences and are widely popular since they need only a few assumptions about models. Conversely, methods based on petrophysical links rely mostly on the property values themselves and can provide a strong coupling between models, but they need to be treated carefully because specific direct relationship must be known or assumed. While some petrophysical relationships are widely accepted, it remains the question whether we may be able to detect them directly from the geophysical data. Currently, there is no reported development that takes full advantage of the flexibility of jointly estimating in-situ empirical relationships and geophysical models for a given geological scenario. We thus developed an algorithm for the two dimensional joint inversion of gravity and magnetotelluric data that seeks simultaneously for a density-resistivity relationship optimal for each studied site described trough a polynomial function. The iterative two-dimensional scheme is tested using synthetic and field data from Cerro Prieto, Mexico. The resulting models show an enhanced resolution with an increased structural and petrophysical correlation. We show that by fitting a functional relationship we increased significantly the coupled geological sense of the models at a little cost in terms of data misfit.

Coupled Analysis of In Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship

PubMed Central

Acar, Evrim; Plopper, George E.; Yener, Bülent

2012-01-01

The structure/function relationship is fundamental to our understanding of biological systems at all levels, and drives most, if not all, techniques for detecting, diagnosing, and treating disease. However, at the tissue level of biological complexity we encounter a gap in the structure/function relationship: having accumulated an extraordinary amount of detailed information about biological tissues at the cellular and subcellular level, we cannot assemble it in a way that explains the correspondingly complex biological functions these structures perform. To help close this information gap we define here several quantitative temperospatial features that link tissue structure to its corresponding biological function. Both histological images of human tissue samples and fluorescence images of three-dimensional cultures of human cells are used to compare the accuracy of in vitro culture models with their corresponding human tissues. To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples. Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues. We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models. PMID:22479315

Mapping the Structure-Function Relationship in Glaucoma and Healthy Patients Measured with Spectralis OCT and Humphrey Perimetry

PubMed Central

Muñoz–Negrete, Francisco J.; Oblanca, Noelia; Rebolleda, Gema

2018-01-01

Purpose To study the structure-function relationship in glaucoma and healthy patients assessed with Spectralis OCT and Humphrey perimetry using new statistical approaches. Materials and Methods Eighty-five eyes were prospectively selected and divided into 2 groups: glaucoma (44) and healthy patients (41). Three different statistical approaches were carried out: (1) factor analysis of the threshold sensitivities (dB) (automated perimetry) and the macular thickness (μm) (Spectralis OCT), subsequently applying Pearson's correlation to the obtained regions, (2) nonparametric regression analysis relating the values in each pair of regions that showed significant correlation, and (3) nonparametric spatial regressions using three models designed for the purpose of this study. Results In the glaucoma group, a map that relates structural and functional damage was drawn. The strongest correlation with visual fields was observed in the peripheral nasal region of both superior and inferior hemigrids (r = 0.602 and r = 0.458, resp.). The estimated functions obtained with the nonparametric regressions provided the mean sensitivity that corresponds to each given macular thickness. These functions allowed for accurate characterization of the structure-function relationship. Conclusions Both maps and point-to-point functions obtained linking structure and function damage contribute to a better understanding of this relationship and may help in the future to improve glaucoma diagnosis. PMID:29850196

Individual species affect plant traits structure in their surroundings: evidence of functional mechanisms of assembly.

PubMed

Chacón-Labella, Julia; de la Cruz, Marcelino; Pescador, David S; Escudero, Adrián

2016-04-01

Evaluating community assembly through the use of functional traits is a promising tool for testing predictions arising from Niche and Coexistence theories. Although interactions among neighboring species and their inter-specific differences are known drivers of coexistence with a strong spatial signal, assessing the role of individual species on the functional structure of the community at different spatial scales remains a challenge. Here, we ask whether individual species exert a measurable effect on the spatial organization of different functional traits in local assemblages. We first propose and compute two functions that describe different aspects of functional trait organization around individual species at multiple scales: individual weighted mean area relationship and individual functional diversity area relationship. Secondly, we develop a conceptual model on the relationship and simultaneous variation of these two metrics, providing five alternative scenarios in response to the ability of some target species to modify its neighbor environment and the possible assembly mechanisms involved. Our results show that some species influence the spatial structure of specific functional traits, but their effects were always restricted to the finest spatial scales. In the basis of our conceptual model, the observed patterns point to two main mechanisms driving the functional structure of the community at the fine scale, "biotic" filtering meditated by individual species and resource partitioning driven by indirect facilitation rather than by competitive mechanisms.

Relating retinal nerve fiber thickness to behavioral sensitivity in patients with glaucoma: application of a linear model.

PubMed

Hood, Donald C

2007-05-01

Glaucoma causes damage to the retinal ganglion cells and their axons, and this damage can be detected with both structural and functional tests. The purpose of this study was to better understand the relationship between a structural measure of retinal nerve fiber layer (RNFL) and the most common functional test, behavioral sensitivity with static automated perimetry (SAP). First, a linear model, previously shown to describe the relationship between local visual evoked potentials and SAP sensitivity, was modified to predict the change in RNFL as measured by optical coherence tomography. Second, previous work by others was shown to be consistent with this model.

Structure-Thermodynamics-Antioxidant Activity Relationships of Selected Natural Phenolic Acids and Derivatives: An Experimental and Theoretical Evaluation

PubMed Central

Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media. PMID:25803685

Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation.

PubMed

Chen, Yuzhen; Xiao, Huizhi; Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.

Students' Competencies in Working with Functions in Secondary Mathematics Education-Empirical Examination of a Competence Structure Model

ERIC Educational Resources Information Center

Nitsch, Renate; Fredebohm, Anneke; Bruder, Regina; Kelava, Augustin; Naccarella, Dominik; Leuders, Timo; Wirtz, Markus

2015-01-01

In the subject matter of functional relationships, a student's ability to translate from one form of representation to another is seen as a central competence. In the course of the HEUREKO project (heuristic work with representations of functional relationships and the diagnosis of mathematical competencies of students), a theoretical competence…

Response of rocky invertebrate diversity, structure and function to the vertical layering of vegetation

NASA Astrophysics Data System (ADS)

Bustamante, María; Tajadura, Javier; Gorostiaga, José María; Saiz-Salinas, José Ignacio

2014-06-01

Macroalgae comprise a prominent part of the rocky benthos where many invertebrates develop, and are believed to be undergoing severe declines worldwide. In order to investigate how the vegetation structure (crustose, basal and canopy layers) contributes to the diversity, structure and function of benthic invertebrates, a total of 31 subtidal transects were sampled along the northeast Atlantic coast of Spain. Significant positive relationships were found between the canopy layer and faunal abundance, taxonomic diversity and functional group diversity. Canopy forming algae were also related to epiphytic invertebrates, medium size forms, colonial strategy and suspensivores. By contrast, basal algae showed negative relationships with all variables tested except for detritivores. Multivariate multiple regression analyses (DISTLM) point to crustose as well as canopy layers as the best link between seaweeds and invertebrate assemblage structure. A close relationship was found between taxonomic and functional diversities. In general, low levels of taxonomic redundancy were detected for functional groups correlated with vegetation structure. A conceptual model based on the results is proposed, describing distinct stages of invertebrate assemblages in relation to the vertical structure of vegetation.

Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

ERIC Educational Resources Information Center

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

Numerical simulation of intelligent compaction technology for construction quality control.

DOT National Transportation Integrated Search

2015-02-01

For eciently updating models of large-scale structures, the response surface (RS) method based on radial basis : functions (RBFs) is proposed to model the input-output relationship of structures. The key issues for applying : the proposed method a...

The relationship between Gross Primary Productivity and Sun-Induced Fluorescence in a nutrient manipulated Mediterranean grassland is controlled primarily by canopy structure

NASA Astrophysics Data System (ADS)

Migliavacca, Mirco

2017-04-01

Recent studies have shown how human induced N/P imbalances affect essential ecosystem processes, and might be particularly important in water-limited ecosystems. Hyperspectral information can be used to directly infer nutrient-induces variation in structural and functional changes of vegetation under different nutrient availability. Among those, sun-induced fluorescence in the far-red region provides a new non-invasive measurement approach that has the potential to quantify dynamic changes in light-use efficiency and photosynthetic carbon dioxide uptake (Gross Primary Production, GPP). However, the mechanistic link between GPP and sun-induced fluorescence under different environmental conditions is not completely understood. In this contribution we investigated the structural and functional factors controlling the emission of SIF at 760 nm in a Mediterranean grassland with different levels of nutrient availability (Nitrogen (N), Phosphorous (P), and Nitrogen and Phosphorous (NP)). We showed how nutrient-induced changes in canopy structure (i.e. changes in plant forms abundance that influence leaf inclination distribution function, LIDF) and functional traits (e.g. nitrogen content per dry mass of leaves, N%, Chlorophyll ab concentration - Cab, and maximum carboxylation capacity, Vcmax) affected the observed relationship between SIF and GPP. Simultaneous measurements of canopy scale GPP and SIF were conducted with transparent transient-state canopy chambers and narrow-band spectrometers, respectively. To disentangle the main drivers of the GPP-SIF relationship we performed a factorial modeling exercise with the Soil-Canopy Observation of Photosynthesis and Energy (SCOPE) model. We conclude that the addition of nutrients imposed a change in the abundance of different plant forms and biochemistry of the canopy. This lead to changes in canopy structure (leaf area index, leaf inclinaton distribution function LIDF parameters) and functional traits (N%, P%, Cab and Vcmax) that eventually controlled the spatial patterns of SIF. Changes in LIDF mainly control the GPP-SIF relationship, with a secondary control of Cab and Vcmax. In order to exploit SIF data to model GPP at global/regional scale canopy structural variability, plant community, and plant functional traits are important confounding factors that have to be considered to correct the plant-functional type specific relationship between sun-induced fluorescence and GPP.

Do Demographic Factors, School Functioning, and Quality of Student-Teacher Relationships as Rated by Teachers Predict Internalising and Externalising Problems among Norwegian Schoolchildren?

ERIC Educational Resources Information Center

Drugli, May Britt; Klokner, Christian; Larsson, Bo

2011-01-01

The present study explored the association between child internalising and externalising problems in schools and demographic factors (sex and age), school functioning (academic performance and adaptive functioning) and teacher-reported student-teacher relationship quality in a cross-sectional study using structural equation modelling. The study…

On the role of general system theory for functional neuroimaging

PubMed Central

Stephan, Klaas Enno

2004-01-01

One of the most important goals of neuroscience is to establish precise structure–function relationships in the brain. Since the 19th century, a major scientific endeavour has been to associate structurally distinct cortical regions with specific cognitive functions. This was traditionally accomplished by correlating microstructurally defined areas with lesion sites found in patients with specific neuropsychological symptoms. Modern neuroimaging techniques with high spatial resolution have promised an alternative approach, enabling non-invasive measurements of regionally specific changes of brain activity that are correlated with certain components of a cognitive process. Reviewing classic approaches towards brain structure–function relationships that are based on correlational approaches, this article argues that these approaches are not sufficient to provide an understanding of the operational principles of a dynamic system such as the brain but must be complemented by models based on general system theory. These models reflect the connectional structure of the system under investigation and emphasize context-dependent couplings between the system elements in terms of effective connectivity. The usefulness of system models whose parameters are fitted to measured functional imaging data for testing hypotheses about structure–function relationships in the brain and their potential for clinical applications is demonstrated by several empirical examples. PMID:15610393

Drug Release Kinetics and Transport Mechanisms of Non-degradable and Degradable Polymeric Delivery Systems

PubMed Central

Fu, Yao; Kao, Weiyuan John

2010-01-01

Importance of the field The advancement in material design and engineering has led to the rapid development of novel materials with increasing complexity and functions. Both non-degradable and degradable polymers have found wide applications in the controlled delivery field. Studies on drug release kinetics provide important information into the function of material systems. To elucidate the detailed transport mechanism and the structure-function relationship of a material system, it is critical to bridge the gap between the macroscopic data and the transport behavior at the molecular level. Areas covered in this review The structure and function information of selected non-degradable and degradable polymers have been collected and summarized from literatures published after 1990s. The release kinetics of selected drug compounds from various material systems will be discussed in case studies. Recent progresses in the mathematical models based on different transport mechanisms will be highlighted. What the reader will gain This article aims to provide an overview of structure-function relationships of selected non-degradable and degradable polymers as drug delivery matrices. Take home message Understanding the structure-function relationship of the material system is key to the successful design of a delivery system for a particular application. Moreover, developing complex polymeric matrices requires more robust mathematical models to elucidate the solute transport mechanisms. PMID:20331353

Structural-functional relationships between eye orbital imaging biomarkers and clinical visual assessments

NASA Astrophysics Data System (ADS)

Yao, Xiuya; Chaganti, Shikha; Nabar, Kunal P.; Nelson, Katrina; Plassard, Andrew; Harrigan, Rob L.; Mawn, Louise A.; Landman, Bennett A.

2017-02-01

Eye diseases and visual impairment affect millions of Americans and induce billions of dollars in annual economic burdens. Expounding upon existing knowledge of eye diseases could lead to improved treatment and disease prevention. This research investigated the relationship between structural metrics of the eye orbit and visual function measurements in a cohort of 470 patients from a retrospective study of ophthalmology records for patients (with thyroid eye disease, orbital inflammation, optic nerve edema, glaucoma, intrinsic optic nerve disease), clinical imaging, and visual function assessments. Orbital magnetic resonance imaging (MRI) and computed tomography (CT) images were retrieved and labeled in 3D using multi-atlas label fusion. Based on the 3D structures, both traditional radiology measures (e.g., Barrett index, volumetric crowding index, optic nerve length) and novel volumetric metrics were computed. Using stepwise regression, the associations between structural metrics and visual field scores (visual acuity, functional acuity, visual field, functional field, and functional vision) were assessed. Across all models, the explained variance was reasonable (R2 0.1-0.2) but highly significant (p < 0.001). Instead of analyzing a specific pathology, this study aimed to analyze data across a variety of pathologies. This approach yielded a general model for the connection between orbital structural imaging biomarkers and visual function.

The Role of Family Functioning in the Stress Process of Dementia Caregivers: A Structural Family Framework

ERIC Educational Resources Information Center

Mitrani, Victoria B.; Lewis, John E.; Feaster, Daniel J.; Czaja, Sara J.; Eisdorfer, Carl; Schulz, Richard; Szapocznik, Jose

2006-01-01

Purpose: The purpose of the study was to evaluate the role of family functioning in the stress process in a sample of caregivers of dementia patients by using a structural family framework. The stress-process model of caregiver distress included family functioning as an intervening variable in the relationship between objective burden and…

Plant functional traits and canopy structure control the relationship between photosynthetic CO2 uptake and far-red sun-induced fluorescence in a Mediterranean grassland under different nutrient availability.

PubMed

Migliavacca, Mirco; Perez-Priego, Oscar; Rossini, Micol; El-Madany, Tarek S; Moreno, Gerardo; van der Tol, Christiaan; Rascher, Uwe; Berninger, Anna; Bessenbacher, Verena; Burkart, Andreas; Carrara, Arnaud; Fava, Francesco; Guan, Jin-Hong; Hammer, Tiana W; Henkel, Kathrin; Juarez-Alcalde, Enrique; Julitta, Tommaso; Kolle, Olaf; Martín, M Pilar; Musavi, Talie; Pacheco-Labrador, Javier; Pérez-Burgueño, Andrea; Wutzler, Thomas; Zaehle, Sönke; Reichstein, Markus

2017-05-01

Sun-induced fluorescence (SIF) in the far-red region provides a new noninvasive measurement approach that has the potential to quantify dynamic changes in light-use efficiency and gross primary production (GPP). However, the mechanistic link between GPP and SIF is not completely understood. We analyzed the structural and functional factors controlling the emission of SIF at 760 nm (F 760 ) in a Mediterranean grassland manipulated with nutrient addition of nitrogen (N), phosphorous (P) or nitrogen-phosphorous (NP). Using the soil-canopy observation of photosynthesis and energy (SCOPE) model, we investigated how nutrient-induced changes in canopy structure (i.e. changes in plant forms abundance that influence leaf inclination distribution function, LIDF) and functional traits (e.g. N content in dry mass of leaves, N%, Chlorophyll a+b concentration (Cab) and maximum carboxylation capacity (V cmax )) affected the observed linear relationship between F 760 and GPP. We conclude that the addition of nutrients imposed a change in the abundance of different plant forms and biochemistry of the canopy that controls F 760 . Changes in canopy structure mainly control the GPP-F 760 relationship, with a secondary effect of Cab and V cmax . In order to exploit F 760 data to model GPP at the global/regional scale, canopy structural variability, biodiversity and functional traits are important factors that have to be considered. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Emergent structure-function relations in emphysema and asthma.

PubMed

Winkler, Tilo; Suki, Béla

2011-01-01

Structure-function relationships in the respiratory system are often a result of the emergence of self-organized patterns or behaviors that are characteristic of certain respiratory diseases. Proper description of such self-organized behavior requires network models that include nonlinear interactions among different parts of the system. This review focuses on 2 models that exhibit self-organized behavior: a network model of the lung parenchyma during the progression of emphysema that is driven by mechanical force-induced breakdown, and an integrative model of bronchoconstriction in asthma that describes interactions among airways within the bronchial tree. Both models suggest that the transition from normal to pathologic states is a nonlinear process that includes a tipping point beyond which interactions among the system components are reinforced by positive feedback, further promoting the progression of pathologic changes. In emphysema, the progressive destruction of tissue is irreversible, while in asthma, it is possible to recover from a severe bronchoconstriction. These concepts may have implications for pulmonary medicine. Specifically, we suggest that structure-function relationships emerging from network behavior across multiple scales should be taken into account when the efficacy of novel treatments or drug therapy is evaluated. Multiscale, computational, network models will play a major role in this endeavor.

Development of a Conceptual Model for Smoking Cessation: Physical Activity, Neurocognition, and Executive Functioning.

PubMed

Loprinzi, Paul D; Herod, Skyla M; Walker, Jerome F; Cardinal, Bradley J; Mahoney, Sara E; Kane, Christy

2015-01-01

Considerable research has shown adverse neurobiological effects of chronic alcohol use, including long-term and potentially permanent changes in the structure and function of the brain; however, much less is known about the neurobiological consequences of chronic smoking, as it has largely been ignored until recently. In this article, we present a conceptual model proposing the effects of smoking on neurocognition and the role that physical activity may play in this relationship as well as its role in smoking cessation. Pertinent published peer-reviewed articles deposited in PubMed delineating the pathways in the proposed model were reviewed. The proposed model, which is supported by emerging research, demonstrates a bidirectional relationship between smoking and executive functioning. In support of our conceptual model, physical activity may moderate this relationship and indirectly influence smoking behavior through physical activity-induced changes in executive functioning. Our model may have implications for aiding smoking cessation efforts through the promotion of physical activity as a mechanism for preventing smoking-induced deficits in neurocognition and executive function.

A Structural Equation Model on Korean Adolescents' Excessive Use of Smartphones.

PubMed

Lee, Hana; Kim, JooHyun

2018-03-31

We develop a unified structural model that defines multi-relationships between systematic factors causing excessive use of smartphones and the corresponding results. We conducted a survey with adolescents who live in Seoul, Pusan, Gangneung, Donghae, and Samcheok from Feb. to Mar. 2016. We utilized SPSS Ver. 22 and Amos Ver. 22 to analyze the survey result at a 0.05 significance level. To investigate demographic characteristics of the participants and their variations, we employed descriptive analysis. We adopted the maximum likelihood estimate method to verify the fitness of the hypothetical model and the hypotheses therein. We used χ 2 statistics, GFI, AGFI, CFI, NFI, IFI, RMR, and RMSEA to verify the fitness of our structural model. (1) Our proposed structural model demonstrated a fine fitness level. (2) Our proposed structural model could describe the excessive use of a smartphone with 88.6% accuracy. (3) The absence of the family function and relationship between friends, impulsiveness, and low self-esteem were confirmed as key factors that cause excessive use of smartphones. (4) Further, impulsiveness and low self-esteem are closely related to the absence of family functions and relations between friends by 68.3% and 54.4%, respectively. We suggest that nursing intervention programs from various angles are required to reduce adolescents' excessive use of smartphones. For example, family communication programs would be helpful for both parents and children. Consultant programs about friend relationship also meaningful for the program. Copyright © 2018. Published by Elsevier B.V.

Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities

PubMed Central

Estrela, Sylvie; Brown, Sam P.

2013-01-01

Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships), and species spatial organization (structural relationships) are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource) is traded for detoxification (service) and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition), and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies. PMID:24385891

Sequence-structure relationship study in all-α transmembrane proteins using an unsupervised learning approach.

PubMed

Esque, Jérémy; Urbain, Aurélie; Etchebest, Catherine; de Brevern, Alexandre G

2015-11-01

Transmembrane proteins (TMPs) are major drug targets, but the knowledge of their precise topology structure remains highly limited compared with globular proteins. In spite of the difficulties in obtaining their structures, an important effort has been made these last years to increase their number from an experimental and computational point of view. In view of this emerging challenge, the development of computational methods to extract knowledge from these data is crucial for the better understanding of their functions and in improving the quality of structural models. Here, we revisit an efficient unsupervised learning procedure, called Hybrid Protein Model (HPM), which is applied to the analysis of transmembrane proteins belonging to the all-α structural class. HPM method is an original classification procedure that efficiently combines sequence and structure learning. The procedure was initially applied to the analysis of globular proteins. In the present case, HPM classifies a set of overlapping protein fragments, extracted from a non-redundant databank of TMP 3D structure. After fine-tuning of the learning parameters, the optimal classification results in 65 clusters. They represent at best similar relationships between sequence and local structure properties of TMPs. Interestingly, HPM distinguishes among the resulting clusters two helical regions with distinct hydrophobic patterns. This underlines the complexity of the topology of these proteins. The HPM classification enlightens unusual relationship between amino acids in TMP fragments, which can be useful to elaborate new amino acids substitution matrices. Finally, two challenging applications are described: the first one aims at annotating protein functions (channel or not), the second one intends to assess the quality of the structures (X-ray or models) via a new scoring function deduced from the HPM classification.

ALAMEDA, a Structural–Functional Model for Faba Bean Crops: Morphological Parameterization and Verification

PubMed Central

RUIZ-RAMOS, MARGARITA; MÍNGUEZ, M. INÉS

2006-01-01

• Background Plant structural (i.e. architectural) models explicitly describe plant morphology by providing detailed descriptions of the display of leaf and stem surfaces within heterogeneous canopies and thus provide the opportunity for modelling the functioning of plant organs in their microenvironments. The outcome is a class of structural–functional crop models that combines advantages of current structural and process approaches to crop modelling. ALAMEDA is such a model. • Methods The formalism of Lindenmayer systems (L-systems) was chosen for the development of a structural model of the faba bean canopy, providing both numerical and dynamic graphical outputs. It was parameterized according to the results obtained through detailed morphological and phenological descriptions that capture the detailed geometry and topology of the crop. The analysis distinguishes between relationships of general application for all sowing dates and stem ranks and others valid only for all stems of a single crop cycle. • Results and Conclusions The results reveal that in faba bean, structural parameterization valid for the entire plant may be drawn from a single stem. ALAMEDA was formed by linking the structural model to the growth model ‘Simulation d'Allongement des Feuilles’ (SAF) with the ability to simulate approx. 3500 crop organs and components of a group of nine plants. Model performance was verified for organ length, plant height and leaf area. The L-system formalism was able to capture the complex architecture of canopy leaf area of this indeterminate crop and, with the growth relationships, generate a 3D dynamic crop simulation. Future development and improvement of the model are discussed. PMID:16390842

Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure.

PubMed

Abdelnour, Farras; Dayan, Michael; Devinsky, Orrin; Thesen, Thomas; Raj, Ashish

2018-05-15

How structural connectivity (SC) gives rise to functional connectivity (FC) is not fully understood. Here we mathematically derive a simple relationship between SC measured from diffusion tensor imaging, and FC from resting state fMRI. We establish that SC and FC are related via (structural) Laplacian spectra, whereby FC and SC share eigenvectors and their eigenvalues are exponentially related. This gives, for the first time, a simple and analytical relationship between the graph spectra of structural and functional networks. Laplacian eigenvectors are shown to be good predictors of functional eigenvectors and networks based on independent component analysis of functional time series. A small number of Laplacian eigenmodes are shown to be sufficient to reconstruct FC matrices, serving as basis functions. This approach is fast, and requires no time-consuming simulations. It was tested on two empirical SC/FC datasets, and was found to significantly outperform generative model simulations of coupled neural masses. Copyright © 2018. Published by Elsevier Inc.

Evaluation of Two Teaching Programs Based on Structural Learning Principles.

ERIC Educational Resources Information Center

Haussler, Peter

1978-01-01

Structural learning theory and the Rasch model measured learning gain, retention, and transfer in 1,037 students, grades 7-10. Students learned nine functional relationships with either spontaneous or synthetic algorithms. The Rasch model gave the better description of the data. The hypothesis that the synthetic method was superior was refuted.…

Structural diversity in the dandelion (Taraxacum officinale) polyphenol oxidase family results in different responses to model substrates.

PubMed

Dirks-Hofmeister, Mareike E; Singh, Ratna; Leufken, Christine M; Inlow, Jennifer K; Moerschbacher, Bruno M

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure-function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a "selector" for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates.

Linking social anxiety and adolescent romantic relationship functioning: indirect effects and the importance of peers.

PubMed

Hebert, Karen R; Fales, Jessica; Nangle, Douglas W; Papadakis, Alison A; Grover, Rachel L

2013-11-01

Peer relationships undergo dramatic shifts in form and function during adolescence, at the same time the incidence of socially evaluative fears sharply rises. Despite well-established links between social anxiety and broader interpersonal functioning, there is a dearth of research evaluating the impact of social anxiety on functioning in close relationships during this developmental stage. The present study examines the impact of social anxiety on functioning in close friendships and romantic relationships during adolescence. From a developmental psychopathology perspective, it was expected that social anxiety would influence functioning (quality, length, satisfaction) in romantic relationships through its influence on functioning in same- and other-sex friendships. Participants included 314 adolescents (60.5% female, 14-19 years of age) with a prior or current history of romantic relationship involvement. Structural equation modeling was used to test a mediation model positing an indirect pathway from social anxiety to romantic relationship functioning through functioning in close same- and other-sex friendships. Given known gender differences in social anxiety and relationship functioning, gender also was explored as a potential moderator. Results supported the hypothesized indirect pathway whereby social anxiety was associated with impairment in same-sex friendships; functioning in same-sex friendships was associated with functioning in other-sex friendships, which was associated, in turn, with functioning in romantic relationships. While the hypothesized indirect pathway was significant among both boys and girls, there was greater continuity of functioning between same- and other-sex friendships for girls. These findings highlight the importance of examining the multiple downstream effects of social anxiety on perceived social functioning in adolescence, and suggest that continuity may exist for maladaptive patterns of socialization, particularly across developmentally salient close relationships.

Modelling protein functional domains in signal transduction using Maude

NASA Technical Reports Server (NTRS)

Sriram, M. G.

2003-01-01

Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

Hierarchical modularization of biochemical pathways using fuzzy-c means clustering.

PubMed

de Luis Balaguer, Maria A; Williams, Cranos M

2014-08-01

Biological systems that are representative of regulatory, metabolic, or signaling pathways can be highly complex. Mathematical models that describe such systems inherit this complexity. As a result, these models can often fail to provide a path toward the intuitive comprehension of these systems. More coarse information that allows a perceptive insight of the system is sometimes needed in combination with the model to understand control hierarchies or lower level functional relationships. In this paper, we present a method to identify relationships between components of dynamic models of biochemical pathways that reside in different functional groups. We find primary relationships and secondary relationships. The secondary relationships reveal connections that are present in the system, which current techniques that only identify primary relationships are unable to show. We also identify how relationships between components dynamically change over time. This results in a method that provides the hierarchy of the relationships among components, which can help us to understand the low level functional structure of the system and to elucidate potential hierarchical control. As a proof of concept, we apply the algorithm to the epidermal growth factor signal transduction pathway, and to the C3 photosynthesis pathway. We identify primary relationships among components that are in agreement with previous computational decomposition studies, and identify secondary relationships that uncover connections among components that current computational approaches were unable to reveal.

Bio-mimicking galactose oxidase and hemocyanin, two dioxygen-processing copper proteins.

PubMed

Gamez, Patrick; Koval, Iryna A; Reedijk, Jan

2004-12-21

The modelling of the active sites of metalloproteins is one of the most challenging tasks in bio-inorganic chemistry. Copper proteins form part of this stimulating field of research as copper enzymes are mainly involved in oxidation bio-reactions. Thus, the understanding of the structure-function relationship of their active sites will allow the design of effective and environmental friendly oxidation catalysts. This perspective illustrates some outstanding structural and functional synthetic models of the active site of copper proteins, with special attention given to models of galactose oxidase and hemocyanin.

Nonparametric Transfer Function Models

PubMed Central

Liu, Jun M.; Chen, Rong; Yao, Qiwei

2009-01-01

In this paper a class of nonparametric transfer function models is proposed to model nonlinear relationships between ‘input’ and ‘output’ time series. The transfer function is smooth with unknown functional forms, and the noise is assumed to be a stationary autoregressive-moving average (ARMA) process. The nonparametric transfer function is estimated jointly with the ARMA parameters. By modeling the correlation in the noise, the transfer function can be estimated more efficiently. The parsimonious ARMA structure improves the estimation efficiency in finite samples. The asymptotic properties of the estimators are investigated. The finite-sample properties are illustrated through simulations and one empirical example. PMID:20628584

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations.

PubMed

Ramasubramanian, Smiruthi; Rudy, Yoram

2018-06-05

Relating ion channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of artificial intelligence machine learning. Using this approach, we studied molecular processes that underlie human IKs voltage-mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (a pore-forming tetramer) and KCNE1 (an auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating-charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage relationship. Mechanistic insights include the following: 1) pore energy profile determines iCh subconductance; 2) the entire protein structure, not limited to the pore, contributes to pore energy and channel subconductance; 3) interactions with KCNE1 result in two distinct VS movements, causing gating-charge saturation at positive membrane voltages and current activation delay; and 4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Diagnosis and sensor validation through knowledge of structure and function

NASA Technical Reports Server (NTRS)

Scarl, Ethan A.; Jamieson, John R.; Delaune, Carl I.

1987-01-01

The liquid oxygen expert system 'LES' is proposed as the first capable of diagnostic reasoning from sensor data, using model-based knowledge of structure and function to find the expected state of all system objects, including sensors. The approach is generally algorithmic rather than heuristic, and represents uncertainties as sets of possibilities. Functional relationships are inverted to determine hypothetical values for potentially faulty objects, and may include conditional functions not normally considered to have inverses.

Determinants of quality of life in patients with fibromyalgia: A structural equation modeling approach.

PubMed

Lee, Jeong-Won; Lee, Kyung-Eun; Park, Dong-Jin; Kim, Seong-Ho; Nah, Seong-Su; Lee, Ji Hyun; Kim, Seong-Kyu; Lee, Yeon-Ah; Hong, Seung-Jae; Kim, Hyun-Sook; Lee, Hye-Soon; Kim, Hyoun Ah; Joung, Chung-Il; Kim, Sang-Hyon; Lee, Shin-Seok

2017-01-01

Health-related quality of life (HRQOL) in patients with fibromyalgia (FM) is lower than in patients with other chronic diseases and the general population. Although various factors affect HRQOL, no study has examined a structural equation model of HRQOL as an outcome variable in FM patients. The present study assessed relationships among physical function, social factors, psychological factors, and HRQOL, and the effects of these variables on HRQOL in a hypothesized model using structural equation modeling (SEM). HRQOL was measured using SF-36, and the Fibromyalgia Impact Questionnaire (FIQ) was used to assess physical dysfunction. Social and psychological statuses were assessed using the Beck Depression Inventory (BDI), the State-Trait Anxiety Inventory (STAI), the Arthritis Self-Efficacy Scale (ASES), and the Social Support Scale. SEM analysis was used to test the structural relationships of the model using the AMOS software. Of the 336 patients, 301 (89.6%) were women with an average age of 47.9±10.9 years. The SEM results supported the hypothesized structural model (χ2 = 2.336, df = 3, p = 0.506). The final model showed that Physical Component Summary (PCS) was directly related to self-efficacy and inversely related to FIQ, and that Mental Component Summary (MCS) was inversely related to FIQ, BDI, and STAI. In our model of FM patients, HRQOL was affected by physical, social, and psychological variables. In these patients, higher levels of physical function and self-efficacy can improve the PCS of HRQOL, while physical function, depression, and anxiety negatively affect the MCS of HRQOL.

Determinants of quality of life in patients with fibromyalgia: A structural equation modeling approach

PubMed Central

Lee, Jeong-Won; Lee, Kyung-Eun; Park, Dong-Jin; Kim, Seong-Ho; Nah, Seong-Su; Lee, Ji Hyun; Kim, Seong-Kyu; Lee, Yeon-Ah; Hong, Seung-Jae; Kim, Hyun-Sook; Lee, Hye-Soon; Kim, Hyoun Ah; Joung, Chung-Il; Kim, Sang-Hyon

2017-01-01

Objective Health-related quality of life (HRQOL) in patients with fibromyalgia (FM) is lower than in patients with other chronic diseases and the general population. Although various factors affect HRQOL, no study has examined a structural equation model of HRQOL as an outcome variable in FM patients. The present study assessed relationships among physical function, social factors, psychological factors, and HRQOL, and the effects of these variables on HRQOL in a hypothesized model using structural equation modeling (SEM). Methods HRQOL was measured using SF-36, and the Fibromyalgia Impact Questionnaire (FIQ) was used to assess physical dysfunction. Social and psychological statuses were assessed using the Beck Depression Inventory (BDI), the State-Trait Anxiety Inventory (STAI), the Arthritis Self-Efficacy Scale (ASES), and the Social Support Scale. SEM analysis was used to test the structural relationships of the model using the AMOS software. Results Of the 336 patients, 301 (89.6%) were women with an average age of 47.9±10.9 years. The SEM results supported the hypothesized structural model (χ2 = 2.336, df = 3, p = 0.506). The final model showed that Physical Component Summary (PCS) was directly related to self-efficacy and inversely related to FIQ, and that Mental Component Summary (MCS) was inversely related to FIQ, BDI, and STAI. Conclusions In our model of FM patients, HRQOL was affected by physical, social, and psychological variables. In these patients, higher levels of physical function and self-efficacy can improve the PCS of HRQOL, while physical function, depression, and anxiety negatively affect the MCS of HRQOL. PMID:28158289

Comparative analysis of the mechanical signals in lung development and compensatory growth.

PubMed

Hsia, Connie C W

2017-03-01

This review compares the manner in which physical stress imposed on the parenchyma, vasculature and thorax and the thoraco-pulmonary interactions, drive both developmental and compensatory lung growth. Re-initiation of anatomical lung growth in the mature lung is possible when the loss of functioning lung units renders the existing physiologic-structural reserves insufficient for maintaining adequate function and physical stress on the remaining units exceeds a critical threshold. The appropriate spatial and temporal mechanical interrelationships and the availability of intra-thoracic space, are crucial to growth initiation, follow-on remodeling and physiological outcome. While the endogenous potential for compensatory lung growth is retained and may be pharmacologically augmented, supra-optimal mechanical stimulation, unbalanced structural growth, or inadequate remodeling may limit functional gain. Finding ways to optimize the signal-response relationships and resolve structure-function discrepancies are major challenges that must be overcome before the innate compensatory ability could be fully realized. Partial pneumonectomy reproducibly removes a known fraction of functioning lung units and remains the most robust model for examining the adaptive mechanisms, structure-function consequences and plasticity of the remaining functioning lung units capable of regeneration. Fundamental mechanical stimulus-response relationships established in the pneumonectomy model directly inform the exploration of effective approaches to maximize compensatory growth and function in chronic destructive lung diseases, transplantation and bioengineered lungs.

Comparative Analysis of the Mechanical Signals in Lung Development and Compensatory Growth

PubMed Central

Hsia, Connie C.W.

2017-01-01

This review compares the manner in which physical stress imposed on the parenchyma, vasculature and thorax, and the thoraco-pulmonary interactions, drive both developmental and compensatory lung growth. Re-initiation of anatomical lung growth in the mature lung is possible when the loss of functioning lung units renders the existing physiologic-structural reserves insufficient for maintaining adequate function and physical stress on the remaining units exceeds a critical threshold. The appropriate spatial and temporal mechanical interrelationships, and the availability of intra-thoracic space, are crucial to growth initiation, follow-on remodeling and physiological outcome. While the endogenous potential for compensatory lung growth is retained and may be pharmacologically augmented, supra-optimal mechanical stimulation, unbalanced structural growth, or inadequate remodeling, may limit functional gain. Finding ways to optimize the signal-response relationships and resolve structure-function discrepancies are major challenges that must be overcome before the innate compensatory ability could be fully realized. Partial pneumonectomy reproducibly removes a known fraction of functioning lung units and remains the most robust model for examining the adaptive mechanisms, structure-function consequences, and plasticity of the remaining functioning lung units capable of regeneration. Fundamental mechanical stimulus-response relationships established in the pneumonectomy model directly inform the exploration of effective approaches to maximize compensatory growth and function in chronic destructive lung diseases, transplantation and bioengineered lungs. PMID:28084523

Brandon Knott | NREL

Science.gov Websites

-6223 Research Interests Molecular mechanisms of cellulose-degrading enzymes Structure-function relationships of biomass-derived polymers Structure-function relationships in glycoside hydrolases Methane potential protein engineering targets. Structure-Function Relationships of Biomass-Derived Polymers

Structural Equation Modeling of Motor Impairment, Gross Motor Function, and the Functional Outcome in Children with Cerebral Palsy

ERIC Educational Resources Information Center

Park, Eun-Young; Kim, Won-Ho

2013-01-01

Physical therapy intervention for children with cerebral palsy (CP) is focused on reducing neurological impairments, improving strength, and preventing the development of secondary impairments in order to improve functional outcomes. However, relationship between motor impairments and functional outcome has not been proved definitely. This study…

Childhood adversity and social functioning in psychosis: Exploring clinical and cognitive mediators.

PubMed

Palmier-Claus, Jasper; Berry, Katherine; Darrell-Berry, Hannah; Emsley, Richard; Parker, Sophie; Drake, Richard; Bucci, Sandra

2016-04-30

Childhood adversity may increase risk of impaired social functioning across the continuum of psychosis. However, the pathways by which adversity dictates functional outcome remain underexplored. This study investigated the association between childhood adversity and social functioning, and the clinical and cognitive mediators of this relationship. Fifty-four clinical (20 chronic, 20 first episode, 14 at ultra-high risk) and 120 non-clinical participants completed standardised questionnaires, semi-structured interviews and tests of theory of mind ability. The authors used multiple group structural equation modelling to fit mediation models allowing for differential relationships between the clinical and non-clinical samples. When examining each pathway separately, depression, paranoia and anxious attachment mediated the effect of childhood adversity on social functioning. In a combined model, depression was the only significant mediating variable with greater adversity predicting lower mood across groups. Childhood adversity did not significantly predict theory of mind ability in any of the models. This is the first study to indicate that childhood adversity acts on social functioning by increasing levels of depression, suggesting a common mechanism across the spectrum of psychosis. Clinical interventions should target low mood in order to improve social functioning at all stages of psychotic disorder. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

PubMed Central

Toffano-Nioche, Claire; Gautheret, Daniel; Leclerc, Fabrice

2015-01-01

A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea. PMID:26240384

Successful Aging and Subjective Well-Being Among Oldest-Old Adults

PubMed Central

Cho, Jinmyoung; Martin, Peter; Poon, Leonard W.

2015-01-01

Purpose of the Study: This research integrates successful aging and developmental adaptation models to empirically define the direct and indirect effects of 2 distal (i.e., education and past life experiences) and 5 proximal influences (i.e., physical functioning, cognitive functioning, physical health impairment, social resources, and perceived economic status) on subjective well-being. The proximal influences involved predictors outlined in most extant models of successful aging (e.g., Rowe & Kahn, 1998 [Rowe, J. W., & Kahn, R. L. (1998). Successful aging. New York: Pantheon Books.]). Our model extends such models by including distal impact as well as interactions between distal and proximal impacts. Design and Methods: Data were obtained from 234 centenarians and 72 octogenarians in the Georgia Centenarian Study. Structural equation modeling was conducted with Mplus 6.1. Results: Results showed significant direct effects of physical health impairment and social resources on positive aspects of subjective well-being among oldest-old adults. We also found significant indirect effects of cognitive functioning and education on positive affect among oldest-old adults. Social resources mediated the relationship between cognitive functioning and positive affect; and cognitive functioning and social resources mediated the relationship between education and positive affect. In addition, physical health impairment mediated the relationship between cognitive functioning and positive affect; and cognitive functioning and physical health impairment mediated the relationship between education and positive affect. Implications: Integrating 2 different models (i.e., successful aging and developmental adaptation) provided a comprehensive view of adaptation from a developmental perspective. PMID:25112594

Scottish Schools Science Equipment Research Centre, Bulletin No. 56, June 1972.

ERIC Educational Resources Information Center

1972

A model demonstrating the relationship between the structure of blood vessels and the flow of blood is described and illustrated in the biology section of the newsletter. The apparatus also contains a functional (but not structural) model of the heart. Suggestions for the preparation of a relatively permanent dialysis bag from visking tubing are…

Developing sensor activity relationships for the JPL electronic nose sensors using molecular modeling and QSAR techniques

NASA Technical Reports Server (NTRS)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Jewell, A. D.; Zhou, H.; Manatt, K.; Kisor, A. K.

2005-01-01

We report a Quantitative Structure-Activity Relationships (QSAR) study using Genetic Function Approximations (GFA) to describe the polymer-carbon composite sensor activities in the JPL Electronic Nose, when exposed to chemical vapors at parts-per-million concentration levels.

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

DOE PAGES

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu; ...

2016-06-30

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Adolescent Executive Dysfunction in Daily Life: Relationships to Risks, Brain Structure and Substance Use

PubMed Central

Clark, Duncan B.; Chung, Tammy; Martin, Christopher S.; Hasler, Brant P.; Fitzgerald, Douglas H.; Luna, Beatriz; Brown, Sandra A.; Tapert, Susan F.; Brumback, Ty; Cummins, Kevin; Pfefferbaum, Adolf; Sullivan, Edith V.; Pohl, Kilian M.; Colrain, Ian M.; Baker, Fiona C.; De Bellis, Michael D.; Nooner, Kate B.; Nagel, Bonnie J.

2017-01-01

During adolescence, problems reflecting cognitive, behavioral and affective dysregulation, such as inattention and emotional dyscontrol, have been observed to be associated with substance use disorder (SUD) risks and outcomes. Prior studies have typically been with small samples, and have typically not included comprehensive measurement of executive dysfunction domains. The relationships of executive dysfunction in daily life with performance based testing of cognitive skills and structural brain characteristics, thought to be the basis for executive functioning, have not been definitively determined. The aims of this study were to determine the relationships between executive dysfunction in daily life, measured by the Behavior Rating Inventory of Executive Function (BRIEF), cognitive skills and structural brain characteristics, and SUD risks, including a global SUD risk indicator, sleep quality, and risky alcohol and cannabis use. In addition to bivariate relationships, multivariate models were tested. The subjects (n = 817; ages 12 through 21) were participants in the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) study. The results indicated that executive dysfunction was significantly related to SUD risks, poor sleep quality, risky alcohol use and cannabis use, and was not significantly related to cognitive skills or structural brain characteristics. In multivariate models, the relationship between poor sleep quality and risky substance use was mediated by executive dysfunction. While these cross-sectional relationships need to be further examined in longitudinal analyses, the results suggest that poor sleep quality and executive dysfunction may be viable preventive intervention targets to reduce adolescent substance use. PMID:29180956

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

PubMed

Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

2015-02-10

Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

Studying dyadic structure-function relationships: a review of current modeling approaches and new insights into Ca2+ (mis)handling.

PubMed

Maleckar, Mary M; Edwards, Andrew G; Louch, William E; Lines, Glenn T

2017-01-01

Excitation-contraction coupling in cardiac myocytes requires calcium influx through L-type calcium channels in the sarcolemma, which gates calcium release through sarcoplasmic reticulum ryanodine receptors in a process known as calcium-induced calcium release, producing a myoplasmic calcium transient and enabling cardiomyocyte contraction. The spatio-temporal dynamics of calcium release, buffering, and reuptake into the sarcoplasmic reticulum play a central role in excitation-contraction coupling in both normal and diseased cardiac myocytes. However, further quantitative understanding of these cells' calcium machinery and the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease requires accurate knowledge of cardiac ultrastructure, protein distribution and subcellular function. As current imaging techniques are limited in spatial resolution, limiting insight into changes in calcium handling, computational models of excitation-contraction coupling have been increasingly employed to probe these structure-function relationships. This review will focus on the development of structural models of cardiac calcium dynamics at the subcellular level, orienting the reader broadly towards the development of models of subcellular calcium handling in cardiomyocytes. Specific focus will be given to progress in recent years in terms of multi-scale modeling employing resolved spatial models of subcellular calcium machinery. A review of the state-of-the-art will be followed by a review of emergent insights into calcium-dependent etiologies in heart disease and, finally, we will offer a perspective on future directions for related computational modeling and simulation efforts.

Confidence Intervals for a Semiparametric Approach to Modeling Nonlinear Relations among Latent Variables

ERIC Educational Resources Information Center

Pek, Jolynn; Losardo, Diane; Bauer, Daniel J.

2011-01-01

Compared to parametric models, nonparametric and semiparametric approaches to modeling nonlinearity between latent variables have the advantage of recovering global relationships of unknown functional form. Bauer (2005) proposed an indirect application of finite mixtures of structural equation models where latent components are estimated in the…

Structure-function relationship between the octopus perimeter cluster mean sensitivity and sector retinal nerve fiber layer thickness measured with the RTVue optical coherence tomography and scanning laser polarimetry.

PubMed

Naghizadeh, Farzaneh; Garas, Anita; Vargha, Péter; Holló, Gábor

2014-01-01

To determine structure-function relationship between each of 16 Octopus perimeter G2 program clusters and the corresponding 16 peripapillary sector retinal nerve fiber layer thickness (RNFLT) values measured with the RTVue-100 Fourier-domain optical coherence tomography (RTVue OCT) and scanning laser polarimetry with variable corneal compensation (GDx-VCC) and enhanced corneal compensation (GDx-ECC) corneal compensation. One eye of 110 white patients (15 healthy, 20 ocular hypertensive, and 75 glaucoma eyes) were investigated. The Akaike information criterion and the F test were used to identify the best fitting model. Parabolic relationship with logarithmic cluster mean sensitivity and linear sector RNFLT values provided the best fit. For RTVue OCT, significant (P<0.0001) coefficients of determination (R) were found for all 16 RNFLT sectors. The R values were highest for the temporal, superotemporal, and inferotemporal RNFLT sectors (0.4483 to 0.5186). For GDx-VCC/ECC, significant (P<0.01) parabolic relationship was seen for all but the temporal and nasal RNFLT sectors. The overall highest R value (0.6943) was found for a superotemporal RNFLT sector with GDx-ECC. For some RNFLT sectors, the goodness of fit differed significantly between the imaging methods. Structure-function relationship was similar for the total population and the glaucoma subgroup, whereas no relationship (P>0.05) was found for the control eyes. Mean sensitivity of the Octopus visual field clusters showed significant parabolic relationship with the corresponding peripapillary RNFLT sectors. The relationship was more general with the RTVue OCT than GDx-VCC or GDx-ECC. The results show that visual field clusters of the Octopus G program can be applied for detailed structure-function research.

Metacognition as a Mediating Variable Between Neurocognition and Functional Outcome in First Episode Psychosis.

PubMed

Davies, Geoff; Fowler, David; Greenwood, Kathryn

2017-07-01

Neurocognitive and functional outcome deficits have long been acknowledged in schizophrenia and neurocognition has been found to account for functional disability to a greater extent than psychopathology. Much of the variance in functional outcome however still remains unexplained and metacognition may mediate the relationship between neurocognition, functional capacity, and self-reported social and occupational function. Eighty first episode psychosis participants were recruited and completed measures of neurocognition (memory, executive function, and intelligence quotient), metacognition (Beck Cognitive Insight Scale, Metacognitive Awareness Interview), psychopathology (PANSS), and both functional capacity (UPSA) and real-life social and occupational function (The Time Use Survey). Path analyses investigated the relationships between variables through structural equation modeling. A series of path models demonstrated that metacognition partially mediates the relationship between neurocognition and functional capacity, and fully mediates the relationship between functional capacity and social and occupational function. The present study findings identify that metacognition may be critical to translating cognitive and functional skills into real-world contexts, and this relationship is found at early stages of illness. Understanding how individuals translate cognitive and functional skills into the real-world (the competence-performance gap) may offer valuable guidance to intervention programs. This finding is important to models of recovery as it suggests that intervention programs that focus on enhancing metacognition abilities may have a greater impact than traditional rehabilitation programs focusing on cognitive abilities, on social and occupational outcomes. © The Author 2016. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

PubMed

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

Novel approaches to determine contractile function of the isolated adult zebrafish ventricular cardiac myocyte.

PubMed

Dvornikov, Alexey V; Dewan, Sukriti; Alekhina, Olga V; Pickett, F Bryan; de Tombe, Pieter P

2014-05-01

The zebrafish (Danio rerio) has been used extensively in cardiovascular biology, but mainly in the study of heart development. The relative ease of its genetic manipulation may indicate the suitability of this species as a cost-effective model system for the study of cardiac contractile biology. However, whether the zebrafish heart is an appropriate model system for investigations pertaining to mammalian cardiac contractile structure-function relationships remains to be resolved. Myocytes were isolated from adult zebrafish hearts by enzymatic digestion, attached to carbon rods, and twitch force and intracellular Ca(2+) were measured. We observed the modulation of twitch force, but not of intracellular Ca(2+), by both extracellular [Ca(2+)] and sarcomere length. In permeabilized cells/myofibrils, we found robust myofilament length-dependent activation. Moreover, modulation of myofilament activation-relaxation and force redevelopment kinetics by varied Ca(2+) activation levels resembled that found previously in mammalian myofilaments. We conclude that the zebrafish is a valid model system for the study of cardiac contractile structure-function relationships.

Plant functional trait diversity regulates the nonlinear response of productivity to regional climate change in Tibetan alpine grasslands.

PubMed

Wu, Jianshuang; Wurst, Susanne; Zhang, Xianzhou

2016-10-19

The biodiversity-productivity relationship is still under debate for alpine grasslands on the Tibetan Plateau. We know little about direct and indirect effects of biotic and abiotic drivers on this relationship, especially in regard to plant functional trait diversity. Here, we examine how aboveground net primary productivity (ANPP) and precipitation use efficiency (PUE) respond to climate, soil and community structure across alpine grasslands on the Northern Tibetan Plateau. We found that both ANPP and PUE showed nonlinear patterns along water availability and site altitude variation, which together accounted for 80.3% and 68.8% of variation in ANPP and PUE, respectively, by optimal generalized additive models. Functional trait divergence (FTD) and community weighted mean (CWM) of plant functional traits were as important as plant species diversity (PSD) for explaining the nonlinear productivity-climate relationship. These findings were confirmed by results from principal component analyses and structural equation models. We also found that FTD was negatively correlated with PSD across different alpine grasslands. Our results implicate: first, the combinatorial influences of temperature and precipitation gradients are important for predicting alpine grassland dynamics; second, the convergence and divergence of plant functional traits may have the potential to elucidate the effect of plant diversity on ecosystem functionality.

Plant functional trait diversity regulates the nonlinear response of productivity to regional climate change in Tibetan alpine grasslands

PubMed Central

Wu, Jianshuang; Wurst, Susanne; Zhang, Xianzhou

2016-01-01

The biodiversity-productivity relationship is still under debate for alpine grasslands on the Tibetan Plateau. We know little about direct and indirect effects of biotic and abiotic drivers on this relationship, especially in regard to plant functional trait diversity. Here, we examine how aboveground net primary productivity (ANPP) and precipitation use efficiency (PUE) respond to climate, soil and community structure across alpine grasslands on the Northern Tibetan Plateau. We found that both ANPP and PUE showed nonlinear patterns along water availability and site altitude variation, which together accounted for 80.3% and 68.8% of variation in ANPP and PUE, respectively, by optimal generalized additive models. Functional trait divergence (FTD) and community weighted mean (CWM) of plant functional traits were as important as plant species diversity (PSD) for explaining the nonlinear productivity-climate relationship. These findings were confirmed by results from principal component analyses and structural equation models. We also found that FTD was negatively correlated with PSD across different alpine grasslands. Our results implicate: first, the combinatorial influences of temperature and precipitation gradients are important for predicting alpine grassland dynamics; second, the convergence and divergence of plant functional traits may have the potential to elucidate the effect of plant diversity on ecosystem functionality. PMID:27759112

Using Case Studies as a Semester-Long Tool to Teach Neuroanatomy and Structure-Function Relationships to Undergraduates

PubMed Central

Kennedy, Susan

2013-01-01

In addition to being inherently interesting to students, case studies can serve as useful tools to teach neuroanatomy and demonstrate important relationships between brain structure and function. In most undergraduate courses, however, neuroanatomy is presented to students as a “unit” or chapter, much like other topics (e.g., receptors, pharmacology) covered in the course, over a period of a week or two. In this article, a relatively simple model of teaching neuroanatomy is described in which students are actively engaged in the presentation and discussion of case studies throughout the semester, following a general introduction to the structure of the nervous system. In this way, the teaching of neuroanatomy is “distributed” throughout the semester and put into a more user-friendly context for students as additional topics are introduced. Generally, students report enjoying learning brain structure using this method, and commented positively on the class activities associated with learning brain anatomy. Advantages and disadvantages of such a model are presented, as are suggestions for implementing similar models of undergraduate neuroanatomy education. PMID:24319386

Imidazole derivatives as angiotensin II AT1 receptor blockers: Benchmarks, drug-like calculations and quantitative structure-activity relationships modeling

NASA Astrophysics Data System (ADS)

Alloui, Mebarka; Belaidi, Salah; Othmani, Hasna; Jaidane, Nejm-Eddine; Hochlaf, Majdi

2018-03-01

We performed benchmark studies on the molecular geometry, electron properties and vibrational analysis of imidazole using semi-empirical, density functional theory and post Hartree-Fock methods. These studies validated the use of AM1 for the treatment of larger systems. Then, we treated the structural, physical and chemical relationships for a series of imidazole derivatives acting as angiotensin II AT1 receptor blockers using AM1. QSAR studies were done for these imidazole derivatives using a combination of various physicochemical descriptors. A multiple linear regression procedure was used to design the relationships between molecular descriptor and the activity of imidazole derivatives. Results validate the derived QSAR model.

Computational modeling of the obstructive lung diseases asthma and COPD

PubMed Central

2014-01-01

Asthma and chronic obstructive pulmonary disease (COPD) are characterized by airway obstruction and airflow limitation and pose a huge burden to society. These obstructive lung diseases impact the lung physiology across multiple biological scales. Environmental stimuli are introduced via inhalation at the organ scale, and consequently impact upon the tissue, cellular and sub-cellular scale by triggering signaling pathways. These changes are propagated upwards to the organ level again and vice versa. In order to understand the pathophysiology behind these diseases we need to integrate and understand changes occurring across these scales and this is the driving force for multiscale computational modeling. There is an urgent need for improved diagnosis and assessment of obstructive lung diseases. Standard clinical measures are based on global function tests which ignore the highly heterogeneous regional changes that are characteristic of obstructive lung disease pathophysiology. Advances in scanning technology such as hyperpolarized gas MRI has led to new regional measurements of ventilation, perfusion and gas diffusion in the lungs, while new image processing techniques allow these measures to be combined with information from structural imaging such as Computed Tomography (CT). However, it is not yet known how to derive clinical measures for obstructive diseases from this wealth of new data. Computational modeling offers a powerful approach for investigating this relationship between imaging measurements and disease severity, and understanding the effects of different disease subtypes, which is key to developing improved diagnostic methods. Gaining an understanding of a system as complex as the respiratory system is difficult if not impossible via experimental methods alone. Computational models offer a complementary method to unravel the structure-function relationships occurring within a multiscale, multiphysics system such as this. Here we review the current state-of-the-art in techniques developed for pulmonary image analysis, development of structural models of the respiratory system and predictions of function within these models. We discuss application of modeling techniques to obstructive lung diseases, namely asthma and emphysema and the use of models to predict response to therapy. Finally we introduce a large European project, AirPROM that is developing multiscale models to investigate structure-function relationships in asthma and COPD. PMID:25471125

Multilevel examination of facility characteristics, social integration, and health for older adults living in nursing homes.

PubMed

Leedahl, Skye N; Chapin, Rosemary K; Little, Todd D

2015-01-01

Testing a model based on past research and theory, this study assessed relationships between facility characteristics (i.e., culture change efforts, social workers) and residents' social networks and social support across nursing homes; and examined relationships between multiple aspects of social integration (i.e., social networks, social capital, social engagement, social support) and mental and functional health for older adults in nursing homes. Data were collected at nursing homes using a planned missing data design with random sampling techniques. Data collection occurred at the individual-level through in-person structured interviews with older adult nursing home residents (N = 140) and at the facility-level (N = 30) with nursing home staff. The best fitting multilevel structural equation model indicated that the culture change subscale for relationships significantly predicted differences in residents' social networks. Additionally, social networks had a positive indirect relationship with mental and functional health among residents primarily via social engagement. Social capital had a positive direct relationship with both health outcomes. To predict better social integration and mental and functional health outcomes for nursing homes residents, study findings support prioritizing that close relationships exist among staff, residents, and the community as well as increased resident social engagement and social trust. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Sedentary Screen Time and Left Ventricular Structure and Function: the CARDIA Study

PubMed Central

Gibbs, Bethany Barone; Reis, Jared P.; Schelbert, Erik B.; Craft, Lynette L.; Sidney, Steve; Lima, Joao; Lewis, Cora E.

2013-01-01

Sedentary screen time (watching TV or using a computer) predicts cardiovascular outcomes independently from moderate and vigorous physical activity and could impact left ventricular structure and function through the adverse consequences of sedentary behavior. Purpose To determine whether sedentary screen time is associated with measures of left ventricular structure and function. Methods The Coronary Artery Risk Development in Young Adults (CARDIA) Study measured screen time by questionnaire and left ventricular structure and function by echocardiography in 2,854 black and white participants, aged 43–55 years, in 2010–2011. Generalized linear models evaluated cross-sectional trends for echocardiography measures across higher categories of screen time and adjusting for demographics, smoking, alcohol, and physical activity. Further models adjusted for potential intermediate factors (blood pressure, antihypertensive medication use, diabetes, and body mass index (BMI). Results The relationship between screen time and left ventricular mass(LVM) differed in blacks vs. whites. Among whites, higher screen time was associated with larger LVM (P<0.001), after adjustment for height, demographics, and lifestyle variables. Associations between screen time and LVM persisted when adjusting for blood pressure, antihypertensive medication use, and diabetes (P=0.008) but not with additional adjustment for BMI (P=0.503). Similar relationships were observed for screen time with LVM indexed to height2.7, relative wall thickness, and mass-to-volume ratio. Screen time was not associated with left ventricular structure among blacks or left ventricular function in either race group. Conclusions Sedentary screen time is associated with greater LVM in white adults and this relationship was largely explained by higher overall adiposity. The lack of association in blacks supports a potential qualitative difference in the cardiovascular consequences of sedentary screen-based behavior. PMID:23863618

A Combination of Hand-Held Models and Computer Imaging Programs Helps Students Answer Oral Questions about Molecular Structure and Function: A Controlled Investigation of Student Learning

ERIC Educational Resources Information Center

Harris, Michelle A.; Peck, Ronald F.; Colton, Shannon; Morris, Jennifer; Neto, Elias Chaibub; Kallio, Julie

2009-01-01

We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging…

Integrated Modeling for Watershed Ecosystem Services Assessment and Forecasting

EPA Science Inventory

Regional scale watershed management decisions must be informed by the science-based relationship between anthropogenic activities on the landscape and the change in ecosystem structure, function, and services that occur as a result. We applied process-based models that represent...

Relational-interdependent self-construal as a predictor of relationship quality: the mediating roles of one's own behaviors and perceptions of the fulfillment of friendship functions.

PubMed

Morry, Marian M; Kito, Mie

2009-06-01

Relational-interdependent self-construal (RISC) is the tendency to think of oneself in terms of relationships with close others, and it influences relationship cognitions (e.g., closeness, commitment, perceived similarity). The authors expected individuals high in RISC to report more relationship supportive behaviors (RSB; e.g., higher levels of trust, more intimate disclosures), experience greater fulfillment of friendship functions (FrFu; e.g., help, emotional security, stimulating companionship), and report higher relationship quality than individuals low in RISC. The authors also hypothesized that RSB would mediate the RISC-friendship function and the RISC-relationship quality relations and that FrFu would mediate the relation between RSB and relationship quality. Structural equation modeling supported the authors' hypotheses. These effects did not differ across friendship type (same or cross sex). The authors discuss the importance of self-construal for relationship research.

Structure-Function Network Mapping and Its Assessment via Persistent Homology

PubMed Central

2017-01-01

Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal. We demonstrate that our approach can uncover the direct and indirect structural paths for predicting functional connectivity, and our network similarity measure outperforms other currently available methods. We systematically validate our approach with (1) a comparison of regularized vs. non-regularized procedures, (2) a null model of the degree-preserving random rewired structural matrix, (3) different network types (binary vs. weighted matrices), and (4) different brain parcellation schemes (low vs. high resolutions). Finally, we evaluate the scalability of our method with relatively large matrices (2514x2514) of structural and functional connectivity obtained from 12 healthy human subjects measured non-invasively while at rest. Our results reveal a nonlinear structure-function relationship, suggesting that the resting-state functional connectivity depends on direct structural connections, as well as relatively parsimonious indirect connections via polysynaptic pathways. PMID:28046127

Structural Diversity in the Dandelion (Taraxacum officinale) Polyphenol Oxidase Family Results in Different Responses to Model Substrates

PubMed Central

Dirks-Hofmeister, Mareike E.; Singh, Ratna; Leufken, Christine M.; Inlow, Jennifer K.; Moerschbacher, Bruno M.

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure–function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a “selector” for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates. PMID:24918587

Chemometric strategy for modeling metabolic biological space along the gastrointestinal tract and assessing microbial influences.

PubMed

Martin, François-Pierre J; Montoliu, Ivan; Kochhar, Sunil; Rezzi, Serge

2010-12-01

Over the past decade, the analysis of metabolic data with advanced chemometric techniques has offered the potential to explore functional relationships among biological compartments in relation to the structure and function of the intestine. However, the employed methodologies, generally based on regression modeling techniques, have given emphasis to region-specific metabolic patterns, while providing only limited insights into the spatiotemporal metabolic features of the complex gastrointestinal system. Hence, novel approaches are needed to analyze metabolic data to reconstruct the metabolic biological space associated with the evolving structures and functions of an organ such as the gastrointestinal tract. Here, we report the application of multivariate curve resolution (MCR) methodology to model metabolic relationships along the gastrointestinal compartments in relation to its structure and function using data from our previous metabonomic analysis. The method simultaneously summarizes metabolite occurrence and contribution to continuous metabolic signatures of the different biological compartments of the gut tract. This methodology sheds new light onto the complex web of metabolic interactions with gut symbionts that modulate host cell metabolism in surrounding gut tissues. In the future, such an approach will be key to provide new insights into the dynamic onset of metabolic deregulations involved in region-specific gastrointestinal disorders, such as Crohn's disease or ulcerative colitis.

The mediating effect of social relationships on the association between socioeconomic status and subjective health - results from the Heinz Nixdorf Recall cohort study.

PubMed

Vonneilich, Nico; Jöckel, Karl-Heinz; Erbel, Raimund; Klein, Jens; Dragano, Nico; Siegrist, Johannes; von dem Knesebeck, Olaf

2012-04-17

Socioeconomic status (SES) is an important determinant of population health. Explanatory approaches on how SES determines health have so far included numerous factors, amongst them psychosocial factors such as social relationships. However, it is unclear whether social relationships can help explain socioeconomic differences in general subjective health. Do different aspects of social relationships contribute differently to the explanation? Based on a cohort study of middle and older aged residents (45 to 75 years) from the Ruhr Area in Germany our study tries to clarify the matter. For the analyses data from the population-based prospective Heinz Nixdorf Recall (HNR) Study is used. As indicators of SES education, equivalent household income and occupational status were employed. Social relations were assessed by including structural as well as functional aspects. Structural aspects were estimated by the Social Integration Index (SII) and functional aspects were measured by availability of emotional and instrumental support. Data on general subjective health status was available for both baseline examination (2000-2003) and a 5-year follow-up (2006-2008). The sample consists of 4,146 men and women. Four logistic regression models were calculated: in the first model we controlled for age and subjective health at baseline, while in models 2 and 3, either functional or structural aspects of social relationships were introduced separately. Model 4 then included all variables. As former studies indicated different health effects of SES and social relations in men and women, analyses were conducted with the overall sample as well as for each gender alone. Prospective associations of SES and subjective health were reduced after introducing social relationships into the regression models. Percentage reductions between 2% and 30% were observed in the overall sample when all aspects of social relations were included. The percentage reductions were strongest in the lowest SES group. Gender specific analyses revealed mediating effects of social relationships in women and men. The magnitude of mediating effects varied depending on the indicators of SES and social relations. Social relationships substantially contribute to the explanation of SES differences in subjective health. Interventions for improving social relations which especially focus on socially deprived groups are likely to help reducing socioeconomic disparities in health.

A structural equation model relating impaired sensorimotor function, fear of falling and gait patterns in older people.

PubMed

Menz, Hylton B; Lord, Stephen R; Fitzpatrick, Richard C

2007-02-01

Many falls in older people occur while walking, however the mechanisms responsible for gait instability are poorly understood. Therefore, the aim of this study was to develop a plausible model describing the relationships between impaired sensorimotor function, fear of falling and gait patterns in older people. Temporo-spatial gait parameters and acceleration patterns of the head and pelvis were obtained from 100 community-dwelling older people aged between 75 and 93 years while walking on an irregular walkway. A theoretical model was developed to explain the relationships between these variables, assuming that head stability is a primary output of the postural control system when walking. This model was then tested using structural equation modeling, a statistical technique which enables the testing of a set of regression equations simultaneously. The structural equation model indicated that: (i) reduced step length has a significant direct and indirect association with reduced head stability; (ii) impaired sensorimotor function is significantly associated with reduced head stability, but this effect is largely indirect, mediated by reduced step length, and; (iii) fear of falling is significantly associated with reduced step length, but has little direct influence on head stability. These findings provide useful insights into the possible mechanisms underlying gait characteristics and risk of falling in older people. Particularly important is the indication that fear-related step length shortening may be maladaptive.

Stability and the Evolvability of Function in a Model Protein

PubMed Central

Bloom, Jesse D.; Wilke, Claus O.; Arnold, Frances H.; Adami, Christoph

2004-01-01

Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to evolve the function of binding to a ligand. Although our model contains no built-in tradeoff between stability and function, proteins evolved function more efficiently when the stability requirement was relaxed. Proteins with both high stability and high function evolved more efficiently when the stability requirement was gradually increased than when there was constant selection for high stability. These results show that in our model, the evolution of function is enhanced by allowing proteins to explore sequences corresponding to marginally stable structures, and that it is easier to improve stability while maintaining high function than to improve function while maintaining high stability. Our model also demonstrates that even in the absence of a fundamental biophysical tradeoff between stability and function, the speed with which function can evolve is limited by the stability requirement imposed on the protein. PMID:15111394

Mechanism of Resilin Elasticity

PubMed Central

Qin, Guokui; Hu, Xiao; Cebe, Peggy; Kaplan, David L.

2012-01-01

Resilin is critical in the flight and jumping systems of insects as a polymeric rubber-like protein with outstanding elasticity. However, insight into the underlying molecular mechanisms responsible for resilin elasticity remains undefined. Here we report the structure and function of resilin from Drosophila CG15920. A reversible beta-turn transition was identified in the peptide encoded by exon III and for full length resilin during energy input and release, features that correlate to the rapid deformation of resilin during functions in vivo. Micellar structures and nano-porous patterns formed after beta-turn structures were present via changes in either the thermal or mechanical inputs. A model is proposed to explain the super elasticity and energy conversion mechanisms of resilin, providing important insight into structure-function relationships for this protein. Further, this model offers a view of elastomeric proteins in general where beta-turn related structures serve as fundamental units of the structure and elasticity. PMID:22893127

Does the Use of Connective Words in Written Assessments Predict High School Students' Reading and Writing Achievement?

ERIC Educational Resources Information Center

Duggleby, Sandra J.; Tang, Wei; Kuo-Newhouse, Amy

2016-01-01

This study examined the relationship between ninth-grade students' use of connectives (temporal, causal, adversative, and additive) in functional writing and performance on standards-based/criterion-referenced measures of reading and writing. Specifically, structural equation modeling (SEM) techniques were used to examine the relationship between…

Relationships between structural complexity, coral traits, and reef fish assemblages

NASA Astrophysics Data System (ADS)

Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

2017-06-01

With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

Uncovering the structure-function relationship in spider silk

NASA Astrophysics Data System (ADS)

Yarger, Jeffery L.; Cherry, Brian R.; van der Vaart, Arjan

2018-03-01

All spiders produce protein-based biopolymer fibres that we call silk. The most studied of these silks is spider dragline silk, which is very tough and relatively abundant compared with other types of spider silks. Considerable research has been devoted to understanding the relationship between the molecular structure and mechanical properties of spider dragline silks. In this Review, we overview experimental and computational studies that have provided a wealth of detail at the molecular level on the highly conserved repetitive core and terminal regions of spider dragline silk. We also discuss the role of the nanocrystalline β-sheets and amorphous regions in determining the properties of spider silk fibres, endowing them with strength and elasticity. Additionally, we outline imaging techniques and modelling studies that elucidate the importance of the hierarchical structure of silk fibres at the molecular level. These insights into structure-function relationships can guide the reverse engineering of spider silk to enable the production of superior synthetic fibres.

Social cognition as a mediator variable between neurocognition and functional outcome in schizophrenia: empirical review and new results by structural equation modeling.

PubMed

Schmidt, Stefanie J; Mueller, Daniel R; Roder, Volker

2011-09-01

Cognitive impairments are currently regarded as important determinants of functional domains and are promising treatment goals in schizophrenia. Nevertheless, the exact nature of the interdependent relationship between neurocognition and social cognition as well as the relative contribution of each of these factors to adequate functioning remains unclear. The purpose of this article is to systematically review the findings and methodology of studies that have investigated social cognition as a mediator variable between neurocognitive performance and functional outcome in schizophrenia. Moreover, we carried out a study to evaluate this mediation hypothesis by the means of structural equation modeling in a large sample of 148 schizophrenia patients. The review comprised 15 studies. All but one study provided evidence for the mediating role of social cognition both in cross-sectional and in longitudinal designs. Other variables like motivation and social competence additionally mediated the relationship between social cognition and functional outcome. The mean effect size of the indirect effect was 0.20. However, social cognitive domains were differentially effective mediators. On average, 25% of the variance in functional outcome could be explained in the mediation model. The results of our own statistical analysis are in line with these conclusions: Social cognition mediated a significant indirect relationship between neurocognition and functional outcome. These results suggest that research should focus on differential mediation pathways. Future studies should also consider the interaction with other prognostic factors, additional mediators, and moderators in order to increase the predictive power and to target those factors relevant for optimizing therapy effects.

The relationship between leadership, teamworking, structure, burnout and attitude to patients on acute psychiatric wards

PubMed Central

Nijman, Henk; Simpson, Alan; Jones, Julia

2010-01-01

Background Conflict (aggression, substance use, absconding, etc.) and containment (coerced medication, manual restraint, etc.) threaten the safety of patients and staff on psychiatric wards. Previous work has suggested that staff variables may be significant in explaining differences between wards in their rates of these behaviours, and that structure (ward organisation, rules and daily routines) might be the most critical of these. This paper describes the exploration of a large dataset to assess the relationship between structure and other staff variables. Methods A multivariate cross-sectional design was utilised. Data were collected from staff on 136 acute psychiatric wards in 26 NHS Trusts in England, measuring leadership, teamwork, structure, burnout and attitudes towards difficult patients. Relationships between these variables were explored through principal components analysis (PCA), structural equation modelling and cluster analysis. Results Principal components analysis resulted in the identification of each questionnaire as a separate factor, indicating that the selected instruments assessed a number of non-overlapping items relevant for ward functioning. Structural equation modelling suggested a linear model in which leadership influenced teamwork, teamwork structure; structure burnout; and burnout feelings about difficult patients. Finally, cluster analysis identified two significantly distinct groups of wards: the larger of which had particularly good leadership, teamwork, structure, attitudes towards patients and low burnout; and the second smaller proportion which was poor on all variables and high on burnout. The better functioning cluster of wards had significantly lower rates of containment events. Conclusion The overall performance of staff teams is associated with differing rates of containment on wards. Interventions to reduce rates of containment on wards may need to address staff issues at every level, from leadership through to staff attitudes. PMID:20082064

Direct ink writing of 3D conductive polyaniline structures and rheological modelling

NASA Astrophysics Data System (ADS)

Holness, F. Benjamin; Price, Aaron D.

2018-01-01

The intractable nature of conjugated polymers (CP) leads to practical limitations in the fabrication of CP-based transducers having complex three-dimensional geometries. Conventional CP device fabrication processes have focused primarily on thin-film deposition techniques; this study explores novel additive manufacturing processes specifically developed for CP with the ultimate goal of increasing the functionality of CP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures was enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder to fabricate high-resolution 3D conductive PANI structures. The required processability of PANI was achieved by means of a counterion-induced thermal doping method. The effect of thermal doping on the PANI-DBSA paste by means of a constitutive relationship to describe the paste flow as a function of the thermal doping time is explored. This relationship is incorporated within a flow model to predict the extruded track width as a function of various process parameters including: print speed, gauge pressure, nozzle diameter, and pre-extrusion thermal doping time.

Functional traits and structural controls on the relationship between photosynthetic CO2 uptake and sun-induced fluorescence in a Mediterranean grassland under different nutrient availability

NASA Astrophysics Data System (ADS)

Migliavacca, Mirco

2016-04-01

Recent studies have shown how human induced nitrogen (N) and phosphorous (P) imbalances affect essential ecosystem processes, and might be particularly important in water-limited ecosystems. Hyperspectral information can be used to directly infer nutrient-induced variation in structural and functional changes of vegetation under different nutrient availability. However, several uncertainties still hamper the direct link between photosynthetic CO2 uptake (gross primary productivity, GPP) and hyperspectral reflectance. Sun-induced fluorescence (SIF) provides a new non-invasive measurement approach that has the potential to quantify dynamic changes in light use efficiency and photosynthetic CO2 uptake. In this contribution we will present an experiment conducted in a Mediterranean grassland, where 16 plots of 8x8 meters were manipulated by adding nutrient (N, P, and NP). Almost simultaneous estimates of canopy scale GPP and SIF were conducted with transparent transient-state canopy chambers and high resolution spectrometers, respectively. We investigated the response of GPP and SIF to different nutrient availability and plant stoichiometry. The second objective was to identify how structural (LAI, leaf angle distribution, and biodiversity) and canopy biochemical properties (e.g. N and chlorophyll content - Chl) control the functional relationship between GPP and SIF. To test the different hypotheses the SCOPE radiative transfer model was used. We ran a factorial experiment with SCOPE to disentangle the main drivers (structure vs biochemistry) of the relationship GPP-SIF. The results showed significant differences in GPP values between N and without N addition plots. We also found that vegetation indices sensitive to pigment variations and physiology (such as photochemical reflectance index PRI) and SIF showed differences between different treatments. SCOPE showed very good agreement with the observed data (R2=0.71). The observed variability in SIF was mainly related to changes in functional traits of the vegetation (changes in N and P content and Chl). However, beside changes in functional traits, changes in canopy structure (and in particular variation in plant forms abundance after fertilization) controlled the GPP-SIF relationship. According to these results, plant N/P stoichiometry and structure should be considered when modelling GPP assuming a linear relationship with SIF at grasslands sites.

Information model construction of MES oriented to mechanical blanking workshop

NASA Astrophysics Data System (ADS)

Wang, Jin-bo; Wang, Jin-ye; Yue, Yan-fang; Yao, Xue-min

2016-11-01

Manufacturing Execution System (MES) is one of the crucial technologies to implement informatization management in manufacturing enterprises, and the construction of its information model is the base of MES database development. Basis on the analysis of the manufacturing process information in mechanical blanking workshop and the information requirement of MES every function module, the IDEF1X method was adopted to construct the information model of MES oriented to mechanical blanking workshop, and a detailed description of the data structure feature included in MES every function module and their logical relationship was given from the point of view of information relationship, which laid the foundation for the design of MES database.

Computer memory management system

DOEpatents

Kirk, III, Whitson John

2002-01-01

A computer memory management system utilizing a memory structure system of "intelligent" pointers in which information related to the use status of the memory structure is designed into the pointer. Through this pointer system, The present invention provides essentially automatic memory management (often referred to as garbage collection) by allowing relationships between objects to have definite memory management behavior by use of coding protocol which describes when relationships should be maintained and when the relationships should be broken. In one aspect, the present invention system allows automatic breaking of strong links to facilitate object garbage collection, coupled with relationship adjectives which define deletion of associated objects. In another aspect, The present invention includes simple-to-use infinite undo/redo functionality in that it has the capability, through a simple function call, to undo all of the changes made to a data model since the previous `valid state` was noted.

Intergenerational Transmission of Neuropsychological Executive Functioning

ERIC Educational Resources Information Center

Jester, Jennifer M.; Nigg, Joel T.; Puttler, Leon I.; Long, Jeffrey C.; Fitzgerald, Hiram E.; Zucker, Robert A.

2009-01-01

Relationships between parent and child executive functioning were examined, controlling for the critical potential confound of IQ, in a family study involving 434 children (130 girls and 304 boys) and 376 parents from 204 community recruited families at high risk for the development of substance use disorder. Structural equation modeling found…

Relationship of amotivation to neurocognition, self-efficacy and functioning in first-episode psychosis: a structural equation modeling approach.

PubMed

Chang, W C; Kwong, V W Y; Hui, C L M; Chan, S K W; Lee, E H M; Chen, E Y H

2017-03-01

Better understanding of the complex interplay among key determinants of functional outcome is crucial to promoting recovery in psychotic disorders. However, this is understudied in the early course of illness. We aimed to examine the relationships among negative symptoms, neurocognition, general self-efficacy and global functioning in first-episode psychosis (FEP) patients using structural equation modeling (SEM). Three hundred and twenty-one Chinese patients aged 26-55 years presenting with FEP to an early intervention program in Hong Kong were recruited. Assessments encompassing symptom profiles, functioning, perceived general self-efficacy and a battery of neurocognitive tests were conducted. Negative symptom measurement was subdivided into amotivation and diminished expression (DE) domain scores based on the ratings in the Scale for the Assessment of Negative Symptoms. An initial SEM model showed no significant association between functioning and DE which was removed from further analysis. A final trimmed model yielded very good model fit (χ2 = 15.48, p = 0.63; comparative fit index = 1.00; root mean square error of approximation <0.001) and demonstrated that amotivation, neurocognition and general self-efficacy had a direct effect on global functioning. Amotivation was also found to mediate a significant indirect effect of neurocognition and general self-efficacy on functioning. Neurocognition was not significantly related to general self-efficacy. Our results indicate a critical intermediary role of amotivation in linking neurocognitive impairment to functioning in FEP. General self-efficacy may represent a promising treatment target for improvement of motivational deficits and functional outcome in the early illness stage.

Parabolic quantitative structure-activity relationships and photodynamic therapy: application of a three-compartment model with clearance to the in vivo quantitative structure-activity relationships of a congeneric series of pyropheophorbide derivatives used as photosensitizers for photodynamic therapy.

PubMed

Potter, W R; Henderson, B W; Bellnier, D A; Pandey, R K; Vaughan, L A; Weishaupt, K R; Dougherty, T J

1999-11-01

An open three-compartment pharmacokinetic model was applied to the in vivo quantitative structure-activity relationship (QSAR) data of a homologous series of pyropheophorbide photosensitizers for photodynamic therapy (PDT). The physical model was a lipid compartment sandwiched between two identical aqueous compartments. The first compartment was assumed to clear irreversibly at a rate K0. The measured octanol-water partition coefficients, P(i) (where i is the number of carbons in the alkyl chain) and the clearance rate K0 determined the clearance kinetics of the drugs. Solving the coupled differential equations of the three-compartment model produced clearance kinetics for each of the sensitizers in each of the compartments. The third compartment was found to contain the target of PDT. This series of compounds is quite lipophilic. Therefore these drugs are found mainly in the second compartment. The drug level in the third compartment represents a small fraction of the tissue level and is thus not accessible to direct measurement by extraction. The second compartment of the model accurately predicted the clearance from the serum of mice of the hexyl ether of pyropheophorbide a, one member of this series of compounds. The diffusion and clearance rate constants were those found by fitting the pharmacokinetics of the third compartment to the QSAR data. This result validated the magnitude and mechanistic significance of the rate constants used to model the QSAR data. The PDT response to dose theory was applied to the kinetic behavior of the target compartment drug concentration. This produced a pharmacokinetic-based function connecting PDT response to dose as a function of time postinjection. This mechanistic dose-response function was fitted to published, single time point QSAR data for the pheophorbides. As a result, the PDT target threshold dose together with the predicted QSAR as a function of time postinjection was found.

Series of structural and functional models for the ES (enzyme-substrate) complex of the Co(II)-containing quercetin 2,3-dioxygenase.

PubMed

Sun, Ying-Ji; Huang, Qian-Qian; Zhang, Jian-Jun

2014-03-17

A series of mononuclear Co(II)-flavonolate complexes [Co(II)L(R)(fla)] (L(R)H = 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-p/m-R-benzoic acid; R = p-OMe (1), p-Me (2), m-Br (4), and m-NO2 (5); fla = flavonolate) were designed and synthesized as structural and functional models for the ES (enzyme-substrate) complexes to mimic the active site of the Co(II)-containing quercetin 2,3-dioxygenase (Co-2,3-QD). The metal center Co(II) ion in each complex shows a similar distorted octahedral geometry. The model complexes display high enzyme-type dioxygenation reactivity (oxidative O-heterocyclic ring opening of the coordinated substrate flavonolate) at low temperature, presumably due to the attached carboxylate group in the ligands. The reactivity exhibits a substituent group dependent order of -OMe (1) > -Me (2) > -H (3)14b > -Br (4) > -NO2 (5), and the Hammett plot is linear (ρ = -0.78). This can be explained as the electronic nature of the substituent group in the ligands may influence the conformation and redox potential of the bound flavonolate and finally bring different reactivity. The structures, properties, and reactivity of the model complexes show some dependence on the substituent group in the supporting model ligands, and there is some relationship among them. This study is the first example of a series of structural and functional ES models of Co-2,3-QD, with focus on the effects of the electronic nature of substituted groups and the carboxylate group of the ligands to the dioxygenation reactivity, that will provide important insights into the structure-property-reactivity relationship and the catalytic role of Co-2,3-QD.

[The cultural history of palliative care in primitive societies: an integrative review].

PubMed

Siles González, José; Solano Ruiz, Maria Del Carmen

2012-08-01

The objective of this study is to describe the evolution of palliative care in order to reflect on the possibility of its origin in primitive cultures and their relationship with the beginnings of the cult of the dead. It describes the change in the symbolic structures and social interactions involved in palliative care during prehistory: functional unit, functional framework and functional element. The theoretical framework is based on cultural history, the dialectical structural model and symbolic interactionism. Categorization techniques, cultural history and dialectic structuralism analyses were performed. Palliative care existed in primitive societies, mostly associated with the rites of passage with a high symbolic content. The social structures - functional unit, functional framework and functional element - are the pillars that supported palliative care in prehistory societies.

Structural elements and organization of the ancestral translational machinery

NASA Technical Reports Server (NTRS)

Rein, R.; Srinivasan, S.; Mcdonald, J.; Raghunathan, G.; Shibata, M.

1987-01-01

The molecular mechanisms of the primitive translational apparatus are discussed in the framework of present-day protein biosynthesis. The structural necessities of an early adaptor and the multipoint recognition properties of such an adaptor are investigated on the basis of structure/function relationships found in a contemporary system and a molecular model of the contemporary transpeptidation complex. A model of the tRNA(Tyr)-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed; the model is used to illustrate the required recognition properties of the ancestor aminoacyl synthetase.

Mediators of sexual functioning and marital quality in chronically depressed adults with and without a history of childhood sexual abuse.

PubMed

Dunlop, Boadie W; Hill, Eric; Johnson, Benjamin N; Klein, Daniel N; Gelenberg, Alan J; Rothbaum, Barbara O; Thase, Michael E; Kocsis, James H

2015-03-01

Sexual dysfunction is common among depressed adults. Childhood sexual abuse (CSA) and depressive symptomology are among the risk factors for sexual dysfunction, and these factors may interact to predict adult relationship functioning. Several models have been developed postulating interactions between these variables. We tested models of the effects of CSA and elucidate the associations between CSA, sexual dysfunction, depression severity, anxiety, and relationship quality in chronically depressed adults. Baseline data from 808 chronically depressed outpatients enrolled in the Research Evaluating the Value of Augmenting Medication with Psychotherapy study were evaluated using structural equation modeling. The Inventory of Depressive Symptomology, self-report version (IDS-SR) assessed depression severity, and the Mood and Anxiety Symptom Questionnaire Anxious Arousal subscale assessed anxiety. Sexual function was assessed with the Arizona Sexual Experiences Scale (ASEX), and the Quality of Marriage Index (QMI) assessed relationship quality for patients in stable relationships. CSA scores predicted depression severity on the IDS-SR, as well as lower relationship quality and sexual satisfaction. ASEX scores were significantly associated with depression severity but were not correlated with the QMI. Two models were evaluated to elucidate these associations, revealing that (i) depression severity and anxious arousal mediated the relationship between CSA and adult sexual function, (ii) anxious arousal and sexual functioning mediated the association between CSA and depression symptoms, and (iii) when these models were combined, anxious arousal emerged as the most important mediator of CSA on depression which, in turn, mediated associations with adult sexual satisfaction and relationship quality. Although CSA predicts lower relationship and sexual satisfaction among depressed adults, the long-term effects of CSA appear to be mediated by depressive and anxious symptoms. It is important to address depression and anxiety symptoms when treating patients with CSA who present with sexual dysfunction or marital concerns. © 2014 International Society for Sexual Medicine.

Computational studies of novel chymase inhibitors against cardiovascular and allergic diseases: mechanism and inhibition.

PubMed

Arooj, Mahreen; Thangapandian, Sundarapandian; John, Shalini; Hwang, Swan; Park, Jong K; Lee, Keun W

2012-12-01

To provide a new idea for drug design, a computational investigation is performed on chymase and its novel 1,4-diazepane-2,5-diones inhibitors that explores the crucial molecular features contributing to binding specificity. Molecular docking studies of inhibitors within the active site of chymase were carried out to rationalize the inhibitory properties of these compounds and understand their inhibition mechanism. The density functional theory method was used to optimize molecular structures with the subsequent analysis of highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential maps, which revealed that negative potentials near 1,4-diazepane-2,5-diones ring are essential for effective binding of inhibitors at active site of enzyme. The Bayesian model with receiver operating curve statistic of 0.82 also identified arylsulfonyl and aminocarbonyl as the molecular features favoring and not favoring inhibition of chymase, respectively. Moreover, genetic function approximation was applied to construct 3D quantitative structure-activity relationships models. Two models (genetic function approximation model 1 r(2) = 0.812 and genetic function approximation model 2 r(2) = 0.783) performed better in terms of correlation coefficients and cross-validation analysis. In general, this study is used as example to illustrate how combinational use of 2D/3D quantitative structure-activity relationships modeling techniques, molecular docking, frontier molecular orbital density fields (highest occupied molecular orbital and lowest unoccupied molecular orbital), and molecular electrostatic potential analysis may be useful to gain an insight into the binding mechanism between enzyme and its inhibitors. © 2012 John Wiley & Sons A/S.

Reasoning=working Memory<>attention

ERIC Educational Resources Information Center

Buehner, M.; Krumm, S.; Pick, M.

2005-01-01

The purpose of this study was to clarify the relationship between attention, components of working memory, and reasoning. Therefore, twenty working memory tests, two attention tests, and nine intelligence subtests were administered to 135 students. Using structural equation modeling, we were able to replicate a functional model of working memory…

Gene, Brain, and Behavior Relationships in Fragile X Syndrome: Evidence from Neuroimaging Studies

ERIC Educational Resources Information Center

Lightbody, Amy A.; Reiss, Allan L.

2009-01-01

Fragile X syndrome (FraX) remains the most common inherited cause of intellectual disability and provides a valuable model for studying gene-brain-behavior relationships. Over the past 15 years, structural and functional magnetic resonance imaging studies have emerged with the goal of better understanding the neural pathways contributing to the…

Clinical Components of Borderline Personality Disorder and Personality Functioning.

PubMed

Ferrer, Marc; Andión, Óscar; Calvo, Natalia; Hörz, Susanne; Fischer-Kern, Melitta; Kapusta, Nestor D; Schneider, Gudrun; Clarkin, John F; Doering, Stephan

2018-01-01

Impairment in personality functioning (PF) represents a salient criterion of the DSM-5 alternative diagnostic model for personality disorders (AMPD). The main goal of this study is to analyze the relationship of the borderline personality disorder (BPD) clinical components derived from the DSM-5 categorical diagnostic model (affective dysregulation, behavioral dysregulation, and disturbed relatedness) with personality organization (PO), i.e., PF, assessed by the Structured Interview of Personality Organization (STIPO). STIPO and the Structured Clinical Interviews for DSM-IV (SCID-I and -II) were administered to 206 BPD patients. The relationship between PO and BPD components were studied using Spearman correlations and independent linear regression analyses. Significant positive correlations were observed between STIPO scores and several DSM-5 BPD criteria and comorbid psychiatric disorders. STIPO dimensions mainly correlated with disturbed relatedness and, to a lesser extent, affective dysregulation components. Each BPD clinical component was associated with specific STIPO dimensions. Both diagnostic models, DSM-5 BPD criteria and PO, are not only related but complementary concepts. The results of this study particularly recommend STIPO for the assessment of relational functioning, which is a major domain of the Personality Functioning Scale Levels of the DSM-5 AMPD. © 2018 S. Karger AG, Basel.

Functional diversity supports the physiological tolerance hypothesis for plant species richness along climatic gradients

USGS Publications Warehouse

Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

2013-01-01

1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Modelling dynamics in protein crystal structures by ensemble refinement

PubMed Central

Burnley, B Tom; Afonine, Pavel V; Adams, Paul D; Gros, Piet

2012-01-01

Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated Rfree values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a ‘molten core’ likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships. DOI: http://dx.doi.org/10.7554/eLife.00311.001 PMID:23251785

Relationship between chemical structure and the occupational asthma hazard of low molecular weight organic compounds

PubMed Central

Jarvis, J; Seed, M; Elton, R; Sawyer, L; Agius, R

2005-01-01

Aims: To investigate quantitatively, relationships between chemical structure and reported occupational asthma hazard for low molecular weight (LMW) organic compounds; to develop and validate a model linking asthma hazard with chemical substructure; and to generate mechanistic hypotheses that might explain the relationships. Methods: A learning dataset used 78 LMW chemical asthmagens reported in the literature before 1995, and 301 control compounds with recognised occupational exposures and hazards other than respiratory sensitisation. The chemical structures of the asthmagens and control compounds were characterised by the presence of chemical substructure fragments. Odds ratios were calculated for these fragments to determine which were associated with a likelihood of being reported as an occupational asthmagen. Logistic regression modelling was used to identify the independent contribution of these substructures. A post-1995 set of 21 asthmagens and 77 controls were selected to externally validate the model. Results: Nitrogen or oxygen containing functional groups such as isocyanate, amine, acid anhydride, and carbonyl were associated with an occupational asthma hazard, particularly when the functional group was present twice or more in the same molecule. A logistic regression model using only statistically significant independent variables for occupational asthma hazard correctly assigned 90% of the model development set. The external validation showed a sensitivity of 86% and specificity of 99%. Conclusions: Although a wide variety of chemical structures are associated with occupational asthma, bifunctional reactivity is strongly associated with occupational asthma hazard across a range of chemical substructures. This suggests that chemical cross-linking is an important molecular mechanism leading to the development of occupational asthma. The logistic regression model is freely available on the internet and may offer a useful but inexpensive adjunct to the prediction of occupational asthma hazard. PMID:15778257

Chemical Sensor Array Response Modeling Using Quantitative Structure-Activity Relationships Technique

NASA Astrophysics Data System (ADS)

Shevade, Abhijit V.; Ryan, Margaret A.; Homer, Margie L.; Zhou, Hanying; Manfreda, Allison M.; Lara, Liana M.; Yen, Shiao-Pin S.; Jewell, April D.; Manatt, Kenneth S.; Kisor, Adam K.

We have developed a Quantitative Structure-Activity Relationships (QSAR) based approach to correlate the response of chemical sensors in an array with molecular descriptors. A novel molecular descriptor set has been developed; this set combines descriptors of sensing film-analyte interactions, representing sensor response, with a basic analyte descriptor set commonly used in QSAR studies. The descriptors are obtained using a combination of molecular modeling tools and empirical and semi-empirical Quantitative Structure-Property Relationships (QSPR) methods. The sensors under investigation are polymer-carbon sensing films which have been exposed to analyte vapors at parts-per-million (ppm) concentrations; response is measured as change in film resistance. Statistically validated QSAR models have been developed using Genetic Function Approximations (GFA) for a sensor array for a given training data set. The applicability of the sensor response models has been tested by using it to predict the sensor activities for test analytes not considered in the training set for the model development. The validated QSAR sensor response models show good predictive ability. The QSAR approach is a promising computational tool for sensing materials evaluation and selection. It can also be used to predict response of an existing sensing film to new target analytes.

Reverse engineering the gap gene network of Drosophila melanogaster.

PubMed

Perkins, Theodore J; Jaeger, Johannes; Reinitz, John; Glass, Leon

2006-05-01

A fundamental problem in functional genomics is to determine the structure and dynamics of genetic networks based on expression data. We describe a new strategy for solving this problem and apply it to recently published data on early Drosophila melanogaster development. Our method is orders of magnitude faster than current fitting methods and allows us to fit different types of rules for expressing regulatory relationships. Specifically, we use our approach to fit models using a smooth nonlinear formalism for modeling gene regulation (gene circuits) as well as models using logical rules based on activation and repression thresholds for transcription factors. Our technique also allows us to infer regulatory relationships de novo or to test network structures suggested by the literature. We fit a series of models to test several outstanding questions about gap gene regulation, including regulation of and by hunchback and the role of autoactivation. Based on our modeling results and validation against the experimental literature, we propose a revised network structure for the gap gene system. Interestingly, some relationships in standard textbook models of gap gene regulation appear to be unnecessary for or even inconsistent with the details of gap gene expression during wild-type development.

Proton channel models

PubMed Central

Pupo, Amaury; Baez-Nieto, David; Martínez, Agustín; Latorre, Ramón; González, Carlos

2014-01-01

Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins. PMID:24755912

Structure and functions of internal working models of attachment and their role for emotion regulation.

PubMed

Zimmermann, P

1999-12-01

The concept of organization in the service of adaptation has been applied to attachment theory (Sroufe & Waters, 1977) as well as to a variety of life sciences (Ryan, Kuhi & Deci, 1997). Internal working models (IWMs) are postulated as providing organizing structure to the attachment behavior system controlling attachment behaviors toward caregivers and, with increasing age, autonomous individual adaptation. While many theoretical specifications have been suggested on that topic (e.g. Bretherton, 1987, 1990; Bretherton & Munholland, 1999; Main, Kaplan & Cassidy, 1985; Sroufe & Fleeson, 1986), empirical studies focusing directly on the structure or functions of internal working models are rare. Knowledge about the structure and functioning of IWMs could add to the understanding of the developmental influences of the attachment organization across the life-span. In this paper two topics will be addressed shortly and related to an empirical investigation concerning the relationship between attachment representations during late adolescence and emotion regulation patterns: (1) structure and functions of IWMs in terms of information-processing and emotion and behavior regulation; and (2) the transfer from IWMs of self-with-attachment figures to adaptive personality structures based on autonomous self-regulation.

A novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China

PubMed Central

Yang, Yanzheng; Zhu, Qiuan; Peng, Changhui; Wang, Han; Xue, Wei; Lin, Guanghui; Wen, Zhongming; Chang, Jie; Wang, Meng; Liu, Guobin; Li, Shiqing

2016-01-01

Increasing evidence indicates that current dynamic global vegetation models (DGVMs) have suffered from insufficient realism and are difficult to improve, particularly because they are built on plant functional type (PFT) schemes. Therefore, new approaches, such as plant trait-based methods, are urgently needed to replace PFT schemes when predicting the distribution of vegetation and investigating vegetation sensitivity. As an important direction towards constructing next-generation DGVMs based on plant functional traits, we propose a novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China. The results demonstrated that a Gaussian mixture model (GMM) trained with a LMA-Nmass-LAI data combination yielded an accuracy of 72.82% in simulating vegetation distribution, providing more detailed parameter information regarding community structures and ecosystem functions. The new approach also performed well in analyses of vegetation sensitivity to different climatic scenarios. Although the trait-climate relationship is not the only candidate useful for predicting vegetation distributions and analysing climatic sensitivity, it sheds new light on the development of next-generation trait-based DGVMs. PMID:27052108

Investigating attachment, caregiving, and mental health: a model of maternal-fetal relationships.

PubMed

Walsh, Judi; Hepper, Erica G; Marshall, Benjamin J

2014-11-19

Maternal-fetal relationships have been associated with psychosocial outcomes for women and children, but there has been a lack of conceptual clarity about the nature of the maternal relationship with the unborn child, and inconsistent findings assessing its predictors. We proposed and tested a model whereby maternal-fetal relationship quality was predicted by factors relating to the quality of the couple relationship and psychological health. We hypothesized that the contribution of individual differences in romantic attachment shown in past research would be mediated by romantic caregiving responsiveness, as maternal-fetal relationships reflect the beginnings of the caregiving system. 258 women in pregnancy (13, 23, and 33-weeks gestation) completed online measures of attachment to partner, caregiving responsiveness to partner, mental health, and thoughts about their unborn baby. Structural equation modeling was used to test a model of maternal-fetal relationships. Maternal-fetal relationship quality was higher for women at 23-weeks than 13-weeks gestation. Women in first pregnancies had higher self-reported scores of psychological functioning and quality of maternal-fetal relationships than women in subsequent pregnancies. Structural equation models indicated that the quality of the maternal-fetal relationship was best predicted by romantic caregiving responsiveness to partner and women's own psychological health, and that the association between adult romantic attachment avoidance and maternal-fetal relationships was fully mediated by caregiving responsiveness to partner, even after controlling for other factors. These data support the hypothesis that maternal-fetal relationships better reflect the operation of the caregiving system than the care-seeking (i.e., attachment) system. Models of maternal-fetal relationships and interventions with couples should consider the role of caregiving styles of mothers to partners and the relationship between expectant parents alongside other known predictors, particularly psychological health.

3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

ERIC Educational Resources Information Center

Meyer, Scott C.

2015-01-01

An upper-division undergraduate laboratory experiment is described that explores the structure/function relationship of protein domains, namely leucine zippers, through a molecular graphics computer program and physical models fabricated by 3D printing. By generating solvent accessible surfaces and color-coding hydrophobic, basic, and acidic amino…

A Posteriori Comparison of Natural and Surgical Destabilization Models of Canine Osteoarthritis

PubMed Central

Pelletier, Jean-Pierre; d'Anjou, Marc-André; Blond, Laurent; Pelletier, Johanne-Martel; del Castillo, Jérôme R. E.

2013-01-01

For many years Canis familiaris, the domestic dog, has drawn particular interest as a model of osteoarthritis (OA). Here, we optimized the dog model of experimental OA induced by cranial cruciate ligament sectioning. The usefulness of noninvasive complementary outcome measures, such as gait analysis for the limb function and magnetic resonance imaging for structural changes, was demonstrated in this model. Relationships were established between the functional impairment and the severity of structural changes including the measurement of cartilage thinning. In the dog model of naturally occurring OA, excellent test-retest reliability was denoted for the measurement of the limb function. A criterion to identify clinically meaningful responders to therapy was determined for privately owned dogs undergoing clinical trials. In addition, the recording of accelerometer-based duration of locomotor activity showed strong and complementary agreement with the biomechanical limb function. The translation potential of these models to the human OA condition is underlined. A preclinical testing protocol which combines the dog model of experimental OA induced by cranial cruciate ligament transection and the Dog model of naturally occurring OA offers the opportunity to further investigate the structural and functional benefits of disease-modifying strategies. Ultimately, a better prediction of outcomes for human clinical trials would be brought. PMID:24288664

Ties that bind: implications of social support for rural, partnered African American women's health functioning.

PubMed

Black, Angela R; Cook, Jennifer L; Murry, Velma McBride; Cutrona, Carolyn E

2005-01-01

Ecological theory was used to explore the pathways through which intimate relationship quality influenced health functioning among rural, partnered African American women. Structural equation modeling was used to analyze data from 349 women in Georgia and Iowa. Women's intimate relationship quality was positively associated with their psychological and physical health functioning. Support from community residents moderated this link, which was strongest for women who felt most connected with their neighbors and for women who believed their neighborhood to have a sense of communal responsibility. Future research should identify other factors salient to health functioning among members of this population.

Can genetics help psychometrics? Improving dimensionality assessment through genetic factor modeling.

PubMed

Franić, Sanja; Dolan, Conor V; Borsboom, Denny; Hudziak, James J; van Beijsterveldt, Catherina E M; Boomsma, Dorret I

2013-09-01

In the present article, we discuss the role that quantitative genetic methodology may play in assessing and understanding the dimensionality of psychological (psychometric) instruments. Specifically, we study the relationship between the observed covariance structures, on the one hand, and the underlying genetic and environmental influences giving rise to such structures, on the other. We note that this relationship may be such that it hampers obtaining a clear estimate of dimensionality using standard tools for dimensionality assessment alone. One situation in which dimensionality assessment may be impeded is that in which genetic and environmental influences, of which the observed covariance structure is a function, differ from each other in structure and dimensionality. We demonstrate that in such situations settling dimensionality issues may be problematic, and propose using quantitative genetic modeling to uncover the (possibly different) dimensionalities of the underlying genetic and environmental structures. We illustrate using simulations and an empirical example on childhood internalizing problems.

Functional and Structural Optimality in Plant Growth: A Crop Modelling Case Study

NASA Astrophysics Data System (ADS)

Caldararu, S.; Purves, D. W.; Smith, M. J.

2014-12-01

Simple mechanistic models of vegetation processes are essential both to our understanding of plant behaviour and to our ability to predict future changes in vegetation. One concept that can take us closer to such models is that of plant optimality, the hypothesis that plants aim to achieve an optimal state. Conceptually, plant optimality can be either structural or functional optimality. A structural constraint would mean that plants aim to achieve a certain structural characteristic such as an allometric relationship or nutrient content that allows optimal function. A functional condition refers to plants achieving optimal functionality, in most cases by maximising carbon gain. Functional optimality conditions are applied on shorter time scales and lead to higher plasticity, making plants more adaptable to changes in their environment. In contrast, structural constraints are optimal given the specific environmental conditions that plants are adapted to and offer less flexibility. We exemplify these concepts using a simple model of crop growth. The model represents annual cycles of growth from sowing date to harvest, including both vegetative and reproductive growth and phenology. Structural constraints to growth are represented as an optimal C:N ratio in all plant organs, which drives allocation throughout the vegetative growing stage. Reproductive phenology - i.e. the onset of flowering and grain filling - is determined by a functional optimality condition in the form of maximising final seed mass, so that vegetative growth stops when the plant reaches maximum nitrogen or carbon uptake. We investigate the plants' response to variations in environmental conditions within these two optimality constraints and show that final yield is most affected by changes during vegetative growth which affect the structural constraint.

Hearing Loss Is Negatively Related to Episodic and Semantic Long-Term Memory but Not to Short-Term Memory

ERIC Educational Resources Information Center

Ronnberg, Jerker; Danielsson, Henrik; Rudner, Mary; Arlinger, Stig; Sternang, Ola; Wahlin, Ake; Nilsson, Lars-Goran

2011-01-01

Purpose: To test the relationship between degree of hearing loss and different memory systems in hearing aid users. Method: Structural equation modeling (SEM) was used to study the relationship between auditory and visual acuity and different cognitive and memory functions in an age-hetereogenous subsample of 160 hearing aid users without…

The development of executive functions and early mathematics: a dynamic relationship.

PubMed

Van der Ven, Sanne H G; Kroesbergen, Evelyn H; Boom, Jan; Leseman, Paul P M

2012-03-01

The relationship between executive functions and mathematical skills has been studied extensively, but results are inconclusive, and how this relationship evolves longitudinally is largely unknown. The aim was to investigate the factor structure of executive functions in inhibition, shifting, and updating; the longitudinal development of executive functions and mathematics; and the relation between them. A total of 211 children in grade 2 (7-8 years old) from 10 schools in the Netherlands. Children were followed in grade 1 and 2 of primary education. Executive functions and mathematics were measured four times. The test battery contained multiple tasks for each executive function: Animal stroop, local global, and Simon task for inhibition; Animal Shifting, Trail Making Test in Colours, and Sorting Task for shifting; and Digit Span Backwards, Odd One Out, and Keep Track for updating. The factor structure of executive functions was assessed and relations with mathematics were investigated using growth modelling. Confirmatory factor analysis (CFA) showed that inhibition and shifting could not be distinguished from each other. Updating was a separate factor, and its development was strongly related to mathematical development while inhibition and shifting did not predict mathematics in the presence of the updating factor. The strong relationship between updating and mathematics suggest that updating skills play a key role in the maths learning process. This makes updating a promising target for future intervention studies. ©2011 The British Psychological Society.

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

Local and average structure of Mn- and La-substituted BiFeO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

Modeling human target acquisition in ground-to-air weapon systems

NASA Technical Reports Server (NTRS)

Phatak, A. V.; Mohr, R. L.; Vikmanis, M.; Wei, K. C.

1982-01-01

The problems associated with formulating and validating mathematical models for describing and predicting human target acquisition response are considered. In particular, the extension of the human observer model to include the acquisition phase as well as the tracking segment is presented. Relationship of the Observer model structure to the more complex Standard Optimal Control model formulation and to the simpler Transfer Function/Noise representation is discussed. Problems pertinent to structural identifiability and the form of the parameterization are elucidated. A systematic approach toward the identification of the observer acquisition model parameters from ensemble tracking error data is presented.

Robust biological parametric mapping: an improved technique for multimodal brain image analysis

NASA Astrophysics Data System (ADS)

Yang, Xue; Beason-Held, Lori; Resnick, Susan M.; Landman, Bennett A.

2011-03-01

Mapping the quantitative relationship between structure and function in the human brain is an important and challenging problem. Numerous volumetric, surface, region of interest and voxelwise image processing techniques have been developed to statistically assess potential correlations between imaging and non-imaging metrics. Recently, biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. To enable widespread application of this approach, we introduce robust regression and robust inference in the neuroimaging context of application of the general linear model. Through simulation and empirical studies, we demonstrate that our robust approach reduces sensitivity to outliers without substantial degradation in power. The robust approach and associated software package provides a reliable way to quantitatively assess voxelwise correlations between structural and functional neuroimaging modalities.

Design, synthesis and exploring the quantitative structure-activity relationship of some antioxidant flavonoid analogues.

PubMed

Das, Sreeparna; Mitra, Indrani; Batuta, Shaikh; Niharul Alam, Md; Roy, Kunal; Begum, Naznin Ara

2014-11-01

A series of flavonoid analogues were synthesized and screened for the in vitro antioxidant activity through their ability to quench 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical. The activity of these compounds, measured in comparison to the well-known standard antioxidants (29-32), their precursors (38-42) and other bioactive moieties (38-42) resembling partially the flavone skeleton was analyzed further to develop Quantitative Structure-Activity Relationship (QSAR) models using the Genetic Function Approximation (GFA) technique. Based on the essential structural requirements predicted by the QSAR models, some analogues were designed, synthesized and tested for activity. The predicted and experimental activities of these compounds were well correlated. Flavone analogue 20 was found to be the most potent antioxidant. Copyright © 2014 Elsevier Ltd. All rights reserved.

Relating Anaerobic Digestion Microbial Community and Process Function.

PubMed

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

An overview of multiphase cartilage mechanical modelling and its role in understanding function and pathology.

PubMed

Klika, Václav; Gaffney, Eamonn A; Chen, Ying-Chun; Brown, Cameron P

2016-09-01

There is a long history of mathematical and computational modelling with the objective of understanding the mechanisms governing cartilage׳s remarkable mechanical performance. Nonetheless, despite sophisticated modelling development, simulations of cartilage have consistently lagged behind structural knowledge and thus the relationship between structure and function in cartilage is not fully understood. However, in the most recent generation of studies, there is an emerging confluence between our structural knowledge and the structure represented in cartilage modelling. This raises the prospect of further refinement in our understanding of cartilage function and also the initiation of an engineering-level understanding for how structural degradation and ageing relates to cartilage dysfunction and pathology, as well as informing the potential design of prospective interventions. Aimed at researchers entering the field of cartilage modelling, we thus review the basic principles of cartilage models, discussing the underlying physics and assumptions in relatively simple settings, whilst presenting the derivation of relatively parsimonious multiphase cartilage models consistent with our discussions. We proceed to consider modern developments that start aligning the structure captured in the models with observed complexities. This emphasises the challenges associated with constitutive relations, boundary conditions, parameter estimation and validation in cartilage modelling programmes. Consequently, we further detail how both experimental interrogations and modelling developments can be utilised to investigate and reduce such difficulties before summarising how cartilage modelling initiatives may improve our understanding of cartilage ageing, pathology and intervention. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Posttraumatic Stress Disorder Symptoms, Relationship Adjustment, and Relationship Aggression in a Sample of Female Flood Victims

PubMed Central

Monson, Candice M.; Schumm, Jeremiah A.; Watkins, Laura E.; Panuzio, Jillian; Resick, Patricia A.

2010-01-01

This study tested a model examining the interrelationships among posttraumatic stress disorder (PTSD) symptoms, intimate relationship adjustment, and intimate relationship aggression in a sample of 205 adult female flood victims. At the bivariate level, higher PTSD symptoms were associated with higher physical and psychological aggression victimization, poorer relationship adjustment, and higher physical and psychological aggression perpetration. Results from structural equation modeling (SEM) analyses indicated that relationship aggression victimization influenced aggression perpetration directly, and in the case of physical aggression, indirectly through its relationship with PTSD symptoms and relationship adjustment. The influence of PTSD symptoms on physical aggression perpetration was fully explained by poorer relationship adjustment. These findings extend prior work from other traumatized populations documenting associations between variables reflecting PTSD symptomatology and indices of relationship functioning, and indicate a need for further investigation in this area of inquiry. PMID:21057584

EEG functional connectivity is partially predicted by underlying white matter connectivity

PubMed Central

Chu, CJ; Tanaka, N; Diaz, J; Edlow, BL; Wu, O; Hämäläinen, M; Stufflebeam, S; Cash, SS; Kramer, MA.

2015-01-01

Over the past decade, networks have become a leading model to illustrate both the anatomical relationships (structural networks) and the coupling of dynamic physiology (functional networks) linking separate brain regions. The relationship between these two levels of description remains incompletely understood and an area of intense research interest. In particular, it is unclear how cortical currents relate to underlying brain structural architecture. In addition, although theory suggests that brain communication is highly frequency dependent, how structural connections influence overlying functional connectivity in different frequency bands has not been previously explored. Here we relate functional networks inferred from statistical associations between source imaging of EEG activity and underlying cortico-cortical structural brain connectivity determined by probabilistic white matter tractography. We evaluate spontaneous fluctuating cortical brain activity over a long time scale (minutes) and relate inferred functional networks to underlying structural connectivity for broadband signals, as well as in seven distinct frequency bands. We find that cortical networks derived from source EEG estimates partially reflect both direct and indirect underlying white matter connectivity in all frequency bands evaluated. In addition, we find that when structural support is absent, functional connectivity is significantly reduced for high frequency bands compared to low frequency bands. The association between cortical currents and underlying white matter connectivity highlights the obligatory interdependence of functional and structural networks in the human brain. The increased dependence on structural support for the coupling of higher frequency brain rhythms provides new evidence for how underlying anatomy directly shapes emergent brain dynamics at fast time scales. PMID:25534110

Molecular Modeling as a Self-Taught Component of a Conventional Undergraduate Chemical Reaction Engineering Course

ERIC Educational Resources Information Center

Rothe, Erhard W.; Zygmunt, William E.

2016-01-01

We inserted a self-taught molecular modeling project into an otherwise conventional undergraduate chemical-reaction-engineering course. Our objectives were that students should (a) learn with minimal instructor intervention, (b) gain an appreciation for the relationship between molecular structure and, first, macroscopic state functions in…

The ISO Edi Conceptual Model Activity and Its Relationship to OSI.

ERIC Educational Resources Information Center

Fincher, Judith A.

1990-01-01

The edi conceptual model is being developed to define common structures, services, and processes that syntax-specific standards like X12 and EDIFACT could adopt. Open Systems Interconnection (OSI) is of interest to edi because of its potential to help enable global interoperability across Electronic Data Interchange (EDI) functional groups. A…

Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy.

PubMed

Wirsich, Jonathan; Perry, Alistair; Ridley, Ben; Proix, Timothée; Golos, Mathieu; Bénar, Christian; Ranjeva, Jean-Philippe; Bartolomei, Fabrice; Breakspear, Michael; Jirsa, Viktor; Guye, Maxime

2016-01-01

The in vivo structure-function relationship is key to understanding brain network reorganization due to pathologies. This relationship is likely to be particularly complex in brain network diseases such as temporal lobe epilepsy, in which disturbed large-scale systems are involved in both transient electrical events and long-lasting functional and structural impairments. Herein, we estimated this relationship by analyzing the correlation between structural connectivity and functional connectivity in terms of analytical network communication parameters. As such, we targeted the gradual topological structure-function reorganization caused by the pathology not only at the whole brain scale but also both in core and peripheral regions of the brain. We acquired diffusion (dMRI) and resting-state fMRI (rsfMRI) data in seven right-lateralized TLE (rTLE) patients and fourteen healthy controls and analyzed the structure-function relationship by using analytical network communication metrics derived from the structural connectome. In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information) in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

External validation of structure-biodegradation relationship (SBR) models for predicting the biodegradability of xenobiotics.

PubMed

Devillers, J; Pandard, P; Richard, B

2013-01-01

Biodegradation is an important mechanism for eliminating xenobiotics by biotransforming them into simple organic and inorganic products. Faced with the ever growing number of chemicals available on the market, structure-biodegradation relationship (SBR) and quantitative structure-biodegradation relationship (QSBR) models are increasingly used as surrogates of the biodegradation tests. Such models have great potential for a quick and cheap estimation of the biodegradation potential of chemicals. The Estimation Programs Interface (EPI) Suite™ includes different models for predicting the potential aerobic biodegradability of organic substances. They are based on different endpoints, methodologies and/or statistical approaches. Among them, Biowin 5 and 6 appeared the most robust, being derived from the largest biodegradation database with results obtained only from the Ministry of International Trade and Industry (MITI) test. The aim of this study was to assess the predictive performances of these two models from a set of 356 chemicals extracted from notification dossiers including compatible biodegradation data. Another set of molecules with no more than four carbon atoms and substituted by various heteroatoms and/or functional groups was also embodied in the validation exercise. Comparisons were made with the predictions obtained with START (Structural Alerts for Reactivity in Toxtree). Biowin 5 and Biowin 6 gave satisfactorily prediction results except for the prediction of readily degradable chemicals. A consensus model built with Biowin 1 allowed the diminution of this tendency.

From Patterns to Function in Living Systems: Dryland Ecosystems as a Case Study

NASA Astrophysics Data System (ADS)

Meron, Ehud

2018-03-01

Spatial patterns are ubiquitous in animate matter. Besides their intricate structure and beauty they generally play functional roles. The capacity of living systems to remain functional in changing environments is a question of utmost importance, but its intimate relationship to pattern formation is largely unexplored. Here, we address this relationship using dryland vegetation as a case study. Following a brief introduction to pattern-formation theory, we describe a mathematical model that captures several mechanisms of vegetation pattern formation and discuss ecological contexts that showcase different mechanisms. Using this model, we unravel the different vegetation patterns that keep dryland ecosystems viable along the rainfall gradient, identify multistability ranges where fronts separating domains of alternative stable states exist, and highlight the roles of front dynamics in mitigating or reversing desertification. The utility of satellite images in testing model predictions is discussed. An outlook on outstanding open problems concludes this paper.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Exploring the relationships between International Classification of Functioning, Disability and Health (ICF) constructs of Impairment, Activity Limitation and Participation Restriction in people with osteoarthritis prior to joint replacement.

PubMed

Pollard, Beth; Johnston, Marie; Dieppe, Paul

2011-05-16

The International Classification of Functioning, Disability and Health (ICF) proposes three main constructs, impairment (I), activity limitation (A) and participation restriction (P). The ICF model allows for all paths between the constructs to be explored, with significant paths likely to vary for different conditions. The relationships between I, A and P have been explored in some conditions but not previously in people with osteoarthritis prior to joint replacement. The aim of this paper is to examine these relationships using separate measures of each construct and structural equation modelling. A geographical cohort of 413 patients with osteoarthritis about to undergo hip and knee joint replacement completed the Aberdeen measures of Impairment, Activity Limitation and Participation Restriction (Ab-IAP). Confirmatory factor analysis was used to test the three factor (I, A, P) measurement model. Structural equation modelling was used to explore the I, A and P pathways in the ICF model. There was support from confirmatory factor analysis for the three factor I, A, P measurement model. The structural equation model had good fit [S-B Chi-square = 439.45, df = 149, CFI robust = 0.91, RMSEA robust = 0.07] and indicated significant pathways between I and A (standardised coefficient = 0.76 p < 0.0001) and between A and P (standardised coefficient = 0.75 p < 0.0001). However, the path between I and P was not significant (standardised coefficient = 0.01). The significant pathways suggest that treatments and interventions aimed at reducing impairment, such as joint replacement, may only affect P indirectly, through A, however, longitudinal data would be needed to establish this.

The Relationship between Symptom Relief and Psychosocial Functional Improvement during Acute Electroconvulsive Therapy for Patients with Major Depressive Disorder.

PubMed

Lin, Ching-Hua; Yang, Wei-Cheng

2017-07-01

We aimed to compare the degree of symptom relief to psychosocial functional (abbreviated as "functional") improvement and explore the relationships between symptom relief and functional improvement during acute electroconvulsive therapy for patients with major depressive disorder. Major depressive disorder inpatients (n=130) requiring electroconvulsive therapy were recruited. Electroconvulsive therapy was generally performed for a maximum of 12 treatments. Symptom severity, using the 17-item Hamilton Depression Rating Scale, and psychosocial functioning (abbreviated as "functioning"), using the Modified Work and Social Adjustment Scale, were assessed before electroconvulsive therapy, after every 3 electroconvulsive therapy treatments, and after the final electroconvulsive therapy. Both 17-item Hamilton Depression Rating Scale and Modified Work and Social Adjustment Scale scores were converted to T-score units to compare the degrees of changes between depressive symptoms and functioning after electroconvulsive therapy. Structural equation modeling was used to test the relationships between 17-item Hamilton Depression Rating Scale and Modified Work and Social Adjustment Scale during acute electroconvulsive therapy. One hundred sixteen patients who completed at least the first 3 electroconvulsive therapy treatments entered the analysis. Reduction of 17-item Hamilton Depression Rating Scale T-scores was significantly greater than that of Modified Work and Social Adjustment Scale T-scores at assessments 2, 3, 4, and 5. The model analyzed by structural equation modeling satisfied all indices of goodness-of-fit (chi-square = 32.882, P =.107, TLI = 0.92, CFI = 0.984, RMSEA = 0.057). The 17-item Hamilton Depression Rating Scale change did not predict subsequent Modified Work and Social Adjustment Scale change. Functioning improved less than depressive symptoms during acute electroconvulsive therapy. Symptom reduction did not predict subsequent functional improvement. Depressive symptoms and functional impairment are distinct domains and should be assessed independently to accurately reflect the effectiveness of electroconvulsive therapy. © The Author 2017. Published by Oxford University Press on behalf of CINP.

Disease Severity and Domain Specific Arthritis Self-Efficacy: Relationships to Pain and Functioning in Rheumatoid Arthritis Patients

PubMed Central

Somers, Tamara J.; Shelby, Rebecca A.; Keefe, Francis J.; Godiwala, Neha; Lumley, Mark A.; Mosley-Williams, Angelia; Rice, John R.; Caldwell, David

2010-01-01

Objective Examining the degree to which disease severity and domains of self-efficacy (pain, function, other symptoms) explain pain and functioning in rheumatoid arthritis patients. Methods Patients (N=263) completed the Arthritis Impact Measurements Scales-2 to assess pain and functioning (physical, affective, and social), the Arthritis Self-Efficacy Scale to assess three self-efficacy domains (pain, physical function, other); disease severity was assessed with C-reactive protein, physician's rating, abnormal joint count. Structural equation modeling was used to examine hypotheses: 1) does disease severity have a direct relationship with pain and each area of functioning, 2) does disease severity have a direct relationship with each arthritis self-efficacy domain, and 3) do the self-efficacy domains mediate the relationship between disease severity and RA pain and each area of functioning. Results Disease severity was related to pain, physical functioning, and each self-efficacy domain (β's=.28-.56; p's<.001). Each self-efficacy domain was related to its respective domain of functioning (e.g., self-efficacy for pain was related to pain) (β's=.36-.54; p's<.001). Self-efficacy mediated the relationship between disease severity and pain and functioning (β's=.12-.19; p's<.001). Self-efficacy for pain control and to perform functional tasks accounted for 32-42% of disease severity's total effect on their respective outcomes (e.g., self-efficacy for pain control accounted for 32% of disease severity's total effect on pain). Variance accounted for by the total model was 52% for pain, 53% for physical functioning, and 44% for affective and social functioning. Conclusions Disease severity and self-efficacy both impact RA functioning and intervening in these areas may lead to better outcomes. PMID:20535796

The effect of the gastrocnemius on the plantar fascia.

PubMed

Pascual Huerta, Javier

2014-12-01

Although anatomic and functional relationship has been established between the gastrocnemius muscle, via the Achilles tendon, and the plantar fascia, the exact role of gastrocnemius tightness in foot and plantar fascia problems is not completely understood. This article summarizes past and current literature linking these 2 structures and gives a mechanical explanation based on functional models of the relationship between gastrocnemius tightness and plantar fascia. The effect of gastrocnemius tightness on the sagittal behavior of the foot is also discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

A predictive multi-linear regression model for organic micropollutants, based on a laboratory-scale column study simulating the river bank filtration process.

PubMed

Bertelkamp, C; Verliefde, A R D; Reynisson, J; Singhal, N; Cabo, A J; de Jonge, M; van der Hoek, J P

2016-03-05

This study investigated relationships between OMP biodegradation rates and the functional groups present in the chemical structure of a mixture of 31 OMPs. OMP biodegradation rates were determined from lab-scale columns filled with soil from RBF site Engelse Werk of the drinking water company Vitens in The Netherlands. A statistically significant relationship was found between OMP biodegradation rates and the functional groups of the molecular structures of OMPs in the mixture. The OMP biodegradation rate increased in the presence of carboxylic acids, hydroxyl groups, and carbonyl groups, but decreased in the presence of ethers, halogens, aliphatic ethers, methyl groups and ring structures in the chemical structure of the OMPs. The predictive model obtained from the lab-scale soil column experiment gave an accurate qualitative prediction of biodegradability for approximately 70% of the OMPs monitored in the field (80% excluding the glymes). The model was found to be less reliable for the more persistent OMPs (OMPs with predicted biodegradation rates lower or around the standard error=0.77d(-1)) and OMPs containing amide or amine groups. These OMPs should be carefully monitored in the field to determine their removal during RBF. Copyright © 2015 Elsevier B.V. All rights reserved.

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

PubMed

Shim, Jihyun; Mackerell, Alexander D

2011-05-01

A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more detailed presentation of issues and limitations associated with empirical energy functions and conformational sampling methods.

The NEO Five-Factor Inventory: latent structure and relationships with dimensions of anxiety and depressive disorders in a large clinical sample.

PubMed

Rosellini, Anthony J; Brown, Timothy A

2011-03-01

The present study evaluated the latent structure of the NEO Five-Factor Inventory (NEO FFI) and relations between the five-factor model (FFM) of personality and dimensions of DSM-IV anxiety and depressive disorders (panic disorder, generalized anxiety disorder [GAD], obsessive-compulsive disorder, social phobia [SOC], major depressive disorder [MDD]) in a large sample of outpatients (N = 1,980). Exploratory structural equation modeling (ESEM) was used to show that a five-factor solution provided acceptable model fit, albeit with some poorly functioning items. Neuroticism demonstrated significant positive associations with all but one of the disorder constructs whereas Extraversion was inversely related to SOC and MDD. Conscientiousness was inversely related to MDD but demonstrated a positive relationship with GAD. Results are discussed in regard to potential revisions to the NEO FFI, the evaluation of other NEO instruments using ESEM, and clinical implications of structural paths between FFM domains and specific emotional disorders.

The NEO Five-Factor Inventory: Latent Structure and Relationships With Dimensions of Anxiety and Depressive Disorders in a Large Clinical Sample

PubMed Central

Rosellini, Anthony J.; Brown, Timothy A.

2017-01-01

The present study evaluated the latent structure of the NEO Five-Factor Inventory (NEO FFI) and relations between the five-factor model (FFM) of personality and dimensions of DSM-IV anxiety and depressive disorders (panic disorder, generalized anxiety disorder [GAD], obsessive–compulsive disorder, social phobia [SOC], major depressive disorder [MDD]) in a large sample of outpatients (N = 1,980). Exploratory structural equation modeling (ESEM) was used to show that a five-factor solution provided acceptable model fit, albeit with some poorly functioning items. Neuroticism demonstrated significant positive associations with all but one of the disorder constructs whereas Extraversion was inversely related to SOC and MDD. Conscientiousness was inversely related to MDD but demonstrated a positive relationship with GAD. Results are discussed in regard to potential revisions to the NEO FFI, the evaluation of other NEO instruments using ESEM, and clinical implications of structural paths between FFM domains and specific emotional disorders. PMID:20881102

A structural equation model of patient-healthcare provider relationships and HIV-infected patient outcomes in Chinese populations.

PubMed

Chen, Wei-Ti; Shiu, Chengshi; Yang, Joyce P; Chuang, Peing; Zhang, Lin; Bao, Meijuan; Lu, Hongzhou

2018-03-01

Obtaining maximum antiretroviral therapy (ART) adherence is critical for maintaining a high CD4 count and strong immune function in PLWHA. Key factors for achieving optimum adherence include good medication self-efficacy, decreased medication-taking difficulties, and positive patient-healthcare provider (HCP) relationships. Limited studies have analyzed the correlation of these factors and ART adherence in Chinese population. In this paper, structural equation modeling was performed to assess the proposed model of relations between patient-HCP relationships and adherence. Audio Computer-Assisted Self-Interview (ACASI) software was used to collect data on ART adherence and patient variables among 227 PLWHA in Shanghai and Taipei. Participants completed a one-time 60-minute ACASI survey that consisted of standardized measures to assess demographics, recent CD4 counts, self-efficacy, patient-HCP relationship, adherence, and medication-taking difficulties. The data shown the relationship between patient-HCP relationships and adherence was significantly consistent with mediation by medication self-efficacy. However, patient-HCP interaction did not directly influence medication-taking difficulties, and medication-taking difficulties did not significantly affect CD4 counts. Furthermore, patient-HCP interactions did not directly impact CD4 counts; rather, the relation was consistent with mediation (by either better medication self-efficacy or better adherence) or by improved adherence alone. Future interventions should be designed to enhance self-management and provide better patient-HCP communication. This improved communication will enhance medication self-efficacy and decrease medication-taking difficulties. This in turn will improve medication adherence and immune function among PLWHA.

Field- and Remote Sensing-based Structural Attributes Measured at Multiple Scales Influence the Relationship Between Nitrogen and Reflectance of Forest Canopies

NASA Astrophysics Data System (ADS)

Sullivan, F.; Ollinger, S. V.; Palace, M. W.; Ouimette, A.; Sanders-DeMott, R.; Lepine, L. C.

2017-12-01

The correlation between near-infrared reflectance and forest canopy nitrogen concentration has been demonstrated at varying scales using a range of optical sensors on airborne and satellite platforms. Although the mechanism underpinning the relationship is unclear, at its basis are biologically-driven functional relationships of multiple plant traits that affect canopy chemistry and structure. The link between near-infrared reflectance and canopy nitrogen has been hypothesized to be partially driven by covariation of canopy nitrogen with canopy structure. In this study, we used a combination of airborne LiDAR data and field measured leaf and canopy chemical and structural traits to explore interrelationships between canopy nitrogen, near-infrared reflectance, and canopy structure on plots at Bartlett Experimental Forest in the White Mountain National Forest, New Hampshire. Over each plot, we developed a 1-meter resolution canopy height profile and a 1-meter resolution canopy height model. From canopy height profiles and canopy height models, we calculated a set of metrics describing the plot-level variability, breadth, depth, and arrangement of LiDAR returns. This combination of metrics was used to describe both vertical and horizontal variation in structure. In addition, we developed and measured several field-based metrics of leaf and canopy structure at the plot scale by directly measuring the canopy or by weighting leaf-level metrics by species leaf area contribution. We assessed relationships between leaf and structural metrics, near-infrared reflectance and canopy nitrogen concentration using multiple linear regression and mixed effects modeling. Consistent with our hypothesis, we found moderately strong links between both near-infrared reflectance and canopy nitrogen concentration with LiDAR-derived structural metrics, and we additionally found that leaf-level metrics scaled to the plot level share an important role in canopy reflectance. We suggest that canopy structure has a governing role in canopy reflectance, reducing maximum potential reflectance as structural complexity increases, and therefore also influences the relationship between canopy nitrogen and NIR reflectance.

Forecasting Urban Forest Ecosystem Structure, Function, and Vulnerability

NASA Astrophysics Data System (ADS)

Steenberg, James W. N.; Millward, Andrew A.; Nowak, David J.; Robinson, Pamela J.; Ellis, Alexis

2017-03-01

The benefits derived from urban forest ecosystems are garnering increasing attention in ecological research and municipal planning. However, because of their location in heterogeneous and highly-altered urban landscapes, urban forests are vulnerable and commonly suffer disproportionate and varying levels of stress and disturbance. The objective of this study is to assess and analyze the spatial and temporal changes, and potential vulnerability, of the urban forest resource in Toronto, Canada. This research was conducted using a spatially-explicit, indicator-based assessment of vulnerability and i-Tree Forecast modeling of temporal changes in forest structure and function. Nine scenarios were simulated for 45 years and model output was analyzed at the ecosystem and municipal scale. Substantial mismatches in ecological processes between spatial scales were found, which can translate into unanticipated loss of function and social inequities if not accounted for in planning and management. At the municipal scale, the effects of Asian longhorned beetle and ice storm disturbance were far less influential on structure and function than changes in management actions. The strategic goals of removing invasive species and increasing tree planting resulted in a decline in carbon storage and leaf biomass. Introducing vulnerability parameters in the modeling increased the spatial heterogeneity in structure and function while expanding the disparities of resident access to ecosystem services. There was often a variable and uncertain relationship between vulnerability and ecosystem structure and function. Vulnerability assessment and analysis can provide strategic planning initiatives with valuable insight into the processes of structural and functional change resulting from management intervention.

Forecasting Urban Forest Ecosystem Structure, Function, and Vulnerability.

PubMed

Steenberg, James W N; Millward, Andrew A; Nowak, David J; Robinson, Pamela J; Ellis, Alexis

2017-03-01

The benefits derived from urban forest ecosystems are garnering increasing attention in ecological research and municipal planning. However, because of their location in heterogeneous and highly-altered urban landscapes, urban forests are vulnerable and commonly suffer disproportionate and varying levels of stress and disturbance. The objective of this study is to assess and analyze the spatial and temporal changes, and potential vulnerability, of the urban forest resource in Toronto, Canada. This research was conducted using a spatially-explicit, indicator-based assessment of vulnerability and i-Tree Forecast modeling of temporal changes in forest structure and function. Nine scenarios were simulated for 45 years and model output was analyzed at the ecosystem and municipal scale. Substantial mismatches in ecological processes between spatial scales were found, which can translate into unanticipated loss of function and social inequities if not accounted for in planning and management. At the municipal scale, the effects of Asian longhorned beetle and ice storm disturbance were far less influential on structure and function than changes in management actions. The strategic goals of removing invasive species and increasing tree planting resulted in a decline in carbon storage and leaf biomass. Introducing vulnerability parameters in the modeling increased the spatial heterogeneity in structure and function while expanding the disparities of resident access to ecosystem services. There was often a variable and uncertain relationship between vulnerability and ecosystem structure and function. Vulnerability assessment and analysis can provide strategic planning initiatives with valuable insight into the processes of structural and functional change resulting from management intervention.

Population density of North American elk: effects on plant diversity.

PubMed

Stewart, Kelley M; Bowyer, R Terry; Kie, John G; Dick, Brian L; Ruess, Roger W

2009-08-01

Large, herbivorous mammals have profound effects on ecosystem structure and function and often act as keystone species in ecosystems they inhabit. Density-dependent processes associated with population structure of large mammals may interact with ecosystem functioning to increase or decrease biodiversity, depending on the relationship of herbivore populations relative to the carrying capacity (K) of the ecosystem. We tested for indirect effects of population density of large herbivores on plant species richness and diversity in a montane ecosystem, where increased net aboveground primary productivity (NAPP) in response to low levels of herbivory has been reported. We documented a positive, linear relationship between plant-species diversity and richness with NAPP. Structural equation modeling revealed significant indirect relationships between population density of herbivores, NAPP, and species diversity. We observed an indirect effect of density-dependent processes in large, herbivorous mammals and species diversity of plants through changes in NAPP in this montane ecosystem. Changes in species diversity of plants in response to herbivory may be more indirect in ecosystems with long histories of herbivory. Those subtle or indirect effects of herbivory may have strong effects on ecosystem functioning, but may be overlooked in plant communities that are relatively resilient to herbivory.

Ego-resiliency reloaded: a three-component model of general resiliency.

PubMed

Farkas, Dávid; Orosz, Gábor

2015-01-01

Ego-resiliency (ER) is a capacity that enables individuals to adapt to constantly changing environmental demands. The goal of our research was to identify components of Ego-resiliency, and to test the reliability and the structural and convergent validity of the refined version of the ER11 Ego-resiliency scale. In Study 1 we used a factor analytical approach to assess structural validity and to identify factors of Ego-resiliency. Comparing alternative factor-structures, a hierarchical model was chosen including three factors: Active Engagement with the World (AEW), Repertoire of Problem Solving Strategies (RPSS), and Integrated Performance under Stress (IPS). In Study 2, the convergent and divergent validity of the ER11 scale and its factors and their relationship with resilience were tested. The results suggested that resiliency is a double-faced construct, with one function to keep the personality system stable and intact, and the other function to adjust the personality system in an adaptive way to the dynamically changing environment. The stability function is represented by the RPSS and IPS components of ER. Their relationship pattern is similar to other constructs of resilience, e.g. the Revised Connor-Davidson Resilience Scale (R-CD-RISC). The flexibility function is represented by the unit of RPSS and AEW components. In Study 3 we tested ER11 on a Hungarian online representative sample and integrated the results in a model of general resiliency. This framework allows us to grasp both the stability-focused and the plasticity-focused nature of resiliency.

Ego-Resiliency Reloaded: A Three-Component Model of General Resiliency

PubMed Central

Farkas, Dávid; Orosz, Gábor

2015-01-01

Ego-resiliency (ER) is a capacity that enables individuals to adapt to constantly changing environmental demands. The goal of our research was to identify components of Ego-resiliency, and to test the reliability and the structural and convergent validity of the refined version of the ER11 Ego-resiliency scale. In Study 1 we used a factor analytical approach to assess structural validity and to identify factors of Ego-resiliency. Comparing alternative factor-structures, a hierarchical model was chosen including three factors: Active Engagement with the World (AEW), Repertoire of Problem Solving Strategies (RPSS), and Integrated Performance under Stress (IPS). In Study 2, the convergent and divergent validity of the ER11 scale and its factors and their relationship with resilience were tested. The results suggested that resiliency is a double-faced construct, with one function to keep the personality system stable and intact, and the other function to adjust the personality system in an adaptive way to the dynamically changing environment. The stability function is represented by the RPSS and IPS components of ER. Their relationship pattern is similar to other constructs of resilience, e.g. the Revised Connor-Davidson Resilience Scale (R-CD-RISC). The flexibility function is represented by the unit of RPSS and AEW components. In Study 3 we tested ER11 on a Hungarian online representative sample and integrated the results in a model of general resiliency. This framework allows us to grasp both the stability-focused and the plasticity-focused nature of resiliency. PMID:25815881

Public Opinion as Collective Coorientation.

ERIC Educational Resources Information Center

Tipton, Leonard; And Others

To conceptualize public opinion as something other than "mere aggregation" of individual opinions requires systemic models that identify component parts of public opinion and their structural/functional relationships. Operationalization requires asking respondents not only their individual opinion, but also their perception of public…

Specifications of insilicoML 1.0: a multilevel biophysical model description language.

PubMed

Asai, Yoshiyuki; Suzuki, Yasuyuki; Kido, Yoshiyuki; Oka, Hideki; Heien, Eric; Nakanishi, Masao; Urai, Takahito; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

2008-12-01

An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

Determinants of cation transport selectivity: Equilibrium binding and transport kinetics

PubMed Central

2015-01-01

The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules. PMID:26078056

Treatment Concerns and Functional Impairment in Pediatric Anxiety.

PubMed

Wu, Monica S; Salloum, Alison; Lewin, Adam B; Selles, Robert R; McBride, Nicole M; Crawford, Erika A; Storch, Eric A

2016-08-01

Although there are efficacious, evidence-based treatments for anxiety disorders, youth often experience delays in seeking therapy. Myriad reasons may contribute to this lag in treatment initiation, with some youth possessing concerns about therapy. Treatment concerns are broadly characterized by worries/ambivalence about seeking treatment, including concerns about the negative reactions, consequences, and inconvenience of treatment. As no studies exist for youth with anxiety disorders, this study examined the phenomenology of treatment concerns in 119 treatment-seeking, anxious youth and utilized a structural equation model to examine the relationship between child anxiety, depressive symptoms, treatment concerns, and anxiety-related functional impairment. Over 90 % of the children positively endorsed some type of treatment-related fear, with the most frequently expressed concern being that therapy would take too much time (50.4 %). Based on the model, both child anxiety and depressive symptoms predicted functional impairment, and treatment concerns mediated the relationship between child anxiety and functional impairment.

Direct and Indirect Links Between Childhood Maltreatment, Posttraumatic Stress Disorder, and Women’s Health

PubMed Central

Lang, Ariel J.; Aarons, Gregory A.; Gearity, James; Laffaye, Charlene; Satz, Leslie; Dresselhaus, Timothy R.; Stein, Murray B.

2008-01-01

The authors evaluated the relationships among childhood maltreatment, sexual trauma in adulthood, posttraumatic stress disorder (PTSD), and health functioning in women. Female Veterans’ Affairs (VA) primary care patients (N = 200) completed self-report measures of childhood maltreatment, adult sexual trauma, PTSD symptoms, and current health functioning. The authors used structural equation modeling to test models of the relationship among these variables. Childhood nonsexual maltreatment and adult sexual assault were positively associated with PTSD. Childhood nonsexual maltreatment (β = −.20) and PTSD (β = −.75) were significantly associated with poorer physical and mental health functioning. Adult sexual assault negatively affected health functioning through its association with PTSD. Thus, poor health outcomes associated with childhood maltreatment in women may be conveyed through PTSD. These findings should strengthen efforts directed at identifying and treating PTSD in female victims of childhood maltreatment with the aim of preventing or attenuating poor health outcomes. PMID:18316270

Structured penalties for functional linear models-partially empirical eigenvectors for regression.

PubMed

Randolph, Timothy W; Harezlak, Jaroslaw; Feng, Ziding

2012-01-01

One of the challenges with functional data is incorporating geometric structure, or local correlation, into the analysis. This structure is inherent in the output from an increasing number of biomedical technologies, and a functional linear model is often used to estimate the relationship between the predictor functions and scalar responses. Common approaches to the problem of estimating a coefficient function typically involve two stages: regularization and estimation. Regularization is usually done via dimension reduction, projecting onto a predefined span of basis functions or a reduced set of eigenvectors (principal components). In contrast, we present a unified approach that directly incorporates geometric structure into the estimation process by exploiting the joint eigenproperties of the predictors and a linear penalty operator. In this sense, the components in the regression are 'partially empirical' and the framework is provided by the generalized singular value decomposition (GSVD). The form of the penalized estimation is not new, but the GSVD clarifies the process and informs the choice of penalty by making explicit the joint influence of the penalty and predictors on the bias, variance and performance of the estimated coefficient function. Laboratory spectroscopy data and simulations are used to illustrate the concepts.

Discovering rules for protein-ligand specificity using support vector inductive logic programming.

PubMed

Kelley, Lawrence A; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

2009-09-01

Structural genomics initiatives are rapidly generating vast numbers of protein structures. Comparative modelling is also capable of producing accurate structural models for many protein sequences. However, for many of the known structures, functions are not yet determined, and in many modelling tasks, an accurate structural model does not necessarily tell us about function. Thus, there is a pressing need for high-throughput methods for determining function from structure. The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, is often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and to function design. We present a new general method for discovering the features of binding pockets that confer specificity for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of inductive logic programming with the statistical learning power of support vector machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind NAD on a large benchmark set given only the geometry and composition of the backbone of the binding pocket without the use of docking. In addition, we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggests that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/.

The Significance of G Protein-Coupled Receptor Crystallography for Drug Discovery

PubMed Central

Salon, John A.; Lodowski, David T.

2011-01-01

Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination. PMID:21969326

High-throughput screening of chemicals as functional ...

EPA Pesticide Factsheets

Identifying chemicals that provide a specific function within a product, yet have minimal impact on the human body or environment, is the goal of most formulation chemists and engineers practicing green chemistry. We present a methodology to identify potential chemical functional substitutes from large libraries of chemicals using machine learning based models. We collect and analyze publicly available information on the function of chemicals in consumer products or industrial processes to identify a suite of harmonized function categories suitable for modeling. We use structural and physicochemical descriptors for these chemicals to build 41 quantitative structure–use relationship (QSUR) models for harmonized function categories using random forest classification. We apply these models to screen a library of nearly 6400 chemicals with available structure information for potential functional substitutes. Using our Functional Use database (FUse), we could identify uses for 3121 chemicals; 4412 predicted functional uses had a probability of 80% or greater. We demonstrate the potential application of the models to high-throughput (HT) screening for “candidate alternatives” by merging the valid functional substitute classifications with hazard metrics developed from HT screening assays for bioactivity. A descriptor set could be obtained for 6356 Tox21 chemicals that have undergone a battery of HT in vitro bioactivity screening assays. By applying QSURs, we wer

Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context.

PubMed

Wang, Yong-Cui; Wang, Yong; Yang, Zhi-Xia; Deng, Nai-Yang

2011-06-20

Enzymes are known as the largest class of proteins and their functions are usually annotated by the Enzyme Commission (EC), which uses a hierarchy structure, i.e., four numbers separated by periods, to classify the function of enzymes. Automatically categorizing enzyme into the EC hierarchy is crucial to understand its specific molecular mechanism. In this paper, we introduce two key improvements in predicting enzyme function within the machine learning framework. One is to introduce the efficient sequence encoding methods for representing given proteins. The second one is to develop a structure-based prediction method with low computational complexity. In particular, we propose to use the conjoint triad feature (CTF) to represent the given protein sequences by considering not only the composition of amino acids but also the neighbor relationships in the sequence. Then we develop a support vector machine (SVM)-based method, named as SVMHL (SVM for hierarchy labels), to output enzyme function by fully considering the hierarchical structure of EC. The experimental results show that our SVMHL with the CTF outperforms SVMHL with the amino acid composition (AAC) feature both in predictive accuracy and Matthew's correlation coefficient (MCC). In addition, SVMHL with the CTF obtains the accuracy and MCC ranging from 81% to 98% and 0.82 to 0.98 when predicting the first three EC digits on a low-homologous enzyme dataset. We further demonstrate that our method outperforms the methods which do not take account of hierarchical relationship among enzyme categories and alternative methods which incorporate prior knowledge about inter-class relationships. Our structure-based prediction model, SVMHL with the CTF, reduces the computational complexity and outperforms the alternative approaches in enzyme function prediction. Therefore our new method will be a useful tool for enzyme function prediction community.

Which Working Memory Functions Predict Intelligence?

ERIC Educational Resources Information Center

Oberauer, Klaus; Sub, Heinz-Martin; Wilhelm, Oliver; Wittmann, Werner W.

2008-01-01

Investigates the relationship between three factors of working memory (storage and processing, relational integration, and supervision) and four factors of intelligence (reasoning, speed, memory, and creativity) using structural equation models. Relational integration predicted reasoning ability at least as well as the storage-and-processing…

Statistical self-similarity of width function maxima with implications to floods

USGS Publications Warehouse

Veitzer, S.A.; Gupta, V.K.

2001-01-01

Recently a new theory of random self-similar river networks, called the RSN model, was introduced to explain empirical observations regarding the scaling properties of distributions of various topologic and geometric variables in natural basins. The RSN model predicts that such variables exhibit statistical simple scaling, when indexed by Horton-Strahler order. The average side tributary structure of RSN networks also exhibits Tokunaga-type self-similarity which is widely observed in nature. We examine the scaling structure of distributions of the maximum of the width function for RSNs for nested, complete Strahler basins by performing ensemble simulations. The maximum of the width function exhibits distributional simple scaling, when indexed by Horton-Strahler order, for both RSNs and natural river networks extracted from digital elevation models (DEMs). We also test a powerlaw relationship between Horton ratios for the maximum of the width function and drainage areas. These results represent first steps in formulating a comprehensive physical statistical theory of floods at multiple space-time scales for RSNs as discrete hierarchical branching structures. ?? 2001 Published by Elsevier Science Ltd.

Applications of large-scale density functional theory in biology

NASA Astrophysics Data System (ADS)

Cole, Daniel J.; Hine, Nicholas D. M.

2016-10-01

Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

A simulator for evaluating methods for the detection of lesion-deficit associations

NASA Technical Reports Server (NTRS)

Megalooikonomou, V.; Davatzikos, C.; Herskovits, E. H.

2000-01-01

Although much has been learned about the functional organization of the human brain through lesion-deficit analysis, the variety of statistical and image-processing methods developed for this purpose precludes a closed-form analysis of the statistical power of these systems. Therefore, we developed a lesion-deficit simulator (LDS), which generates artificial subjects, each of which consists of a set of functional deficits, and a brain image with lesions; the deficits and lesions conform to predefined distributions. We used probability distributions to model the number, sizes, and spatial distribution of lesions, to model the structure-function associations, and to model registration error. We used the LDS to evaluate, as examples, the effects of the complexities and strengths of lesion-deficit associations, and of registration error, on the power of lesion-deficit analysis. We measured the numbers of recovered associations from these simulated data, as a function of the number of subjects analyzed, the strengths and number of associations in the statistical model, the number of structures associated with a particular function, and the prior probabilities of structures being abnormal. The number of subjects required to recover the simulated lesion-deficit associations was found to have an inverse relationship to the strength of associations, and to the smallest probability in the structure-function model. The number of structures associated with a particular function (i.e., the complexity of associations) had a much greater effect on the performance of the analysis method than did the total number of associations. We also found that registration error of 5 mm or less reduces the number of associations discovered by approximately 13% compared to perfect registration. The LDS provides a flexible framework for evaluating many aspects of lesion-deficit analysis.

Non-Linear Relationship between Economic Growth and CO2 Emissions in China: An Empirical Study Based on Panel Smooth Transition Regression Models

PubMed Central

Wang, Zheng-Xin; Hao, Peng; Yao, Pei-Yi

2017-01-01

The non-linear relationship between provincial economic growth and carbon emissions is investigated by using panel smooth transition regression (PSTR) models. The research indicates that, on the condition of separately taking Gross Domestic Product per capita (GDPpc), energy structure (Es), and urbanisation level (Ul) as transition variables, three models all reject the null hypothesis of a linear relationship, i.e., a non-linear relationship exists. The results show that the three models all contain only one transition function but different numbers of location parameters. The model taking GDPpc as the transition variable has two location parameters, while the other two models separately considering Es and Ul as the transition variables both contain one location parameter. The three models applied in the study all favourably describe the non-linear relationship between economic growth and CO2 emissions in China. It also can be seen that the conversion rate of the influence of Ul on per capita CO2 emissions is significantly higher than those of GDPpc and Es on per capita CO2 emissions. PMID:29236083

Non-Linear Relationship between Economic Growth and CO₂ Emissions in China: An Empirical Study Based on Panel Smooth Transition Regression Models.

PubMed

Wang, Zheng-Xin; Hao, Peng; Yao, Pei-Yi

2017-12-13

The non-linear relationship between provincial economic growth and carbon emissions is investigated by using panel smooth transition regression (PSTR) models. The research indicates that, on the condition of separately taking Gross Domestic Product per capita (GDPpc), energy structure (Es), and urbanisation level (Ul) as transition variables, three models all reject the null hypothesis of a linear relationship, i.e., a non-linear relationship exists. The results show that the three models all contain only one transition function but different numbers of location parameters. The model taking GDPpc as the transition variable has two location parameters, while the other two models separately considering Es and Ul as the transition variables both contain one location parameter. The three models applied in the study all favourably describe the non-linear relationship between economic growth and CO₂ emissions in China. It also can be seen that the conversion rate of the influence of Ul on per capita CO₂ emissions is significantly higher than those of GDPpc and Es on per capita CO₂ emissions.

Defining functional distance using manifold embeddings of gene ontology annotations

PubMed Central

Lerman, Gilad; Shakhnovich, Boris E.

2007-01-01

Although rigorous measures of similarity for sequence and structure are now well established, the problem of defining functional relationships has been particularly daunting. Here, we present several manifold embedding techniques to compute distances between Gene Ontology (GO) functional annotations and consequently estimate functional distances between protein domains. To evaluate accuracy, we correlate the functional distance to the well established measures of sequence, structural, and phylogenetic similarities. Finally, we show that manual classification of structures into folds and superfamilies is mirrored by proximity in the newly defined function space. We show how functional distances place structure–function relationships in biological context resulting in insight into divergent and convergent evolution. The methods and results in this paper can be readily generalized and applied to a wide array of biologically relevant investigations, such as accuracy of annotation transference, the relationship between sequence, structure, and function, or coherence of expression modules. PMID:17595300

Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure-property relationship analysis.

PubMed

Watkins, Marquita; Sizochenko, Natalia; Moore, Quentarius; Golebiowski, Marek; Leszczynska, Danuta; Leszczynski, Jerzy

2017-02-01

The presence of chlorophenols in drinking water can be hazardous to human health. Understanding the mechanisms of adsorption under specific experimental conditions would be beneficial when developing methods to remove toxic substances from drinking water during water treatment in order to limit human exposure to these contaminants. In this study, we investigated the sorption of chlorophenols on multi-walled carbon nanotubes using a density functional theory (DFT) approach. This was applied to study selected interactions between six solvents, five types of nanotubes, and six chlorophenols. Experimental data were used to construct structure-adsorption relationship (SAR) models that describe the recovery process. Specific interactions between solvents and chlorophenols were taken into account in the calculations by using novel specific mixture descriptors.

Modeling coding-sequence evolution within the context of residue solvent accessibility.

PubMed

Scherrer, Michael P; Meyer, Austin G; Wilke, Claus O

2012-09-12

Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

Factors Influencing Laboratory Information System Effectiveness Through Strategic Planning in Shiraz Teaching Hospitals.

PubMed

Bahador, Fateme; Sharifian, Roxana; Farhadi, Payam; Jafari, Abdosaleh; Nematolahi, Mohtram; Shokrpour, Nasrin

This study aimed to develop and test a research model that examined 7effective factors on the effectiveness of laboratory information system (LIS) through strategic planning. This research was carried out on total laboratory staff, information technology staff, and laboratory managers in Shiraz (a city in the south of Iran) teaching hospitals by structural equation modeling approach in 2015. The results revealed that there was no significant positive relationship between decisions based on cost-benefit analysis and LIS functionality with LIS effectiveness, but there was a significant positive relationship between other factors and LIS effectiveness. As expected, high levels of strategic information system planning result in increasing LIS effectiveness. The results also showed that the relationship between cost-benefit analysis, LIS functionality, end-user involvement, and information technology-business alignment with strategic information system planning was significant and positive.

Use of an Ecological Model to Study Sexual Satisfaction in a Heterosexual Spanish Sample.

PubMed

Del Mar Sánchez-Fuentes, María; Salinas, José María; Sierra, Juan Carlos

2016-11-01

Sexual satisfaction is a key factor in sexual health and has been associated with quality of life. However, few studies have focused on the factors related to sexual satisfaction in the population in Spain. The main goal of this research was to analyze the predictive capacity of an ecological model for the study of sexual satisfaction in a Spanish sample of 723 men and 851 women, with mean age equal to 36.28 (SD = 12.59) and who were in a heterosexual relationship. We analyzed, using structural equation modeling, the degree to which sexual satisfaction was related to different variables. These variables were the following: personal variables (depression and sexual attitudes); interpersonal variables (relationship satisfaction, sexual function, and sexual assertiveness); social variables (social support, parenthood, and annual income); and cultural variables (political ideology, religion, and religious practice). In men, sexual satisfaction was directly predicted by relationship satisfaction and sexual function. Furthermore, political ideology, religious practice, social support, annual income, initiation sexual assertiveness, and sexual attitudes were indirectly associated with sexual satisfaction. In women, sexual satisfaction was directly predicted by relationship satisfaction, sexual function, sexual assertiveness, and sexual attitudes. In addition, political ideology, religious practice, and social support were indirectly associated with sexual satisfaction. Implications for research and therapy are also discussed.

Phylogenetic profiles reveal structural/functional determinants of TRPC3 signal-sensing antennae

PubMed Central

Ko, Kyung Dae; Bhardwaj, Gaurav; Hong, Yoojin; Chang, Gue Su; Kiselyov, Kirill

2009-01-01

Biochemical assessment of channel structure/function is incredibly challenging. Developing computational tools that provide these data would enable translational research, accelerating mechanistic experimentation for the bench scientist studying ion channels. Starting with the premise that protein sequence encodes information about structure, function and evolution (SF&E), we developed a unified framework for inferring SF&E from sequence information using a knowledge-based approach. The Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST) provides phylogenetic profiles that can model, ab initio, SF&E relationships of biological sequences at the whole protein, single domain and single-amino acid level.1,2 In our recent paper,4 we have applied GDDA-BLAST analysis to study canonical TRP (TRPC) channels1 and empirically validated predicted lipid-binding and trafficking activities contained within the TRPC3 TRP_2 domain of unknown function. Overall, our in silico, in vitro, and in vivo experiments support a model in which TRPC3 has signal-sensing antennae which are adorned with lipid-binding, trafficking and calmodulin regulatory domains. In this Addendum, we correlate our functional domain analysis with the cryo-EM structure of TRPC3.3 In addition, we synthesize recent studies with our new findings to provide a refined model on the mechanism(s) of TRPC3 activation/deactivation. PMID:19704910

Maternal Parenting Stress and Child Perception of Family Functioning Among Families Affected by HIV.

PubMed

Schulte, Marya T; Armistead, Lisa; Marelich, William D; Payne, Diana L; Goodrum, Nada M; Murphy, Debra A

Mothers living with HIV (MLWH) experience stressors inherent to parenting, often within a context characterized by poverty, stigma, and/or limited social support. Our study assessed the relationship between parenting stress and child perceptions of family functioning in families with MLWH who have healthy school-age children. MLWH and their children (N = 102 pairs) completed measures addressing parenting stress and perceptions of family functioning (i.e., parent-child communication, family routines, and family cohesion). We used covariance structural modeling to evaluate the relationship between these factors, with results showing greater maternal parenting stress associated with poorer family functioning outcomes (reported by both the child and the mother). Findings offer support for the parenting stress-family functioning relationship by providing the child perspective along with the maternal perspective, and point to the need for interventions aimed at minimizing the impact of maternal parenting stress on family functioning. Copyright © 2017 Association of Nurses in AIDS Care. Published by Elsevier Inc. All rights reserved.

Structural connectivity allows for multi-threading during rest: the structure of the cortex leads to efficient alternation between resting state exploratory behavior and default mode processing.

PubMed

Senden, Mario; Goebel, Rainer; Deco, Gustavo

2012-05-01

Despite the absence of stimulation or task conditions the cortex exhibits highly structured spatio-temporal activity patterns. These patterns are known as resting state networks (RSNs) and emerge as low-frequency fluctuations (<0.1 Hz) observed in the fMRI signal of human subjects during rest. We are interested in the relationship between structural connectivity of the cortex and the fluctuations exhibited during resting conditions. We are especially interested in the effect of degree of connectivity on resting state dynamics as the default mode network (DMN) is highly connected. We find in experimental resting fMRI data that the DMN is the functional network that is most frequently active and for the longest time. In large-scale computational simulations of the cortex based on the corresponding underlying DTI/DSI based neuroanatomical connectivity matrix, we additionally find a strong correlation between the mean degree of functional networks and the proportion of time they are active. By artificially modifying different types of neuroanatomical connectivity matrices in the model, we were able to demonstrate that only models based on structural connectivity containing hubs give rise to this relationship. We conclude that, during rest, the cortex alternates efficiently between explorations of its externally oriented functional repertoire and internally oriented processing as a consequence of the DMN's high degree of connectivity. Copyright © 2012 Elsevier Inc. All rights reserved.

Flexible link functions in nonparametric binary regression with Gaussian process priors.

PubMed

Li, Dan; Wang, Xia; Lin, Lizhen; Dey, Dipak K

2016-09-01

In many scientific fields, it is a common practice to collect a sequence of 0-1 binary responses from a subject across time, space, or a collection of covariates. Researchers are interested in finding out how the expected binary outcome is related to covariates, and aim at better prediction in the future 0-1 outcomes. Gaussian processes have been widely used to model nonlinear systems; in particular to model the latent structure in a binary regression model allowing nonlinear functional relationship between covariates and the expectation of binary outcomes. A critical issue in modeling binary response data is the appropriate choice of link functions. Commonly adopted link functions such as probit or logit links have fixed skewness and lack the flexibility to allow the data to determine the degree of the skewness. To address this limitation, we propose a flexible binary regression model which combines a generalized extreme value link function with a Gaussian process prior on the latent structure. Bayesian computation is employed in model estimation. Posterior consistency of the resulting posterior distribution is demonstrated. The flexibility and gains of the proposed model are illustrated through detailed simulation studies and two real data examples. Empirical results show that the proposed model outperforms a set of alternative models, which only have either a Gaussian process prior on the latent regression function or a Dirichlet prior on the link function. © 2015, The International Biometric Society.

Flexible Link Functions in Nonparametric Binary Regression with Gaussian Process Priors

PubMed Central

Li, Dan; Lin, Lizhen; Dey, Dipak K.

2015-01-01

Summary In many scientific fields, it is a common practice to collect a sequence of 0-1 binary responses from a subject across time, space, or a collection of covariates. Researchers are interested in finding out how the expected binary outcome is related to covariates, and aim at better prediction in the future 0-1 outcomes. Gaussian processes have been widely used to model nonlinear systems; in particular to model the latent structure in a binary regression model allowing nonlinear functional relationship between covariates and the expectation of binary outcomes. A critical issue in modeling binary response data is the appropriate choice of link functions. Commonly adopted link functions such as probit or logit links have fixed skewness and lack the flexibility to allow the data to determine the degree of the skewness. To address this limitation, we propose a flexible binary regression model which combines a generalized extreme value link function with a Gaussian process prior on the latent structure. Bayesian computation is employed in model estimation. Posterior consistency of the resulting posterior distribution is demonstrated. The flexibility and gains of the proposed model are illustrated through detailed simulation studies and two real data examples. Empirical results show that the proposed model outperforms a set of alternative models, which only have either a Gaussian process prior on the latent regression function or a Dirichlet prior on the link function. PMID:26686333

The power of social networks and social support in promotion of physical activity and body mass index among African American adults.

PubMed

Flórez, Karen R; Richardson, Andrea S; Ghosh-Dastidar, Madhumita Bonnie; Troxel, Wendy; DeSantis, Amy; Colabianchi, Natalie; Dubowitz, Tamara

2018-04-01

Social support and social networks can elucidate important structural and functional aspects of social relationships that are associated with health-promoting behaviors, including Physical Activity (PA) and weight. A growing number of studies have investigated the relationship between social support, social networks, PA and obesity specifically among African Americans; however, the evidence is mixed and many studies focus exclusively on African American women. Most studies have also focused on either functional or structural aspects of social relationships (but not both) and few have objectively measured moderate-to-vigorous physical activity (MVPA) and body mass index (BMI). Cross-sectional surveys of adult African American men and women living in two low-income predominantly African American neighborhoods in Pittsburgh, PA (N = 799) measured numerous structural features as well as functional aspects of social relationships. Specifically, structural features included social isolation, and social network size and diversity. Functional aspects included perceptions of social support for physical activity from the social network in general as well as from family and friends specifically. Height, weight, and PA were objectively measured. From these, we derived Body Mass Index (BMI) and moderate-to-vigorous physical activity (MVPA). All regression models were stratified by gender, and included age, income, education, employment, marital status, physical limitations, and a neighborhood indicator. Greater social isolation was a significant predictor of lower BMI among men only. Among women only, social isolation was significantly associated with increased MVPA whereas, network diversity was significantly associated with reduced MVPA. Future research would benefit from in-depth qualitative investigations to understand how social networks may act to influence different types of physical activity among African Americans, as well as understand how they can be possible levers for health promotion and prevention.

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

ERIC Educational Resources Information Center

Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

2018-01-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

David W. Mulder, Ph.D. | NREL

Science.gov Websites

an emphasis on identifying unique structure-functions relationships and molecular determinates of exploring structure-function relationships of redox metalloenzymes Designated Area Representative of the ]-hydrogenase H-cluster assembly revealed in the structure of HydAΔEFG" Nature (2010) Illustration labeled

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Integrating affective and cognitive correlates of heart rate variability: A structural equation modeling approach

PubMed Central

Mann, Sarah L.; Selby, Edward A.; Bates, Marsha E.; Contrada, Richard J.

2016-01-01

High frequency heart rate variability (HRV) is a measure of neurocardiac communication thought to reflect predominantly parasympathetic cardiac regulation. Low HRV has been associated empirically with clinical and subclinical levels of anxiety and depression and, more recently, high levels of HRV have been associated with better performance on some measures of executive functioning (EF). These findings have offered support for theories proposing HRV as an index measure of a broad, self-regulatory capacity underlying aspects of emotion regulation and executive control. This study sought to test that proposition by using a structural equation modeling approach to examine the relationships of HRV to negative affect (NA) and EF in a large sample of U.S. adults ages 30s–80s. HRV was modeled as a predictor of an NA factor (self-reported trait anxiety and depression symptoms) and an EF factor (performance on three neuropsychological tests tapping facets of executive abilities). Alternative models also were tested to determine the utility of HRV for predicting NA and EF, with and without statistical control of demographic and health-related covariates. In the initial structural model, HRV showed a significant positive relationship to EF and a nonsignificant relationship to NA. In a covariate-adjusted model, HRV’s associations with both constructs were nonsignificant. Age emerged as the only significant predictor of NA and EF in the final model, showing inverse relationships to both. Findings may reflect population and methodological differences from prior research; they also suggest refinements to the interpretations of earlier findings and theoretical claims regarding HRV. PMID:26168884

Religion, kinship and health behaviors of African American women.

PubMed

Coe, Kathryn; Keller, Colleen; Walker, Jenelle R

2015-02-01

A positive relationship exists between functional health and religion. We present an empirical definition of religion and describe the key elements of religious behavior, building a model that can be used to explore the presumed relationship between religion and health. Semi-structured interactive interviews were conducted with 22 participants over a 6-month period. Head Start programs and churches located in the inner city of a large metropolitan area. Twenty-two African American women were aged from 21 to 45. We focus on social relationships and propose that prophet-created religions mimic kinship relationships and encourage kinship-like cooperation between members.

Biochemical changes in bone in a model of weightlessness

NASA Technical Reports Server (NTRS)

Mechanic, Gerald L.

1986-01-01

The amounts of nonmineralized and mineralized collagen in bone from control, immobilized, and immobilized reambulated monkeys were examined. In order to understand structure function relationships of bone collagen and the reponse of a variety of conditions on control of the three dimensional structure of the collagen fibril, the stereochemistry of the cross-linking reactions as well as the stereospecific packing of the collagen molecules were studied.

Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.

PubMed

Zhou, Peng; Wang, Congcong; Tian, Feifei; Ren, Yanrong; Yang, Chao; Huang, Jian

2013-01-01

Quantitative structure-activity relationship (QSAR), a regression modeling methodology that establishes statistical correlation between structure feature and apparent behavior for a series of congeneric molecules quantitatively, has been widely used to evaluate the activity, toxicity and property of various small-molecule compounds such as drugs, toxicants and surfactants. However, it is surprising to see that such useful technique has only very limited applications to biomacromolecules, albeit the solved 3D atom-resolution structures of proteins, nucleic acids and their complexes have accumulated rapidly in past decades. Here, we present a proof-of-concept paradigm for the modeling, prediction and interpretation of the binding affinity of 144 sequence-nonredundant, structure-available and affinity-known protein complexes (Kastritis et al. Protein Sci 20:482-491, 2011) using a biomacromolecular QSAR (BioQSAR) scheme. We demonstrate that the modeling performance and predictive power of BioQSAR are comparable to or even better than that of traditional knowledge-based strategies, mechanism-type methods and empirical scoring algorithms, while BioQSAR possesses certain additional features compared to the traditional methods, such as adaptability, interpretability, deep-validation and high-efficiency. The BioQSAR scheme could be readily modified to infer the biological behavior and functions of other biomacromolecules, if their X-ray crystal structures, NMR conformation assemblies or computationally modeled structures are available.

Methodology to Support Dynamic Function Allocation Policies Between Humans and Flight Deck Automation

NASA Technical Reports Server (NTRS)

Johnson, Eric N.

2012-01-01

Function allocation assigns work functions to all agents in a team, both human and automation. Efforts to guide function allocation systematically have been studied in many fields such as engineering, human factors, team and organization design, management science, cognitive systems engineering. Each field focuses on certain aspects of function allocation, but not all; thus, an independent discussion of each does not address all necessary aspects of function allocation. Four distinctive perspectives have emerged from this comprehensive review of literature on those fields: the technology-centered, human-centered, team-oriented, and work-oriented perspectives. Each perspective focuses on different aspects of function allocation: capabilities and characteristics of agents (automation or human), structure and strategy of a team, and work structure and environment. This report offers eight issues with function allocation that can be used to assess the extent to which each of issues exist on a given function allocation. A modeling framework using formal models and simulation was developed to model work as described by the environment, agents, their inherent dynamics, and relationships among them. Finally, to validate the framework and metrics, a case study modeled four different function allocations between a pilot and flight deck automation during the arrival and approach phases of flight.

Quantitative structure-property relationship (correlation analysis) of phosphonic acid-based chelates in design of MRI contrast agent.

PubMed

Tiwari, Anjani K; Ojha, Himanshu; Kaul, Ankur; Dutta, Anupama; Srivastava, Pooja; Shukla, Gauri; Srivastava, Rakesh; Mishra, Anil K

2009-07-01

Nuclear magnetic resonance imaging is a very useful tool in modern medical diagnostics, especially when gadolinium (III)-based contrast agents are administered to the patient with the aim of increasing the image contrast between normal and diseased tissues. With the use of soft modelling techniques such as quantitative structure-activity relationship/quantitative structure-property relationship after a suitable description of their molecular structure, we have studied a series of phosphonic acid for designing new MRI contrast agent. Quantitative structure-property relationship studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors of the phosphonic acid-based chelating agent and their stability constants. The final quantitative structure-property relationship mathematical models were found as--quantitative structure-property relationship Model for phosphonic acid series (Model 1)--log K(ML) = {5.00243(+/-0.7102)}- MR {0.0263(+/-0.540)}n = 12 l r l = 0.942 s = 0.183 F = 99.165 quantitative structure-property relationship Model for phosphonic acid series (Model 2)--log K(ML) = {5.06280(+/-0.3418)}- MR {0.0252(+/- .198)}n = 12 l r l = 0.956 s = 0.186 F = 99.256.

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates*S⃞

PubMed Central

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej; McAuliffe, Jon D.; Turner, Kevin R.; Di Lullo, Gloria A.; Chen, Steven; Antipova, Olga; Perumal, Shiamalee; Ala-Kokko, Leena; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; Marini, Joan C.; Antonio, James D. San

2008-01-01

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The “cell interaction domain” is proposed to regulate dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The “matrix interaction domain” may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging. PMID:18487200

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The 'cell interaction domain' is proposed to regulatemore » dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The 'matrix interaction domain' may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging.« less

Social relationships and health: the relative roles of family functioning and social support.

PubMed

Franks, P; Campbell, T L; Shields, C G

1992-04-01

The associations between social relationships and health have been examined using two major research traditions. Using a social epidemiological approach, much research has shown the beneficial effect of social supports on health and health behaviors. Family interaction research, which has grown out of a more clinical tradition, has shown the complex effects of family functioning on health, particularly mental health. No studies have examined the relative power of these two approaches in explicating the connections between social relationships and health. We hypothesized that social relationships (social support and family functioning) would exert direct and indirect (through depressive symptoms) effects on health behaviors. We also hypothesized that the effects of social relationships on health would be more powerfully explicated by family functioning than by social support. We mailed a pilot survey to a random sample of patients attending a family practice center, including questions on depressive symptoms, cardiovascular health behaviors, demographics, social support using the ISEL scale, and family functioning using the FEICS scale. FEICS is a self-report questionnaire designed to assess family emotional involvement and criticism, the media elements of family expressed emotion. Eighty-three useable responses were obtained. Regression analyses and structural modelling showed both direct and indirect statistically significant paths from social relationships to health behaviors. Family criticism was directly associated (standardized coefficient = 0.29) with depressive symptoms, and family emotional involvement was directly associated with both depressive symptoms (coefficient = 0.35) and healthy cardiovascular behaviors (coefficient = 0.32). The results support the primacy of family functioning factors in understanding the associations among social relationships, mental health, and health behaviors. The contrasting relationships between emotional involvement and depressive symptoms on the one hand and emotional involvement and health behaviors on the other suggest the need for a more complex model to understand the connections between social relationships and health.

What can volumes reveal about human brain evolution? A framework for bridging behavioral, histometric, and volumetric perspectives

PubMed Central

de Sousa, Alexandra A.; Proulx, Michael J.

2014-01-01

An overall relationship between brain size and cognitive ability exists across primates. Can more specific information about neural function be gleaned from cortical area volumes? Numerous studies have found significant relationships between brain structures and behaviors. However, few studies have speculated about brain structure-function relationships from the microanatomical to the macroanatomical level. Here we address this problem in comparative neuroanatomy, where the functional relevance of overall brain size and the sizes of cortical regions have been poorly understood, by considering comparative psychology, with measures of visual acuity and the perception of visual illusions. We outline a model where the macroscopic size (volume or surface area) of a cortical region (such as the primary visual cortex, V1) is related to the microstructure of discrete brain regions. The hypothesis developed here is that an absolutely larger V1 can process more information with greater fidelity due to having more neurons to represent a field of space. This is the first time that the necessary comparative neuroanatomical research at the microstructural level has been brought to bear on the issue. The evidence suggests that as the size of V1 increases: the number of neurons increases, the neuron density decreases, and the density of neuronal connections increases. Thus, we describe how information about gross neuromorphology, using V1 as a model for the study of other cortical areas, may permit interpretations of cortical function. PMID:25009469

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions.

PubMed

Kohn, Kathryn P; Underwood, Sonia M; Cooper, Melanie M

2018-06-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively. Fourteen university students concurrently enrolled in introductory chemistry and biology courses were interviewed to explore their perceptions regarding 1) the meaning of structure, properties, and function; 2) the presentation of these concepts in their courses; and 3) how these concepts might be related. Findings suggest that the concepts of structure and properties were interpreted similarly between chemistry and biology, but students more closely associated the discussion of structure-property relationships with their chemistry courses and structure-function with biology. Despite receiving little in the way of instructional support, nine students proposed a coherent conceptual relationship, indicating that structure determines properties, which determine function. Furthermore, students described ways in which they connected and benefited from their understanding. Though many students are prepared to make these connections, we would encourage instructors to engage in cross-disciplinary conversations to understand the shared goals and disciplinary distinctions regarding these important concepts in an effort to better support students unable to construct these connections for themselves.

Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

NASA Astrophysics Data System (ADS)

Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

2001-12-01

Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

The Cajal body and the nucleolus: "In a relationship" or "It's complicated"?

PubMed

Trinkle-Mulcahy, Laura; Sleeman, Judith E

2017-06-03

From their initial identification as 'nucleolar accessory bodies' more than a century ago, the relationship between Cajal bodies and nucleoli has been a subject of interest and controversy. In this review, we seek to place recent developments in the understanding of the physical and functional relationships between the 2 structures in the context of historical observations. Biophysical models of nuclear body formation, the molecular nature of CB/nucleolus interactions and the increasing list of joint roles for CBs and nucleoli, predominantly in assembling ribonucleoprotein (RNP) complexes, are discussed.

Computational biomechanics changes our view on insect head evolution.

PubMed

Blanke, Alexander; Watson, Peter J; Holbrey, Richard; Fagan, Michael J

2017-02-08

Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to objectively identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution. © 2017 The Author(s).

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

PubMed Central

Cai, Yizhi; Lux, Matthew W.; Adam, Laura; Peccoud, Jean

2009-01-01

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology. PMID:19816554

Applied Computational Chemistry for the Blind and Visually Impaired

ERIC Educational Resources Information Center

Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

2012-01-01

We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

PubMed

Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

2009-06-01

The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

Pathways between profiles of family functioning, child security in the interparental subsystem, and child psychological problems.

PubMed

Davies, Patrick T; Cummings, E Mark; Winter, Marcia A

2004-01-01

This study was designed to delineate pathways between systems profiles of family functioning, children's emotional insecurity in the interparental relationship, and their psychological adjustment in a sample of 221 children and their parents. Consistent with family systems theory, cluster analyses conducted with assessments of marital, coparental, and parent-child functioning indicated that families fit into one of four profiles: (a) cohesive families, characterized by warmth, affection, and flexible well-defined boundaries in family relationships; (b) disengaged families, reflected in high levels of adversity and low levels of support across family subsystems; (c) enmeshed families, evidenced by high levels of discord and weak maintenance of relationship boundaries in the family unit; and (d) adequate families, defined by elevated parental psychological control within a larger family context of low discord and high warmth. In comparison to children in cohesive families, children in enmeshed and disengaged families exhibited greater signs of insecurity in the interparental relationship concurrently and internalizing and externalizing symptoms both concurrently and 1 year later. Structural equation models revealed that a latent, multimethod measure of insecurity in the interparental relationship partially mediated associations between family enmeshment and disengagement and children's psychological symptoms 1 year later. Results are discussed in relation to how they inform and refine a family-wide model of the emotional security hypothesis.

Spiders in Motion: Demonstrating Adaptation, Structure-Function Relationships, and Trade-Offs in Invertebrates

ERIC Educational Resources Information Center

Bowlin, Melissa S.; McLeer, Dorothy F.; Danielson-Francois, Anne M.

2014-01-01

Evolutionary history and structural considerations constrain all aspects of animal physiology. Constraints on invertebrate locomotion are especially straightforward for students to observe and understand. In this exercise, students use spiders to investigate the concepts of adaptation, structure-function relationships, and trade-offs. Students…

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study

PubMed Central

Raethong, Nachon; Wong-ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa

2016-01-01

Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction. PMID:27274991

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study.

PubMed

Raethong, Nachon; Wong-Ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa

2016-01-01

Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H(+)-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.

Structure of marginally jammed polydisperse packings of frictionless spheres

NASA Astrophysics Data System (ADS)

Zhang, Chi; O'Donovan, Cathal B.; Corwin, Eric I.; Cardinaux, Frédéric; Mason, Thomas G.; Möbius, Matthias E.; Scheffold, Frank

2015-03-01

We model the packing structure of a marginally jammed bulk ensemble of polydisperse spheres. To this end we expand on the granocentric model [Clusel et al., Nature (London) 460, 611 (2009), 10.1038/nature08158], explicitly taking into account rattlers. This leads to a relationship between the characteristic parameters of the packing, such as the mean number of neighbors and the fraction of rattlers, and the radial distribution function g (r ) . We find excellent agreement between the model predictions for g (r ) and packing simulations, as well as experiments on jammed emulsion droplets. The observed quantitative agreement opens the path towards a full structural characterization of jammed particle systems for imaging and scattering experiments.

Phytoplankton Pigment Communities Can be Modeled Using Unique Relationships With Spectral Absorption Signatures in a Dynamic Coastal Environment

NASA Astrophysics Data System (ADS)

Catlett, D.; Siegel, D. A.

2018-01-01

Understanding the roles of phytoplankton community composition in the functioning of marine ecosystems and ocean biogeochemical cycles is important for many ocean science problems of societal relevance. Remote sensing currently offers the only feasible method for continuously assessing phytoplankton community structure on regional to global scales. However, methods are presently hindered by the limited spectral resolution of most satellite sensors and by uncertainties associated with deriving quantitative indices of phytoplankton community structure from phytoplankton pigment concentrations. Here we analyze a data set of concurrent phytoplankton pigment concentrations and phytoplankton absorption coefficient spectra from the Santa Barbara Channel, California, to develop novel optical oceanographic models for retrieving metrics of phytoplankton community composition. Cluster and Empirical Orthogonal Function analyses of phytoplankton pigment concentrations are used to define up to five phytoplankton pigment communities as a representation of phytoplankton functional types. Unique statistical relationships are found between phytoplankton pigment communities and absorption features isolated using spectral derivative analysis and are the basis of predictive models. Model performance is substantially better for phytoplankton pigment community indices compared with determinations of the contributions of individual pigments or taxa to chlorophyll a. These results highlight the application of data-driven chemotaxonomic approaches for developing and validating bio-optical algorithms and illustrate the potential and limitations for retrieving phytoplankton community composition from hyperspectral satellite ocean color observations.

Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

Advances in Homology Protein Structure Modeling

PubMed Central

Xiang, Zhexin

2007-01-01

Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function. PMID:16787261

Examination of the Positive and Negative Syndrome Scale factor structure and longitudinal relationships with functioning in early psychosis.

PubMed

Best, Michael W; Grossman, Michael; Oyewumi, L Kola; Bowie, Christopher R

2016-04-01

We examined the factor structure of the Positive and Negative Syndrome Scale (PANSS) in early-episode psychosis and its relationships with functioning at baseline and follow-up. A total of 240 consecutive admissions to an early intervention in psychosis clinic were assessed at intake to the program with the PANSS, Global Assessment of Functioning (GAF) and Social and Occupational Functioning Assessment Scale (SOFAS). Seventy individuals were reassessed at follow-up. A maximum likelihood factor analysis was conducted on baseline PANSS scores and the ability of each factor to predict baseline and follow-up GAF and SOFAS was examined. A five-factor model with varimax rotation was the best fit to our data and was largely congruent with factors found previously. The negative symptom factor was the best predictor of GAF and SOFAS at baseline and follow-up. Negative symptoms are the best symptomatic predictor of functioning in individuals with early psychosis and are an important treatment target to improve recovery. © 2014 Wiley Publishing Asia Pty Ltd.

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks.

PubMed

Honegger, Thibault; Thielen, Moritz I; Feizi, Soheil; Sanjana, Neville E; Voldman, Joel

2016-06-22

The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry.

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

NASA Astrophysics Data System (ADS)

Honegger, Thibault; Thielen, Moritz I.; Feizi, Soheil; Sanjana, Neville E.; Voldman, Joel

2016-06-01

The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry.

Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.; Spiteller, Michael

2012-09-01

A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

Consumer and case manager perspectives of service empowerment: relationship to mental health recovery.

PubMed

Crane-Ross, Dushka; Lutz, Wilma J; Roth, Dee

2006-04-01

This study examines the relationship between service empowerment and recovery. Service empowerment is defined as the extent to which consumers participate in service decisions and the level of reciprocity and respect within the relationship with their case managers. Assessments were made from two perspectives: consumers and their case managers. Structural equation models were developed to examine the direct and indirect effects of service empowerment on four recovery outcomes: Quality of Life, Level of Functioning, Consumer-Reported Symptomatology, and Case Manager-Reported Symptomatology. Consumers' perceptions of service empowerment were the most powerful predictor of recovery outcomes across the four models. Consumers' and case managers' perceptions were related but the magnitude of the relationship was small, indicating that considerable differences exist between their perceptions of service empowerment.

Obesity and Aging: Consequences for Cognition, Brain Structure, and Brain Function.

PubMed

Bischof, Gérard N; Park, Denise C

2015-01-01

This review focuses on the relationship between obesity and aging and how these interact to affect cognitive function. The topics covered are guided by the Scaffolding Theory of Aging and Cognition (STAC [Park and Reuter-Lorenz. Annu Rev Psychol 2009;60:173-96]-a conceptual model designed to relate brain structure and function to one's level of cognitive ability. The initial literature search was focused on normal aging and was guided by the key words, "aging, cognition, and obesity" in PubMed. In a second search, we added key words related to neuropathology including words "Alzheimer's disease," "vascular dementia," and "mild cognitive impairment." The data suggest that being overweight or obese in midlife may be more detrimental to subsequent age-related cognitive decline than being overweight or obese at later stages of the life span. These effects are likely mediated by the accelerated effects obesity has on the integrity of neural structures, including both gray and white matter. Further epidemiological studies have provided evidence that obesity in midlife is linked to an increased risk for Alzheimer's disease and vascular dementia, most likely via an increased accumulation of Alzheimer's disease pathology. Although it is clear that obesity negatively affects cognition, more work is needed to better understand how aging plays a role and how brain structure and brain function might mediate the relationship of obesity and age on cognition. Guided by the STAC and the STAC-R models, we provide a roadmap for future investigations of the role of obesity on cognition across the life span.

Obesity and Aging: Consequences for Cognition, Brain Structure and Brain Function

PubMed Central

Bischof, Gérard N.; Park, Denise C.

2017-01-01

Objective This review focuses on the relationship between obesity and aging and how these interact together to affect cognitive function. The topics covered are guided by the Scaffolding Theory of Aging and Cognition (STAC; Park & Reuter-Lorenz, 2009—a conceptual model designed to relate brain structure and function to one’s level of cognitive ability. Methods The initial literature search was focused on normal aging and was guided by the key words, “aging, cognition, and obesity” in “PUBMED”. In a second search we added key words related to neuropathology including words “Alzheimer’s Disease”, “Vascular dementia” (VaD) and “Mild Cognitive Impairment” (MCI). Results The data suggest that being overweight or obese in midlife may be more detrimental to subsequent age-related cognitive decline than being overweight or obese at later stages of the lifespan. These effects are likely mediated by the accelerated effects obesity has on the integrity of neural structures, including both gray and white matter. Further epidemiological studies have provided evidence that obesity in mid-life is linked to an increased risk for AD and VaD, most likely via an increased accumulation of AD pathology. Conclusion While it is clear that obesity negatively affects cognition, more work is needed to better understand how aging plays a role and how brain structure and brain function might mediate the relationship of obesity and age on cognition. Guided by the STAC and the STAC-R models, we provide a roadmap for future investigations of the role of obesity on cognition across the lifespan. PMID:26107577

Parent-Reported Behavioral and Psychiatric Problems Mediate the Relationship between Sleep-Disordered Breathing and Cognitive Deficits in School-Aged Children.

PubMed

Smith, Dale L; Gozal, David; Hunter, Scott J; Kheirandish-Gozal, Leila

2017-01-01

Numerous studies over the past several decades have illustrated that children who suffer from sleep-disordered breathing (SDB) are at greater risk for cognitive, behavioral, and psychiatric problems. Although behavioral problems have been proposed as a potential mediator between SDB and cognitive functioning, these relationships have not been critically examined. This analysis is based on a community-based cohort of 1,115 children who underwent overnight polysomnography, and cognitive and behavioral phenotyping. Structural model of the relationships between SDB, behavior, and cognition, and two recently developed mediation approaches based on propensity score weighting and resampling were used to assess the mediational role of parent-reported behavior and psychiatric problems in the relationship between SDB and cognitive functioning. Multiple models utilizing two different SDB definitions further explored direct effects of SDB on cognition as well as indirect effects through behavioral pathology. All models were adjusted for age, sex, race, BMI z -score, and asthma status. Indirect effects of SDB through behavior problems were significant in all mediation models, while direct effects of SDB on cognition were not. The findings were consistent across different mediation procedures and remained essentially unaltered when different criteria for SDB, behavior, and cognition were used. Potential effects of SDB on cognitive functioning appear to occur through behavioral problems that are detectable in this pediatric population. Thus, early attentional or behavioral pathology may be implicated in the cognitive functioning deficits associated with SDB, and may present an early morbidity-related susceptibility biomarker.

Perceived Discrimination and Social Relationship Functioning among Sexual Minorities: Structural Stigma as a Moderating Factor

PubMed Central

Doyle, David Matthew; Molix, Lisa

2015-01-01

Work on structural stigma shows how public policy affects health outcomes for members of devalued groups, including sexual minorities. In the current research, structural stigma is proposed as a moderating variable that strengthens deleterious associations between perceived discrimination and social relationship functioning. Hypotheses were tested in two cross-sectional studies, including both online (N = 214; Study 1) and community (N = 94; Study 2) samples of sexual minority men and women residing throughout the United States. Structural stigma was coded from policy related to sexual minority rights within each state. Confirming hypotheses, support for the moderating role of structural stigma was found via multilevel models across studies. Specifically, associations between perceived discrimination and friendship strain, loneliness (Study 1) and familial strain (Study 2) were increased for those who resided in states with greater levels of structural stigma and attenuated for those who resided in states with lesser levels. In Study 1, these results were robust to state-level covariates (conservatism and religiosity), but conservatism emerged as a significant moderator in lieu of structural stigma in Study 2. Results are discussed in the context of the shifting landscape of public policy related to sexual minority rights within the United States. PMID:26807046

Development of a stock-recruitment model and assessment of biological reference points for the Lake Erie walleye fishery

USGS Publications Warehouse

Zhao, Yingming; Kocovsky, Patrick M.; Madenjian, Charles P.

2013-01-01

We developed an updated stock–recruitment relationship for Lake Erie Walleye Sander vitreus using the Akaike information criterion model selection approach. Our best stock–recruitment relationship was a Ricker spawner–recruit function to which spring warming rate was added as an environmental variable, and this regression model explained 39% of the variability in Walleye recruitment over the 1978 through 2006 year-classes. Thus, most of the variability in Lake Erie Walleye recruitment appeared to be attributable to factors other than spawning stock size and spring warming rate. The abundance of age-0 Gizzard Shad Dorosoma cepedianum, which was an important term in previous models, may still be an important factor for Walleye recruitment, but poorer ability to monitor Gizzard Shad since the late 1990s could have led to that term failing to appear in our best model. Secondly, we used numerical simulation to demonstrate how to use the stock recruitment relationship to characterize the population dynamics (such as stable age structure, carrying capacity, and maximum sustainable yield) and some biological reference points (such as fishing rates at different important biomass or harvest levels) for an age-structured population in a deterministic way.

Quantitative structure-activity relationships studies of CCR5 inhibitors and toxicity of aromatic compounds using gene expression programming.

PubMed

Shi, Weimin; Zhang, Xiaoya; Shen, Qi

2010-01-01

Quantitative structure-activity relationship (QSAR) study of chemokine receptor 5 (CCR5) binding affinity of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas and toxicity of aromatic compounds have been performed. The gene expression programming (GEP) was used to select variables and produce nonlinear QSAR models simultaneously using the selected variables. In our GEP implementation, a simple and convenient method was proposed to infer the K-expression from the number of arguments of the function in a gene, without building the expression tree. The results were compared to those obtained by artificial neural network (ANN) and support vector machine (SVM). It has been demonstrated that the GEP is a useful tool for QSAR modeling. Copyright 2009 Elsevier Masson SAS. All rights reserved.

Gene function prediction based on the Gene Ontology hierarchical structure.

PubMed

Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

2014-01-01

The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

The interface of protein structure, protein biophysics, and molecular evolution

PubMed Central

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

The Relationships Between Functional Limitation, Depression, Suicidal Ideation, and Coping in Older Korean Immigrants.

PubMed

Ahn, Joonhee; Kim, Bum Jung

2015-12-01

Older adults with functional limitations may be at higher risk for depression and suicidal ideation compared to their counterparts without such limits. This study examined the structural relationships between functional limitation, depression, suicidal ideation, and coping strategies in older Korean immigrants. Using data from 220 community dwelling Korean immigrants (age ≧ 65) in Los Angeles County, path analysis was conducted to test the study hypotheses. The resulting model accounted for 56% of the variance in suicidal ideation, with functional limitation making significant contribution to suicidal ideation. Meanwhile, depression, which had the strongest direct effects on suicidal ideation, also played a significant role in mediating between functional limitation and suicidal ideation. Furthermore, adaptive coping was significantly associated with both functional limitation and suicidal ideation. Findings provide implications for implementing suicide-prevention programs for older Korean immigrants, especially those living with functional disability.

Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elrod, D.W.

1992-01-01

Computational neural networks (CNNs) are a computational paradigm inspired by the brain's massively parallel network of highly interconnected neurons. The power of computational neural networks derives not so much from their ability to model the brain as from their ability to learn by example and to map highly complex, nonlinear functions, without the need to explicitly specify the functional relationship. Two central questions about CNNs were investigated in the context of predicting chemical reactions: (1) the mapping properties of neural networks and (2) the representation of chemical information for use in CNNs. Chemical reactivity is here considered an example ofmore » a complex, nonlinear function of molecular structure. CNN's were trained using modifications of the back propagation learning rule to map a three dimensional response surface similar to those typically observed in quantitative structure-activity and structure-property relationships. The computational neural network's mapping of the response surface was found to be robust to the effects of training sample size, noisy data and intercorrelated input variables. The investigation of chemical structure representation led to the development of a molecular structure-based connection-table representation suitable for neural network training. An extension of this work led to a BE-matrix structure representation that was found to be general for several classes of reactions. The CNN prediction of chemical reactivity and regiochemistry was investigated for electrophilic aromatic substitution reactions, Markovnikov addition to alkenes, Saytzeff elimination from haloalkanes, Diels-Alder cycloaddition, and retro Diels-Alder ring opening reactions using these connectivity-matrix derived representations. The reaction predictions made by the CNNs were more accurate than those of an expert system and were comparable to predictions made by chemists.« less

Geometry and Function Definition for Discrete Analysis and Its Relationship to the Design Data Base.

DTIC Science & Technology

1977-08-01

clarif y its dependenc e on the design process as a whole . The model generation capabilities of a state—of—the—art structural analysis system ( GIFTS ...a whole. The model generat ion capabilit ies of a state—of—the—art structural analysis system ( GIFTS 4), heav ily oriented toward s pre— and post...independentl y at a later stage. Ii . 1,1 ~1E TP IC HIER.ARCHY ~)F DEFINITION IN GIFTS ‘+ A three-d imensional object , to be designed or analyz ed

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers.

PubMed

Da, Yang

2015-12-18

The amount of functional genomic information has been growing rapidly but remains largely unused in genomic selection. Genomic prediction and estimation using haplotypes in genome regions with functional elements such as all genes of the genome can be an approach to integrate functional and structural genomic information for genomic selection. Towards this goal, this article develops a new haplotype approach for genomic prediction and estimation. A multi-allelic haplotype model treating each haplotype as an 'allele' was developed for genomic prediction and estimation based on the partition of a multi-allelic genotypic value into additive and dominance values. Each additive value is expressed as a function of h - 1 additive effects, where h = number of alleles or haplotypes, and each dominance value is expressed as a function of h(h - 1)/2 dominance effects. For a sample of q individuals, the limit number of effects is 2q - 1 for additive effects and is the number of heterozygous genotypes for dominance effects. Additive values are factorized as a product between the additive model matrix and the h - 1 additive effects, and dominance values are factorized as a product between the dominance model matrix and the h(h - 1)/2 dominance effects. Genomic additive relationship matrix is defined as a function of the haplotype model matrix for additive effects, and genomic dominance relationship matrix is defined as a function of the haplotype model matrix for dominance effects. Based on these results, a mixed model implementation for genomic prediction and variance component estimation that jointly use haplotypes and single markers is established, including two computing strategies for genomic prediction and variance component estimation with identical results. The multi-allelic genetic partition fills a theoretical gap in genetic partition by providing general formulations for partitioning multi-allelic genotypic values and provides a haplotype method based on the quantitative genetics model towards the utilization of functional and structural genomic information for genomic prediction and estimation.

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecul...

An Undergraduate Laboratory Activity on Molecular Dynamics Simulations

ERIC Educational Resources Information Center

Spitznagel, Benjamin; Pritchett, Paige R.; Messina, Troy C.; Goadrich, Mark; Rodriguez, Juan

2016-01-01

Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we…

Parental Problem Drinking and Adolescent Externalizing Behaviors: The Mediating Role of Family Functioning

PubMed Central

Schulz, Jessica; Gordon, Mellissa S.; Ohannessian, Christine McCauley

2015-01-01

This study explored relationships among parental problem drinking, family functioning, and adolescent externalizing behaviors. The unique effects of maternal and paternal drinking were examined separately for girls and boys. The sample included 14-19 year old U.S. adolescents (Mage=16.15; SD=.75; 52.5% female) and their parents. Participants completed surveys in the spring of 2007 and 2008. Structural equation modelling was used to conduct path analysis models. Results showed the distinctive and adverse effects of parental problem drinking on adolescent alcohol use, drug use, rule breaking, and aggressive behavior over time. Findings also highlighted the indirect and mediating roles of family functioning. For both girls and boys, family cohesion mediated the relationship between parental problem drinking and adolescent externalizing behaviors. For girls, adolescent-father communication predicted increased externalizing behaviors over time. These findings draw attention to the importance of exploring adolescent and parent gender when examining parental problem drinking, family functioning, and externalizing behaviors. PMID:26073673

Proposal of a socio-cognitive-behavioral structural equation model of internalized stigma in people with severe and persistent mental illness.

PubMed

Muñoz, Manuel; Sanz, María; Pérez-Santos, Eloísa; Quiroga, María de Los Ángeles

2011-04-30

The social stigma of mental illness has received much attention in recent years and its effects on diverse variables such as psychiatric symptoms, social functioning, self-esteem, self-efficacy, quality of life, and social integration are well established. However, internalized stigma in people with severe and persistent mental illness has not received the same attention. The aim of the present work was to study the relationships between the principal variables involved in the functioning of internalized stigma (sociodemographic and clinical variables, social stigma, psychosocial functioning, recovery expectations, empowerment, and discrimination experiences) in a sample of people with severe and persistent mental illness (N=108). The main characteristics of the sample and the differences between groups with high and low internalized stigma were analyzed, a correlation analysis of the variables was performed, and a structural equation model, integrating variables of social, cognitive, and behavioral content, was proposed and tested. The results indicate the relationships among social stigma, discrimination experiences, recovery expectation, and internalized stigma and their role in the psychosocial and behavioral outcomes in schizophrenia spectrum disorders. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Relationship between Scanning Laser Polarimetry with Enhanced Corneal Compensation and with Variable Corneal Compensation

PubMed Central

Kim, Kyung Hoon; Choi, Jaewan; Lee, Chang Hwan; Cho, Beom-Jin; Kook, Michael S.

2008-01-01

Purpose To evaluate the structure-function relationships between retinal sensitivity measured by Humphrey visual field analyzer (HVFA) and the retinal nerve fiber layer (RNFL) thickness measured by scanning laser polarimetry (SLP) with variable corneal compensation (VCC) and enhanced corneal compensation (ECC) in glaucomatous and healthy eyes. Methods Fifty-three eyes with an atypical birefringence pattern (ABP) based on SLP-VCC (28 glaucomatous eyes and 25 normal healthy eyes) were enrolled in this cross-sectional study. RNFL thickness was measured by both VCC and ECC techniques, and the visual field was examined by HVFA with 24-2 full-threshold program. The relationships between RNFL measurements in superior and inferior sectors and corresponding retinal mean sensitivity were sought globally and regionally with linear regression analysis in each group. Coefficients of the determination were calculated and compared between VCC and ECC techniques. Results In eyes with ABP, R2 values for the association between SLP parameters and retinal sensitivity were 0.06-0.16 with VCC, whereas they were 0.21-0.48 with ECC. The association of RNFL thickness with retinal sensitivity was significantly better with ECC than with VCC in 5 out of 8 regression models between SLP parameters and HVF parameters (P<0.05). Conclusions The strength of the structure-function association was higher with ECC than with VCC in eyes with ABP, which suggests that the ECC algorithm is a better approach for evaluating the structure-function relationship in eyes with ABP. PMID:18323701

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

PubMed

Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

2017-04-15

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Impact of airway morphological changes on pulmonary flows in scoliosis

NASA Astrophysics Data System (ADS)

Farrell, James; Garrido, Enrique; Valluri, Prashant

2016-11-01

The relationship between thoracic deformity in scoliosis and lung function is poorly understood. In a pilot study, we reviewed computed tomography (CT) routine scans of patients undergoing scoliosis surgery. The CT scans were processed to segment the anatomy of the airways, lung and spine. A three-dimensional model was created to study the anatomical relationship. Preliminary analysis showed significant airway morphological differences depending on the anterior position of the spine. A computational fluid dynamics (CFD) study was also conducted on the airway geometry using the inspiratory scans. The CFD model assuming non-compliant airway walls was capable of showing pressure drops in areas of high airway resistance, but was unable to predict regional ventilation differences. Our results indicate a dependence between the dynamic deformation of the airway during breathing and lung function. Dynamic structural deformation must therefore be incorporated within any modelling approaches to guide clinicians on the decision to perform surgical correction of the scoliosis.

Design, Fabrication, Characterization and Modeling of Integrated Functional Materials

DTIC Science & Technology

2010-10-19

ribbons: A relationship between the soft magnetic properties and GMI effect has been established in Co69Fe4.5R1.5Si10B15 (R = Ni, Al , Cr) amorphous... deposition . A strain compression-relaxation mechanism has been proposed in order to explain the structure- property relationships in the CFO-PZT bilayer...being pursued. The new Laser Assisted Spray process chamber for co- deposition of QDs and polymer films is shown in Fig. 55. Fig. 55

Relationships between cortical myeloarchitecture and electrophysiological networks

PubMed Central

Hunt, Benjamin A. E.; Tewarie, Prejaas K.; Mougin, Olivier E.; Geades, Nicolas; Singh, Krish D.; Morris, Peter G.; Gowland, Penny A.; Brookes, Matthew J.

2016-01-01

The human brain relies upon the dynamic formation and dissolution of a hierarchy of functional networks to support ongoing cognition. However, how functional connectivities underlying such networks are supported by cortical microstructure remains poorly understood. Recent animal work has demonstrated that electrical activity promotes myelination. Inspired by this, we test a hypothesis that gray-matter myelin is related to electrophysiological connectivity. Using ultra-high field MRI and the principle of structural covariance, we derive a structural network showing how myelin density differs across cortical regions and how separate regions can exhibit similar myeloarchitecture. Building upon recent evidence that neural oscillations mediate connectivity, we use magnetoencephalography to elucidate networks that represent the major electrophysiological pathways of communication in the brain. Finally, we show that a significant relationship exists between our functional and structural networks; this relationship differs as a function of neural oscillatory frequency and becomes stronger when integrating oscillations over frequency bands. Our study sheds light on the way in which cortical microstructure supports functional networks. Further, it paves the way for future investigations of the gray-matter structure/function relationship and its breakdown in pathology. PMID:27830650

The Relationship between Maternal Nutrition during Pregnancy and Offspring Kidney Structure and Function in Humans: A Systematic Review

PubMed Central

Lee, Yu Qi; Collins, Clare E.; Gordon, Adrienne; Rae, Kym M.; Pringle, Kirsty G.

2018-01-01

The intrauterine environment is critical for fetal growth and organ development. Evidence from animal models indicates that the developing kidney is vulnerable to suboptimal maternal nutrition and changes in health status. However, evidence from human studies are yet to be synthesised. Therefore, the aim of the current study was to systematically review current research on the relationship between maternal nutrition during pregnancy and offspring kidney structure and function in humans. A search of five databases identified 9501 articles, of which three experimental and seven observational studies met the inclusion criteria. Nutrients reviewed to date included vitamin A (n = 3), folate and vitamin B12 (n = 2), iron (n = 1), vitamin D (n = 1), total energy (n = 2) and protein (n = 1). Seven studies were assessed as being of “positive” and three of “neutral” quality. A variety of populations were studied, with limited studies investigating maternal nutrition during pregnancy, while measurements of offspring kidney outcomes were diverse across studies. There was a lack of consistency in the timing of follow-up for offspring kidney structure and/or function assessments, thus limiting comparability between studies. Deficiencies in maternal folate, vitamin A, and total energy during pregnancy were associated with detrimental impacts on kidney structure and function, measured by kidney volume, proteinuria, eGFRcystC and mean creatinine clearance in the offspring. Additional experimental and longitudinal prospective studies are warranted to confirm this relationship, especially in Indigenous populations where the risk of renal disease is greater. PMID:29466283

Validity of semi-quantitative scale for brain MRI in unilateral cerebral palsy due to periventricular white matter lesions: Relationship with hand sensorimotor function and structural connectivity.

PubMed

Fiori, Simona; Guzzetta, Andrea; Pannek, Kerstin; Ware, Robert S; Rossi, Giuseppe; Klingels, Katrijn; Feys, Hilde; Coulthard, Alan; Cioni, Giovanni; Rose, Stephen; Boyd, Roslyn N

2015-01-01

To provide first evidence of construct validity of a semi-quantitative scale for brain structural MRI (sqMRI scale) in children with unilateral cerebral palsy (UCP) secondary to periventricular white matter (PWM) lesions, by examining the relationship with hand sensorimotor function and whole brain structural connectivity. Cross-sectional study of 50 children with UCP due to PWM lesions using 3 T (MRI), diffusion MRI and assessment of hand sensorimotor function. We explored the relationship of lobar, hemispheric and global scores on the sqMRI scale, with fractional anisotropy (FA), as a measure of brain white matter microstructure, and with hand sensorimotor measures (Assisting Hand Assessment, AHA; Jebsen-Taylor Test for Hand Function, JTTHF; Melbourne Assessment of Unilateral Upper Limb Function, MUUL; stereognosis; 2-point discrimination). Lobar and hemispheric scores on the sqMRI scale contralateral to the clinical side of hemiplegia correlated with sensorimotor paretic hand function measures and FA of a number of brain structural connections, including connections of brain areas involved in motor control (postcentral, precentral and paracentral gyri in the parietal lobe). More severe lesions correlated with lower sensorimotor performance, with the posterior limb of internal capsule score being the strongest contributor to impaired hand function. The sqMRI scale demonstrates first evidence of construct validity against impaired motor and sensory function measures and brain structural connectivity in a cohort of children with UCP due to PWM lesions. More severe lesions correlated with poorer paretic hand sensorimotor function and impaired structural connectivity in the hemisphere contralateral to the clinical side of hemiplegia. The quantitative structural MRI scoring may be a useful clinical tool for studying brain structure-function relationships but requires further validation in other populations of CP.

Annual grass invasion in sagebrush-steppe: The relative importance of climate, soil properties and biotic interactions

USGS Publications Warehouse

Bansal, Sheel; Sheley, Roger L.

2016-01-01

The invasion by winter-annual grasses (AGs) such as Bromus tectorum into sagebrush steppe throughout the western USA is a classic example of a biological invasion with multiple, interacting climate, soil and biotic factors driving the invasion, although few studies have examined all components together. Across a 6000-km2 area of the northern Great Basin, we conducted a field assessment of 100 climate, soil, and biotic (functional group abundances, diversity) factors at each of 90 sites that spanned an invasion gradient ranging from 0 to 100 % AG cover. We first determined which biotic and abiotic factors had the strongest correlative relationships with AGs and each resident functional group. We then used regression and structural equation modeling to explore how multiple ecological factors interact to influence AG abundance. Among biotic interactions, we observed negative relationships between AGs and biodiversity, perennial grass cover, resident species richness, biological soil crust cover and shrub density, whereas perennial and annual forb cover, tree cover and soil microbial biomass had no direct linkage to AG. Among abiotic factors, AG cover was strongly related to climate (increasing cover with increasing temperature and aridity), but had weak relationships with soil factors. Our structural equation model showed negative effects of perennial grasses and biodiversity on AG cover while integrating the negative effects of warmer climate and positive influence of belowground processes on resident functional groups. Our findings illustrate the relative importance of biotic interactions and climate on invasive abundance, while soil properties appear to have stronger relationships with resident biota than with invasives.

A structural equation modeling of executive functions, IQ and mathematical skills in primary students: Differential effects on number production, mental calculus and arithmetical problems.

PubMed

Arán Filippetti, Vanessa; Richaud, María Cristina

2017-10-01

Though the relationship between executive functions (EFs) and mathematical skills has been well documented, little is known about how both EFs and IQ differentially support diverse math domains in primary students. Inconsistency of results may be due to the statistical techniques employed, specifically, if the analysis is conducted with observed variables, i.e., regression analysis, or at the latent level, i.e., structural equation modeling (SEM). The current study explores the contribution of both EFs and IQ in mathematics through an SEM approach. A total of 118 8- to 12-year-olds were administered measures of EFs, crystallized (Gc) and fluid (Gf) intelligence, and math abilities (i.e., number production, mental calculus and arithmetical problem-solving). Confirmatory factor analysis (CFA) offered support for the three-factor solution of EFs: (1) working memory (WM), (2) shifting, and (3) inhibition. Regarding the relationship among EFs, IQ and math abilities, the results of the SEM analysis showed that (i) WM and age predict number production and mental calculus, and (ii) shifting and sex predict arithmetical problem-solving. In all of the SEM models, EFs partially or totally mediated the relationship between IQ, age and math achievement. These results suggest that EFs differentially supports math abilities in primary-school children and is a more significant predictor of math achievement than IQ level.

Automated method for relating regional pulmonary structure and function: integration of dynamic multislice CT and thin-slice high-resolution CT

NASA Astrophysics Data System (ADS)

Tajik, Jehangir K.; Kugelmass, Steven D.; Hoffman, Eric A.

1993-07-01

We have developed a method utilizing x-ray CT for relating pulmonary perfusion to global and regional anatomy, allowing for detailed study of structure to function relationships. A thick slice, high temporal resolution mode is used to follow a bolus contrast agent for blood flow evaluation and is fused with a high spatial resolution, thin slice mode to obtain structure- function detail. To aid analysis of blood flow, we have developed a software module, for our image analysis package (VIDA), to produce the combined structure-function image. Color coded images representing blood flow, mean transit time, regional tissue content, regional blood volume, regional air content, etc. are generated and imbedded in the high resolution volume image. A text file containing these values along with a voxel's 3-D coordinates is also generated. User input can be minimized to identifying the location of the pulmonary artery from which the input function to a blood flow model is derived. Any flow model utilizing one input and one output function can be easily added to a user selectable list. We present examples from our physiologic based research findings to demonstrate the strengths of combining dynamic CT and HRCT relative to other scanning modalities to uniquely characterize pulmonary normal and pathophysiology.

Critical zone structure controls concentration-discharge relationships and solute generation in forested tropical montane watersheds

NASA Astrophysics Data System (ADS)

Wymore, Adam S.; Brereton, Richard L.; Ibarra, Daniel E.; Maher, Kate; McDowell, William H.

2017-07-01

Concentration-discharge (C-Q) relationships are poorly known for tropical watersheds, even though the tropics contribute a disproportionate amount of solutes to the global ocean. The Luquillo Mountains in Puerto Rico offer an ideal environment to examine C-Q relationships across a heterogeneous tropical landscape. We use 10-30 years of weekly stream chemistry data across 10 watersheds to examine C-Q relationships for weathering products (SiO2(aq), Ca2+, Mg2+, and Na+) and biologically controlled solutes (dissolved organic carbon [DOC], dissolved organic nitrogen [DON], NH4+, NO3-, PO43-, K+, and SO42-). We analyze C-Q relationships using power law equations and a solute production model and use principal component analysis to test hypotheses regarding how the structure of the critical zone controls solute generation. Volcaniclastic watersheds had higher concentrations of weathering solutes and smaller tributaries were approximately threefold more efficient at generating these solutes than larger rivers. Lithology and vegetation explained a significant amount of variation in the theoretical maximum concentrations of weathering solutes (r2 = 0.43-0.48) and in the C-Q relationships of PO43- (r2 = 0.63) and SiO2(aq) (r2 = 0.47). However, the direction and magnitude of these relationships varied. Across watersheds, various forms of N and P displayed variable C-Q relationships, while DOC was consistently enriched with increasing discharge. Results suggest that PO43- may be a useful indicator of watershed function. Relationships between C-Q and landscape characteristics indicate the extent to which the structure and function of the Critical zone controls watershed solute fluxes.

Shopper marketing: a new challenge for Spanish community pharmacies.

PubMed

Gavilan, Diana; Avello, Maria; Abril, Carmen

2014-01-01

Changes that have occurred over the past few decades in retailing and in the health care sector--namely, a drastic reduction in drug profit-margins, and a more critical use of health services by patients--have created a scenario characterized by rising competitiveness. This new context is necessitating community pharmacies (hereafter, pharmacies) to improve their business model through new strategies. Shopper marketing has proven invaluable in other retail settings and therefore, could be a critical element for new practices in pharmacies. First, to analyze how shopping experiences in pharmacies based on new practices in shopper marketing affect shopping behavior. Second, to study the mediating effect of customer satisfaction on the relationship between shopping experiences and shopping behavior. A self-reported questionnaire was developed to measure four concepts: hedonic experience (enjoyable), functional experience (goal-oriented), customer satisfaction and shopping behavior. Data were collected from 28 different pharmacies dispersed throughout Spain. Structural equation modeling (SEM) was used to test the relationships in the theoretical model. First, the measurement model was estimated to assess model fit, reliability, convergent and discriminant validity. Then, the parameters of the structural model were estimated and the mediation effects were subsequently tested. Functional experience and hedonic experience each significantly and positively correlate with consumer satisfaction and with customer shopping behavior (purchases and loyalty). Moreover, the effects of each type of experience on shopping behavior are partially mediated by customer satisfaction. The results suggest that even in Spanish pharmacies, which have traditionally been considered as strictly functional retailers, ensuring customer satisfaction and enhancing shopping behavior now demand more than just functional experiences. Moreover, a customer's experience at a pharmacy can itself trigger a shopping cycle; therefore, pharmacists should consider prioritizing investments in hedonic experiences. Copyright © 2014 Elsevier Inc. All rights reserved.

Extracurricular participation among children with epilepsy in Canada.

PubMed

Kamath, Sangita; Fayed, Nora; Goodman, Carly; Streiner, David L; Ronen, Gabriel M

2016-03-01

Participation in extracurricular activities creates opportunities for children to foster friendships, promote a sense of belonging, and improve physical and mental well-being. The objective of this study was to determine the relationship(s) of personal factors, seizure variables, and social supports with extracurricular participation in children with epilepsy (CWE). Baseline analysis of the QUALITÉ longitudinal study cohort of children aged 8-14 years (N=426) was conducted. Variables hypothesized to be related to the participation of CWE were classified using the International Classification of Functioning, Disability and Health according to body functions (presence of generalized tonic-clonic seizures in the past month, on/off AEDs, and seizure severity), environmental factors (perceived social support from parents and friends), and personal factors (sex, age, family structure, and family income). Analysis of variables related to extracurricular participation was conducted with regression modeling. Personal factors of age, gender, and family structure as well as body function variables of generalized tonic-clonic seizures and seizure severity were found to be the most important to extracurricular participation based on how frequently they were included in the final models (16/16 and 13/16 times, respectively). When parental support was found to be related to participation, the association was negative in 6 out of 16 models. The personal factors that are related to extracurricular participation among children with epilepsy mirror samples based on the general population, although seizures also play an important role. The relationship between perceived parental support and actual participation levels warrants further exploration. Copyright © 2015 Elsevier Inc. All rights reserved.

Use of Random and Site-Directed Mutagenesis to Probe Protein Structure-Function Relationships: Applied Techniques in the Study of Helicobacter pylori.

PubMed

Whitmire, Jeannette M; Merrell, D Scott

2017-01-01

Mutagenesis is a valuable tool to examine the structure-function relationships of bacterial proteins. As such, a wide variety of mutagenesis techniques and strategies have been developed. This chapter details a selection of random mutagenesis methods and site-directed mutagenesis procedures that can be applied to an array of bacterial species. Additionally, the direct application of the techniques to study the Helicobacter pylori Ferric Uptake Regulator (Fur) protein is described. The varied approaches illustrated herein allow the robust investigation of the structural-functional relationships within a protein of interest.

In vivo Visuotopic Brain Mapping with Manganese-Enhanced MRI and Resting-State Functional Connectivity MRI

PubMed Central

Chan, Kevin C.; Fan, Shu-Juan; Chan, Russell W.; Cheng, Joe S.; Zhou, Iris Y.; Wu, Ed X.

2014-01-01

The rodents are an increasingly important model for understanding the mechanisms of development, plasticity, functional specialization and disease in the visual system. However, limited tools have been available for assessing the structural and functional connectivity of the visual brain network globally, in vivo and longitudinally. There are also ongoing debates on whether functional brain connectivity directly reflects structural brain connectivity. In this study, we explored the feasibility of manganese-enhanced MRI (MEMRI) via 3 different routes of Mn2+ administration for visuotopic brain mapping and understanding of physiological transport in normal and visually deprived adult rats. In addition, resting-state functional connectivity MRI (RSfcMRI) was performed to evaluate the intrinsic functional network and structural-functional relationships in the corresponding anatomical visual brain connections traced by MEMRI. Upon intravitreal, subcortical, and intracortical Mn2+ injection, different topographic and layer-specific Mn enhancement patterns could be revealed in the visual cortex and subcortical visual nuclei along retinal, callosal, cortico-subcortical, transsynaptic and intracortical horizontal connections. Loss of visual input upon monocular enucleation to adult rats appeared to reduce interhemispheric polysynaptic Mn2+ transfer but not intra- or inter-hemispheric monosynaptic Mn2+ transport after Mn2+ injection into visual cortex. In normal adults, both structural and functional connectivity by MEMRI and RSfcMRI was stronger interhemispherically between bilateral primary/secondary visual cortex (V1/V2) transition zones (TZ) than between V1/V2 TZ and other cortical nuclei. Intrahemispherically, structural and functional connectivity was stronger between visual cortex and subcortical visual nuclei than between visual cortex and other subcortical nuclei. The current results demonstrated the sensitivity of MEMRI and RSfcMRI for assessing the neuroarchitecture, neurophysiology and structural-functional relationships of the visual brains in vivo. These may possess great potentials for effective monitoring and understanding of the basic anatomical and functional connections in the visual system during development, plasticity, disease, pharmacological interventions and genetic modifications in future studies. PMID:24394694

Finite Element Analysis and Understanding the Biomechanics and Evolution of Living and Fossil Organisms

NASA Astrophysics Data System (ADS)

Rayfield, Emily J.

2007-05-01

Finite element analysis (FEA) is a technique that reconstructs stress, strain, and deformation in a digital structure. Although commonplace in engineering and orthopedic science for more than 30 years, only recently has it begun to be adopted in the zoological and paleontological sciences to address questions of organismal morphology, function, and evolution. Current research tends to focus on either deductive studies that assume a close relationship between form and function or inductive studies that aim to test this relationship, although explicit hypothesis-testing bridges these two standpoints. Validation studies have shown congruence between in vivo or in vitro strain and FE-inferred strain. Future validation work on a broad range of taxa will assist in phylogenetically bracketing our extinct animal FE-models to increase confidence in our input parameters, although currently, FEA has much potential in addressing questions of form-function relationships, providing appropriate questions are asked of the existing data.

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bo; Selbach, Sverre M., E-mail: selbach@ntnu.no

2017-06-15

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.« less

TRP channels in calcium homeostasis: from hormonal control to structure-function relationship of TRPV5 and TRPV6.

PubMed

van Goor, Mark K C; Hoenderop, Joost G J; van der Wijst, Jenny

2017-06-01

Maintaining plasma calcium levels within a narrow range is of vital importance for many physiological functions. Therefore, calcium transport processes in the intestine, bone and kidney are tightly regulated to fine-tune the rate of absorption, storage and excretion. The TRPV5 and TRPV6 calcium channels are viewed as the gatekeepers of epithelial calcium transport. Several calciotropic hormones control the channels at the level of transcription, membrane expression, and function. Recent technological advances have provided the first near-atomic resolution structural models of several TRPV channels, allowing insight into their architecture. While this field is still in its infancy, it has increased our understanding of molecular channel regulation and holds great promise for future structure-function studies of these ion channels. This review will summarize the mechanisms that control the systemic calcium balance, as well as extrapolate structural views to the molecular functioning of TRPV5/6 channels in epithelial calcium transport. Copyright © 2016. Published by Elsevier B.V.

Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance.

PubMed

Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas

2016-10-01

The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of maximum plant height, reflecting the importance of forest vertical stratification for diversity-carbon relationship. We therefore argue for stronger complementary effects that would be induced also by complementary light-use efficiency of tree and species growing in the understory layer.

The Creation and Statistical Evaluation of a Deterministic Model of the Human Bronchial Tree from HRCT Images.

PubMed

Montesantos, Spyridon; Katz, Ira; Pichelin, Marine; Caillibotte, Georges

2016-01-01

A quantitative description of the morphology of lung structure is essential prior to any form of predictive modeling of ventilation or aerosol deposition implemented within the lung. The human lung is a very complex organ, with airway structures that span two orders of magnitude and having a multitude of interfaces between air, tissue and blood. As such, current medical imaging protocols cannot provide medical practitioners and researchers with in-vivo knowledge of deeper lung structures. In this work a detailed algorithm for the generation of an individualized 3D deterministic model of the conducting part of the human tracheo-bronchial tree is described. Distinct initial conditions were obtained from the high-resolution computed tomography (HRCT) images of seven healthy volunteers. The algorithm developed is fractal in nature and is implemented as a self-similar space sub-division procedure. The expansion process utilizes physiologically realistic relationships and thresholds to produce an anatomically consistent human airway tree. The model was validated through extensive statistical analysis of the results and comparison of the most common morphological features with previously published morphometric studies and other equivalent models. The resulting trees were shown to be in good agreement with published human lung geometric characteristics and can be used to study, among other things, structure-function relationships in simulation studies.

Online adaptive decision trees: pattern classification and function approximation.

PubMed

Basak, Jayanta

2006-09-01

Recently we have shown that decision trees can be trained in the online adaptive (OADT) mode (Basak, 2004), leading to better generalization score. OADTs were bottlenecked by the fact that they are able to handle only two-class classification tasks with a given structure. In this article, we provide an architecture based on OADT, ExOADT, which can handle multiclass classification tasks and is able to perform function approximation. ExOADT is structurally similar to OADT extended with a regression layer. We also show that ExOADT is capable not only of adapting the local decision hyperplanes in the nonterminal nodes but also has the potential of smoothly changing the structure of the tree depending on the data samples. We provide the learning rules based on steepest gradient descent for the new model ExOADT. Experimentally we demonstrate the effectiveness of ExOADT in the pattern classification and function approximation tasks. Finally, we briefly discuss the relationship of ExOADT with other classification models.

Resting-state functional connectivity emerges from structurally and dynamically shaped slow linear fluctuations.

PubMed

Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-07-03

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

The Norwegian Computerized Adaptive Test of Personality Disorder-Static Form (CAT-PD-SF): Reliability, Factor Structure, and Relationships With Personality Functioning.

PubMed

Thimm, Jens C

2017-12-01

The Computerized Adaptive Test of Personality Disorder-Static Form (CAT-PD-SF) is a self-report inventory developed to assess pathological personality traits. The current study explored the reliability and higher order factor structure of the Norwegian version of the CAT-PD-SF and the relationships between the CAT-PD traits and domains of personality functioning in an undergraduate student sample ( N = 375). In addition to the CAT-PD-SF, the short form of the Severity Indices of Personality Problems and the Brief Symptom Inventory were administered. The results showed that the Norwegian CAT-PD-SF has good score reliability. Factor analysis of the CAT-PD-SF scales indicated five superordinate factors that correspond to the trait domains of the alternative DSM-5 model for personality disorders. The CAT-PD traits were highly predictive of impaired personality functioning after controlling for psychological distress. It is concluded that the CAT-PD-SF is a promising tool for the assessment of personality disorder traits.

The relationship between multilevel models and non-parametric multilevel mixture models: Discrete approximation of intraclass correlation, random coefficient distributions, and residual heteroscedasticity.

PubMed

Rights, Jason D; Sterba, Sonya K

2016-11-01

Multilevel data structures are common in the social sciences. Often, such nested data are analysed with multilevel models (MLMs) in which heterogeneity between clusters is modelled by continuously distributed random intercepts and/or slopes. Alternatively, the non-parametric multilevel regression mixture model (NPMM) can accommodate the same nested data structures through discrete latent class variation. The purpose of this article is to delineate analytic relationships between NPMM and MLM parameters that are useful for understanding the indirect interpretation of the NPMM as a non-parametric approximation of the MLM, with relaxed distributional assumptions. We define how seven standard and non-standard MLM specifications can be indirectly approximated by particular NPMM specifications. We provide formulas showing how the NPMM can serve as an approximation of the MLM in terms of intraclass correlation, random coefficient means and (co)variances, heteroscedasticity of residuals at level 1, and heteroscedasticity of residuals at level 2. Further, we discuss how these relationships can be useful in practice. The specific relationships are illustrated with simulated graphical demonstrations, and direct and indirect interpretations of NPMM classes are contrasted. We provide an R function to aid in implementing and visualizing an indirect interpretation of NPMM classes. An empirical example is presented and future directions are discussed. © 2016 The British Psychological Society.

From Green to Blue: Site-Directed Mutagenesis of the Green Fluorescent Protein to Teach Protein Structure-Function Relationships

ERIC Educational Resources Information Center

Giron, Maria D.; Salto, Rafael

2011-01-01

Structure-function relationship studies in proteins are essential in modern Cell Biology. Laboratory exercises that allow students to familiarize themselves with basic mutagenesis techniques are essential in all Genetic Engineering courses to teach the relevance of protein structure. We have implemented a laboratory course based on the…

The Relationship between Cranial Structure, Biomechanical Performance and Ecological Diversity in Varanoid Lizards

PubMed Central

McCurry, Matthew R.; Mahony, Michael; Clausen, Phillip D.; Quayle, Michelle R.; Walmsley, Christopher W.; Jessop, Tim S.; Wroe, Stephen; Richards, Heather; McHenry, Colin R.

2015-01-01

Skull structure is intimately associated with feeding ability in vertebrates, both in terms of specific performance measures and general ecological characteristics. This study quantitatively assessed variation in the shape of the cranium and mandible in varanoid lizards, and its relationship to structural performance (von Mises strain) and interspecific differences in feeding ecology. Geometric morphometric and linear morphometric analyses were used to evaluate morphological differences, and finite element analysis was used to quantify variation in structural performance (strain during simulated biting, shaking and pulling). This data was then integrated with ecological classes compiled from relevant scientific literature on each species in order to establish structure-function relationships. Finite element modelling results showed that variation in cranial morphology resulted in large differences in the magnitudes and locations of strain in biting, shaking and pulling load cases. Gracile species such as Varanus salvadorii displayed high strain levels during shaking, especially in the areas between the orbits. All models exhibit less strain during pull back loading compared to shake loading, even though a larger force was applied (pull =30N, shake = 20N). Relationships were identified between the morphology, performance, and ecology. Species that did not feed on hard prey clustered in the gracile region of cranial morphospace and exhibited significantly higher levels of strain during biting (P = 0.0106). Species that fed on large prey clustered in the elongate area of mandible morphospace. This relationship differs from those that have been identified in other taxonomic groups such as crocodiles and mammals. This difference may be due to a combination of the open ‘space-frame’ structure of the varanoid lizard skull, and the ‘pull back’ behaviour that some species use for processing large prey. PMID:26106889

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.

PubMed

Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W

2017-06-01

Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.

Flexible multibody simulation of automotive systems with non-modal model reduction techniques

NASA Astrophysics Data System (ADS)

Shiiba, Taichi; Fehr, Jörg; Eberhard, Peter

2012-12-01

The stiffness of the body structure of an automobile has a strong relationship with its noise, vibration, and harshness (NVH) characteristics. In this paper, the effect of the stiffness of the body structure upon ride quality is discussed with flexible multibody dynamics. In flexible multibody simulation, the local elastic deformation of the vehicle has been described traditionally with modal shape functions. Recently, linear model reduction techniques from system dynamics and mathematics came into the focus to find more sophisticated elastic shape functions. In this work, the NVH-relevant states of a racing kart are simulated, whereas the elastic shape functions are calculated with modern model reduction techniques like moment matching by projection on Krylov-subspaces, singular value decomposition-based reduction techniques, and combinations of those. The whole elastic multibody vehicle model consisting of tyres, steering, axle, etc. is considered, and an excitation with a vibration characteristics in a wide frequency range is evaluated in this paper. The accuracy and the calculation performance of those modern model reduction techniques is investigated including a comparison of the modal reduction approach.

Correspondence between theoretical models and dual energy x-ray absorptiometry measurements of femoral cross-sectional growth during adolescence

NASA Technical Reports Server (NTRS)

van der Meulen, M. C.; Marcus, R.; Bachrach, L. K.; Carter, D. R.

1997-01-01

We have developed an analytical model of long bone cross-sectional ontogeny in which appositional growth of the diaphysis is primarily driven by mechanical stimuli associated with increasing body mass during growth and development. In this study, our goal was to compare theoretical predictions of femoral diaphyseal structure from this model with measurements of femoral bone mineral and geometry by dual energy x-ray absorptiometry. Measurements of mid-diaphyseal femoral geometry and structure were made previously in 101 Caucasian adolescents and young adults 9-26 years of age. The data on measured bone mineral content and calculated section modulus were compared with the results of our analytical model of cross-sectional development of the human femur over the same age range. Both bone mineral content and section modulus showed good correspondence with experimental measurements when the relationships with age and body mass were examined. Strong linear relationships were evident for both parameters when examined as a function of body mass.

Modeling G Protein-Coupled Receptors: a Concrete Possibility

PubMed Central

Costanzi, Stefano

2010-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that are involved in the regulation of a wide range of physiological functions and constitute the most common target for therapeutic intervention. Due to the paucity of crystal structures, homology modeling has become a widespread technique for the construction of GPCR models, which have been applied to the study of their structure-function relationships and to the identification of lead ligands through virtual screening. Rhodopsin has been for years the only available template. However, recent breakthroughs in GPCR crystallography have led to the solution of the structures of a few additional receptors. In light of these newly elucidated crystal structures, we have been able to produce a substantial amount of data to demonstrate that accurate models of GPCRs in complex with their ligands can be constructed through homology modeling followed by fully flexible molecular docking. These results have been confirmed by our success in the first blind assessment of GPCR modeling and docking, organized in coordination with the solution of the X-ray structure of the adenosine A2A receptor. Taken together, these data indicate that: a) the transmembrane helical bundle can be modeled with considerable accuracy; b) predicting the binding mode of a ligand, although doable, is challenging; c) modeling of the extracellular and intracellular loops is still problematic. PMID:21253444

Social relationships and physician utilization among older adults-A systematic review.

PubMed

Bremer, Daniel; Inhestern, Laura; von dem Knesebeck, Olaf

2017-01-01

In older age health needs and demand for health services utilization increase. Individual's social relationships can play a decisive role regarding the utilization of outpatient health care services. This systematic review examines the associations of structural and functional dimensions of social relationships with outpatient health services use of older adults. The databases PubMed, CINAHL, SocINDEX, PsycINFO, International Bibliography of the Social Sciences (IBSS), Sociological Abstracts, and Applied Social Sciences Index and Abstracts (ASSIA) were searched in February 2016. The methodological and reporting quality of the articles was assessed and the results were synthesized descriptively and systematically. Out of 1.392 hits, 36 articles (35 studies) were included in the systematic review. The methodological and reporting quality of the included articles was reasonable. Various structural and functional characteristics of social relationships were associated with the use (yes/no) and the frequency of using outpatient care among older adults. The majority of the associations between structural dimensions of social relationships and the use of physicians were positive and moderate in strength. The associations between functional dimensions of social relationships and the probability of using physician services were inconsistent and varied in strength. For the most part, social relationship variables assigned to the structural dimension were positively and weakly to moderately associated with the frequency of physician visits. Functional aspects of social relationships also tended to have positive associations with the frequency of physician utilization. The associations were weak to moderate in strength. Measuring social relationships and their influence on health services use is a challenging methodological endeavor indicated by the inconclusive results. The results suggest that the outpatient care utilization behavior of older individuals being structurally and functionally integrated in social relationships is different to older adults being socially isolated or having no social support. All in all, the current status of quantitative data was insufficient. Future health services research should accentuate social ties in more detail, especially according to quality aspects of social relationships.

Establishing a relationship between maximum torque production of isolated joints to simulate EVA ratchet push-pull maneuver: A case study

NASA Technical Reports Server (NTRS)

Pandya, Abhilash; Maida, James; Hasson, Scott; Greenisen, Michael; Woolford, Barbara

1993-01-01

As manned exploration of space continues, analytical evaluation of human strength characteristics is critical. These extraterrestrial environments will spawn issues of human performance which will impact the designs of tools, work spaces, and space vehicles. Computer modeling is an effective method of correlating human biomechanical and anthropometric data with models of space structures and human work spaces. The aim of this study is to provide biomechanical data from isolated joints to be utilized in a computer modeling system for calculating torque resulting from any upper extremity motions: in this study, the ratchet wrench push-pull operation (a typical extravehicular activity task). Established here are mathematical relationships used to calculate maximum torque production of isolated upper extremity joints. These relationships are a function of joint angle and joint velocity.

Modeling the Prospective Relationships of Impairment, Injury Severity, and Participation to Quality of Life Following Traumatic Brain Injury

PubMed Central

Kalpinski, Ryan J.; Williamson, Meredith L. C.; Elliott, Timothy R.; Berry, Jack W.; Underhill, Andrea T.; Fine, Philip R.

2013-01-01

Identifying reliable predictors of positive adjustment following traumatic brain injury (TBI) remains an important area of inquiry. Unfortunately, much of available research examines direct relationships between predictor variables and outcomes without attending to the contextual relationships that can exist between predictor variables. Relying on theoretical models of well-being, we examined a theoretical model of adjustment in which the capacity to engage in intentional activities would be prospectively associated with greater participation, which in turn would predict subsequent life satisfaction and perceived health assessed at a later time. Structural equation modeling of data collected from 312 individuals (226 men, 86 women) with TBI revealed that two elements of participation—mobility and occupational activities—mediated the prospective influence of functional independence and injury severity to optimal adjustment 60 months following medical discharge for TBI. The model accounted for 21% of the variance in life satisfaction and 23% of the variance in self-rated health. Results indicate that the effects of functional independence and injury severity to optimal adjustment over time may be best understood in the context of participation in meaningful, productive activities. Implications for theoretical models of well-being and for clinical interventions that promote adjustmentafter TBI are discussed. PMID:24199186

Mediators of Aggression Among Young Adult Offspring of Depressed Mothers

PubMed Central

Keenan-Miller, Danielle; Hammen, Constance; Brennan, Patricia A.

2010-01-01

The current paper explores the connection between maternal depression and offspring aggression during the transition to adulthood, expanding the scope of prior research on this topic. Both family-level factors (including parent-child relationship quality and maternal relationship quality) and youth factors (including depression history and social functioning in mid-adolescence) were tested as potential mediators in a longitudinal community sample of 710 youth at ages 15 and 20. The results suggest that maternal depression confers a risk for higher levels of aggressive behavior by offspring at age 20. Structural Equation Models suggested that the association between maternal depression and youth aggression is fully mediated by youth history of depression by mid-adolescence, even when accounting for the stability of aggression between ages 15 and 20. Parent-child relationship quality, youth social functioning, and maternal relationship quality were not unique mediators of this association. Limitations and implications are discussed. PMID:20919790

Function does not follow form in gene regulatory circuits.

PubMed

Payne, Joshua L; Wagner, Andreas

2015-08-20

Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine who regulates whom. Studies that have focused on the gene expression patterns (functions) of circuits with a given structure (form) have examined just a few structures or gene expression patterns. Here, we use a computational model to exhaustively characterize the gene expression patterns of nearly 17 million three-gene circuits in order to systematically explore the relationship between circuit form and function. Three main conclusions emerge. First, function does not follow form. A circuit of any one structure can have between twelve and nearly thirty thousand distinct gene expression patterns. Second, and conversely, form does not follow function. Most gene expression patterns can be realized by more than one circuit structure. And third, multifunctionality severely constrains circuit form. The number of circuit structures able to drive multiple gene expression patterns decreases rapidly with the number of these patterns. These results indicate that it is generally not possible to infer circuit function from circuit form, or vice versa.

The brief family relationship scale: a brief measure of the relationship dimension in family functioning.

PubMed

Fok, Carlotta Ching Ting; Allen, James; Henry, David

2014-02-01

The Relationship dimension of the Family Environment Scale, which consists of the Cohesion, Expressiveness, and Conflict subscales, measures a person's perception of the quality of his or her family relationship functioning. This study investigates an adaptation of the Relationship dimension of the Family Environment Scale for Alaska Native youth. The authors tested the adapted measure, the Brief Family Relationship Scale, for psychometric properties and internal structure with 284 12- to 18-year-old predominately Yup'ik Eskimo Alaska Native adolescents from rural, remote communities. This non-Western cultural group is hypothesized to display higher levels of collectivism traditionally organized around an extended kinship family structure. Results demonstrate a subset of the adapted items function satisfactorily, a three-response alternative format provided meaningful information, and the subscale's underlying structure is best described through three distinct first-order factors, organized under one higher order factor. Convergent and discriminant validity of the Brief Family Relationship Scale was assessed through correlational analysis.

Impact of Adolescents' Filial Self-Efficacy on Quality of Family Functioning and Satisfaction

ERIC Educational Resources Information Center

Caprara, Gian Vittorio; Pastorelli, Concetta; Regalia, Camillo; Scabini, Eugenia; Bandura, Albert

2005-01-01

In this prospective study, we tested a structural model in which adolescents' perceived self-efficacy to manage parental relationships affected their satisfaction with family life both directly, and indirectly, through its impact on family practices. Findings based on 380 Italian adolescents showed that perceived filial self-efficacy was linked…

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient

NASA Technical Reports Server (NTRS)

Gomez, Elena del V.; Garland, Jay L.; Roberts, Michael S.

2004-01-01

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential. c2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Double dissociation of structure-function relationships in memory and fluid intelligence observed with magnetic resonance elastography.

PubMed

Johnson, Curtis L; Schwarb, Hillary; Horecka, Kevin M; McGarry, Matthew D J; Hillman, Charles H; Kramer, Arthur F; Cohen, Neal J; Barbey, Aron K

2018-05-01

Brain tissue mechanical properties, measured in vivo with magnetic resonance elastography (MRE), have proven to be sensitive metrics of neural tissue integrity. Recently, our group has reported on the positive relationship between viscoelasticity of the hippocampus and performance on a relational memory task in healthy young adults, which highlighted the potential of sensitive MRE measures for studying brain health and its relation to cognitive function; however, structure-function relationships outside of the hippocampus have not yet been explored. In this study, we examined the relationships between viscoelasticity of both the hippocampus and the orbitofrontal cortex and performance on behavioral assessments of relational memory and fluid intelligence. In a sample of healthy, young adults (N = 53), there was a significant, positive relationship between orbitofrontal cortex viscoelasticity and fluid intelligence performance (r = 0.42; p = .002). This finding is consistent with the previously reported relationship between hippocampal viscoelasticity and relational memory performance (r = 0.41; p = .002). Further, a significant double dissociation between the orbitofrontal-fluid intelligence relationship and the hippocampal-relational memory relationship was observed. These data support the specificity of regional brain MRE measures in support of separable cognitive functions. This report of a structure-function relationship observed with MRE beyond the hippocampus suggests a future role for MRE as a sensitive neuroimaging technique for brain mapping. Copyright © 2018 Elsevier Inc. All rights reserved.

Functional networks inference from rule-based machine learning models.

PubMed

Lazzarini, Nicola; Widera, Paweł; Williamson, Stuart; Heer, Rakesh; Krasnogor, Natalio; Bacardit, Jaume

2016-01-01

Functional networks play an important role in the analysis of biological processes and systems. The inference of these networks from high-throughput (-omics) data is an area of intense research. So far, the similarity-based inference paradigm (e.g. gene co-expression) has been the most popular approach. It assumes a functional relationship between genes which are expressed at similar levels across different samples. An alternative to this paradigm is the inference of relationships from the structure of machine learning models. These models are able to capture complex relationships between variables, that often are different/complementary to the similarity-based methods. We propose a protocol to infer functional networks from machine learning models, called FuNeL. It assumes, that genes used together within a rule-based machine learning model to classify the samples, might also be functionally related at a biological level. The protocol is first tested on synthetic datasets and then evaluated on a test suite of 8 real-world datasets related to human cancer. The networks inferred from the real-world data are compared against gene co-expression networks of equal size, generated with 3 different methods. The comparison is performed from two different points of view. We analyse the enriched biological terms in the set of network nodes and the relationships between known disease-associated genes in a context of the network topology. The comparison confirms both the biological relevance and the complementary character of the knowledge captured by the FuNeL networks in relation to similarity-based methods and demonstrates its potential to identify known disease associations as core elements of the network. Finally, using a prostate cancer dataset as a case study, we confirm that the biological knowledge captured by our method is relevant to the disease and consistent with the specialised literature and with an independent dataset not used in the inference process. The implementation of our network inference protocol is available at: http://ico2s.org/software/funel.html.

Hierarchy of Dysfunction Related to Dressing Performance in Stroke Patients: A Path Analysis Study.

PubMed

Fujita, Takaaki; Nagayama, Hirofumi; Sato, Atsushi; Yamamoto, Yuichi; Yamane, Kazuhiro; Otsuki, Koji; Tsuchiya, Kenji; Tozato, Fusae

2016-01-01

Previous reports indicated that various dysfunctions caused by stroke affect the level of independence in dressing. These dysfunctions can be hierarchical, and these effects on dressing performance can be complicated in stroke patients. However, there are no published reports focusing on the hierarchical structure of the relationships between the activities of daily living and balance function, motor and sensory functions of the affected lower limb, strength of the abdominal muscles and knee extension on the unaffected side, and visuospatial deficits. The purpose of this study was to elucidate the hierarchical and causal relationships between dressing performance and these dysfunctions in stroke patients. This retrospective study included 104 first-time stroke patients. The causal relationship between the dressing performance and age, time post stroke, balance function, motor and sensory functions of the affected lower limb, strength of the abdominal muscles and knee extension on the unaffected side, and visuospatial deficits were examined using path analysis. A hypothetical path model was created based on previous studies, and the goodness of fit between the data and model were verified. A modified path model was created that achieved an almost perfect fit to the data. Balance function and abdominal muscle strength have direct effects on dressing performance, with standardized direct effect estimates of 0.78 and 0.15, respectively. Age, motor and sensory functions of the affected lower limb, and strength of abdominal muscle and knee extension on the unaffected side have indirect effects on dressing by influencing balance function. Our results suggest that dressing performance depends strongly on balance function, and it is mainly influenced by the motor function of the affected lower limb.

Photon echo spectroscopy reveals structure-dynamics relationships in carotenoids

NASA Astrophysics Data System (ADS)

Christensson, N.; Polivka, T.; Yartsev, A.; Pullerits, T.

2009-06-01

Based on simultaneous analysis of the frequency-resolved transient grating, peak shift, and echo width signals, we present a model for the third-order optical response of carotenoids including population dynamics and system-bath interactions. Our frequency-resolved photon echo experiments show that the model needs to incorporate the excited-state absorption from both the S2 and the S1 states. We apply our model to analyze the experimental results on astaxanthin and lycopene, aiming to elucidate the relation between structure and system-bath interactions. Our analysis allows us to relate structural motifs to changes in the energy-gap correlation functions. We find that the terminal rings of astaxanthin lead to increased coupling between slow molecular motions and the electronic transition. We also find evidence for stronger coupling to higher frequency overdamped modes in astaxanthin, pointing to the importance of the functional groups in providing coupling to fluctuations influencing the dynamics in the passage through the conical intersection governing the S2-S1 relaxation.

VarMod: modelling the functional effects of non-synonymous variants

PubMed Central

Pappalardo, Morena; Wass, Mark N.

2014-01-01

Unravelling the genotype–phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein interfaces and protein–ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod. PMID:24906884

Modeling Spatial Dependencies and Semantic Concepts in Data Mining

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vatsavai, Raju

Data mining is the process of discovering new patterns and relationships in large datasets. However, several studies have shown that general data mining techniques often fail to extract meaningful patterns and relationships from the spatial data owing to the violation of fundamental geospatial principles. In this tutorial, we introduce basic principles behind explicit modeling of spatial and semantic concepts in data mining. In particular, we focus on modeling these concepts in the widely used classification, clustering, and prediction algorithms. Classification is the process of learning a structure or model (from user given inputs) and applying the known model to themore » new data. Clustering is the process of discovering groups and structures in the data that are ``similar,'' without applying any known structures in the data. Prediction is the process of finding a function that models (explains) the data with least error. One common assumption among all these methods is that the data is independent and identically distributed. Such assumptions do not hold well in spatial data, where spatial dependency and spatial heterogeneity are a norm. In addition, spatial semantics are often ignored by the data mining algorithms. In this tutorial we cover recent advances in explicitly modeling of spatial dependencies and semantic concepts in data mining.« less

Electrophysiological Modeling of Cardiac Ventricular Function: From Cell to Organ

PubMed Central

Winslow, R. L.; Scollan, D. F.; Holmes, A.; Yung, C. K.; Zhang, J.; Jafri, M. S.

2005-01-01

Three topics of importance to modeling the integrative function of the heart are reviewed. The first is modeling of the ventricular myocyte. Emphasis is placed on excitation-contraction coupling and intracellular Ca2+ handling, and the interpretation of experimental data regarding interval-force relationships. Second, data on use of diffusion tensor magnetic resonance (DTMR) imaging for measuring the anatomical structure of the cardiac ventricles are presented. A method for the semi-automated reconstruction of the ventricles using a combination of gradient recalled acquisition in the steady state (GRASS) and DTMR images is described. Third, we describe how these anatomically and biophysically based models of the cardiac ventricles can be implemented on parallel computers. PMID:11701509

Inferring multi-scale neural mechanisms with brain network modelling

PubMed Central

Schirner, Michael; McIntosh, Anthony Randal; Jirsa, Viktor; Deco, Gustavo

2018-01-01

The neurophysiological processes underlying non-invasive brain activity measurements are incompletely understood. Here, we developed a connectome-based brain network model that integrates individual structural and functional data with neural population dynamics to support multi-scale neurophysiological inference. Simulated populations were linked by structural connectivity and, as a novelty, driven by electroencephalography (EEG) source activity. Simulations not only predicted subjects' individual resting-state functional magnetic resonance imaging (fMRI) time series and spatial network topologies over 20 minutes of activity, but more importantly, they also revealed precise neurophysiological mechanisms that underlie and link six empirical observations from different scales and modalities: (1) resting-state fMRI oscillations, (2) functional connectivity networks, (3) excitation-inhibition balance, (4, 5) inverse relationships between α-rhythms, spike-firing and fMRI on short and long time scales, and (6) fMRI power-law scaling. These findings underscore the potential of this new modelling framework for general inference and integration of neurophysiological knowledge to complement empirical studies. PMID:29308767

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Demographic and obstetric factors affecting women's sexual functioning during pregnancy.

PubMed

Abouzari-Gazafroodi, Kobra; Najafi, Fatemeh; Kazemnejad, Ehsan; Rahnama, Parvin; Montazeri, Ali

2015-08-19

Sexual desire and frequency of sexual relationships during pregnancy remains challenging. This study aimed to assess factors that affect women's sexual functioning during pregnancy. This was a cross sectional study carried out at prenatal care clinics of public health services in Iran. An author-designed structured questionnaire including items on socio-demographic characteristics, obstetric history, the current pregnancy, and women's sexual functioning during pregnancy was used to collect data. The generalized linear model was performed in order to find out factors that affect women's sexual functioning during pregnancy. In all, 518 pregnant women participated in the study. The mean age of participants was 26.4 years (SD = 4.7). Overall 309 women (59.7%) scored less than mean on sexual functioning. The results obtained from generalized linear model demonstrated that that lower education, unwanted pregnancy, earlier stage of pregnancy, older age, and longer duration of marriage were the most important factors contributing to disturbed sexual functioning among couples. The findings suggest that sexual function during pregnancy might be disturbed due to several factors. Indeed issues on sexual relationship should be included as part of prenatal care and reproductive health programs for every woman.

Lightning Strike Ablation Damage Influence Factors Analysis of Carbon Fiber/Epoxy Composite Based on Coupled Electrical-Thermal Simulation

NASA Astrophysics Data System (ADS)

Yin, J. J.; Chang, F.; Li, S. L.; Yao, X. L.; Sun, J. R.; Xiao, Y.

2017-10-01

According to the mathematical analysis model constructed on the basis of energy-balance relationship in lightning strike, and accompany with the simplified calculation strategy of composite resin pyrolysis degree dependent electrical conductivity, an effective three dimensional thermal-electrical coupling analysis finite element model of composite laminate suffered from lightning current was established based on ABAQUS, to elucidate the effects of lighting current waveform parameters and thermal/electrical properties of composite laminate on the extent of ablation damage. Simulated predictions agree well with the composite lightning strike directed effect experimental data, illustrating the potential accuracy of the constructed model. The analytical results revealed that extent of composite lightning strike ablation damage can be characterized by action integral validly, there exist remarkable power function relationships between action integral and visual damage area, projected damage area, maximum damage depth and damage volume of ablation damage, and enhancing the electrical conductivity and specific heat of composite, ablation damage will be descended obviously, power function relationships also exist between electrical conductivity, specific heat and ablation damage, however, the impact of thermal conductivity on the extent of ablation damage is not notable. The conclusions obtained provide some guidance for composite anti-lightning strike structure-function integration design.

Design and Structure-Function Characterization of 3D Printed Synthetic Porous Biomaterials for Tissue Engineering.

PubMed

Kelly, Cambre N; Miller, Andrew T; Hollister, Scott J; Guldberg, Robert E; Gall, Ken

2018-04-01

3D printing is now adopted for use in a variety of industries and functions. In biomedical engineering, 3D printing has prevailed over more traditional manufacturing methods in tissue engineering due to its high degree of control over both macro- and microarchitecture of porous tissue scaffolds. However, with the improved flexibility in design come new challenges in characterizing the structure-function relationships between various architectures and both mechanical and biological properties in an assortment of clinical applications. Presently, the field of tissue engineering lacks a comprehensive body of literature that is capable of drawing meaningful relationships between the designed structure and resulting function of 3D printed porous biomaterial scaffolds. This work first discusses the role of design on 3D printed porous scaffold function and then reviews characterization of these structure-function relationships for 3D printed synthetic metallic, polymeric, and ceramic biomaterials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential effects of genetically distinct mechanisms of elevating amylose on barley starch characteristics.

PubMed

Regina, Ahmed; Blazek, Jaroslav; Gilbert, Elliot; Flanagan, Bernadine M; Gidley, Michael J; Cavanagh, Colin; Ral, Jean-Philippe; Larroque, Oscar; Bird, Anthony R; Li, Zhongyi; Morell, Matthew K

2012-07-01

The relationships between starch structure and functionality are important in underpinning the industrial and nutritional utilisation of starches. In this work, the relationships between the biosynthesis, structure, molecular organisation and functionality have been examined using a series of defined genotypes in barley with low (<20%), standard (20-30%), elevated (30-50%) and high (>50%) amylose starches. A range of techniques have been employed to determine starch physical features, higher order structure and functionality. The two genetic mechanisms for generating high amylose contents (down-regulation of branching enzymes and starch synthases, respectively) yielded starches with very different amylopectin structures but similar gelatinisation and viscosity properties driven by reduced granular order and increased amylose content. Principal components analysis (PCA) was used to elucidate the relationships between genotypes and starch molecular structure and functionality. Parameters associated with granule order (PC1) accounted for a large percentage of the variance (57%) and were closely related to amylose content. Parameters associated with amylopectin fine structure accounted for 18% of the variance but were less closely aligned to functionality parameters. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structural Equation Modeling: A Framework for Ocular and Other Medical Sciences Research

PubMed Central

Christ, Sharon L.; Lee, David J.; Lam, Byron L.; Diane, Zheng D.

2017-01-01

Structural equation modeling (SEM) is a modeling framework that encompasses many types of statistical models and can accommodate a variety of estimation and testing methods. SEM has been used primarily in social sciences but is increasingly used in epidemiology, public health, and the medical sciences. SEM provides many advantages for the analysis of survey and clinical data, including the ability to model latent constructs that may not be directly observable. Another major feature is simultaneous estimation of parameters in systems of equations that may include mediated relationships, correlated dependent variables, and in some instances feedback relationships. SEM allows for the specification of theoretically holistic models because multiple and varied relationships may be estimated together in the same model. SEM has recently expanded by adding generalized linear modeling capabilities that include the simultaneous estimation of parameters of different functional form for outcomes with different distributions in the same model. Therefore, mortality modeling and other relevant health outcomes may be evaluated. Random effects estimation using latent variables has been advanced in the SEM literature and software. In addition, SEM software has increased estimation options. Therefore, modern SEM is quite general and includes model types frequently used by health researchers, including generalized linear modeling, mixed effects linear modeling, and population average modeling. This article does not present any new information. It is meant as an introduction to SEM and its uses in ocular and other health research. PMID:24467557

Cognitive predictors of a common multitasking ability: Contributions from working memory, attention control, and fluid intelligence.

PubMed

Redick, Thomas S; Shipstead, Zach; Meier, Matthew E; Montroy, Janelle J; Hicks, Kenny L; Unsworth, Nash; Kane, Michael J; Hambrick, D Zachary; Engle, Randall W

2016-11-01

Previous research has identified several cognitive abilities that are important for multitasking, but few studies have attempted to measure a general multitasking ability using a diverse set of multitasks. In the final dataset, 534 young adult subjects completed measures of working memory (WM), attention control, fluid intelligence, and multitasking. Correlations, hierarchical regression analyses, confirmatory factor analyses, structural equation models, and relative weight analyses revealed several key findings. First, although the complex tasks used to assess multitasking differed greatly in their task characteristics and demands, a coherent construct specific to multitasking ability was identified. Second, the cognitive ability predictors accounted for substantial variance in the general multitasking construct, with WM and fluid intelligence accounting for the most multitasking variance compared to attention control. Third, the magnitude of the relationships among the cognitive abilities and multitasking varied as a function of the complexity and structure of the various multitasks assessed. Finally, structural equation models based on a multifaceted model of WM indicated that attention control and capacity fully mediated the WM and multitasking relationship. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Modeling species-abundance relationships in multi-species collections

USGS Publications Warehouse

Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

2003-01-01

Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

The structure and statistics of interstellar turbulence

NASA Astrophysics Data System (ADS)

Kritsuk, A. G.; Ustyugov, S. D.; Norman, M. L.

2017-06-01

We explore the structure and statistics of multiphase, magnetized ISM turbulence in the local Milky Way by means of driven periodic box numerical MHD simulations. Using the higher order-accurate piecewise-parabolic method on a local stencil (PPML), we carry out a small parameter survey varying the mean magnetic field strength and density while fixing the rms velocity to observed values. We quantify numerous characteristics of the transient and steady-state turbulence, including its thermodynamics and phase structure, kinetic and magnetic energy power spectra, structure functions, and distribution functions of density, column density, pressure, and magnetic field strength. The simulations reproduce many observables of the local ISM, including molecular clouds, such as the ratio of turbulent to mean magnetic field at 100 pc scale, the mass and volume fractions of thermally stable Hi, the lognormal distribution of column densities, the mass-weighted distribution of thermal pressure, and the linewidth-size relationship for molecular clouds. Our models predict the shape of magnetic field probability density functions (PDFs), which are strongly non-Gaussian, and the relative alignment of magnetic field and density structures. Finally, our models show how the observed low rates of star formation per free-fall time are controlled by the multiphase thermodynamics and large-scale turbulence.

Connectivity and functional profiling of abnormal brain structures in pedophilia

PubMed Central

Poeppl, Timm B.; Eickhoff, Simon B.; Fox, Peter T.; Laird, Angela R.; Rupprecht, Rainer; Langguth, Berthold; Bzdok, Danilo

2015-01-01

Despite its 0.5–1% lifetime prevalence in men and its general societal relevance, neuroimaging investigations in pedophilia are scarce. Preliminary findings indicate abnormal brain structure and function. However, no study has yet linked structural alterations in pedophiles to both connectional and functional properties of the aberrant hotspots. The relationship between morphological alterations and brain function in pedophilia as well as their contribution to its psychopathology thus remain unclear. First, we assessed bimodal connectivity of structurally altered candidate regions using meta-analytic connectivity modeling (MACM) and resting-state correlations employing openly accessible data. We compared the ensuing connectivity maps to the activation likelihood estimation (ALE) maps of a recent quantitative meta-analysis of brain activity during processing of sexual stimuli. Second, we functionally characterized the structurally altered regions employing meta-data of a large-scale neuroimaging database. Candidate regions were functionally connected to key areas for processing of sexual stimuli. Moreover, we found that the functional role of structurally altered brain regions in pedophilia relates to nonsexual emotional as well as neurocognitive and executive functions, previously reported to be impaired in pedophiles. Our results suggest that structural brain alterations affect neural networks for sexual processing by way of disrupted functional connectivity, which may entail abnormal sexual arousal patterns. The findings moreover indicate that structural alterations account for common affective and neurocognitive impairments in pedophilia. The present multi-modal integration of brain structure and function analyses links sexual and nonsexual psychopathology in pedophilia. PMID:25733379

Connectivity and functional profiling of abnormal brain structures in pedophilia.

PubMed

Poeppl, Timm B; Eickhoff, Simon B; Fox, Peter T; Laird, Angela R; Rupprecht, Rainer; Langguth, Berthold; Bzdok, Danilo

2015-06-01

Despite its 0.5-1% lifetime prevalence in men and its general societal relevance, neuroimaging investigations in pedophilia are scarce. Preliminary findings indicate abnormal brain structure and function. However, no study has yet linked structural alterations in pedophiles to both connectional and functional properties of the aberrant hotspots. The relationship between morphological alterations and brain function in pedophilia as well as their contribution to its psychopathology thus remain unclear. First, we assessed bimodal connectivity of structurally altered candidate regions using meta-analytic connectivity modeling (MACM) and resting-state correlations employing openly accessible data. We compared the ensuing connectivity maps to the activation likelihood estimation (ALE) maps of a recent quantitative meta-analysis of brain activity during processing of sexual stimuli. Second, we functionally characterized the structurally altered regions employing meta-data of a large-scale neuroimaging database. Candidate regions were functionally connected to key areas for processing of sexual stimuli. Moreover, we found that the functional role of structurally altered brain regions in pedophilia relates to nonsexual emotional as well as neurocognitive and executive functions, previously reported to be impaired in pedophiles. Our results suggest that structural brain alterations affect neural networks for sexual processing by way of disrupted functional connectivity, which may entail abnormal sexual arousal patterns. The findings moreover indicate that structural alterations account for common affective and neurocognitive impairments in pedophilia. The present multimodal integration of brain structure and function analyses links sexual and nonsexual psychopathology in pedophilia. © 2015 Wiley Periodicals, Inc.

Computational models of the pulmonary circulation: Insights and the move towards clinically directed studies

PubMed Central

Tawhai, Merryn H.; Clark, Alys R.; Burrowes, Kelly S.

2011-01-01

Biophysically-based computational models provide a tool for integrating and explaining experimental data, observations, and hypotheses. Computational models of the pulmonary circulation have evolved from minimal and efficient constructs that have been used to study individual mechanisms that contribute to lung perfusion, to sophisticated multi-scale and -physics structure-based models that predict integrated structure-function relationships within a heterogeneous organ. This review considers the utility of computational models in providing new insights into the function of the pulmonary circulation, and their application in clinically motivated studies. We review mathematical and computational models of the pulmonary circulation based on their application; we begin with models that seek to answer questions in basic science and physiology and progress to models that aim to have clinical application. In looking forward, we discuss the relative merits and clinical relevance of computational models: what important features are still lacking; and how these models may ultimately be applied to further increasing our understanding of the mechanisms occurring in disease of the pulmonary circulation. PMID:22034608

Sleep Disturbance, Daytime Symptoms, and Functional Performance in Patients With Stable Heart Failure: A Mediation Analysis.

PubMed

Jeon, Sangchoon; Redeker, Nancy S

2016-01-01

Sleep disturbance is common among patients with heart failure (HF) who also experience symptom burden and poor functional performance. We evaluated the extent to which sleep-related, daytime symptoms (fatigue, excessive daytime sleepiness, and depressive symptoms) mediate the relationship between sleep disturbance and functional performance among patients with stable HF. We recruited patients with stable HF for this secondary analysis of data from a cross-sectional, observational study. Participants completed unattended ambulatory polysomnography from which the Respiratory Disturbance Index was calculated, along with a Six-Minute Walk Test, questionnaires to elicit sleep disturbance (Pittsburgh Sleep Quality Index, Insomnia Symptoms from the Sleep Habits Questionnaire), daytime symptoms (Center for Epidemiologic Studies Depression Scale, Global Fatigue Index, Epworth Sleepiness Scale), and self-reported functional performance (Medical Outcomes Study SF36 V2 Physical Function Scale). We used structural equation modeling with latent variables for the key analysis. Follow-up, exploratory regression analysis with bootstrapped samples was used to examine the extent to which individual daytime symptoms mediated effects of sleep disturbance on functional performance after controlling for clinical and demographic covariates. The sample included 173 New York Heart Association Class I-IV HF patients (n = 60/34.7% women; M = 60.7, SD = 16.07 years of age). Daytime symptoms mediated the relationship between sleep disturbance and functional performance. Fatigue and depression mediated the relationship between insomnia symptoms and self-reported functional performance, whereas fatigue and sleepiness mediated the relationship between sleep quality and functional performance. Sleepiness mediated the relationship between the respiratory index and self-reported functional performance only in people who did not report insomnia. Daytime symptoms explain the relationships between sleep disturbance and functional performance in stable HF.

Structural and Molecular Modeling Features of P2X Receptors

PubMed Central

Alves, Luiz Anastacio; da Silva, João Herminio Martins; Ferreira, Dinarte Neto Moreira; Fidalgo-Neto, Antonio Augusto; Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; Caffarena, Ernesto Raúl; de Freitas, Mônica Santos

2014-01-01

Currently, adenosine 5′-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors. PMID:24637936

Intergenerational Transmission of Neuropsychological Executive Functioning

PubMed Central

Jester, Jennifer M.; Nigg, Joel T.; Puttler, Leon I.; Long, Jeffrey C.; Fitzgerald, Hiram E.; Zucker, Robert A.

2009-01-01

Relationships between parent and child executive functioning were examined, controlling for the critical potential confound of IQ, in a family study involving 434 children (130 girls, 304 boys) and 376 parents from 204 community recruited families at high risk for the development of substance use disorder. Structural equation modeling found evidence of separate executive functioning and intelligence (IQ) latent variables. Mother’s and father’s executive functioning were associated with child’s executive functioning (beta = 0.34 for father-child, 0.51 for mother-child), independently of parental IQ, which as expected was associated with child’s IQ (beta = 0.52 for father-child, 0.54 for mother-child). Familial correlations also showed a significant relationship of executive functioning between parents and offspring. These findings clarify that key elements of the executive functioning construct are reliably differentiable from IQ, and are transmitted in families. This work supports the utility of the construct of executive function in further study of the mechanisms and etiology of externalizing psychopathologies. PMID:19243871

Insights into the structural/conformational requirements of cytotoxic oxadiazoles as potential chemotherapeutic target binding agents

NASA Astrophysics Data System (ADS)

Alikhani, Radin; Razzaghi-Asl, Nima; Ramazani, Ali; Hosseinzadeh, Zahra

2018-07-01

A few novel previously synthesized 2,5-disubstituted 1,3,4-oxadiazoles with cytotoxic activity (1-17) were subjected to combined docking/quantum mechanical studies against chemotherapeutic targets. Selected macromolecular targets were those that were previously known to be inhibited by 1,3,4-oxadiazoles. Within this work, favorable binding modes/affinities of the oxadiazoles toward validated cancer targets were elucidated. Some oxadiazole structures exhibited ΔGbs comparable to or stronger than crystallographic ligands that were previously demonstrated to inhibit such targets. On the basis of obtained results, a general structure activity/binding relationship (SAR/SBR) was developed and a few 2,5-disubstituted 1,3,4-oxadiazole structures were proposed and virtually validated as potential cytotoxic candidates. To get more insight into structure binding relationship of candidate molecules within best correlated targets, docked conformation of the best in silico in vitro correlated oxadiazole structure was analyzed in terms of intermolecular binding energy components by functional B3LYP in association with split valence basis set using polarization functions (Def2-SVP). We believe that such modeling studies may be complementary to our previous results on the synthesis and cytotoxicity assessment of novel 1,3,4-oxadiazole derivatives through extending the scope of privileged structures toward designing new potential anti-tumor compounds.

Using combined hydrological variables for extracting functional signatures of catchments to better assess the acceptability of model structures in conceptual catchment modelling

NASA Astrophysics Data System (ADS)

Fovet, O.; Hrachowitz, M.; RUIZ, L.; Gascuel-odoux, C.; Savenije, H.

2013-12-01

While most hydrological models reproduce the general flow dynamics of a system, they frequently fail to adequately mimic system internal processes. This is likely to make them inadequate to simulate solutes transport. For example, the hysteresis between storage and discharge, which is often observed in shallow hard-rock aquifers, is rarely well reproduced by models. One main reason is that this hysteresis has little weight in the calibration because objective functions are based on time series of individual variables. This reduces the ability of classical calibration/validation procedures to assess the relevance of the conceptual hypothesis associated with hydrological models. Calibrating models on variables derived from the combination of different individual variables (like stream discharge and groundwater levels) is a way to insure that models will be accepted based on their consistency. Here we therefore test the value of this more systems-like approach to test different hypothesis on the behaviour of a small experimental low-land catchment in French Brittany (ORE AgrHys) where a high hysteresis is observed on the stream flow vs. shallow groundwater level relationship. Several conceptual models were applied to this site, and calibrated using objective functions based on metrics of this hysteresis. The tested model structures differed with respect to the storage function in each reservoir, the storage-discharge function in each reservoir, the deep loss expressions (as constant or variable fraction), the number of reservoirs (from 1 to 4) and their organization (parallel, series). The observed hysteretic groundwater level-discharge relationship was not satisfactorily reproduced by most of the tested models except for the most complex ones. Those were thus more consistent, their underlying hypotheses are probably more realistic even though their performance for simulating observed stream flow was decreased. Selecting models based on such systems-like approach is likely to improve their efficiency for environmental application e.g. on solute transport issues. The next step would be to apply the same approach with variables combining hydrological and biogeochemical variables.

Structure-Function Perturbation and Dissociation of Tetrameric Urate Oxidase by High Hydrostatic Pressure

PubMed Central

Girard, Eric; Marchal, Stéphane; Perez, Javier; Finet, Stéphanie; Kahn, Richard; Fourme, Roger; Marassio, Guillaume; Dhaussy, Anne-Claire; Prangé, Thierry; Giffard, Marion; Dulin, Fabienne; Bonneté, Françoise; Lange, Reinhard; Abraini, Jacques H.; Mezouar, Mohamed; Colloc'h, Nathalie

2010-01-01

Abstract Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms. PMID:20483346

Scoring functions for protein-protein interactions.

PubMed

Moal, Iain H; Moretti, Rocco; Baker, David; Fernández-Recio, Juan

2013-12-01

The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

Game Theory, Conditional Preferences, and Social Influence

PubMed Central

Stirling, Wynn C.; Felin, Teppo

2013-01-01

Neoclassical noncooperative game theory is based on a simple, yet powerful synthesis of mathematical and logical concepts: unconditional and immutable preference orderings and individual rationality. Although this structure has proven useful for characterizing competitive multi-player behavior, its applicability to scenarios involving complex social relationships is problematic. In this paper we directly address this limitation by the introduction of a conditional preference structure that permits players to modulate their preference orderings as functions of the preferences of other players. Embedding this expanded preference structure in a formal and graphical framework provides a systematic approach for characterizing a complex society. The result is an influence network that allows conditional preferences to propagate through the community, resulting in an emergent social model which characterizes all of the social relationships that exist and which leads to solution concepts that account for both group and individual interests. The Ultimatum game is presented as an example of how social influence can be modeled with conditional preferences. PMID:23451078

Game theory, conditional preferences, and social influence.

PubMed

Stirling, Wynn C; Felin, Teppo

2013-01-01

Neoclassical noncooperative game theory is based on a simple, yet powerful synthesis of mathematical and logical concepts: unconditional and immutable preference orderings and individual rationality. Although this structure has proven useful for characterizing competitive multi-player behavior, its applicability to scenarios involving complex social relationships is problematic. In this paper we directly address this limitation by the introduction of a conditional preference structure that permits players to modulate their preference orderings as functions of the preferences of other players. Embedding this expanded preference structure in a formal and graphical framework provides a systematic approach for characterizing a complex society. The result is an influence network that allows conditional preferences to propagate through the community, resulting in an emergent social model which characterizes all of the social relationships that exist and which leads to solution concepts that account for both group and individual interests. The Ultimatum game is presented as an example of how social influence can be modeled with conditional preferences.

Depression and resilience mediates the effect of family function on quality of life of the elderly.

PubMed

Lu, Canjie; Yuan, Lexin; Lin, Weiquan; Zhou, Ying; Pan, Shengmao

2017-07-01

Family function, which improves individual resilience and strongly link to quality of life (QOL) among the elderly, increases the risk of depression. Because of these demonstrated relationships, it can be hypothesized that both depression and resilience are mediators of the association between family function and QOL. To test this hypothesis, the structural equation model (SEM) constructed by Amos 21.0 was employed to assess the indirect effect of depression (Geriatric Depression Scale, GDS) and resilience (Connor-Davidson Resilience Scale, CD-RISC) on the relationship between family function (Family APGAR Score, APGAR) and QOL (12-item Short Form health survey, SF-12) in 474 elderly adults from three communities in Guangzhou, China. Correlation matrix showed that depression is significantly negatively correlated with family functioning (r=-0.54, P<0.01), resilience (r=-0.46, P<0.01) and QOL (r=-0.63, P<0.01), while resilience is significantly positively correlated with family functioning (r=0.35, P<0.01) and QOL (r=0.40, P<0.01). SEM indicated that Family functioning appeared to have significant indirect effects through resilience (β=0.089) and depression (β=0.307; combined β=0.056) on QOL (R 2 =0.55). The model fit indices showed a good fit of the model of the data (χ 2 /df=1.362, P>0.05, SRMR=0.023, RMSEA=0.028, GFI=0.985, NFI=0.987, TLI=0.993, CFI=0.996). The finding supports the assumption that depression and resilience are consistent intermediary factors of the relationship between family function and QOL among the elderly. Copyright © 2017 Elsevier B.V. All rights reserved.

Cognitive aging on latent constructs for visual processing capacity: a novel structural equation modeling framework with causal assumptions based on a theory of visual attention.

PubMed

Nielsen, Simon; Wilms, L Inge

2014-01-01

We examined the effects of normal aging on visual cognition in a sample of 112 healthy adults aged 60-75. A testbattery was designed to capture high-level measures of visual working memory and low-level measures of visuospatial attention and memory. To answer questions of how cognitive aging affects specific aspects of visual processing capacity, we used confirmatory factor analyses in Structural Equation Modeling (SEM; Model 2), informed by functional structures that were modeled with path analyses in SEM (Model 1). The results show that aging effects were selective to measures of visual processing speed compared to visual short-term memory (VSTM) capacity (Model 2). These results are consistent with some studies reporting selective aging effects on processing speed, and inconsistent with other studies reporting aging effects on both processing speed and VSTM capacity. In the discussion we argue that this discrepancy may be mediated by differences in age ranges, and variables of demography. The study demonstrates that SEM is a sensitive method to detect cognitive aging effects even within a narrow age-range, and a useful approach to structure the relationships between measured variables, and the cognitive functional foundation they supposedly represent.

The Development of Executive Functions and Early Mathematics: A Dynamic Relationship

ERIC Educational Resources Information Center

Van der Ven, Sanne H. G.; Kroesbergen, Evelyn H.; Boom, Jan; Leseman, Paul P. M.

2012-01-01

Background: The relationship between executive functions and mathematical skills has been studied extensively, but results are inconclusive, and how this relationship evolves longitudinally is largely unknown. Aim: The aim was to investigate the factor structure of executive functions in inhibition, shifting, and updating; the longitudinal…

A case study examination of structure and function in a state health department chronic disease unit.

PubMed

Alongi, Jeanne

2015-04-01

I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness.

A Case Study Examination of Structure and Function in a State Health Department Chronic Disease Unit

PubMed Central

2015-01-01

Objectives. I explored the structural and operational practices of the chronic disease prevention and control unit of a state health department and proposed a conceptual model of structure, function, and effectiveness for future study. Methods. My exploratory case study examined 7 elements of organizational structure and practice. My interviews with staff and external stakeholders of a single chronic disease unit yielded quantitative and qualitative data that I coded by perspective, process, relationship, and activity. I analyzed these for patterns and emerging themes. Results. Chi-square analysis revealed significant correlations among collaboration with goal ambiguity, political support, and responsiveness, and evidence-based decisions with goal ambiguity and responsiveness. Conclusions. Although my study design did not permit conclusions about causality, my findings suggested that some elements of the model might facilitate effectiveness for chronic disease units and should be studied further. My findings might have important implications for identifying levers around which capacity can be built that may strengthen effectiveness. PMID:25689211

A structural comparison of 'real' and 'model' calmodulin clarified allosteric interactions regulating domain motion.

PubMed

Shimoyama, Hiromitsu

2018-05-07

Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates various biochemical processes. CaM acts via structural changes and complex forming with its target enzymes. CaM has two globular domains (N-lobe and C-lobe) connected by a long linker region. Upon calcium binding, the N-lobe and C-lobe undergo local conformational changes, after that, entire CaM wraps the target enzyme through a large conformational change. However, the regulation mechanism, such as allosteric interactions regulating the conformational changes, is still unclear. In order to clarify the allosteric interactions, in this study, experimentally obtained 'real' structures are compared to 'model' structures lacking the allosteric interactions. As the allosteric interactions would be absent in calcium-free CaM (apo-CaM), allostery-eliminated calcium-bound CaM (holo-CaM) models were constructed by combining the apo-CaM's linker and the holo-CaM's N- and C-lobe. Before the comparison, the 'real' and 'model' structures were clustered and cluster-cluster relationship was determined by a principal component analysis. The structures were compared based on the relationship, then, a distance map and a contact probability analysis clarified that the inter-domain motion is regulated by several groups of inter-domain contacting residue pairs. The analyses suggested that these residues cause inter-domain translation and rotation, and as a consequence, the motion encourage structural diversity. The resultant diversity would contribute to the functional versatility of CaM.

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

PubMed Central

Akiva, Eyal; Copp, Janine N.; Tokuriki, Nobuhiko; Babbitt, Patricia C.

2017-01-01

Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold. PMID:29078300

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

PubMed

Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

2016-05-01

Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bird functional diversity decreases with time since disturbance: Does patchy prescribed fire enhance ecosystem function?.

PubMed

Sitters, Holly; Di Stefano, Julian; Christie, Fiona; Swan, Matthew; York, Alan

2016-01-01

Animal species diversity is often associated with time since disturbance, but the effects of disturbances such as fire on functional diversity are unknown. Functional diversity measures the range, abundance, and distribution of trait values in a community, and links changes in species composition with the consequences for ecosystem function. Improved understanding of the relationship between time since fire (TSF) and functional diversity is critical given that the frequency of both prescribed fire and wildfire is expected to increase. To address this knowledge gap, we examined responses of avian functional diversity to TSF and two direct measures of environmental heterogeneity, plant diversity, and structural heterogeneity. We surveyed birds across a 70-year chronosequence spanning four vegetation types in southeast Australia. Six bird functional traits were used to derive four functional diversity indices (richness, evenness, divergence, and dispersion) and the effects of TSF, plant diversity and structural heterogeneity on species richness and the functional diversity indices were examined using mixed models. We used a regression tree method to identify traits associated with species more common in young vegetation. Functional richness and dispersion were negatively associated with TSF in all vegetation types, suggesting that recent prescribed fire generates heterogeneous vegetation and provides greater opportunities for resource partitioning. Species richness was not significantly associated with TSF, and is probably an unreliable surrogate for functional diversity in fire-prone systems. A positive, relationship between functional evenness and structural heterogeneity was comnon to all vegetation types, suggesting that fine-scale (tens of meters) structural variation can enhance ecosystem function. Species more common in young vegetation were primarily linked by their specialist diets, indicating that ecosystem services such as seed dispersal and insect control are enhanced in more recently burnt vegetation. We suggest that patchy prescribed fire sustains functional diversity, and that controlled use of patchy fire to break up large expanses of mature vegetation will enhance ecosystem function.

Latent constructs model explaining the attachment-linked variation in autobiographical remembering.

PubMed

Öner, Sezin; Gülgöz, Sami

2016-01-01

In the current study, we proposed a latent constructs model to characterise the qualitative aspects of autobiographical remembering and investigated the structural relations in the model that may vary across individuals. Primarily, we focused on the memories of romantic relationships and argued that attachment anxiety and avoidance would be reflected in the ways that individuals encode, rehearse, or remember autobiographical memories in close relationships. Participants reported two positive and two negative relationship-specific memories and rated the characteristics for each memory. As predicted, the basic memory model yielded appropriate fit, indicating that event characteristics (EC) predicted the frequency of rehearsal (RC) and phenomenology at retrieval (PC). When attachment variables were integrated, the model showed that rehearsal mediated the link between anxiety and PC, especially for negative memories. On the other hand, for avoidance EC was the key factor mediating the link between avoidance and RC, as well as PC. Findings were discussed with respect to autobiographical memory functions emphasising a systematically, integrated framework.

Recovery among Adolescents: Models for Post-Treatment Gains in Drug Abuse Treatments

PubMed Central

Joe, George W.; Knight, Danica Kalling; Becan, Jennifer E.; Flynn, Patrick M.

2013-01-01

Recovery among adolescents undergoing substance abuse treatment was modeled in terms of pre-treatment motivation, therapeutic relationships, psychological functioning, treatment retention, legal pressures, DSM diagnoses, and client demographics. To address between program differences, a within-covariance matrix, based on 547 youth, was used. Applicability of the results across treatment modalities was also examined. The data were from the NIDA-sponsored DATOS Adolescent study. Results from structural equation models (estimated using Mplus) indicated that higher pre-treatment motivation predicted stronger counselor and in-treatment peer relationships, better counselor relationships and retention predicted less illegal drug use at follow-up, and DSM diagnosis was important in the treatment process. Overall, illegal drug use at follow-up was associated with post-treatment alcohol consumption, cigarette use, condom nonuse, psychological distress, criminality, and school non-attendance. The results document the importance of motivation and therapeutic relationships on recovery, even when taking into account the relative effects of legal pressures, DSM diagnoses, and demographics. PMID:24238715

The effect of hippocampal function, volume and connectivity on posterior cingulate cortex functioning during episodic memory fMRI in mild cognitive impairment.

PubMed

Papma, Janne M; Smits, Marion; de Groot, Marius; Mattace Raso, Francesco U; van der Lugt, Aad; Vrooman, Henri A; Niessen, Wiro J; Koudstaal, Peter J; van Swieten, John C; van der Veen, Frederik M; Prins, Niels D

2017-09-01

Diminished function of the posterior cingulate cortex (PCC) is a typical finding in early Alzheimer's disease (AD). It is hypothesized that in early stage AD, PCC functioning relates to or reflects hippocampal dysfunction or atrophy. The aim of this study was to examine the relationship between hippocampus function, volume and structural connectivity, and PCC activation during an episodic memory task-related fMRI study in mild cognitive impairment (MCI). MCI patients (n = 27) underwent episodic memory task-related fMRI, 3D-T1w MRI, 2D T2-FLAIR MRI and diffusion tensor imaging. Stepwise linear regression analysis was performed to examine the relationship between PCC activation and hippocampal activation, hippocampal volume and diffusion measures within the cingulum along the hippocampus. We found a significant relationship between PCC and hippocampus activation during successful episodic memory encoding and correct recognition in MCI patients. We found no relationship between the PCC and structural hippocampal predictors. Our results indicate a relationship between PCC and hippocampus activation during episodic memory engagement in MCI. This may suggest that during episodic memory, functional network deterioration is the most important predictor of PCC functioning in MCI. • PCC functioning during episodic memory relates to hippocampal functioning in MCI. • PCC functioning during episodic memory does not relate to hippocampal structure in MCI. • Functional network changes are an important predictor of PCC functioning in MCI.

Cavitation and Its Discontents: Opportunities for Resolving Current Controversies1[C

PubMed Central

Rockwell, Fulton E.; Wheeler, James K.; Holbrook, N. Michele

2014-01-01

Cavitation has long been recognized as a key constraint on the structure and functional integrity of the xylem. Yet, recent results call into question how well we understand cavitation in plants. Here, we consider embolism formation in angiosperms at two scales. The first focuses on how air-seeding occurs at the level of pit membranes, raising the question of whether capillary failure is an appropriate physical model. The second addresses methodological uncertainties that affect our ability to infer the formation of embolism and its reversal in plant stems. Overall, our goal is to open up fresh perspectives on the structure-function relationships of xylem. PMID:24501002

Machine learnt bond order potential to model metal-organic (Co-C) heterostructures.

PubMed

Narayanan, Badri; Chan, Henry; Kinaci, Alper; Sen, Fatih G; Gray, Stephen K; Chan, Maria K Y; Sankaranarayanan, Subramanian K R S

2017-11-30

A fundamental understanding of the inter-relationships between structure, morphology, atomic scale dynamics, chemistry, and physical properties of mixed metallic-covalent systems is essential to design novel functional materials for applications in flexible nano-electronics, energy storage and catalysis. To achieve such knowledge, it is imperative to develop robust and computationally efficient atomistic models that describe atomic interactions accurately within a single framework. Here, we present a unified Tersoff-Brenner type bond order potential (BOP) for a Co-C system, trained against lattice parameters, cohesive energies, equation of state, and elastic constants of different crystalline phases of cobalt as well as orthorhombic Co 2 C derived from density functional theory (DFT) calculations. The independent BOP parameters are determined using a combination of supervised machine learning (genetic algorithms) and local minimization via the simplex method. Our newly developed BOP accurately describes the structural, thermodynamic, mechanical, and surface properties of both the elemental components as well as the carbide phases, in excellent accordance with DFT calculations and experiments. Using our machine-learnt BOP potential, we performed large-scale molecular dynamics simulations to investigate the effect of metal/carbon concentration on the structure and mechanical properties of porous architectures obtained via self-assembly of cobalt nanoparticles and fullerene molecules. Such porous structures have implications in flexible electronics, where materials with high electrical conductivity and low elastic stiffness are desired. Using unsupervised machine learning (clustering), we identify the pore structure, pore-distribution, and metallic conduction pathways in self-assembled structures at different C/Co ratios. We find that as the C/Co ratio increases, the connectivity between the Co nanoparticles becomes limited, likely resulting in low electrical conductivity; on the other hand, such C-rich hybrid structures are highly flexible (i.e., low stiffness). The BOP model developed in this work is a valuable tool to investigate atomic scale processes, structure-property relationships, and temperature/pressure response of Co-C systems, as well as design organic-inorganic hybrid structures with a desired set of properties.

Disentangling the relationship between children’s motor ability, executive function and academic achievement

PubMed Central

Egger, Fabienne; Benzing, Valentin; Jäger, Katja; Conzelmann, Achim; Roebers, Claudia M.; Pesce, Caterina

2017-01-01

Even though positive relations between children’s motor ability and their academic achievement are frequently reported, the underlying mechanisms are still unclear. Executive function has indeed been proposed, but hardly tested as a potential mediator. The aim of the present study was therefore to examine the mediating role of executive function in the relationship between motor ability and academic achievement, also investigating the individual contribution of specific motor abilities to the hypothesized mediated linkage to academic achievement. At intervals of ten weeks, 236 children aged between 10 and 12 years were tested in terms of their motor ability (t1: cardiovascular endurance, muscular strength, motor coordination), core executive functions (t2: updating, inhibition, shifting), and academic achievement (t3: mathematics, reading, spelling). Structural equation modelling revealed executive function to be a mediator in the relation between motor ability and academic achievement, represented by a significant indirect effect. In separate analyses, each of the three motor abilities were positively related to children’s academic achievement. However, only in the case of children’s motor coordination, the mediation by executive function accounted for a significance percentage of variance of academic achievement data. The results provide evidence in support of models that conceive executive function as a mechanism explaining the relationship that links children’s physical activity-related outcomes to academic achievement and strengthen the advocacy for quality physical activity not merely focused on health-related physical fitness outcomes, but also on motor skill development and learning. PMID:28817625

Causal inference in biology networks with integrated belief propagation.

PubMed

Chang, Rui; Karr, Jonathan R; Schadt, Eric E

2015-01-01

Inferring causal relationships among molecular and higher order phenotypes is a critical step in elucidating the complexity of living systems. Here we propose a novel method for inferring causality that is no longer constrained by the conditional dependency arguments that limit the ability of statistical causal inference methods to resolve causal relationships within sets of graphical models that are Markov equivalent. Our method utilizes Bayesian belief propagation to infer the responses of perturbation events on molecular traits given a hypothesized graph structure. A distance measure between the inferred response distribution and the observed data is defined to assess the 'fitness' of the hypothesized causal relationships. To test our algorithm, we infer causal relationships within equivalence classes of gene networks in which the form of the functional interactions that are possible are assumed to be nonlinear, given synthetic microarray and RNA sequencing data. We also apply our method to infer causality in real metabolic network with v-structure and feedback loop. We show that our method can recapitulate the causal structure and recover the feedback loop only from steady-state data which conventional method cannot.

Finite element modeling of sound transmission with perforations of tympanic membrane

PubMed Central

Gan, Rong Z.; Cheng, Tao; Dai, Chenkai; Yang, Fan; Wood, Mark W.

2009-01-01

A three-dimensional finite element (FE) model of human ear with structures of the external ear canal, middle ear, and cochlea has been developed recently. In this paper, the FE model was used to predict the effect of tympanic membrane (TM) perforations on sound transmission through the middle ear. Two perforations were made in the posterior-inferior quadrant and inferior site of the TM in the model with areas of 1.33 and 0.82 mm2, respectively. These perforations were also created in human temporal bones with the same size and location. The vibrations of the TM (umbo) and stapes footplate were calculated from the model and measured from the temporal bones using laser Doppler vibrometers. The sound pressure in the middle ear cavity was derived from the model and measured from the bones. The results demonstrate that the TM perforations can be simulated in the FE model with geometrical visualization. The FE model provides reasonable predictions on effects of perforation size and location on middle ear transfer function. The middle ear structure-function relationship can be revealed with multi-field coupled FE analysis. PMID:19603881

Network-Level Structure-Function Relationships in Human Neocortex

PubMed Central

Mišić, Bratislav; Betzel, Richard F.; de Reus, Marcel A.; van den Heuvel, Martijn P.; Berman, Marc G.; McIntosh, Anthony R.; Sporns, Olaf

2016-01-01

The dynamics of spontaneous fluctuations in neural activity are shaped by underlying patterns of anatomical connectivity. While numerous studies have demonstrated edge-wise correspondence between structural and functional connections, much less is known about how large-scale coherent functional network patterns emerge from the topology of structural networks. In the present study, we deploy a multivariate statistical technique, partial least squares, to investigate the association between spatially extended structural networks and functional networks. We find multiple statistically robust patterns, reflecting reliable combinations of structural and functional subnetworks that are optimally associated with one another. Importantly, these patterns generally do not show a one-to-one correspondence between structural and functional edges, but are instead distributed and heterogeneous, with many functional relationships arising from nonoverlapping sets of anatomical connections. We also find that structural connections between high-degree hubs are disproportionately represented, suggesting that these connections are particularly important in establishing coherent functional networks. Altogether, these results demonstrate that the network organization of the cerebral cortex supports the emergence of diverse functional network configurations that often diverge from the underlying anatomical substrate. PMID:27102654

Psychological commitment as a mediator of the relationship between involvement and loyalty

Treesearch

Joohyun Lee; Alan Graefe

2002-01-01

This study tested the ill-understood issues of involvement and loyalty relations. Even though many studies have indicated that loyalty is a function of involvement, only minimal agreement has been reached on the extent to which the constructs of involvement would predict repeat participation. A structural model is developed that relates members' involvement and...

Investigating the Structural Relationship for the Determinants of Cloud Computing Adoption in Education

ERIC Educational Resources Information Center

Bhatiasevi, Veera; Naglis, Michael

2016-01-01

This research is one of the first few to investigate the adoption and usage of cloud computing in higher education in the context of developing countries, in this case Thailand. It proposes extending the technology acceptance model to integrate subjective norm, perceived convenience, trust, computer self-efficacy, and software functionality in…

Modeling a Neural Network as a Teaching Tool for the Learning of the Structure-Function Relationship

ERIC Educational Resources Information Center

Salinas, Dino G.; Acevedo, Cristian; Gomez, Christian R.

2010-01-01

The authors describe an activity they have created in which students can visualize a theoretical neural network whose states evolve according to a well-known simple law. This activity provided an uncomplicated approach to a paradigm commonly represented through complex mathematical formulation. From their observations, students learned many basic…

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

Relationships between Child Behavior Problems and Family Functioning: A Literature Review.

ERIC Educational Resources Information Center

van As, N. M. C.; Janssens, J. M. A. M.

2002-01-01

Reviews research examining the relationship between family functioning and child behavior problems. Focuses on parenting styles, intergenerational relationships, family structure, and family interaction patterns. Finds that child behavior problems are related to a lack of parental support, an imbalanced parent- child relationship, a lack of…

A Comparative Structural Equation Modeling Investigation of the Relationships among Teaching, Cognitive and Social Presence

ERIC Educational Resources Information Center

Kozan, Kadir

2016-01-01

The present study investigated the relationships among teaching, cognitive, and social presence through several structural equation models to see which model would better fit the data. To this end, the present study employed and compared several different structural equation models because different models could fit the data equally well. Among…

Structural equation modeling of motor impairment, gross motor function, and the functional outcome in children with cerebral palsy.

PubMed

Park, Eun-Young; Kim, Won-Ho

2013-05-01

Physical therapy intervention for children with cerebral palsy (CP) is focused on reducing neurological impairments, improving strength, and preventing the development of secondary impairments in order to improve functional outcomes. However, relationship between motor impairments and functional outcome has not been proved definitely. This study confirmed the construct of motor impairment and performed structural equation modeling (SEM) between motor impairment, gross motor function, and functional outcomes of regarding activities of daily living in children with CP. 98 children (59 boys, 39 girls) with CP participated in this cross-sectional study. Mean age was 11 y 5 mo (SD 1 y 9 mo). The Manual Muscle Test (MMT), the Modified Ashworth Scale (MAS), range of motion (ROM) measurement, and the selective motor control (SMC) scale were used to assess motor impairments. Gross motor function and functional outcomes were measured using the Gross Motor Function Measure (GMFM) and the Functional Skills domain of the Pediatric Evaluation of Disability Inventory (PEDI) respectively. Measurement of motor impairment was consisted of strength, spasticity, ROM, and SMC. The construct of motor impairment was confirmed though an examination of a measurement model. The proposed SEM model showed good fit indices. Motor impairment effected gross motor function (β=-.0869). Gross motor function and motor impairment affected functional outcomes directly (β=0.890) and indirectly (β=-0.773) respectively. We confirmed that the construct of motor impairment consist of strength, spasticity, ROM, and SMC and it was identified through measurement model analysis. Functional outcomes are best predicted by gross motor function and motor impairments have indirect effects on functional outcomes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Thermostability in rubredoxin and its relationship to mechanical rigidity

NASA Astrophysics Data System (ADS)

Rader, A. J.

2010-03-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

Disentangling the Impact of Artistic Creativity on Creative Thinking, Working Memory, Attention, and Intelligence: Evidence for Domain-Specific Relationships with a New Self-Report Questionnaire

PubMed Central

Lunke, Katrin; Meier, Beat

2016-01-01

The goal of the present study was to take a new look at the relationship between creativity and cognitive functioning. Based on models that have postulated domain- and sub-domain-structures for different forms of creativity, like scientific, technical or artistic creativity with cognitive functions as important basis, we developed a new questionnaire. The Artistic Creativity Domains Compendium (ACDC) assesses interest, ability and performance in a distinct way for different domains of artistic creativity. We present the data of 270 adults tested with the ACDC, standard tests of divergent and convergent thinking, and tests of cognitive functions. We present fine-grained analyses on the internal and external validity of the ACDC and on the relationships between creativity, working memory, attention, and intelligence. Our results indicate domain-specific associations between creativity and attention as well as working memory. We conclude that the ACDC is a valid instrument to assess artistic creativity and that a fine-grained analysis reveals distinct patterns of relationships between separate domains of creativity and cognition. PMID:27516745

Disentangling the Impact of Artistic Creativity on Creative Thinking, Working Memory, Attention, and Intelligence: Evidence for Domain-Specific Relationships with a New Self-Report Questionnaire.

PubMed

Lunke, Katrin; Meier, Beat

2016-01-01

The goal of the present study was to take a new look at the relationship between creativity and cognitive functioning. Based on models that have postulated domain- and sub-domain-structures for different forms of creativity, like scientific, technical or artistic creativity with cognitive functions as important basis, we developed a new questionnaire. The Artistic Creativity Domains Compendium (ACDC) assesses interest, ability and performance in a distinct way for different domains of artistic creativity. We present the data of 270 adults tested with the ACDC, standard tests of divergent and convergent thinking, and tests of cognitive functions. We present fine-grained analyses on the internal and external validity of the ACDC and on the relationships between creativity, working memory, attention, and intelligence. Our results indicate domain-specific associations between creativity and attention as well as working memory. We conclude that the ACDC is a valid instrument to assess artistic creativity and that a fine-grained analysis reveals distinct patterns of relationships between separate domains of creativity and cognition.

A Web-Accessible Protein Structure Prediction Pipeline

DTIC Science & Technology

2009-06-01

Abstract Proteins are the molecular basis of nearly all structural, catalytic, sensory, and regulatory functions in living organisms. The biological...sensory, and regulatory functions in living organisms. The structure of a protein is essential in understanding its function at the molecular level...Characterizing sequence-structure and structure-function relationships have been the goals of molecular biology for more than three decades

Canopy structural complexity as a continental predictor of primary production: Using NEON to transform understanding of forest structure-function

NASA Astrophysics Data System (ADS)

Atkins, J. W.; Fahey, R. T.; Gough, C. M.; Hardiman, B. S.

2016-12-01

Ecosystem structure-function relationships represent a long-standing research area for ecosystem science. Relationships between canopy structural complexity (CSC) and net primary productivity (NPP), have been characterized for a limited number of sites, yet whether these relationships are conserved across eco-climatic boundaries remains unknown. We hypothesize an underlying mechanistic basis for global NPP-CSC linkages to include improved resource-use efficiency as CSC increases, examined here by correlating CSC with measures of light-use efficiency and nitrogen-use efficiency. Here we present a broad, continental scale analysis of CSC-NPP linkages. We are using multiple NEON sites coupled with other sites across a diverse array of temperate forest types spanning six eco-climatic domains of the continental United States to examine CSC-NPP relationships. Portable canopy LiDAR (PCL) data were used to calculate a suite of CSC metrics at the plot-level within each site. Ongoing work compares CSC to co-located measurements of wood net primary production estimated from the incremental change in woody biomass calculated using tree allometries. Results to date show CSC is highly variable across forest sites and may provide additional explanatory power for predicting NPP that is independent of other commonly used forest structural attributes such as leaf area index. CSC metrics such as rugosity vary widely across sites—ranging from high values (30 - 35) in complex canopies such as the Great Smoky Mountains to low values in open, savanna systems like North-Central Florida (< 0.5 - 2). NPP, and light- and nitrogen-use calculations are underway and will be paired with site-level CSC, with the expectation that CSC, resource-use efficiency, and NPP are positively correlated. Advancing understanding of how and why CSC affects forest NPP across a broad spatial dimension could transform mechanistic understanding of ecosystem structure-carbon cycling relationships, and greatly improve carbon cycling models and remote sensing applications, while providing a crucial linkage between the two.

[A process of aquatic ecological function regionalization: The dual tree framework and conceptual model].

PubMed

Guo, Shu Hai; Wu, Bo

2017-12-01

Aquatic ecological regionalization and aquatic ecological function regionalization are the basis of water environmental management of a river basin and rational utilization of an aquatic ecosystem, and have been studied in China for more than ten years. Regarding the common problems in this field, the relationship between aquatic ecological regionalization and aquatic ecological function regionalization was discussed in this study by systematic analysis of the aquatic ecological zoning and the types of aquatic ecological function. Based on the dual tree structure, we put forward the RFCH process and the diamond conceptual model. Taking Liaohe River basin as an example and referring to the results of existing regionalization studies, we classified the aquatic ecological function regions based on three-class aquatic ecological regionalization. This study provided a process framework for aquatic ecological function regionalization of a river basin.

The proteome: structure, function and evolution

PubMed Central

Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J.E

2006-01-01

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family. PMID:16524832

Employee subjective well-being and physiological functioning: An integrative model.

PubMed

Kuykendall, Lauren; Tay, Louis

2015-01-01

Research shows that worker subjective well-being influences physiological functioning-an early signal of poor health outcomes. While several theoretical perspectives provide insights on this relationship, the literature lacks an integrative framework explaining the relationship. We develop a conceptual model explaining the link between subjective well-being and physiological functioning in the context of work. Integrating positive psychology and occupational stress perspectives, our model explains the relationship between subjective well-being and physiological functioning as a result of the direct influence of subjective well-being on physiological functioning and of their common relationships with work stress and personal resources, both of which are influenced by job conditions.

Supercoil Formation During DNA Melting

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avsaroglu, Baris; Kabakcioglu, Alkan

2009-03-01

Supercoil formation plays a key role in determining the structure-function relationship in DNA. Biological and technological processes, such as protein synthesis, polymerase chain reaction, and microarrays relys on separation of the two strands in DNA, which is coupled to the unwinding of the supercoiled structure. This problem has been studied theoretically via Peyrard-Bishop and Poland-Scheraga type models, which include a simple representation of the DNA structural properties. In recent years, computational models, which provide a more realtistic representaion of DNA molecule, have been used to study the melting behavior of short DNA chains. Here, we will present a new coarse-grained model of DNA which is capable of simulating sufficiently long DNA chains for studying the supercoil formation during melting, without sacrificing the local structural properties. Our coarse-grained model successfully reproduces the local geometry of the DNA molecule, such as the 3'-5' directionality, major-minor groove structure, and the helical pitch. We will present our initial results on the dynamics of supercoiling during DNA melting.

Effects of soil water and heat relationship under various snow cover during freezing-thawing periods in Songnen Plain, China.

PubMed

Fu, Qiang; Hou, Renjie; Li, Tianxiao; Jiang, Ruiqi; Yan, Peiru; Ma, Ziao; Zhou, Zhaoqiang

2018-01-22

In this study, the spatial variations of soil water and heat under bare land (BL), natural snow (NS), compacted snow (CS) and thick snow (TS) treatments were analyzed. The relationship curve between soil temperature and water content conforms to the exponential filtering model, by means of the functional form of the model, it was defined as soil water and heat relation function model. On this basis, soil water and heat function models of 10, 20, 40, 60, 100, and 140 cm were established. Finally, a spatial variation law of the relationship effect was described based on analysising of the differences between the predicted and measured results. During freezing period, the effects of external factors on soil were hindered by snow cover. As the snow increased, the accuracy of the function model gradually improved. During melting period, infiltration by snowmelt affected the relationship between the soil temperature and moisture. With the increasing of snow, the accuracy of the function models gradually decreased. The relationship effects of soil water and heat increased with increasing depth within the frozen zone. In contrast, below the frozen layer, the relationship of soil water and heat was weaker, and the function models were less accurate.

Six-month longitudinal associations between cognitive functioning and distress among the community-based elderly in Hong Kong: A cross-lagged panel analysis.

PubMed

Leung, Chantel Joanne; Cheng, Lewis; Yu, Junhong; Yiend, Jenny; Lee, Tatia M C

2018-07-01

Although previous studies have extensively documented the cross-sectional relationship between cognitive impairment and psychological distress, findings relating to their longitudinal associations remains mixed. The present study examines the longitudinal associations and mutual influence between cognitive functioning and psychological distress across six months among community-dwelling elderly in Hong Kong. A total of 162 older adults (40 males; M age  = 69.8 years, SD = 6.4) were administered objective and subjective measures of cognitive functioning, as well as self-reported ratings of distress, at two time points six months apart. Using structural equation modeling, we tested the cross-lagged relationships between cognitive functioning and distress. Our cross-lagged model indicated that cognitive functioning at baseline significantly predicted subsequent psychological distress. However, distress was not significantly associated with subsequent cognitive functioning. Additionally, the objective and subjective measures of cognitive functioning were not significantly correlated. These findings suggested that distress may occur as a consequence of poorer cognitive functioning in elderly, but not vice versa. The lack of correlation between objective and subjective cognitive measures suggested that the participants may not have adequate insight into their cognitive abilities. The implications of these findings are discussed. Copyright © 2018. Published by Elsevier B.V.

Social relationships and physician utilization among older adults—A systematic review

PubMed Central

Inhestern, Laura; von dem Knesebeck, Olaf

2017-01-01

Background In older age health needs and demand for health services utilization increase. Individual’s social relationships can play a decisive role regarding the utilization of outpatient health care services. This systematic review examines the associations of structural and functional dimensions of social relationships with outpatient health services use of older adults. Methods The databases PubMed, CINAHL, SocINDEX, PsycINFO, International Bibliography of the Social Sciences (IBSS), Sociological Abstracts, and Applied Social Sciences Index and Abstracts (ASSIA) were searched in February 2016. The methodological and reporting quality of the articles was assessed and the results were synthesized descriptively and systematically. Results Out of 1.392 hits, 36 articles (35 studies) were included in the systematic review. The methodological and reporting quality of the included articles was reasonable. Various structural and functional characteristics of social relationships were associated with the use (yes/no) and the frequency of using outpatient care among older adults. The majority of the associations between structural dimensions of social relationships and the use of physicians were positive and moderate in strength. The associations between functional dimensions of social relationships and the probability of using physician services were inconsistent and varied in strength. For the most part, social relationship variables assigned to the structural dimension were positively and weakly to moderately associated with the frequency of physician visits. Functional aspects of social relationships also tended to have positive associations with the frequency of physician utilization. The associations were weak to moderate in strength. Conclusions Measuring social relationships and their influence on health services use is a challenging methodological endeavor indicated by the inconclusive results. The results suggest that the outpatient care utilization behavior of older individuals being structurally and functionally integrated in social relationships is different to older adults being socially isolated or having no social support. All in all, the current status of quantitative data was insufficient. Future health services research should accentuate social ties in more detail, especially according to quality aspects of social relationships. PMID:28957429

Space station functional relationships analysis

NASA Technical Reports Server (NTRS)

Tullis, Thomas S.; Bied, Barbra R.

1988-01-01

A systems engineering process is developed to assist Space Station designers to understand the underlying operational system of the facility so that it can be physically arranged and configured to support crew productivity. The study analyzes the operational system proposed for the Space Station in terms of mission functions, crew activities, and functional relationships in order to develop a quantitative model for evaluation of interior layouts, configuration, and traffic analysis for any Station configuration. Development of the model involved identification of crew functions, required support equipment, criteria of assessing functional relationships, and tools for analyzing functional relationship matrices, as well as analyses of crew transition frequency, sequential dependencies, support equipment requirements, potential for noise interference, need for privacy, and overall compatability of functions. The model can be used for analyzing crew functions for the Initial Operating Capability of the Station and for detecting relationships among these functions. Note: This process (FRA) was used during Phase B design studies to test optional layouts of the Space Station habitat module. The process is now being automated as a computer model for use in layout testing of the Space Station laboratory modules during Phase C.

Hot and Spicy versus Cool and Minty as an Example of Organic Structure-Activity Relationships

NASA Astrophysics Data System (ADS)

Kimbrough, Doris R.

1997-07-01

There are two classes of substances that activate neural receptors that are involved in temperature perception. Structures of substances found in spices and food that we normally associate with "hot" (or spicy) and "cool" (or minty) flavors are presented and discussed. Functional group similarities within the two groups provide an interesting example of the relationship between molecular structure and molecular function in organic chemistry.

Functional relationships between wood structure and vulnerability to xylem cavitation in races of Eucalyptus globulus differing in wood density.

PubMed

Barotto, Antonio José; Monteoliva, Silvia; Gyenge, Javier; Martinez-Meier, Alejandro; Fernandez, María Elena

2018-02-01

Wood density can be considered as a measure of the internal wood structure, and it is usually used as a proxy measure of other mechanical and functional traits. Eucalyptus is one of the most important commercial forestry genera worldwide, but the relationship between wood density and vulnerability to cavitation in this genus has been little studied. The analysis is hampered by, among other things, its anatomical complexity, so it becomes necessary to address more complex techniques and analyses to elucidate the way in which the different anatomical elements are functionally integrated. In this study, vulnerability to cavitation in two races of Eucalyptus globulus Labill. with different wood density was evaluated through Path analysis, a multivariate method that allows evaluation of descriptive models of causal relationship between variables. A model relating anatomical variables with wood properties and functional parameters was proposed and tested. We found significant differences in wood basic density and vulnerability to cavitation between races. The main exogenous variables predicting vulnerability to cavitation were vessel hydraulic diameter and fibre wall fraction. Fibre wall fraction showed a direct impact on wood basic density and the slope of vulnerability curve, and an indirect and negative effect over the pressure imposing 50% of conductivity loss (P50) through them. Hydraulic diameter showed a direct negative effect on P50, but an indirect and positive influence over this variable through wood density on one hand, and through maximum hydraulic conductivity (ks max) and slope on the other. Our results highlight the complexity of the relationship between xylem efficiency and safety in species with solitary vessels such as Eucalyptus spp., with no evident compromise at the intraspecific level. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Relationship between Mental Health and Burden among Primary Caregivers of Outpatients with Schizophrenia.

PubMed

Yu, Wenjun; Chen, Jia; Hu, Jize; Hu, JingChu

2018-01-24

There is growing recognition that caring for a patient with schizophrenia often results in high levels of perceived burden and poorer overall mental health for caregivers. A quantitative cross-sectional design and standardized instruments were used to collect data from 355 primary caregivers of adults in outpatient care with schizophrenia in China. Structural equation modeling was used to examine the association between caregiver burden and mental health among primary caregivers and whether this association is influenced by personality, coping style, and family functioning, based on a diathesis-stress perspective. Goodness-of-fit indices (χ 2 /df = 1.406, GFI = 0.919, CFI = 0.957, etc.) confirmed that the modified model fit the data well. In line with the diathesis-stress model, and with this study's hypotheses, we found that caregiver burden was significantly related to mental health outcomes directly. The final model showed that personality traits, coping style, and family function influenced the relationship between caregiver burden and mental health. The neuroticism personality traits have a direct effect on caregiver burden and family functioning in this sample. Coping style had a direct effect on the caregiver burden, and family functioning had a direct effect on the caregiver burden. Our final model about primary caregivers can be applied clinically to predict mental health outcomes from caregiver burden. © 2018 Family Process Institute.

Structural hierarchy in molecular films of two class II hydrophobins.

PubMed

Paananen, Arja; Vuorimaa, Elina; Torkkeli, Mika; Penttilä, Merja; Kauranen, Martti; Ikkala, Olli; Lemmetyinen, Helge; Serimaa, Ritva; Linder, Markus B

2003-05-13

Hydrophobins are highly surface-active proteins that are specific to filamentous fungi. They function as coatings on various fungal structures, enable aerial growth of hyphae, and facilitate attachment to surfaces. Little is known about their structures and structure-function relationships. In this work we show highly organized surface layers of hydrophobins, representing the most detailed structural study of hydrophobin films so far. Langmuir-Blodgett films of class II hydrophobins HFBI and HFBII from Trichoderma reesei were prepared and analyzed by atomic force microscopy. The films showed highly ordered two-dimensional crystalline structures. By combining our recent results on small-angle X-ray scattering of hydrophobin solutions, we found that the unit cells in the films have dimensions similar to those of tetrameric aggregates found in solutions. Further analysis leads to a model in which the building blocks of the two-dimensional crystals are shape-persistent supramolecules consisting of four hydrophobin molecules. The results also indicate functional and structural differences between HFBI and HFBII that help to explain differences in their properties. The possibility that the highly organized surface assemblies of hydrophobins could allow a route for manufacturing functional surfaces is suggested.

Social cognition in schizophrenia: factor structure, clinical and functional correlates.

PubMed

Buck, Benjamin E; Healey, Kristin M; Gagen, Emily C; Roberts, David L; Penn, David L

2016-08-01

Social cognition is consistently impaired in people with schizophrenia, separable from general neurocognition, predictive of real-world functioning and amenable to psychosocial treatment. Few studies have empirically examined its underlying factor structure. This study (1) examines the factor structure of social cognition in both a sample of individuals with schizophrenia-spectrum disorders and non-clinical controls and (2) explores relationships of factors to neurocognition, symptoms and functioning. A factor analysis was conducted on social cognition measures in a sample of 65 individuals with schizophrenia or schizoaffective disorder, and 50 control participants. The resulting factors were examined for their relationships to symptoms and functioning. Results suggested a two-factor structure in the schizophrenia sample (social cognition skill and hostile attributional style) and a three-factor structure in the non-clinical sample (hostile attributional style, higher-level inferential processing and lower-level cue detection). In the schizophrenia sample, the social cognition skill factor was significantly related to negative symptoms and social functioning, whereas hostile attributional style predicted positive and general psychopathology symptoms. The factor structure of social cognition in schizophrenia separates hostile attributional style and social cognition skill, and each show differential relationships to relevant clinical variables in schizophrenia.

Interior phase transformations and mass-radius relationships of silicon-carbon planets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Hugh F.; Militzer, Burkhard, E-mail: hughfw@gmail.com

2014-09-20

Planets such as 55 Cancri e orbiting stars with a high carbon-to-oxygen ratio may consist primarily of silicon and carbon, with successive layers of carbon, silicon carbide, and iron. The behavior of silicon-carbon materials at the extreme pressures prevalent in planetary interiors, however, has not yet been sufficiently understood. In this work, we use simulations based on density functional theory to determine high-pressure phase transitions in the silicon-carbon system, including the prediction of new stable compounds with Si{sub 2}C and SiC{sub 2} stoichiometry at high pressures. We compute equations of state for these silicon-carbon compounds as a function of pressure,more » and hence derive interior structural models and mass-radius relationships for planets composed of silicon and carbon. Notably, we predict a substantially smaller radius for SiC planets than in previous models, and find that mass radius relationships for SiC planets are indistinguishable from those of silicate planets. We also compute a new equation of state for iron. We rederive interior models for 55 Cancri e and are able to place more stringent restrictions on its composition.« less

Validity of semi-quantitative scale for brain MRI in unilateral cerebral palsy due to periventricular white matter lesions: Relationship with hand sensorimotor function and structural connectivity

PubMed Central

Fiori, Simona; Guzzetta, Andrea; Pannek, Kerstin; Ware, Robert S.; Rossi, Giuseppe; Klingels, Katrijn; Feys, Hilde; Coulthard, Alan; Cioni, Giovanni; Rose, Stephen; Boyd, Roslyn N.

2015-01-01

Aim To provide first evidence of construct validity of a semi-quantitative scale for brain structural MRI (sqMRI scale) in children with unilateral cerebral palsy (UCP) secondary to periventricular white matter (PWM) lesions, by examining the relationship with hand sensorimotor function and whole brain structural connectivity. Methods Cross-sectional study of 50 children with UCP due to PWM lesions using 3 T (MRI), diffusion MRI and assessment of hand sensorimotor function. We explored the relationship of lobar, hemispheric and global scores on the sqMRI scale, with fractional anisotropy (FA), as a measure of brain white matter microstructure, and with hand sensorimotor measures (Assisting Hand Assessment, AHA; Jebsen–Taylor Test for Hand Function, JTTHF; Melbourne Assessment of Unilateral Upper Limb Function, MUUL; stereognosis; 2-point discrimination). Results Lobar and hemispheric scores on the sqMRI scale contralateral to the clinical side of hemiplegia correlated with sensorimotor paretic hand function measures and FA of a number of brain structural connections, including connections of brain areas involved in motor control (postcentral, precentral and paracentral gyri in the parietal lobe). More severe lesions correlated with lower sensorimotor performance, with the posterior limb of internal capsule score being the strongest contributor to impaired hand function. Conclusion The sqMRI scale demonstrates first evidence of construct validity against impaired motor and sensory function measures and brain structural connectivity in a cohort of children with UCP due to PWM lesions. More severe lesions correlated with poorer paretic hand sensorimotor function and impaired structural connectivity in the hemisphere contralateral to the clinical side of hemiplegia. The quantitative structural MRI scoring may be a useful clinical tool for studying brain structure–function relationships but requires further validation in other populations of CP. PMID:26106533

Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities

PubMed Central

Messé, Arnaud; Rudrauf, David; Benali, Habib; Marrelec, Guillaume

2014-01-01

Investigating the relationship between brain structure and function is a central endeavor for neuroscience research. Yet, the mechanisms shaping this relationship largely remain to be elucidated and are highly debated. In particular, the existence and relative contributions of anatomical constraints and dynamical physiological mechanisms of different types remain to be established. We addressed this issue by systematically comparing functional connectivity (FC) from resting-state functional magnetic resonance imaging data with simulations from increasingly complex computational models, and by manipulating anatomical connectivity obtained from fiber tractography based on diffusion-weighted imaging. We hypothesized that FC reflects the interplay of at least three types of components: (i) a backbone of anatomical connectivity, (ii) a stationary dynamical regime directly driven by the underlying anatomy, and (iii) other stationary and non-stationary dynamics not directly related to the anatomy. We showed that anatomical connectivity alone accounts for up to 15% of FC variance; that there is a stationary regime accounting for up to an additional 20% of variance and that this regime can be associated to a stationary FC; that a simple stationary model of FC better explains FC than more complex models; and that there is a large remaining variance (around 65%), which must contain the non-stationarities of FC evidenced in the literature. We also show that homotopic connections across cerebral hemispheres, which are typically improperly estimated, play a strong role in shaping all aspects of FC, notably indirect connections and the topographic organization of brain networks. PMID:24651524

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Longitudinal relationships between resources, motivation, and functioning.

PubMed

Hess, Thomas M; Emery, Lisa; Neupert, Shevaun D

2012-05-01

We investigated how fluctuations and linear changes in health and cognitive resources influence the motivation to engage in complex cognitive activity and the extent to which motivation mediated the relationship between changing resources and cognitively demanding activities. Longitudinal data from 332 adults aged 20-85 years were examined. Motivation was assessed using a composite of Need for Cognition and Personal Need for Structure and additional measures of health, sensory functioning, cognitive ability, and self-reported activity engagement. Multilevel modeling revealed that age-typical changes in health, sensory functions, and ability were associated with changes in motivation, with the impact of declining health on motivation being particularly strong in older adulthood. Changes in motivation, in turn, predicted involvement in cognitive and social activities as well as changes in cognitive ability. Finally, motivation was observed to partially mediate the relationship between changes in resources and cognitively demanding activities. Our results suggest that motivation may play an important role in determining the course of cognitive change and involvement in cognitively demanding everyday activities in adulthood.

Structure–property relationships in atomic-scale junctions: Histograms and beyond

DOE PAGES

Mark S. Hybertsen; Venkataraman, Latha

2016-03-03

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Structure–property relationships in atomic-scale junctions: Histograms and beyond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mark S. Hybertsen; Venkataraman, Latha

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Structure–property reduced order model for viscosity prediction in single-component CO 2 -binding organic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu, David C.; Malhotra, Deepika; Koech, Phillip K.

2016-01-01

CO2 capture from power generation with aqueous solvents remains energy intensive due to the high water content of the current technology, or the high viscosity of non-aqueous alternatives. Quantitative reduced models, connecting molecular structure to bulk properties, are key for developing structure-property relationships that enable molecular design. In this work, we describe such a model that quantitatively predicts viscosities of CO2 binding organic liquids (CO2BOLs) based solely on molecular structure and the amount of bound CO2. The functional form of the model correlates the viscosity with the CO2 loading and an electrostatic term describing the charge distribution between the CO2-bearingmore » functional group and the proton-receiving amine. Molecular simulations identify the proton shuttle between these groups within the same molecule to be the critical indicator of low viscosity. The model, developed to allow for quick screening of solvent libraries, paves the way towards the rational design of low viscosity non-aqueous solvent systems for post-combustion CO2 capture. Following these theoretical recommendations, synthetic efforts of promising candidates and viscosity measurement provide experimental validation and verification.« less

Simulation of wheat growth and development based on organ-level photosynthesis and assimilate allocation.

PubMed

Evers, J B; Vos, J; Yin, X; Romero, P; van der Putten, P E L; Struik, P C

2010-05-01

Intimate relationships exist between form and function of plants, determining many processes governing their growth and development. However, in most crop simulation models that have been created to simulate plant growth and, for example, predict biomass production, plant structure has been neglected. In this study, a detailed simulation model of growth and development of spring wheat (Triticum aestivum) is presented, which integrates degree of tillering and canopy architecture with organ-level light interception, photosynthesis, and dry-matter partitioning. An existing spatially explicit 3D architectural model of wheat development was extended with routines for organ-level microclimate, photosynthesis, assimilate distribution within the plant structure according to organ demands, and organ growth and development. Outgrowth of tiller buds was made dependent on the ratio between assimilate supply and demand of the plants. Organ-level photosynthesis, biomass production, and bud outgrowth were simulated satisfactorily. However, to improve crop simulation results more efforts are needed mechanistically to model other major plant physiological processes such as nitrogen uptake and distribution, tiller death, and leaf senescence. Nevertheless, the work presented here is a significant step forwards towards a mechanistic functional-structural plant model, which integrates plant architecture with key plant processes.

Latent structures of female sexual functioning.

PubMed

Carvalho, Joana; Vieira, Armando Luís; Nobre, Pedro

2012-08-01

For the last three decades, male and female sexual responses have been conceptualized as similar, based on separated and sequential phases as proposed by the models of Masters and Johnson (1966) and Kaplan (1979) model. However, there is a growing debate around the need to conceptualize female sexual response and the classification of sexual dysfunction in women, in view of the upcoming editions of the DSM and ICD. The aim of this study was to test, using structural equation modeling, five conceptual, alternative models of female sexual function, using a sample of women with sexual difficulties and a sample of women without sexual problems. A total of 1993 Portuguese women participated in the study and completed a modified version of the Female Sexual Function Index. Findings suggested a four-factor solution as the model that best fit the data regarding women presenting sexual difficulties: (1) desire/arousal; (2) lubrication; (3) orgasm; (4) pain/vaginismus. In relation to sexually healthy women, the best model was a five-factor solution comprising of (1) desire; (2) arousal; (3) lubrication; (4) orgasm; and (5) pain/vaginismus. Discriminant validity between factors was supported, suggesting that these dimensions measure distinct phenomena. Model fit to the data significantly decreased in both samples, as models began to successively consider greater levels of overlap among phases of sexual function, towards a single-factor solution. By suggesting the overlap between pain and vaginismus, results partially support the new classification that is currently being discussed regarding DSM-5. Additionally, results on the relationship between sexual desire and arousal were inconclusive as sexually healthy women were better characterized by a five-factor model that considered the structural independence among these factors, whereas women with sexual difficulties better fit with a four-factor model merging sexual desire and subjective sexual arousal.

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

PubMed Central

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

2012-01-01

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

PubMed

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

2012-09-21

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Using ventricular modeling to robustly probe significant deep gray matter pathologies: Application to cerebral palsy.

PubMed

Pagnozzi, Alex M; Shen, Kaikai; Doecke, James D; Boyd, Roslyn N; Bradley, Andrew P; Rose, Stephen; Dowson, Nicholas

2016-11-01

Understanding the relationships between the structure and function of the brain largely relies on the qualitative assessment of Magnetic Resonance Images (MRIs) by expert clinicians. Automated analysis systems can support these assessments by providing quantitative measures of brain injury. However, the assessment of deep gray matter structures, which are critical to motor and executive function, remains difficult as a result of large anatomical injuries commonly observed in children with Cerebral Palsy (CP). Hence, this article proposes a robust surrogate marker of the extent of deep gray matter injury based on impingement due to local ventricular enlargement on surrounding anatomy. Local enlargement was computed using a statistical shape model of the lateral ventricles constructed from 44 healthy subjects. Measures of injury on 95 age-matched CP patients were used to train a regression model to predict six clinical measures of function. The robustness of identifying ventricular enlargement was demonstrated by an area under the curve of 0.91 when tested against a dichotomised expert clinical assessment. The measures also showed strong and significant relationships for multiple clinical scores, including: motor function (r 2  = 0.62, P < 0.005), executive function (r 2  = 0.55, P < 0.005), and communication (r 2  = 0.50, P < 0.005), especially compared to using volumes obtained from standard anatomical segmentation approaches. The lack of reliance on accurate anatomical segmentations and its resulting robustness to large anatomical variations is a key feature of the proposed automated approach. This coupled with its strong correlation with clinically meaningful scores, signifies the potential utility to repeatedly assess MRIs for clinicians diagnosing children with CP. Hum Brain Mapp 37:3795-3809, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The association between family factors and child behaviour problems using dyadic data.

PubMed

Wang, Y; Pan, J; Zhang, X; Yi, C

2015-11-01

Parental psychopathology and family issues are key influence factors to child behaviour problems. This study aimed to investigate the dyadic impact of maternal and paternal depression and perceived family functioning on child behaviour problems. Both maternal and paternal depression, perceived family functioning and reported child behaviour problems were collected, respectively. Because of the interdependent characteristic of dyadic data, structural equation modelling was used to examine the relationship among all variables and the mutual influence between mother and father. Results showed that father-perceived family functioning mediated the relationship between parental depression and child behaviour problems, but mother-perceived family functioning did not show this mediation effect. Meanwhile, maternal and paternal depression influenced both of their own and their partner's perceived family functioning. The findings indicated that paternal psychopathology and family functioning should not be overlooked in child behaviour development. In addition, this study underscored the importance to investigate the different impact of father and mother on child development within a dyadic unit. © 2014 John Wiley & Sons Ltd.

Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents

DOE PAGES

McNally, Joshua S.; Noll, Bruce; Orme, Christopher J.; ...

2015-05-04

Here, a density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An x-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction withmore » the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo-six membered ring which included both protons.« less

[Species, functional, structural diversity of typical plant communities and their responses to environmental factors in Miao Archipelago, China.

PubMed

Zheng, Li Ting; Su, Tian; Liu, Xiang Yu; Yin, Fang; Guo, Chao; Tuo, Bin; Yan, En Rong

2018-02-01

Island vegetation plays an important role in biodiversity research across the world. The study of plant diversity in island is helpful for understanding the mechanism of plant diversity maintenance under land-sea interaction. Here, four typical plant communities (Quercus acutissima community, Robinia pseudoacacia community, Pinus thunbergii community and Vitex negundo community) in Miao Archipelago were selected to examine the species, functional and structural diversities and their responses to environmental factors at the community scale by using species diversity indices, functional diversity indices, as well as structural diversity indices. The results showed that the species richness and Rao index of P. thunbergii community was higher than that of Q. acutissima community and R. pseudoacacia community, but the structural diversity was lower. The species diversity and structural diversity of V. Negundo shrub were lower than that of forest community, but the functional diversity was higher than some forest communities. The relationship between the diversity of typical plant communities in island area illustrated a significant positive correlation between species richness with Rao index and tree height diversity, however the correlation with functional evenness was significantly negative. The structural diversity and functional evenness were determined by slope with negative and positive relationships, respectively. Functional heterogeneity, functional divergence and species diversity were affected largely by soil physical and chemical properties, displaying the positive relationship with soil bulk density and soil total carbon content, and a negative relationship with soil water content. In conclusion, diversity pattern of plant community in Miao Archipelago reflected not only the characteristics in mainland vegetation but also the special nature of the sea island.

Bipolar disorder type I and II show distinct relationships between cortical thickness and executive function.

PubMed

Abé, C; Rolstad, S; Petrovic, P; Ekman, C-J; Sparding, T; Ingvar, M; Landén, M

2018-06-15

Frontal cortical abnormalities and executive function impairment co-occur in bipolar disorder. Recent studies have shown that bipolar subtypes differ in the degree of structural and functional impairments. The relationships between cognitive performance and cortical integrity have not been clarified and might differ across patients with bipolar disorder type I, II, and healthy subjects. Using a vertex-wise whole-brain analysis, we investigated how cortical integrity, as measured by cortical thickness, correlates with executive performance in patients with bipolar disorder type I, II, and controls (N = 160). We found focal associations between executive function and cortical thickness in the medial prefrontal cortex in bipolar II patients and controls, but not in bipolar I disorder. In bipolar II patients, we observed additional correlations in lateral prefrontal and occipital regions. Our findings suggest that bipolar disorder patients show altered structure-function relationships, and importantly that those relationships may differ between bipolar subtypes. The findings are line with studies suggesting subtype-specific neurobiological and cognitive profiles. This study contributes to a better understanding of brain structure-function relationships in bipolar disorder and gives important insights into the neuropathophysiology of diagnostic subtypes. © 2018 The Authors Acta Psychiatrica Scandinavica Published by John Wiley & Sons Ltd.

Self-esteem as a mediator of the relationship between role functioning and symptoms for individuals with severe mental illness: a prospective analysis of Modified Labeling theory.

PubMed

Davis, Lisa; Kurzban, Seth; Brekke, John

2012-05-01

Despite a growing body of evidence supporting the efficacy of psychosocial rehabilitation for individuals with severe mental illness (SMI), a large proportion of these individuals remain unable to maintain basic social roles such as employee, parent, or spouse. This study investigated whether changes in role functioning over time impact symptom severity indirectly through the mechanism of changes in self-esteem as posited by Modified Labeling theory. The study sample was composed of 148 individuals diagnosed with schizophrenia, schizoaffective disorder, bipolar disorder with psychotic features, and major depression with psychotic features who elected to participate in community-based psychosocial rehabilitation services. Measures of role functioning, self-esteem, and psychiatric symptoms were gathered at baseline and six months through a combination of structured clinical interviews and self-report surveys. SEM results at baseline provided support for a model in which self-esteem fully mediated the relationship between role functioning and psychiatric symptoms. The final model explained 20% of the variance in psychiatric symptoms. Analyses at six months post-baseline (time 2) indicate that changes in self-esteem fully mediated the relationship between changes in role functioning and changes in psychiatric symptoms. The final change model explained 23% of the variance in changes in psychiatric symptoms. Results provide empirical support for the principles underlying Modified Labeling theory. Implications include the need for interventions that focus on social participation as a means of improving self-esteem, thereby decreasing symptom exacerbation and future relapse for people with SMI. Copyright © 2012 Elsevier B.V. All rights reserved.

TENSOR DECOMPOSITIONS AND SPARSE LOG-LINEAR MODELS

PubMed Central

Johndrow, James E.; Bhattacharya, Anirban; Dunson, David B.

2017-01-01

Contingency table analysis routinely relies on log-linear models, with latent structure analysis providing a common alternative. Latent structure models lead to a reduced rank tensor factorization of the probability mass function for multivariate categorical data, while log-linear models achieve dimensionality reduction through sparsity. Little is known about the relationship between these notions of dimensionality reduction in the two paradigms. We derive several results relating the support of a log-linear model to nonnegative ranks of the associated probability tensor. Motivated by these findings, we propose a new collapsed Tucker class of tensor decompositions, which bridge existing PARAFAC and Tucker decompositions, providing a more flexible framework for parsimoniously characterizing multivariate categorical data. Taking a Bayesian approach to inference, we illustrate empirical advantages of the new decompositions. PMID:29332971

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

A multi-scale ''soil water structure'' model based on the pedostructure concept

NASA Astrophysics Data System (ADS)

Braudeau, E.; Mohtar, R. H.; El Ghezal, N.; Crayol, M.; Salahat, M.; Martin, P.

2009-02-01

Current soil water models do not take into account the internal organization of the soil medium and, a fortiori, the physical interaction between the water film surrounding the solid particles of the soil structure, and the surface charges of this structure. In that sense they empirically deal with the physical soil properties that are all generated from this soil water-structure interaction. As a result, the thermodynamic state of the soil water medium, which constitutes the local physical conditions, namely the pedo-climate, for biological and geo-chemical processes in soil, is not defined in these models. The omission of soil structure from soil characterization and modeling does not allow for coupling disciplinary models for these processes with soil water models. This article presents a soil water structure model, Kamel®, which was developed based on a new paradigm in soil physics where the hierarchical soil structure is taken into account allowing for defining its thermodynamic properties. After a review of soil physics principles which forms the basis of the paradigm, we describe the basic relationships and functionality of the model. Kamel® runs with a set of 15 soil input parameters, the pedohydral parameters, which are parameters of the physically-based equations of four soil characteristic curves that can be measured in the laboratory. For cases where some of these parameters are not available, we show how to estimate these parameters from commonly available soil information using published pedotransfer functions. A published field experimental study on the dynamics of the soil moisture profile following a pounded infiltration rainfall event was used as an example to demonstrate soil characterization and Kamel® simulations. The simulated soil moisture profile for a period of 60 days showed very good agreement with experimental field data. Simulations using input data calculated from soil texture and pedotransfer functions were also generated and compared to simulations of the more ideal characterization. The later comparison illustrates how Kamel® can be used and adapt to any case of soil data availability. As physically based model on soil structure, it may be used as a standard reference to evaluate other soil-water models and also pedotransfer functions at a given location or agronomical situation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maurer, K. D.; Bohrer, G.; Kenny, W. T.

Surface roughness parameters, namely the roughness length and displacement height, are an integral input used to model surface fluxes. However, most models assume these parameters to be a fixed property of plant functional type and disregard the governing structural heterogeneity and dynamics. In this study, we use large-eddy simulations to explore, in silico, the effects of canopy-structure characteristics on surface roughness parameters. We performed a virtual experiment to test the sensitivity of resolved surface roughness to four axes of canopy structure: (1) leaf area index, (2) the vertical profile of leaf density, (3) canopy height, and (4) canopy gap fraction.more » We found roughness parameters to be highly variable, but uncovered positive relationships between displacement height and maximum canopy height, aerodynamic canopy height and maximum canopy height and leaf area index, and eddy-penetration depth and gap fraction. We also found negative relationships between aerodynamic canopy height and gap fraction, as well as between eddy-penetration depth and maximum canopy height and leaf area index. We generalized our model results into a virtual "biometric" parameterization that relates roughness length and displacement height to canopy height, leaf area index, and gap fraction. Using a decade of wind and canopy-structure observations in a site in Michigan, we tested the effectiveness of our model-driven biometric parameterization approach in predicting the friction velocity over heterogeneous and disturbed canopies. We compared the accuracy of these predictions with the friction-velocity predictions obtained from the common simple approximation related to canopy height, the values calculated with large-eddy simulations of the explicit canopy structure as measured by airborne and ground-based lidar, two other parameterization approaches that utilize varying canopy-structure inputs, and the annual and decadal means of the surface roughness parameters at the site from meteorological observations. We found that the classical representation of constant roughness parameters (in space and time) as a fraction of canopy height performed relatively well. Nonetheless, of the approaches we tested, most of the empirical approaches that incorporate seasonal and interannual variation of roughness length and displacement height as a function of the dynamics of canopy structure produced more precise and less biased estimates for friction velocity than models with temporally invariable parameters.« less

Model-based metrics of human-automation function allocation in complex work environments

NASA Astrophysics Data System (ADS)

Kim, So Young

Function allocation is the design decision which assigns work functions to all agents in a team, both human and automated. Efforts to guide function allocation systematically has been studied in many fields such as engineering, human factors, team and organization design, management science, and cognitive systems engineering. Each field focuses on certain aspects of function allocation, but not all; thus, an independent discussion of each does not address all necessary issues with function allocation. Four distinctive perspectives emerged from a review of these fields: technology-centered, human-centered, team-oriented, and work-oriented. Each perspective focuses on different aspects of function allocation: capabilities and characteristics of agents (automation or human), team structure and processes, and work structure and the work environment. Together, these perspectives identify the following eight issues with function allocation: 1) Workload, 2) Incoherency in function allocations, 3) Mismatches between responsibility and authority, 4) Interruptive automation, 5) Automation boundary conditions, 6) Function allocation preventing human adaptation to context, 7) Function allocation destabilizing the humans' work environment, and 8) Mission Performance. Addressing these issues systematically requires formal models and simulations that include all necessary aspects of human-automation function allocation: the work environment, the dynamics inherent to the work, agents, and relationships among them. Also, addressing these issues requires not only a (static) model, but also a (dynamic) simulation that captures temporal aspects of work such as the timing of actions and their impact on the agent's work. Therefore, with properly modeled work as described by the work environment, the dynamics inherent to the work, agents, and relationships among them, a modeling framework developed by this thesis, which includes static work models and dynamic simulation, can capture the issues with function allocation. Then, based on the eight issues, eight types of metrics are established. The purpose of these metrics is to assess the extent to which each issue exists with a given function allocation. Specifically, the eight types of metrics assess workload, coherency of a function allocation, mismatches between responsibility and authority, interruptive automation, automation boundary conditions, human adaptation to context, stability of the human's work environment, and mission performance. Finally, to validate the modeling framework and the metrics, a case study was conducted modeling four different function allocations between a pilot and flight deck automation during the arrival and approach phases of flight. A range of pilot cognitive control modes and maximum human taskload limits were also included in the model. The metrics were assessed for these four function allocations and analyzed to validate capability of the metrics to identify important issues in given function allocations. In addition, the design insights provided by the metrics are highlighted. This thesis concludes with a discussion of mechanisms for further validating the modeling framework and function allocation metrics developed here, and highlights where these developments can be applied in research and in the design of function allocations in complex work environments such as aviation operations.

An examination of relationship between neurological soft signs and neurocognition.

PubMed

Solanki, Ram Kumar; Swami, Mukesh Kumar; Singh, Paramjeet

2012-03-01

Neurological soft signs (NSS) and cognitive function had been examined in schizophrenia, but their relationship has remained elusive for several years. We examined the relationship between NSS and cognitive functions in the present study. A cross sectional study was carried out. Subjects were drawn from first degree relatives of schizophrenia patients, admitted as inpatient or attending as an outpatient. Controls were recruited by word of mouth from hospital staff and visitors of hospitalized patients. Those subjects who satisfied the screening process were subjected to Cambridge Neurological Inventory for soft sign assessment and digit span test, paired associate learning test (PALT) and visuo-spatial working memory matrix (VSWMM) for cognitive function assessment. Correlation analysis and structural equation modeling (SEM) was used for analysis. Significant negative correlation of primitive reflexes with PALT; of motor coordination with VSWMM, working memory (WM) and cognitive index; of total NSS with WM and cognitive index among first degree relatives. SEM showed that motor soft signs have important negative influence over WM. The current findings indicate that NSS have significant negative effect on cognitive functioning. Copyright © 2011 Elsevier B.V. All rights reserved.

A mechanism-mediated model for carcinogenicity: Model content and prediction of the outcome of rodent carcinogenicity bioassays currently being conducted on 25 organic chemicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purdy, R.

A hierarchical model consisting of quantitative structure-activity relationships based mainly on chemical reactivity was developed to predict the carcinogenicity of organic chemicals to rodents. The model is comprised of quantitative structure-activity relationships, QSARs based on hypothesized mechanisms of action, metabolism, and partitioning. Predictors included octanol/water partition coefficient, molecular size, atomic partial charge, bond angle strain, atomic acceptor delocalizibility, atomic radical superdelocalizibility, the lowest unoccupied molecular orbital (LUMO) energy of hypothesized intermediate nitrenium ion of primary aromatic amines, difference in charge of ionized and unionized carbon-chlorine bonds, substituent size and pattern on polynuclear aromatic hydrocarbons, the distance between lone electron pairsmore » over a rigid structure, and the presence of functionalities such as nitroso and hydrazine. The model correctly classified 96% of the carcinogens in the training set of 306 chemicals, and 90% of the carcinogens in the test set of 301 chemicals. The test set by chance contained 84% of the positive thiocontaining chemicals. A QSAR for these chemicals was developed. This posttest set modified model correctly predicted 94% of the carcinogens in the test set. This model was used to predict the carcinogenicity of the 25 organic chemicals the U.S. National Toxicology Program was testing at the writing of this article. 12 refs., 3 tabs.« less

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.

PubMed

Machnicka, Magdalena A; Kaminska, Katarzyna H; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2015-10-23

GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA. In this work we applied homology detection, sequence conservation analysis, fold recognition and homology modeling methods to study sequence-structure-function relationships in the GmrSD restriction endonucleases family. We also analyzed the phylogeny and genomic context of the family members. Results of our comparative genomics study show that GmrS exhibits similarity to proteins from the ParB/Srx fold which can have both NTPase and nuclease activity. In contrast to the previous studies though, we attribute the nuclease activity also to GmrD as we found it to contain the HNH endonuclease motif. We revealed residues potentially important for structure and function in both domains. Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements. Finally, phylogenetic reconstructions of GmrS and GmrD domains revealed that they coevolved and only few GmrSD systems appear to be assembled from distantly related GmrS and GmrD components. Our study provides insight into sequence-structure-function relationships in the yet poorly characterized family of Type IV restriction enzymes. Comparative genomics allowed to propose possible role of GmrD domain in the function of the GmrSD enzyme and possible active sites of both GmrS and GmrD domains. Presented results can guide further experimental characterization of these enzymes.

Chiropractic physicians: toward a select conceptual understanding of bureaucratic structures and functions in the health care institution

PubMed Central

Fredericks, Marcel; Kondellas, Bill; Hang, Lam; Fredericks, Janet; Ross, Michael WV

2011-01-01

Objective The purpose of this article is to present select concepts and theories of bureaucratic structures and functions so that chiropractic physicians and other health care professionals can use them in their respective practices. The society-culture-personality model can be applied as an organizational instrument for assisting chiropractors in the diagnosis and treatment of their patients irrespective of locality. Discussion Society-culture-personality and social meaningful interaction are examined in relationship to the structural and functional aspects of bureaucracy within the health care institution of a society. Implicit in the examination of the health care bureaucratic structures and functions of a society is the focus that chiropractic physicians and chiropractic students learn how to integrate, synthesize, and actualize values and virtues such as empathy, integrity, excellence, diversity, compassion, caring, and understanding with a deep commitment to self-reflection. Conclusion It is essential that future and current chiropractic physicians be aware of the structural and functional aspects of an organization so that chiropractic and other health care professionals are able to deliver care that involves the ingredients of quality, affordability, availability, accessibility, and continuity for their patients. PMID:22693481

VarMod: modelling the functional effects of non-synonymous variants.

PubMed

Pappalardo, Morena; Wass, Mark N

2014-07-01

Unravelling the genotype-phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein-protein interfaces and protein-ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Relief of depression and pain improves daily functioning and quality of life in patients with major depressive disorder.

PubMed

Lin, Ching-Hua; Yen, Yung-Chieh; Chen, Ming-Chao; Chen, Cheng-Chung

2013-12-02

The objective of this study was to investigate the effects of depression relief and pain relief on the improvement in daily functioning and quality of life (QOL) for depressed patients receiving a 6-week treatment of fluoxetine. A total of 131 acutely ill inpatients with major depressive disorder (MDD) were enrolled to receive 20mg of fluoxetine daily for 6 weeks. Depression severity, pain severity, daily functioning, and health-related QOL were assessed at baseline and again at week 6. Depression severity, pain severity, and daily functioning were assessed using the 17-item Hamilton Depression Rating Scale, the Short-Form 36 (SF-36) Body Pain Index, and the Work and Social Adjustment Scale. Health-related QOL was assessed by three primary domains of the SF-36, including social functioning, vitality, and general health perceptions. Pearson's correlation and structural equation modeling were used to examine relationships among the study variables. Five models were proposed. In model 1, depression relief alone improved daily functioning and QOL. In model 2, pain relief alone improved daily functioning and QOL. In model 3, depression relief, mediated by pain relief, improved daily functioning and QOL. In model 4, pain relief, mediated by depression relief, improved daily functioning and QOL. In model 5, both depression relief and pain relief improved daily functioning and QOL. One hundred and six patients completed all the measures at baseline and at week 6. Model 5 was the most fitted structural equation model (χ(2) = 8.62, df = 8, p = 0.376, GFI = 0.975, AGFI = 0.935, TLI = 0.992, CFI = 0.996, RMSEA = 0.027). Interventions which relieve depression and pain improve daily functioning and QOL among patients with MDD. The proposed model can provide quantitative estimates of improvement in treating patients with MDD. © 2013 Elsevier Inc. All rights reserved.

Advancing paternal age at birth is associated with poorer social functioning earlier and later in life of schizophrenia patients in a founder population.

PubMed

Liebenberg, Rudolf; van Heerden, Brigitte; Ehlers, René; Du Plessis, Anna M E; Roos, J Louw

2016-09-30

Consistent associations have been found between advanced paternal age and an increased risk of psychiatric disorders, such as schizophrenia, in their offspring. This increase appears to be linear as paternal age increases. The present study investigates the relationship between early deviant behaviour in the first 10 years of life of patients as well as longer term functional outcome and paternal age in sporadic Afrikaner founder population cases of schizophrenia. This might improve our understanding of Paternal Age-Related Schizophrenia (PARS). Follow-up psychiatric diagnoses were confirmed by the Diagnostic Interview for Genetic Studies (DIGS). An early deviant childhood behaviour semi-structured questionnaire and the Specific Level of Functioning Assessment (SLOF) were completed. From the logistic regression models fitted, a significant negative relationship was found between paternal age at birth and social dysfunction as early deviant behaviour. Additionally, regression analysis revealed a significant negative relationship between paternal age at birth and the SLOF for interpersonal relationships later in life. Early social dysfunction may represent a phenotypic trait for PARS. Further research is required to understand the relationship between early social dysfunction and deficits in interpersonal relationships later in life. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Out Drinking the Joneses: Neighborhood Factors Moderating the Effects of Drinking on Relationship Quality over the First Four Years of Marriage.

PubMed

Crasta, Dev; Funk, Janette L; Lee, Soonhee; Rogge, Ronald D

2017-12-27

Neighborhood quality has been cross-sectionally linked to both relationship behaviors and relationship well-being. Consistent with the Vulnerability Stress-Adaptation model of relationship functioning (Karney & Bradbury, 1995), we hypothesized that associations between social behaviors (e.g., drinking) and relationship quality could be moderated by neighborhood factors. Specifically, we characterized neighborhoods along multiple dimensions using multiple methods (self-report, census) to investigate how neighborhood factors might clarify ambiguous effects of alcohol use on marital functioning. A nationally recruited sample of 303 newlywed couples completed a baseline assessment around the time of marriage and was then assessed yearly across the first 4 years of marriage (94% retention). Three level HLM slope-intercept models were used to model changes in relationship satisfaction across the first 4 years of marriage. Results suggested that, for couples living in highly disordered neighborhoods, positive shifts in overall levels of drinking within specific waves of assessment were associated with corresponding negative shifts in satisfaction whereas in neighborhoods without perceived disorder, this effect was reversed. For couples living in neighborhoods with low levels of domestic structures (high census rates of single renters without children), within-couple discrepancies favoring higher rates of husband drinking in specific waves predicted poorer relationship quality for both partners in those same waves whereas those same discrepancies predicted higher satisfaction in high domesticity neighborhoods (high census rates of married homeowners with children). The findings provide insight into the different roles of alcohol use in relationship maintenance and highlight the importance of using external context to understand intradyadic processes. © 2017 Family Process Institute.

Relationship of cardiac structure and function to cardiorespiratory fitness and lean body mass in adolescents and young adults with Type 2 Diabetes

USDA-ARS?s Scientific Manuscript database

To investigate the relationships of cardiac structure and function with body composition and cardiorespiratory fitness (CRF) among adolescents with type 2 diabetes in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) Study Group. Cross-sectional evaluation of 233 participant...

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

NASA Astrophysics Data System (ADS)

Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

2016-11-01

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

Multiphysics and multiscale modelling, data-model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics.

PubMed

Chabiniok, Radomir; Wang, Vicky Y; Hadjicharalambous, Myrianthi; Asner, Liya; Lee, Jack; Sermesant, Maxime; Kuhl, Ellen; Young, Alistair A; Moireau, Philippe; Nash, Martyn P; Chapelle, Dominique; Nordsletten, David A

2016-04-06

With heart and cardiovascular diseases continually challenging healthcare systems worldwide, translating basic research on cardiac (patho)physiology into clinical care is essential. Exacerbating this already extensive challenge is the complexity of the heart, relying on its hierarchical structure and function to maintain cardiovascular flow. Computational modelling has been proposed and actively pursued as a tool for accelerating research and translation. Allowing exploration of the relationships between physics, multiscale mechanisms and function, computational modelling provides a platform for improving our understanding of the heart. Further integration of experimental and clinical data through data assimilation and parameter estimation techniques is bringing computational models closer to use in routine clinical practice. This article reviews developments in computational cardiac modelling and how their integration with medical imaging data is providing new pathways for translational cardiac modelling.

Characterization of articular cartilage by combining microscopic analysis with a fibril-reinforced finite-element model.

PubMed

Julkunen, Petro; Kiviranta, Panu; Wilson, Wouter; Jurvelin, Jukka S; Korhonen, Rami K

2007-01-01

Load-bearing characteristics of articular cartilage are impaired during tissue degeneration. Quantitative microscopy enables in vitro investigation of cartilage structure but determination of tissue functional properties necessitates experimental mechanical testing. The fibril-reinforced poroviscoelastic (FRPVE) model has been used successfully for estimation of cartilage mechanical properties. The model includes realistic collagen network architecture, as shown by microscopic imaging techniques. The aim of the present study was to investigate the relationships between the cartilage proteoglycan (PG) and collagen content as assessed by quantitative microscopic findings, and model-based mechanical parameters of the tissue. Site-specific variation of the collagen network moduli, PG matrix modulus and permeability was analyzed. Cylindrical cartilage samples (n=22) were harvested from various sites of the bovine knee and shoulder joints. Collagen orientation, as quantitated by polarized light microscopy, was incorporated into the finite-element model. Stepwise stress-relaxation experiments in unconfined compression were conducted for the samples, and sample-specific models were fitted to the experimental data in order to determine values of the model parameters. For comparison, Fourier transform infrared imaging and digital densitometry were used for the determination of collagen and PG content in the same samples, respectively. The initial and strain-dependent fibril network moduli as well as the initial permeability correlated significantly with the tissue collagen content. The equilibrium Young's modulus of the nonfibrillar matrix and the strain dependency of permeability were significantly associated with the tissue PG content. The present study demonstrates that modern quantitative microscopic methods in combination with the FRPVE model are feasible methods to characterize the structure-function relationships of articular cartilage.

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method.

PubMed

Li, Yaohang; Rata, Ionel; Chiu, See-wing; Jakobsson, Eric

2010-07-20

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of approximately 20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD < 0.5A from the native) as top-ranked, and selecting at least one near-native model in the top-5-ranked models, respectively. Similar effectiveness of the POC method is also found in the decoy sets from membrane protein loops. Furthermore, the POC method outperforms the other popularly-used consensus strategies in model ranking, such as rank-by-number, rank-by-rank, rank-by-vote, and regression-based methods. By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set.

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

PubMed Central

2010-01-01

Background Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. Results We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of ~20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD < 0.5A from the native) as top-ranked, and selecting at least one near-native model in the top-5-ranked models, respectively. Similar effectiveness of the POC method is also found in the decoy sets from membrane protein loops. Furthermore, the POC method outperforms the other popularly-used consensus strategies in model ranking, such as rank-by-number, rank-by-rank, rank-by-vote, and regression-based methods. Conclusions By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set. PMID:20642859

Functional mixture regression.

PubMed

Yao, Fang; Fu, Yuejiao; Lee, Thomas C M

2011-04-01

In functional linear models (FLMs), the relationship between the scalar response and the functional predictor process is often assumed to be identical for all subjects. Motivated by both practical and methodological considerations, we relax this assumption and propose a new class of functional regression models that allow the regression structure to vary for different groups of subjects. By projecting the predictor process onto its eigenspace, the new functional regression model is simplified to a framework that is similar to classical mixture regression models. This leads to the proposed approach named as functional mixture regression (FMR). The estimation of FMR can be readily carried out using existing software implemented for functional principal component analysis and mixture regression. The practical necessity and performance of FMR are illustrated through applications to a longevity analysis of female medflies and a human growth study. Theoretical investigations concerning the consistent estimation and prediction properties of FMR along with simulation experiments illustrating its empirical properties are presented in the supplementary material available at Biostatistics online. Corresponding results demonstrate that the proposed approach could potentially achieve substantial gains over traditional FLMs.

Effect of head group orientation on phospholipid assembly

NASA Astrophysics Data System (ADS)

Paul, Tanay; Saha, Jayashree

2017-06-01

The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.

Calcitonin-typical suppression of osteoclastic activity by amphioxus calcitonin superfamily peptides and insights into the evolutionary conservation and diversity of their structures.

PubMed

Sekiguchi, Toshio; Shiraishi, Akira; Satake, Honoo; Kuwasako, Kenji; Takahashi, Hiroki; Sato, Masayuki; Urata, Makoto; Wada, Shuichi; Endo, Masato; Ikari, Takahiro; Hattori, Atsuhiko; Srivastav, Ajai K; Suzuki, Nobuo

2017-05-15

Calcitonin (CT) is a hormone that decreases serum calcium level by suppressing osteoclastic activity in the vertebrate bone. In vertebrates, the structure-function relationship of CTs has been studied extensively. We recently identified three CT superfamily peptides, Bf-CTFP1 to 3, and clarified the molecular and functional characteristics of their receptor and receptor activity-modifying protein in amphioxus, Branchiostoma floridae. However, the CT activity of Bf-CTFPs has yet to be investigated. In the present study, a functional analysis of Bf-CTFPs was performed using goldfish scales having both osteoclasts and osteoblasts. All Bf-CTFPs suppressed osteoclastic activity via a goldfish CT receptor. Although the primary amino acid sequences of the Bf-CTFPs showed low sequence similarity to vertebrate CTs, Bf-CTFP1 to 3 share three amino acids, Thr 25 , Thr 27 , and Pro 32 -NH 2 , that are required for receptor binding, with salmon CT. Moreover, homology model analysis revealed that the Bf-CTFPs form alpha-helical structures. The alpha-helical position and length of Bf-CTFP1 and 2 were conserved with those of a highly potent ligand, teleost CT. Interestingly, the composition of the alpha-helix of Bf-CTFP3 differed from those of teleost CT, despite that the action of Bf-CTFP3 on goldfish scales was the same as that of Bf-CTFP1 and 2. Collectively, the present study provides new insights into the structure-function relationship of CT and its functional evolution in chordates. Copyright © 2017 Elsevier Inc. All rights reserved.

3D Printing of Biomolecular Models for Research and Pedagogy

PubMed Central

Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

2017-01-01

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. PMID:28362403

Avoidant coping and self-efficacy mediate relationships between perceived social constraints and symptoms among long-term breast cancer survivors.

PubMed

Adams, Rebecca N; Mosher, Catherine E; Cohee, Andrea A; Stump, Timothy E; Monahan, Patrick O; Sledge, George W; Cella, David; Champion, Victoria L

2017-07-01

Many breast cancer survivors feel constrained in discussing their cancer experience with others. Limited evidence suggests that social constraints (e.g., avoidance and criticism) from loved ones may negatively impact breast cancer survivors' global health, but research has yet to examine relationships between social constraints and common physical symptoms. Informed by social cognitive processing theory, this study examined whether perceived social constraints from partners and healthcare providers (HCPs) were associated with fatigue, sleep disturbance, and attentional functioning among long-term breast cancer survivors (N = 1052). In addition, avoidant coping and self-efficacy for symptom management were examined as potential mediators of these relationships. Long-term breast cancer survivors (mean years since diagnosis = 6) completed questionnaires assessing social constraints from partners and HCPs, avoidant coping, self-efficacy for symptom management, and symptoms (i.e., fatigue, sleep disturbance, and attentional functioning). Structural equation modeling was used to evaluate the hypothesized relationships among variables in two models: one focused on social constraints from partners and one focused on social constraints from HCPs. Both models demonstrated good fit. Consistent with theory and prior research, greater social constraints from both partners and HCPs were associated with greater symptom burden (i.e., greater fatigue and sleep disturbance, poorer attentional functioning). In addition, all relationships were mediated by avoidant coping and self-efficacy for symptom management. Findings are consistent with social cognitive processing theory and suggest that symptom management interventions may be enhanced by addressing the impact of social constraints from survivors' partners and HCPs on their coping and self-efficacy. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Structure-reactivity relationships between fluorescent chromophores and antioxidant activity of grain and sweet sorghum seeds

USDA-ARS?s Scientific Manuscript database

Polyphenolic structures, such as tannins, are the putative cause of a variety of seed functions including bird/insect resistance and antioxidant activity. Structure-reactivity relationships are necessary to understand the influence of polyphenolic chromophore structures on the tannin content and fr...

An exponentiation method for XML element retrieval.

PubMed

Wichaiwong, Tanakorn

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP.

The structural, connectomic and network covariance of the human brain.

PubMed

Irimia, Andrei; Van Horn, John D

2013-02-01

Though it is widely appreciated that complex structural, functional and morphological relationships exist between distinct areas of the human cerebral cortex, the extent to which such relationships coincide remains insufficiently appreciated. Here we determine the extent to which correlations between brain regions are modulated by either structural, connectomic or network-theoretic properties using a structural neuroimaging data set of magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) volumes acquired from N=110 healthy human adults. To identify the linear relationships between all available pairs of regions, we use canonical correlation analysis to test whether a statistically significant correlation exists between each pair of cortical parcels as quantified via structural, connectomic or network-theoretic measures. In addition to this, we investigate (1) how each group of canonical variables (whether structural, connectomic or network-theoretic) contributes to the overall correlation and, additionally, (2) whether each individual variable makes a significant contribution to the test of the omnibus null hypothesis according to which no correlation between regions exists across subjects. We find that, although region-to-region correlations are extensively modulated by structural and connectomic measures, there are appreciable differences in how these two groups of measures drive inter-regional correlation patterns. Additionally, our results indicate that the network-theoretic properties of the cortex are strong modulators of region-to-region covariance. Our findings are useful for understanding the structural and connectomic relationship between various parts of the brain, and can inform theoretical and computational models of cortical information processing. Published by Elsevier Inc.

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations

PubMed Central

Deco, Gustavo; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-01-01

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure–function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure–function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications. PMID:23825427

Structural and Functional Evaluations for the Early Detection of Glaucoma.

PubMed

Lucy, Katie A; Wollstein, Gadi

2016-01-01

The early detection of glaucoma is imperative in order to preserve functional vision. Structural and functional methods are utilized to detect and monitor glaucomatous damage and the vision loss it causes. The relationship between these detection measures is complex and differs between individuals, especially in early glaucoma. Using both measures together is advised in order to ensure the highest probability of glaucoma detection, and new testing methods are continuously developed with the goals of earlier disease detection and improvement of disease monitoring. The purpose of this review is to explore the relationship between structural and functional glaucoma detection and discuss important technological advances for early glaucoma detection.

Structural and Functional Evaluations for the Early Detection of Glaucoma

PubMed Central

Lucy, Katie A.; Wollstein, Gadi

2016-01-01

The early detection of glaucoma is imperative in order to preserve functional vision. Structural and functional methods are utilized to detect and monitor glaucomatous damage and the vision loss it causes. The relationship between these detection measures is complex and differs between individuals, especially in early glaucoma. Using both measures together is advised in order to ensure the highest probability of glaucoma detection, and new testing methods are continuously developed with the goals of earlier disease detection and improvement of disease monitoring. The purpose of this review is to explore the relationship between structural and functional glaucoma detection and discuss important technological advances for early glaucoma detection. PMID:28603546

An in silico algal toxicity model with a wide applicability potential for industrial chemicals and pharmaceuticals.

PubMed

Önlü, Serli; Saçan, Melek Türker

2017-04-01

The authors modeled the 72-h algal toxicity data of hundreds of chemicals with different modes of action as a function of chemical structures. They developed mode of action-based local quantitative structure-toxicity relationship (QSTR) models for nonpolar and polar narcotics as well as a global QSTR model with a wide applicability potential for industrial chemicals and pharmaceuticals. The present study rigorously evaluated the generated models, meeting the Organisation for Economic Co-operation and Development principles of robustness, validity, and transparency. The proposed global model had a broad structural coverage for the toxicity prediction of diverse chemicals (some of which are high-production volume chemicals) with no experimental toxicity data. The global model is potentially useful for endpoint predictions, the evaluation of algal toxicity screening, and the prioritization of chemicals, as well as for the decision of further testing and the development of risk-management measures in a scientific and regulatory frame. Environ Toxicol Chem 2017;36:1012-1019. © 2016 SETAC. © 2016 SETAC.

Analysis of the Explanatory Variables of the Differences in Perceptions of Cyberbullying: A Role-Based-Model Approach.

PubMed

Fernández-Antelo, Inmaculada; Cuadrado-Gordillo, Isabel

2018-04-01

The controversies that exist regarding the delimitation of the cyberbullying construct demonstrate the need for further research focused on determining the criteria that shape the structure of the perceptions that adolescents have of this phenomenon and on seeking explanations of this behavior. The objectives of this study were to (a) construct possible explanatory models of the perception of cyberbullying from identifying and relating the criteria that form this construct and (b) analyze the influence of previous cyber victimization and cyber aggression experiences in the construction of explanatory models of the perception of cyberbullying. The sample consisted of 2,148 adolescents (49.1% girls; SD = 0.5) aged from 12 to 16 years ( M = 13.9 years; SD = 1.2). The results have shown that previous cyber victimization and cyber aggression experiences lead to major differences in the explanatory models to interpret cyber-abusive behavior as cyberbullying episodes, or as social relationship mechanisms, or as a revenge reaction. We note that the aggressors' explanatory model is based primarily on a strong reciprocal relationship between the imbalance of power and intentionality, that it functions as a link promoting indirect causal relationships of the anonymity and repetition factors with the cyberbullying construct. The victims' perceptual structure is based on three criteria-imbalance of power, intentionality, and publicity-where the key factor in this structure is the intention to harm. These results allow to design more effective measures of prevention and intervention closely tailored to addressing directly the factors that are considered to be predictors of risk.

Comparison of main-shock and aftershock fragility curves developed for New Zealand and US buildings

USGS Publications Warehouse

Uma, S.R.; Ryu, H.; Luco, N.; Liel, A.B.; Raghunandan, M.

2011-01-01

Seismic risk assessment involves the development of fragility functions to express the relationship between ground motion intensity and damage potential. In evaluating the risk associated with the building inventory in a region, it is essential to capture 'actual' characteristics of the buildings and group them so that 'generic building types' can be generated for further analysis of their damage potential. Variations in building characteristics across regions/countries largely influence the resulting fragility functions, such that building models are unsuitable to be adopted for risk assessment in any other region where a different set of building is present. In this paper, for a given building type (represented in terms of height and structural system), typical New Zealand and US building models are considered to illustrate the differences in structural model parameters and their effects on resulting fragility functions for a set of main-shocks and aftershocks. From this study, the general conclusion is that the methodology and assumptions used to derive basic capacity curve parameters have a considerable influence on fragility curves.

Employee subjective well-being and physiological functioning: An integrative model

PubMed Central

Tay, Louis

2015-01-01

Research shows that worker subjective well-being influences physiological functioning—an early signal of poor health outcomes. While several theoretical perspectives provide insights on this relationship, the literature lacks an integrative framework explaining the relationship. We develop a conceptual model explaining the link between subjective well-being and physiological functioning in the context of work. Integrating positive psychology and occupational stress perspectives, our model explains the relationship between subjective well-being and physiological functioning as a result of the direct influence of subjective well-being on physiological functioning and of their common relationships with work stress and personal resources, both of which are influenced by job conditions. PMID:28070359

Log-gamma linear-mixed effects models for multiple outcomes with application to a longitudinal glaucoma study

PubMed Central

Zhang, Peng; Luo, Dandan; Li, Pengfei; Sharpsten, Lucie; Medeiros, Felipe A.

2015-01-01

Glaucoma is a progressive disease due to damage in the optic nerve with associated functional losses. Although the relationship between structural and functional progression in glaucoma is well established, there is disagreement on how this association evolves over time. In addressing this issue, we propose a new class of non-Gaussian linear-mixed models to estimate the correlations among subject-specific effects in multivariate longitudinal studies with a skewed distribution of random effects, to be used in a study of glaucoma. This class provides an efficient estimation of subject-specific effects by modeling the skewed random effects through the log-gamma distribution. It also provides more reliable estimates of the correlations between the random effects. To validate the log-gamma assumption against the usual normality assumption of the random effects, we propose a lack-of-fit test using the profile likelihood function of the shape parameter. We apply this method to data from a prospective observation study, the Diagnostic Innovations in Glaucoma Study, to present a statistically significant association between structural and functional change rates that leads to a better understanding of the progression of glaucoma over time. PMID:26075565

Co-localisation of abnormal brain structure and function in specific language impairment

PubMed Central

Badcock, Nicholas A.; Bishop, Dorothy V.M.; Hardiman, Mervyn J.; Barry, Johanna G.; Watkins, Kate E.

2012-01-01

We assessed the relationship between brain structure and function in 10 individuals with specific language impairment (SLI), compared to six unaffected siblings, and 16 unrelated control participants with typical language. Voxel-based morphometry indicated that grey matter in the SLI group, relative to controls, was increased in the left inferior frontal cortex and decreased in the right caudate nucleus and superior temporal cortex bilaterally. The unaffected siblings also showed reduced grey matter in the caudate nucleus relative to controls. In an auditory covert naming task, the SLI group showed reduced activation in the left inferior frontal cortex, right putamen, and in the superior temporal cortex bilaterally. Despite spatially coincident structural and functional abnormalities in frontal and temporal areas, the relationships between structure and function in these regions were different. These findings suggest multiple structural and functional abnormalities in SLI that are differently associated with receptive and expressive language processing. PMID:22137677

Calpain chronicle--an enzyme family under multidisciplinary characterization.

PubMed

Sorimachi, Hiroyuki; Hata, Shoji; Ono, Yasuko

2011-01-01

Calpain is an intracellular Ca2+-dependent cysteine protease (EC 3.4.22.17; Clan CA, family C02) discovered in 1964. It was also called CANP (Ca2+-activated neutral protease) as well as CASF, CDP, KAF, etc. until 1990. Calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. Calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." In the human genome, 15 genes--CAPN1, CAPN2, etc.--encode a calpain-like protease domain. Their products are calpain homologs with divergent structures and various combinations of functional domains, including Ca2+-binding and microtubule-interaction domains. Genetic studies have linked calpain deficiencies to a variety of defects in many different organisms, including lethality, muscular dystrophies, gastropathy, and diabetes. This review of the study of calpains focuses especially on recent findings about their structure-function relationships. These discoveries have been greatly aided by the development of 3D structural studies and genetic models.

First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer

PubMed Central

Arturo, Emilia C.; Gupta, Kushol; Héroux, Annie; Stith, Linda; Cross, Penelope J.; Parker, Emily J.; Loll, Patrick J.; Jaffe, Eileen K.

2016-01-01

Improved understanding of the relationship among structure, dynamics, and function for the enzyme phenylalanine hydroxylase (PAH) can lead to needed new therapies for phenylketonuria, the most common inborn error of amino acid metabolism. PAH is a multidomain homo-multimeric protein whose conformation and multimerization properties respond to allosteric activation by the substrate phenylalanine (Phe); the allosteric regulation is necessary to maintain Phe below neurotoxic levels. A recently introduced model for allosteric regulation of PAH involves major domain motions and architecturally distinct PAH tetramers [Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL, Jr (2013) Arch Biochem Biophys 530(2):73–82]. Herein, we present, to our knowledge, the first X-ray crystal structure for a full-length mammalian (rat) PAH in an autoinhibited conformation. Chromatographic isolation of a monodisperse tetrameric PAH, in the absence of Phe, facilitated determination of the 2.9 Å crystal structure. The structure of full-length PAH supersedes a composite homology model that had been used extensively to rationalize phenylketonuria genotype–phenotype relationships. Small-angle X-ray scattering (SAXS) confirms that this tetramer, which dominates in the absence of Phe, is different from a Phe-stabilized allosterically activated PAH tetramer. The lack of structural detail for activated PAH remains a barrier to complete understanding of phenylketonuria genotype–phenotype relationships. Nevertheless, the use of SAXS and X-ray crystallography together to inspect PAH structure provides, to our knowledge, the first complete view of the enzyme in a tetrameric form that was not possible with prior partial crystal structures, and facilitates interpretation of a wealth of biochemical and structural data that was hitherto impossible to evaluate. PMID:26884182

Structure analysis of tax revenue and inflation rate in Banda Aceh using vector error correction model with multiple alpha

NASA Astrophysics Data System (ADS)

Sofyan, Hizir; Maulia, Eva; Miftahuddin

2017-11-01

A country has several important parameters to achieve economic prosperity, such as tax revenue and inflation rate. One of the largest revenues of the State Budget in Indonesia comes from the tax sector. Meanwhile, the rate of inflation occurring in a country can be used as an indicator, to measure the good and bad economic problems faced by the country. Given the importance of tax revenue and inflation rate control in achieving economic prosperity, it is necessary to analyze the structure of tax revenue relations and inflation rate. This study aims to produce the best VECM (Vector Error Correction Model) with optimal lag using various alpha and perform structural analysis using the Impulse Response Function (IRF) of the VECM models to examine the relationship of tax revenue, and inflation in Banda Aceh. The results showed that the best model for the data of tax revenue and inflation rate in Banda Aceh City using alpha 0.01 is VECM with optimal lag 2, while the best model for data of tax revenue and inflation rate in Banda Aceh City using alpha 0.05 and 0,1 VECM with optimal lag 3. However, the VECM model with alpha 0.01 yielded four significant models of income tax model, inflation rate of Banda Aceh, inflation rate of health and inflation rate of education in Banda Aceh. While the VECM model with alpha 0.05 and 0.1 yielded one significant model that is income tax model. Based on the VECM models, then there are two structural analysis IRF which is formed to look at the relationship of tax revenue, and inflation in Banda Aceh, the IRF with VECM (2) and IRF with VECM (3).

Structure-function relationships during segregated and integrated network states of human brain functional connectivity.

PubMed

Fukushima, Makoto; Betzel, Richard F; He, Ye; van den Heuvel, Martijn P; Zuo, Xi-Nian; Sporns, Olaf

2018-04-01

Structural white matter connections are thought to facilitate integration of neural information across functionally segregated systems. Recent studies have demonstrated that changes in the balance between segregation and integration in brain networks can be tracked by time-resolved functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data and that fluctuations between segregated and integrated network states are related to human behavior. However, how these network states relate to structural connectivity is largely unknown. To obtain a better understanding of structural substrates for these network states, we investigated how the relationship between structural connectivity, derived from diffusion tractography, and functional connectivity, as measured by rs-fMRI, changes with fluctuations between segregated and integrated states in the human brain. We found that the similarity of edge weights between structural and functional connectivity was greater in the integrated state, especially at edges connecting the default mode and the dorsal attention networks. We also demonstrated that the similarity of network partitions, evaluated between structural and functional connectivity, increased and the density of direct structural connections within modules in functional networks was elevated during the integrated state. These results suggest that, when functional connectivity exhibited an integrated network topology, structural connectivity and functional connectivity were more closely linked to each other and direct structural connections mediated a larger proportion of neural communication within functional modules. Our findings point out the possibility of significant contributions of structural connections to integrative neural processes underlying human behavior.

Quantitative structure activity relationship (QSAR) of piperine analogs for bacterial NorA efflux pump inhibitors.

PubMed

Nargotra, Amit; Sharma, Sujata; Koul, Jawahir Lal; Sangwan, Pyare Lal; Khan, Inshad Ali; Kumar, Ashwani; Taneja, Subhash Chander; Koul, Surrinder

2009-10-01

Quantitative structure activity relationship (QSAR) analysis of piperine analogs as inhibitors of efflux pump NorA from Staphylococcus aureus has been performed in order to obtain a highly accurate model enabling prediction of inhibition of S. aureus NorA of new chemical entities from natural sources as well as synthetic ones. Algorithm based on genetic function approximation method of variable selection in Cerius2 was used to generate the model. Among several types of descriptors viz., topological, spatial, thermodynamic, information content and E-state indices that were considered in generating the QSAR model, three descriptors such as partial negative surface area of the compounds, area of the molecular shadow in the XZ plane and heat of formation of the molecules resulted in a statistically significant model with r(2)=0.962 and cross-validation parameter q(2)=0.917. The validation of the QSAR models was done by cross-validation, leave-25%-out and external test set prediction. The theoretical approach indicates that the increase in the exposed partial negative surface area increases the inhibitory activity of the compound against NorA whereas the area of the molecular shadow in the XZ plane is inversely proportional to the inhibitory activity. This model also explains the relationship of the heat of formation of the compound with the inhibitory activity. The model is not only able to predict the activity of new compounds but also explains the important regions in the molecules in quantitative manner.

Deep structure of the Alborz Mountains by joint inversion of P receiver functions and dispersion curves

NASA Astrophysics Data System (ADS)

Rastgoo, Mehdi; Rahimi, Habib; Motaghi, Khalil; Shabanian, Esmaeil; Romanelli, Fabio; Panza, Giuliano F.

2018-04-01

The Alborz Mountains represent a tectonically and seismically active convergent boundary in the Arabia - Eurasia collision zone, in western Asia. The orogenic belt has undergone a long-lasted tectono-magmatic history since the Cretaceous. The relationship between shallow and deep structures in this complex tectonic domain is not straightforward. We present a 2D velocity model constructed by the assemblage of 1D shear wave velocity (Vs) models from 26 seismic stations, mainly distributed along the southern flank of the Alborz Mountains. The shear wave velocity structure has been estimated beneath each station using joint inversion of P-waves receiver functions and Rayleigh wave dispersion curves. A substantiation of the Vs inversion results sits on the modeling of Bouguer gravity anomaly data. Our velocity and density models show low velocity/density anomalies in uppermost mantle of western and central Alborz at a depth range of ∼50-100 km. In deeper parts of the uppermost mantle (depth range of 100-150 km), a high velocity/density anomaly is located beneath most of the Mountain range. The spatial pattern of these low and high velocity/density structures in the upper mantle is interpreted as the result of post collisional delamination of lower part of the western and central Alborz lithosphere.

Developing and applying the adverse outcome pathway ...

EPA Pesticide Factsheets

To support a paradigm shift in regulatory toxicology testing and risk assessment, the Adverse Outcome Pathway (AOP) concept has recently been proposed. This concept is similar to that for Mode of Action (MOA), describing a sequence of measurable key events triggered by a molecular initiating event in which a stressor interacts with a biological target. The resulting cascade of key events includes molecular, cellular, structural and functional changes in biological systems, resulting in a measurable adverse outcome. Thereby, an AOP ideally provides information relevant to chemical structure-activity relationships as a basis to predict effects for structurally similar compounds. AOPs could potentially also form the basis for qualitative and quantitative predictive modeling of the human adverse outcome resulting from molecular initiating or other key events for which higher-throughput testing methods are available or can be developed.A variety of cellular and molecular processes are known to be critical to normal function of the central (CNS) and peripheral nervous systems (PNS). Because of the biological and functional complexity of the CNS and PNS, it has been challenging to establish causative links and quantitative relationships between key events that comprise the pathways leading from chemical exposure to an adverse outcome in the nervous system. Following introduction of principles of the description and assessment of MOA and AOPs, examples of adverse out

Coordination of the EMS system: an organizational theory approach.

PubMed

Narad, R A

1998-01-01

Emergency medical services (EMS) systems include autonomous organizations with high degrees of interdependence. The need to coordinate system participants has long been recognized but seldom achieved. This can be explained by organizational theory--specifically, the study of the relationships among organizations. Existing models identify the total system's functions, but fail to explain roles and relationships among the system's participants. Coordination among organizations is more difficult than coordination within an organization because of lack of an authority structure. The EMS system can be described as "a functionally interdependent system," consisting of multiple autonomous organizations with high degrees of interdependence in their technical functions. Communities have five potential management approaches, varying according to their aggressiveness. These are laissez-faire, where even voluntary coordination efforts are not tried; voluntary cooperation efforts, such as coordinating councils; external planning agencies without regulatory control; "framework organizations" with regulatory control over the system participants; and bureaucratization, placing the system participants within a single organizational hierarchy. The "multicratic organization" is a model for management of multiorganizational systems. A "system lead agency" plans joint activities and manages relationships among system participants in the way that the management of a uniorganization integrates departments. A lead agency is usually a unit of government or organized pursuant to government action, but a managed care organization can also fill this role. In extreme application of the model, the system is viewed as a framework and temporary modules are attached. Their interests are limited, as needed, to optimize the entire system. The lead agency sets policies affecting relationships of modules and policies crossing organizational boundaries.

De novo design of recombinant spider silk proteins for material applications.

PubMed

Zheng, Ke; Ling, Shengjie

2018-05-21

Spider silks are well known for their superior mechanical properties that are stronger and tougher than steel despite being assembled at close to ambient conditions and using water as the solvent. However, it is a significant challenge to utilize spider silks for practical applications due to their limited sources. Fortunately, genetic engineering techniques offer a promising approach to produce useable amounts of spider silk variants. Starting from these recombinant spider silk proteins, a series of experiments and simulations strategies were developed to improve the recombinant spider silk proteins (RSSP) material design and fabrication with the aim of biomimicking the structure-property-function relationships of spider silks. Accordingly, in this review, we first introduce the structure-property-function relationship of spider silks. Then, we discuss the recent progress in the genetic synthesis of RSSPs and summarize their related multiscale self-assembly behaviors. Finally, we outline works utilizing multiscale modeling to assist RSSP material design. This article is protected by copyright. All rights reserved.

Ethnicity, Social Support, and Depression Among Elderly Chilean People.

PubMed

Gallardo-Peralta, Lorena P; Sánchez-Moreno, Esteban; López De Roda, Ana Barrón; Arias Astray, Andrés

2015-01-01

Recent evidence regarding the relationship between social support and depression in elderly people shows the important role of ethnicity. This research describes the characteristics of social support in a sample of elderly people aged 60 and above living in northern Chile (n = 493), and analyzes the differences in the relationship between social support and depression between an indigenous group (Aymara population, n = 147) and a nonindigenous group (white, Caucasian, mestizo, n = 346). Various dimensions of social support were considered: structural elements, functional social support according to source, and community participation. The results show the existence of significant differences in the characteristics and dimensions of social support depending on sex, ethnicity, and marital status. Further, the central role of the family group is observed for both Aymara and nonindigenous elderly people. The hierarchical regression models obtained result in notable differences in the role of the structural, functional, and community elements of support in explaining depression for the ethnic groups considered.

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Impact of functional and structural social relationships on two year depression outcomes: A multivariate analysis.

PubMed

Davidson, Sandra K; Dowrick, Christopher F; Gunn, Jane M

2016-03-15

High rates of persistent depression highlight the need to identify the risk factors associated with poor depression outcomes and to provide targeted interventions to people at high risk. Although social relationships have been implicated in depression course, interventions targeting social relationships have been disappointing. Possibly, interventions have targeted the wrong elements of relationships. Alternatively, the statistical association between relationships and depression course is not causal, but due to shared variance with other factors. We investigated whether elements of social relationships predict major depressive episode (MDE) when multiple relevant variables are considered. Data is from a longitudinal study of primary care patients with depressive symptoms. 494 participants completed questionnaires at baseline and a depression measure (PHQ-9) two years later. Baseline measures included functional (i.e. quality) and structural (i.e. quantity) social relationships, depression, neuroticism, chronic illness, alcohol abuse, childhood abuse, partner violence and sociodemographic characteristics. Logistic regression with generalised estimating equations was used to estimate the association between social relationships and MDE. Both functional and structural social relationships predicted MDE in univariate analysis. Only functional social relationships remained significant in multivariate analysis (OR: 0.87; 95%CI: 0.79-0.97; p=0.01). Other unique predictors of MDE were baseline depression severity, neuroticism, childhood sexual abuse and intimate partner violence. We did not assess how a person's position in their depression trajectory influenced the association between social relationships and depression. Interventions targeting relationship quality may be part of a personalised treatment plan for people at high risk due of persistent depression due to poor social relationships. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigating Supervisory Relationships and Therapeutic Alliances Using Structural Equation Modeling

ERIC Educational Resources Information Center

DePue, Mary Kristina; Lambie, Glenn W.; Liu, Ren; Gonzalez, Jessica

2016-01-01

The authors used structural equation modeling to examine the contribution of supervisees' supervisory relationship levels to therapeutic alliance (TA) scores with their clients in practicum. Results showed that supervisory relationship scores positively contributed to the TA. Client and counselor ratings of the TA also differed.

Precise Network Modeling of Systems Genetics Data Using the Bayesian Network Webserver.

PubMed

Ziebarth, Jesse D; Cui, Yan

2017-01-01

The Bayesian Network Webserver (BNW, http://compbio.uthsc.edu/BNW ) is an integrated platform for Bayesian network modeling of biological datasets. It provides a web-based network modeling environment that seamlessly integrates advanced algorithms for probabilistic causal modeling and reasoning with Bayesian networks. BNW is designed for precise modeling of relatively small networks that contain less than 20 nodes. The structure learning algorithms used by BNW guarantee the discovery of the best (most probable) network structure given the data. To facilitate network modeling across multiple biological levels, BNW provides a very flexible interface that allows users to assign network nodes into different tiers and define the relationships between and within the tiers. This function is particularly useful for modeling systems genetics datasets that often consist of multiscalar heterogeneous genotype-to-phenotype data. BNW enables users to, within seconds or minutes, go from having a simply formatted input file containing a dataset to using a network model to make predictions about the interactions between variables and the potential effects of experimental interventions. In this chapter, we will introduce the functions of BNW and show how to model systems genetics datasets with BNW.

Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction,more » respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.« less

Biomimetic cellular metals-using hierarchical structuring for energy absorption.

PubMed

Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

2016-07-19

Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form-structure-function relationship of the biological concept generators as well as the bio-inspired metal foams was achieved, on deeper hierarchical levels and overarching different levels.

Development of Novel Repellents Using Structure - Activity Modeling of Compounds in the USDA Archival Database

DTIC Science & Technology

2011-01-01

used in efforts to develop QSAR models. Measurement of Repellent Efficacy Screening for Repellency of Compounds with Unknown Toxicology In screening...CPT) were used to develop Quantitative Structure Activity Relationship ( QSAR ) models to predict repellency. Successful prediction of novel...acylpiperidine QSAR models employed 4 descriptors to describe the relationship between structure and repellent duration. The ANN model of the carboxamides did not

Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms

PubMed Central

Taylor, Gregory K.; Stoddard, Barry L.

2012-01-01

Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of phage, bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that collectively span four distinct nuclease catalytic motifs, have been characterized to date. Members of each family display structural homology and functional relationships to a wide variety of proteins from various organisms. The biological functions of those proteins are highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases, DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These relationships suggest that modern day HEs share common ancestors with proteins involved in genome fidelity, maintenance and gene expression. This review summarizes the results of structural studies of HEs and corresponding proteins from host organisms that have illustrated the manner in which these factors are related. PMID:22406833

Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

NASA Astrophysics Data System (ADS)

Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

2012-12-01

Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

Social cognition in schizophrenia: Factor structure, clinical and functional correlates

PubMed Central

Buck, Benjamin E.; Healey, Kristin M.; Gagen, Emily C.; Roberts, David L.; Penn, David L.

2016-01-01

Background Social cognition is consistently impaired in people with schizophrenia, separable from general neurocognition, predictive of real-world functioning, and amenable to psychosocial treatment. Few studies have empirically examined its underlying factor structure. Aims The present study (1) examines the factor structure of social cognition in both a sample of individuals with schizophrenia-spectrum disorders and non-clinical controls, and (2) explores relationships of factors to neurocognition, symptoms and functioning. Method A factor analysis was conducted on social cognition measures in a sample of sixty-five individuals with schizophrenia or schizoaffective disorder, and fifty control participants. The resulting factors were examined for their relationships to symptoms and functioning. Results Results suggested a two-factor structure in the schizophrenia sample (social cognition skill and hostile attributional style) and a three-factor structure in the non-clinical sample (hostile attributional style, higher-level inferential processing, and lower-level cue detection). In the schizophrenia sample, the social cognition skill factor was significantly related to negative symptoms and social functioning, while hostile attributional style predicted positive and general psychopathology symptoms. Conclusions The factor structure of social cognition in schizophrenia separates hostile attributional style and social cognition skill, and each show differential relationships to relevant clinical variables in schizophrenia. PMID:26747063

Harnessing glycomics technologies: integrating structure with function for glycan characterization

PubMed Central

Robinson, Luke N.; Artpradit, Charlermchai; Raman, Rahul; Shriver, Zachary H.; Ruchirawat, Mathuros; Sasisekharan, Ram

2013-01-01

Glycans, or complex carbohydrates, are a ubiquitous class of biological molecules which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships. PMID:22522536

Perceived Social Relationships and Science Learning Outcomes for Taiwanese Eighth Graders: Structural Equation Modeling with a Complex Sampling Consideration

ERIC Educational Resources Information Center

Jen, Tsung-Hau; Lee, Che-Di; Chien, Chin-Lung; Hsu, Ying-Shao; Chen, Kuan-Ming

2013-01-01

Based on the Trends in International Mathematics and Science Study 2007 study and a follow-up national survey, data for 3,901 Taiwanese grade 8 students were analyzed using structural equation modeling to confirm a social-relation-based affection-driven model (SRAM). SRAM hypothesized relationships among students' perceived social relationships in…

Structural diversity promotes productivity of mixed, uneven-aged forests in southwestern Germany.

PubMed

Dănescu, Adrian; Albrecht, Axel T; Bauhus, Jürgen

2016-10-01

Forest diversity-productivity relationships have been intensively investigated in recent decades. However, few studies have considered the interplay between species and structural diversity in driving productivity. We analyzed these factors using data from 52 permanent plots in southwestern Germany with more than 53,000 repeated tree measurements. We used basal area increment as a proxy for productivity and hypothesized that: (1) structural diversity would increase tree and stand productivity, (2) diversity-productivity relationships would be weaker for species diversity than for structural diversity, and (3) species diversity would also indirectly impact stand productivity via changes in size structure. We measured diversity using distance-independent indices. We fitted separate linear mixed-effects models for fir, spruce and beech at the tree level, whereas at the stand level we pooled all available data. We tested our third hypothesis using structural equation modeling. Structural and species diversity acted as direct and independent drivers of stand productivity, with structural diversity being a slightly better predictor. Structural diversity, but not species diversity, had a significant, albeit asymmetric, effect on tree productivity. The functioning of structurally diverse, mixed forests is influenced by both structural and species diversity. These sources of trait diversity contribute to increased vertical stratification and crown plasticity, which in turn diminish competitive interferences and lead to more densely packed canopies per unit area. Our research highlights the positive effects of species diversity and structural diversity on forest productivity and ecosystem dynamics.

Analyzing structure-function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells.

PubMed

Rank, Lisa; Veith, Sebastian; Gwosch, Eva C; Demgenski, Janine; Ganz, Magdalena; Jongmans, Marjolijn C; Vogel, Christopher; Fischbach, Arthur; Buerger, Stefanie; Fischer, Jan M F; Zubel, Tabea; Stier, Anna; Renner, Christina; Schmalz, Michael; Beneke, Sascha; Groettrup, Marcus; Kuiper, Roland P; Bürkle, Alexander; Ferrando-May, Elisa; Mangerich, Aswin

2016-12-01

Genotoxic stress activates PARP1, resulting in the post-translational modification of proteins with poly(ADP-ribose) (PAR). We genetically deleted PARP1 in one of the most widely used human cell systems, i.e. HeLa cells, via TALEN-mediated gene targeting. After comprehensive characterization of these cells during genotoxic stress, we analyzed structure-function relationships of PARP1 by reconstituting PARP1 KO cells with a series of PARP1 variants. Firstly, we verified that the PARP1\\E988K mutant exhibits mono-ADP-ribosylation activity and we demonstrate that the PARP1\\L713F mutant is constitutively active in cells. Secondly, both mutants exhibit distinct recruitment kinetics to sites of laser-induced DNA damage, which can potentially be attributed to non-covalent PARP1-PAR interaction via several PAR binding motifs. Thirdly, both mutants had distinct functional consequences in cellular patho-physiology, i.e. PARP1\\L713F expression triggered apoptosis, whereas PARP1\\E988K reconstitution caused a DNA-damage-induced G2 arrest. Importantly, both effects could be rescued by PARP inhibitor treatment, indicating distinct cellular consequences of constitutive PARylation and mono(ADP-ribosyl)ation. Finally, we demonstrate that the cancer-associated PARP1 SNP variant (V762A) as well as a newly identified inherited PARP1 mutation (F304L\\V762A) present in a patient with pediatric colorectal carcinoma exhibit altered biochemical and cellular properties, thereby potentially supporting human carcinogenesis. Together, we establish a novel cellular model for PARylation research, by revealing strong structure-function relationships of natural and artificial PARP1 variants. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Quantitative theory of hydrophobic effect as a driving force of protein structure

PubMed Central

Perunov, Nikolay; England, Jeremy L

2014-01-01

Various studies suggest that the hydrophobic effect plays a major role in driving the folding of proteins. In the past, however, it has been challenging to translate this understanding into a predictive, quantitative theory of how the full pattern of sequence hydrophobicity in a protein shapes functionally important features of its tertiary structure. Here, we extend and apply such a phenomenological theory of the sequence-structure relationship in globular protein domains, which had previously been applied to the study of allosteric motion. In an effort to optimize parameters for the model, we first analyze the patterns of backbone burial found in single-domain crystal structures, and discover that classic hydrophobicity scales derived from bulk physicochemical properties of amino acids are already nearly optimal for prediction of burial using the model. Subsequently, we apply the model to studying structural fluctuations in proteins and establish a means of identifying ligand-binding and protein–protein interaction sites using this approach. PMID:24408023

Effects of pressure and electrical charge on macromolecular transport across bovine lens basement membrane.

PubMed

Ferrell, Nicholas; Cameron, Kathleen O; Groszek, Joseph J; Hofmann, Christina L; Li, Lingyan; Smith, Ross A; Bian, Aihua; Shintani, Ayumi; Zydney, Andrew L; Fissell, William H

2013-04-02

Molecular transport through the basement membrane is important for a number of physiological functions, and dysregulation of basement membrane architecture can have serious pathological consequences. The structure-function relationships that govern molecular transport in basement membranes are not fully understood. The basement membrane from the lens capsule of the eye is a collagen IV-rich matrix that can easily be extracted and manipulated in vitro. As such, it provides a convenient model for studying the functional relationships that govern molecular transport in basement membranes. Here we investigate the effects of increased transmembrane pressure and solute electrical charge on the transport properties of the lens basement membrane (LBM) from the bovine eye. Pressure-permeability relationships in LBM transport were governed primarily by changes in diffusive and convective contributions to solute flux and not by pressure-dependent changes in intrinsic membrane properties. The solute electrical charge had a minimal but statistically significant effect on solute transport through the LBM that was opposite of the expected electrokinetic behavior. The observed transport characteristics of the LBM are discussed in the context of established membrane transport modeling and previous work on the effects of pressure and electrical charge in other basement membrane systems. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Multidimensional Predictors of Fatigue among Octogenarians and Centenarians

PubMed Central

Cho, Jinmyoung; Martin, Peter; Margrett, Jennifer; MacDonald, Maurice; Johnson, Mary Ann; Poon, Leonard W.

2012-01-01

Background Fatigue is a common and frequently observed complaint among older adults. However, knowledge about the nature and correlates of fatigue in old age is very limited. Objective: This study examined the relationship of functional indicators, psychological and situational factors and fatigue for 210 octogenarians and centenarians from the Georgia Centenarian Study. Methods Three indicators of functional capacity (self-rated health, instrumental activities of daily living, physical activities of daily living), two indicators of psychological well-being (positive and negative affect), two indicators of situational factors (social network and social support), and a multidimensional fatigue scale were used. Blocked multiple regression analyses were computed to examine significant factors related to fatigue. In addition, multi-group analysis in structural equation modeling was used to investigate residential differences (i.e., long-term care facilities vs. private homes) in the relationship between significant factors and fatigue. Results Blocked multiple regression analyses indicated that two indicators of functional capacity, self-rated health and instrumental activities of daily living, both positive and negative affect, and social support were significant predictors of fatigue among oldest-old adults. The multiple group analysis in structural equation modeling revealed a significant difference among oldest-old adults based on residential status. Conclusion The results suggest that we should not consider fatigue as merely an unpleasant physical symptom, but rather adopt a perspective that different factors such as psychosocial aspects can influence fatigue in advanced later life. PMID:22094445

Multidimensional predictors of fatigue among octogenarians and centenarians.

PubMed

Cho, Jinmyoung; Martin, Peter; Margrett, Jennifer; MacDonald, Maurice; Johnson, Mary Ann; Poon, Leonard W; Jazwinski, S M; Green, R C; Gearing, M; Woodard, J L; Tenover, J S; Siegler, I C; Rott, C; Rodgers, W L; Hausman, D; Arnold, J; Davey, A

2012-01-01

Fatigue is a common and frequently observed complaint among older adults. However, knowledge about the nature and correlates of fatigue in old age is very limited. This study examined the relationship of functional indicators, psychological and situational factors and fatigue for 210 octogenarians and centenarians from the Georgia Centenarian Study. Three indicators of functional capacity (self-rated health, instrumental activities of daily living, physical activities of daily living), two indicators of psychological well-being (positive and negative affect), two indicators of situational factors (social network and social support), and a multidimensional fatigue scale were used. Blocked multiple regression analyses were computed to examine significant factors related to fatigue. In addition, multi-group analysis in structural equation modeling was used to investigate residential differences (i.e., long-term care facilities vs. private homes) in the relationship between significant factors and fatigue. Blocked multiple regression analyses indicated that two indicators of functional capacity, self-rated health and instrumental activities of daily living, both positive and negative affect, and social support were significant predictors of fatigue among oldest-old adults. The multiple group analysis in structural equation modeling revealed a significant difference among oldest-old adults based on residential status. The results suggest that we should not consider fatigue as merely an unpleasant physical symptom, but rather adopt a perspective that different factors such as psychosocial aspects can influence fatigue in advanced later life. Copyright © 2011 S. Karger AG, Basel.

Development of uncertainty-based work injury model using Bayesian structural equation modelling.

PubMed

Chatterjee, Snehamoy

2014-01-01

This paper proposed a Bayesian method-based structural equation model (SEM) of miners' work injury for an underground coal mine in India. The environmental and behavioural variables for work injury were identified and causal relationships were developed. For Bayesian modelling, prior distributions of SEM parameters are necessary to develop the model. In this paper, two approaches were adopted to obtain prior distribution for factor loading parameters and structural parameters of SEM. In the first approach, the prior distributions were considered as a fixed distribution function with specific parameter values, whereas, in the second approach, prior distributions of the parameters were generated from experts' opinions. The posterior distributions of these parameters were obtained by applying Bayesian rule. The Markov Chain Monte Carlo sampling in the form Gibbs sampling was applied for sampling from the posterior distribution. The results revealed that all coefficients of structural and measurement model parameters are statistically significant in experts' opinion-based priors, whereas, two coefficients are not statistically significant when fixed prior-based distributions are applied. The error statistics reveals that Bayesian structural model provides reasonably good fit of work injury with high coefficient of determination (0.91) and less mean squared error as compared to traditional SEM.

Application of Functional Use Predictions to Aid in Structure ...

EPA Pesticide Factsheets

Humans are potentially exposed to thousands of anthropogenic chemicals in commerce. Recent work has shown that the bulk of this exposure may occur in near-field indoor environments (e.g., home, school, work, etc.). Advances in suspect screening analyses (SSA) now allow an improved understanding of the chemicals present in these environments. However, due to the nature of suspect screening techniques, investigators are often left with chemical formula predictions, with the possibility of many chemical structures matching to each formula. Here, newly developed quantitative structure-use relationship (QSUR) models are used to identify potential exposure sources for candidate structures. Previously, a suspect screening workflow was introduced and applied to house dust samples collected from the U.S. Department of Housing and Urban Development’s American Healthy Homes Survey (AHHS) [Rager, et al., Env. Int. 88 (2016)]. This workflow utilized the US EPA’s Distributed Structure-Searchable Toxicity (DSSTox) Database to link identified molecular features to molecular formulas, and ultimately chemical structures. Multiple QSUR models were applied to support the evaluation of candidate structures. These QSURs predict the likelihood of a chemical having a functional use commonly associated with consumer products having near-field use. For 3,228 structures identified as possible chemicals in AHHS house dust samples, we were able to obtain the required descriptors to appl

Dynamic Latent Trait Models with Mixed Hidden Markov Structure for Mixed Longitudinal Outcomes.

PubMed

Zhang, Yue; Berhane, Kiros

2016-01-01

We propose a general Bayesian joint modeling approach to model mixed longitudinal outcomes from the exponential family for taking into account any differential misclassification that may exist among categorical outcomes. Under this framework, outcomes observed without measurement error are related to latent trait variables through generalized linear mixed effect models. The misclassified outcomes are related to the latent class variables, which represent unobserved real states, using mixed hidden Markov models (MHMM). In addition to enabling the estimation of parameters in prevalence, transition and misclassification probabilities, MHMMs capture cluster level heterogeneity. A transition modeling structure allows the latent trait and latent class variables to depend on observed predictors at the same time period and also on latent trait and latent class variables at previous time periods for each individual. Simulation studies are conducted to make comparisons with traditional models in order to illustrate the gains from the proposed approach. The new approach is applied to data from the Southern California Children Health Study (CHS) to jointly model questionnaire based asthma state and multiple lung function measurements in order to gain better insight about the underlying biological mechanism that governs the inter-relationship between asthma state and lung function development.

Structure-function relationships in the evolutionary framework of spermine oxidase.

PubMed

Cervelli, Manuela; Salvi, Daniele; Polticelli, Fabio; Amendola, Roberto; Mariottini, Paolo

2013-06-01

Spermine oxidase is a FAD-dependent enzyme that specifically oxidizes spermine, and plays a central role in the highly regulated catabolism of polyamines in vertebrates. The spermine oxidase substrate is specifically spermine, a tetramine that plays mandatory roles in several cell functions, such as DNA synthesis, cellular proliferation, modulation of ion channels function, cellular signalling, nitric oxide synthesis and inhibition of immune responses. The oxidative products of spermine oxidase activity are spermidine, H2O2 and the aldehyde 3-aminopropanal that spontaneously turns into acrolein. In this study the reconstruction of the phylogenetic relationships among spermine oxidase proteins from different vertebrate taxa allowed to infer their molecular evolutionary history, and assisted in elucidating the conservation of structural and functional properties of this enzyme family. The amino acid residues, which have been hypothesized or demonstrated to play a pivotal role in the enzymatic activity, and substrate specificity are here analysed to obtain a comprehensive and updated view of the structure-function relationships in the evolution of spermine oxidase.

The structural and functional connectivity of the grassland plant Lychnis flos-cuculi

PubMed Central

Aavik, T; Holderegger, R; Bolliger, J

2014-01-01

Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity. PMID:24253937

The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems.

PubMed

Lewandowska, Aleksandra M; Biermann, Antje; Borer, Elizabeth T; Cebrián-Piqueras, Miguel A; Declerck, Steven A J; De Meester, Luc; Van Donk, Ellen; Gamfeldt, Lars; Gruner, Daniel S; Hagenah, Nicole; Harpole, W Stanley; Kirkman, Kevin P; Klausmeier, Christopher A; Kleyer, Michael; Knops, Johannes M H; Lemmens, Pieter; Lind, Eric M; Litchman, Elena; Mantilla-Contreras, Jasmin; Martens, Koen; Meier, Sandra; Minden, Vanessa; Moore, Joslin L; Venterink, Harry Olde; Seabloom, Eric W; Sommer, Ulrich; Striebel, Maren; Trenkamp, Anastasia; Trinogga, Juliane; Urabe, Jotaro; Vyverman, Wim; Van de Waal, Dedmer B; Widdicombe, Claire E; Hillebrand, Helmut

2016-05-19

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity. © 2016 The Author(s).

Retrograde tracing and toe spreading after experimental autologous nerve transplantation and crush injury of the sciatic nerve: a descriptive methodological study.

PubMed

van Neerven, Sabien Ga; Bozkurt, Ahmet; O'Dey, Dan Mon; Scheffel, Juliane; Boecker, Arne H; Stromps, Jan-Philipp; Dunda, Sebastian; Brook, Gary A; Pallua, Norbert

2012-04-30

Evaluation of functional and structural recovery after peripheral nerve injury is crucial to determine the therapeutic effect of a nerve repair strategy. In the present study, we examined the relationship between the structural evaluation of regeneration by means of retrograde tracing and the functional analysis of toe spreading. Two standardized rat sciatic nerve injury models were used to address this relationship. As such, animals received either a 2 cm sciatic nerve defect (neurotmesis) followed by autologous nerve transplantation (ANT animals) or a crush injury with spontaneous recovery (axonotmesis; CI animals). Functional recovery of toe spreading was observed over an observation period of 84 days. In contrast to CI animals, ANT animals did not reach pre-surgical levels of toe spreading. After the observation period, the lipophilic dye DiI was applied to label sensory and motor neurons in dorsal root ganglia (DRG; sensory neurons) and spinal cord (motor neurons), respectively. No statistical difference in motor or sensory neuron counts could be detected between ANT and CI animals.In the present study we could indicate that there was no direct relationship between functional recovery (toe spreading) measured by SSI and the number of labelled (motor and sensory) neurons evaluated by retrograde tracing. The present findings demonstrate that a multimodal approach with a variety of independent evaluation tools is essential to understand and estimate the therapeutic benefit of a nerve repair strategy.

Upper extremity function in stroke subjects: relationships between the international classification of functioning, disability, and health domains.

PubMed

Faria-Fortini, Iza; Michaelsen, Stella Maris; Cassiano, Janine Gomes; Teixeira-Salmela, Luci Fuscaldi

2011-01-01

Upper limb (UL) impairments are the most common disabling deficits after stroke and have complex relationships with activity and participation domains. However, relatively few studies have applied the ICF model to identify the contributions of specific UL impairments, such as muscular weakness, pain, and sensory loss, as predictors of activity and participation. The purposes of this predictive study were to evaluate the relationships between UL variables related to body functions/structures, activity, and participation domains and to determine which would best explain activity and participation with 55 subjects with chronic stroke. Body functions/structures were assessed by measures of grip, pinch, and UL strength, finger tactile sensations, shoulder pain, and cognition (MMSE); activity domain by measures of observed performance (BBT, NHPT, and TEMPA); and participation by measures of quality of life (SSQOL). Upper-limb and grip strength were related to all activity measures (0.52

Quantifying the Hydraulic Roughness of Vegetation using Physical Modelling and Through-Water Terrestrial Laser Scanning.

NASA Astrophysics Data System (ADS)

Vasilopoulos, G.; Leyland, J.; Nield, J. M.

2016-12-01

Plants function as large-scale, flexible obstacles that exert additional drag on water flows, affecting local scale turbulence and the structure of the boundary layer. Hence, vegetation plays a significant role controlling surface water flows and modulating geomorphic change. This makes it an important, but often under considered, component when undertaking flood or erosion control actions, or designing river restoration strategies. Vegetative drag varies depending on flow conditions and the associated vegetation structure and temporary reconfiguration of the plant. Whilst several approaches have been developed to describe this relationship, they have been limited due to the difficulty of accurately and precisely characterising the vegetation itself, especially when it is submerged in flow. In practice, vegetative drag is commonly expressed through bulk parameters that are typically derived from lookup tables. Terrestrial Laser Scanning (TLS) has the ability to capture the surface of in situ objects as 3D point clouds, at high resolution (mm), precision and accuracy, even when submerged in water. This allows for the development of workflows capable of quantifying vegetation structure in 3D from dense TLS point cloud data. A physical modelling experiment investigated the impact of a series of structurally variable plants on flow at three different velocities. Acoustic Doppler Velocimetry (ADV) was employed to measure the velocity field and the corresponding fluvial drag of the vegetation was estimated using a bulk roughness function calculated from precise measurements of the water surface slope. Simultaneously, through-water TLS was employed to capture snapshots of plant deformation and distinguish plant structure during flow, using a porosity approach. Although plant type is important, we find a good relationship between plant structure, drag and adjustments of the velocity field.

Staying on Task: Age-Related Changes in the Relationship Between Executive Functioning and Response Time Consistency.

PubMed

Vasquez, Brandon P; Binns, Malcolm A; Anderson, Nicole D

2016-03-01

Little is known about the relationship of executive functioning with age-related increases in response time (RT) distribution indices (intraindividual standard deviation [ISD], and ex-Gaussian parameters mu, sigma, tau). The goals of this study were to (a) replicate findings of age-related changes in response time distribution indices during an engaging touch-screen RT task and (b) investigate age-related changes in the relationship between executive functioning and RT distribution indices. Healthy adults (24 young [aged 18-30], 24 young-old [aged 65-74], and 24 old-old [aged 75-85]) completed a touch-screen attention task and a battery of neuropsychological tests. The relationships between RT performance and executive functions were examined with structural equation modeling (SEM). ISD, mu, and tau, but not sigma, increased with age. SEM revealed tau as the most salient RT index associated with neuropsychological measures of executive functioning. Further analysis demonstrated that correlations between tau and a weighted executive function composite were significant only in the old-old group. Our results replicate findings of greater RT inconsistency in older adults and reveal that executive functioning is related to tau in adults aged 75-85. These results support literature identifying tau as a marker of cognitive control, which deteriorates in old age. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

EPA Science Inventory

Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

Nanoscale Structure and Interaction of Compact Assemblies of Carbon Nano-Materials

NASA Astrophysics Data System (ADS)

Timsina, Raju; Qiu, Xiangyun

Carbon-based nano-materials (CNM) are a diverse family of multi-functional materials under research and development world wide. Our work is further motivated by the predictive power of the physical understanding of the underlying structure-interaction-function relationships. Here we present results form recent studies of the condensed phases of several model CNMs in complexation with biologically derived molecules. Specifically, we employ X-ray diffraction (XRD) to determine nanoscale structures and use the osmotic stress method to quantify their interactions. The systems under investigation are dsDNA-dispersed carbon nanotubes (dsDNA-CNT), bile-salt-dispersed carbon nanotubes, and surfactant-assisted assemblies of graphene oxides. We found that salt and molecular crowding are both effective in condensing CNMs but the resultant structures show disparate phase behaviors. The molecular interactions driving the condensation/assembly sensitively depend on the nature of CNM complex surface chemistry and range from hydrophobic to electrostatic to entropic forces.

Bridging the Gap between the Human and Macaque Connectome: A Quantitative Comparison of Global Interspecies Structure-Function Relationships and Network Topology

PubMed Central

Miranda-Dominguez, Oscar; Mills, Brian D.; Grayson, David; Woodall, Andrew; Grant, Kathleen A.; Kroenke, Christopher D.

2014-01-01

Resting state functional connectivity MRI (rs-fcMRI) may provide a powerful and noninvasive “bridge” for comparing brain function between patients and experimental animal models; however, the relationship between human and macaque rs-fcMRI remains poorly understood. Here, using a novel surface deformation process for species comparisons in the same anatomical space (Van Essen, 2004, 2005), we found high correspondence, but also unique hub topology, between human and macaque functional connectomes. The global functional connectivity match between species was moderate to strong (r = 0.41) and increased when considering the top 15% strongest connections (r = 0.54). Analysis of the match between functional connectivity and the underlying anatomical connectivity, derived from a previous retrograde tracer study done in macaques (Markov et al., 2012), showed impressive structure–function correspondence in both the macaque and human. When examining the strongest structural connections, we found a 70–80% match between structural and functional connectivity matrices in both species. Finally, we compare species on two widely used metrics for studying hub topology: degree and betweenness centrality. The data showed topological agreement across the species, with nodes of the posterior cingulate showing high degree and betweenness centrality. In contrast, nodes in medial frontal and parietal cortices were identified as having high degree and betweenness in the human as opposed to the macaque. Our results provide: (1) a thorough examination and validation for a surface-based interspecies deformation process, (2) a strong theoretical foundation for making interspecies comparisons of rs-fcMRI, and (3) a unique look at topological distinctions between the species. PMID:24741045

Automated, quantitative measures of grey and white matter lesion burden correlates with motor and cognitive function in children with unilateral cerebral palsy.

PubMed

Pagnozzi, Alex M; Dowson, Nicholas; Doecke, James; Fiori, Simona; Bradley, Andrew P; Boyd, Roslyn N; Rose, Stephen

2016-01-01

White and grey matter lesions are the most prevalent type of injury observable in the Magnetic Resonance Images (MRIs) of children with cerebral palsy (CP). Previous studies investigating the impact of lesions in children with CP have been qualitative, limited by the lack of automated segmentation approaches in this setting. As a result, the quantitative relationship between lesion burden has yet to be established. In this study, we perform automatic lesion segmentation on a large cohort of data (107 children with unilateral CP and 18 healthy children) with a new, validated method for segmenting both white matter (WM) and grey matter (GM) lesions. The method has better accuracy (94%) than the best current methods (73%), and only requires standard structural MRI sequences. Anatomical lesion burdens most predictive of clinical scores of motor, cognitive, visual and communicative function were identified using the Least Absolute Shrinkage and Selection operator (LASSO). The improved segmentations enabled identification of significant correlations between regional lesion burden and clinical performance, which conform to known structure-function relationships. Model performance was validated in an independent test set, with significant correlations observed for both WM and GM regional lesion burden with motor function (p < 0.008), and between WM and GM lesions alone with cognitive and visual function respectively (p < 0.008). The significant correlation of GM lesions with functional outcome highlights the serious implications GM lesions, in addition to WM lesions, have for prognosis, and the utility of structural MRI alone for quantifying lesion burden and planning therapy interventions.

Molecular modeling on structure-function analysis of human progesterone receptor modulators.

PubMed

Pal, Ria; Islam, Md Ataul; Hossain, Tabassum; Saha, Achintya

2011-01-01

Considering the significance of progesterone receptor (PR) modulators, the present study is explored to envisage the biophoric signals for binding to selective PR subtype-A using ligand-based quantitative structure activity relationship (QSAR) and pharmacophore space modeling studies on nonsteroidal substituted quinoline and cyclocymopol monomethyl ether derivatives. Consensus QSAR models (Training set (Tr): n(Tr)=100, R(2) (pred)=0.702; test set (Ts): n(Ts)=30, R(2) (pred)=0.705, R(2) (m)=0.635; validation set (Vs): n(Vs)=40, R(2) (pred)=0.715, R(2) (m)=0.680) suggest that molecular topology, atomic polarizability and electronegativity, atomic mass and van der Waals volume of the ligands have influence on the presence of functional atoms (F, Cl, N and O) and consequently contribute significant relations on ligand binding affinity. Receptor independent space modeling study (Tr: n(Tr)=26, Q(2)=0.927; Ts: n(Ts)=60, R(2) (pred)=0.613, R(2) (m)=0.545; Vs: n(Vs)=84, R(2) (pred)=0.611, R(2) (m)=0.507) indicates the importance of aromatic ring, hydrogen bond donor, molecular hydrophobicity and steric influence for receptor binding. The structure-function characterization is adjudged with the receptor-based docking study, explaining the significance of the mapped molecular attributes for ligand-receptor interaction in the catalytic cleft of PR-A.

A Structural Equation Model of the Factors Associated with Influence and Power of IT Departments and Their Relationship to Firm's IT Orientation and Business Performance

ERIC Educational Resources Information Center

Kowshik, Raghu V.

2010-01-01

Although few firms can function without an information technology (IT) department, senior executives often consider IT as secondary. Historically, studies have found IT departments to have low influence and power status compared to other departments. Few, if any, studies have investigated what factors contribute to this subservient position. Three…

A new method to approximate load-displacement relationships of spinal motion segments for patient-specific multi-body models of scoliotic spine.

PubMed

Jalalian, Athena; Tay, Francis E H; Arastehfar, Soheil; Liu, Gabriel

2017-06-01

Load-displacement relationships of spinal motion segments are crucial factors in characterizing the stiffness of scoliotic spine models to mimic the spine responses to loads. Although nonlinear approach to approximation of the relationships can be superior to linear ones, little mention has been made to deriving personalized nonlinear load-displacement relationships in previous studies. A method is developed for nonlinear approximation of load-displacement relationships of spinal motion segments to assist characterizing in vivo the stiffness of spine models. We propose approximation by tangent functions and focus on rotational displacements in lateral direction. The tangent functions are characterized using lateral bending test. A multi-body model was characterized to 18 patients and utilized to simulate four spine positions; right bending, left bending, neutral, and traction. The same was done using linear functions to assess the performance of the proposed tangent function in comparison with the linear function. Root-mean-square error (RMSE) of the displacements estimated by the tangent functions was 44 % smaller than the linear functions. This shows the ability of our tangent function in approximation of the relationships for a range of infinitesimal to large displacements involved in the spine movement to the four positions. In addition, the models based on the tangent functions yielded 67, 55, and 39 % smaller RMSEs of Ferguson angles, locations of vertebrae, and orientations of vertebrae, respectively, implying better estimates of spine responses to loads. Overall, it can be concluded that our method for approximating load-displacement relationships of spinal motion segments can offer good estimates of scoliotic spine stiffness.

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

PubMed Central

Whitlock, Raj

2014-01-01

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

Enhancing the Developmental Appropriateness of Treatment for Depression in Youth: Integrating the Family in Treatment

PubMed Central

Tompson, Martha C.; Boger, Kathryn Dingman; Asarnow, Joan R.

2016-01-01

Youth depression is an impairing and frequently recurrent and persistent disorder that impacts current and later development, resulting in high social and economic costs. Depression and interpersonal stress are frequently transactional, with depression powerfully negatively impacting relationships and relationship stress negatively impacting the course and outcome of depression. In this context, treatment models for youth depression that emphasize interpersonal functioning, particularly family relationships, may be particularly promising. This article has three objectives. It first reviews the current state of knowledge on the efficacy of psychosocial treatments for depression in youth, with an emphasis on the role of family involvement in treatment. Second, it discusses developmental factors that may impact the applicability and structure of family-focused treatment models for preadolescent and adolescent youth. Third, two family-based treatment models that are currently being evaluated in randomized clinical trials are described: one focusing on preadolescent depressed youth and the other on adolescents who have made a recent suicide attempt. PMID:22537731

Computational approaches for drug discovery.

PubMed

Hung, Che-Lun; Chen, Chi-Chun

2014-09-01

Cellular proteins are the mediators of multiple organism functions being involved in physiological mechanisms and disease. By discovering lead compounds that affect the function of target proteins, the target diseases or physiological mechanisms can be modulated. Based on knowledge of the ligand-receptor interaction, the chemical structures of leads can be modified to improve efficacy, selectivity and reduce side effects. One rational drug design technology, which enables drug discovery based on knowledge of target structures, functional properties and mechanisms, is computer-aided drug design (CADD). The application of CADD can be cost-effective using experiments to compare predicted and actual drug activity, the results from which can used iteratively to improve compound properties. The two major CADD-based approaches are structure-based drug design, where protein structures are required, and ligand-based drug design, where ligand and ligand activities can be used to design compounds interacting with the protein structure. Approaches in structure-based drug design include docking, de novo design, fragment-based drug discovery and structure-based pharmacophore modeling. Approaches in ligand-based drug design include quantitative structure-affinity relationship and pharmacophore modeling based on ligand properties. Based on whether the structure of the receptor and its interaction with the ligand are known, different design strategies can be seed. After lead compounds are generated, the rule of five can be used to assess whether these have drug-like properties. Several quality validation methods, such as cost function analysis, Fisher's cross-validation analysis and goodness of hit test, can be used to estimate the metrics of different drug design strategies. To further improve CADD performance, multi-computers and graphics processing units may be applied to reduce costs. © 2014 Wiley Periodicals, Inc.

Prediction of local proximal tibial subchondral bone structural stiffness using subject-specific finite element modeling: Effect of selected density-modulus relationship.

PubMed

Nazemi, S Majid; Amini, Morteza; Kontulainen, Saija A; Milner, Jaques S; Holdsworth, David W; Masri, Bassam A; Wilson, David R; Johnston, James D

2015-08-01

Quantitative computed tomography based subject-specific finite element modeling has potential to clarify the role of subchondral bone alterations in knee osteoarthritis initiation, progression, and pain initiation. Calculation of bone elastic moduli from image data is a basic step when constructing finite element models. However, different relationships between elastic moduli and imaged density (known as density-modulus relationships) have been reported in the literature. The objective of this study was to apply seven different trabecular-specific and two cortical-specific density-modulus relationships from the literature to finite element models of proximal tibia subchondral bone, and identify the relationship(s) that best predicted experimentally measured local subchondral structural stiffness with highest explained variance and least error. Thirteen proximal tibial compartments were imaged via quantitative computed tomography. Imaged bone mineral density was converted to elastic moduli using published density-modulus relationships and mapped to corresponding finite element models. Proximal tibial structural stiffness values were compared to experimentally measured stiffness values from in-situ macro-indentation testing directly on the subchondral bone surface (47 indentation points). Regression lines between experimentally measured and finite element calculated stiffness had R(2) values ranging from 0.56 to 0.77. Normalized root mean squared error varied from 16.6% to 337.6%. Of the 21 evaluated density-modulus relationships in this study, Goulet combined with Snyder and Schneider or Rho appeared most appropriate for finite element modeling of local subchondral bone structural stiffness. Though, further studies are needed to optimize density-modulus relationships and improve finite element estimates of local subchondral bone structural stiffness. Copyright © 2015 Elsevier Ltd. All rights reserved.

Elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks by molecular simulation

NASA Astrophysics Data System (ADS)

Nayak, Kapileswar; Das, Sushanta; Nanavati, Hemant

2008-01-01

We present a framework for the development of elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks, incorporating aspects of the primary molecular structure. Semicrystalline polymeric fiber networks are modeled as sequentially arranged crystalline and amorphous regions. Rotational isomeric states-Monte Carlo simulations of amorphous chains of up to 360 bonds (degree of polymerization, DP =60), confined between and bridging infinite impenetrable crystalline walls, have been characterized by Ω, the probability density of the intercrystal separation h, and Δβ, the polarizability anisotropy. lnΩ and Δβ have been modeled as functions of h, yielding the chain deformation relationships. The development has been extended to the fiber network to yield the photoelasticity relationships. We execute our framework by fitting to experimental stress-elongation data and employing the single fitted parameter to directly predict the birefringence-elongation behavior, without any further fitting. Incorporating the effect of strain-induced crystallization into the framework makes it physically more meaningful and yields accurate predictions of the birefringence-elongation behavior.

The Cajal body and the nucleolus: “In a relationship” or “It's complicated”?

PubMed Central

2017-01-01

ABSTRACT From their initial identification as ‘nucleolar accessory bodies’ more than a century ago, the relationship between Cajal bodies and nucleoli has been a subject of interest and controversy. In this review, we seek to place recent developments in the understanding of the physical and functional relationships between the 2 structures in the context of historical observations. Biophysical models of nuclear body formation, the molecular nature of CB/nucleolus interactions and the increasing list of joint roles for CBs and nucleoli, predominantly in assembling ribonucleoprotein (RNP) complexes, are discussed. PMID:27661468

Structure-Property-Function Relationship in Humic Substances to Explain the Biological Activity in Plants

PubMed Central

García, Andrés Calderín; de Souza, Luiz Gilberto Ambrosio; Pereira, Marcos Gervasio; Castro, Rosane Nora; García-Mina, José María; Zonta, Everaldo; Lisboa, Francy Junior Gonçalves; Berbara, Ricardo Luis Louro

2016-01-01

Knowledge of the structure-property-function relationship of humic substances (HSs) is key for understanding their role in soil. Despite progress, studies on this topic are still under discussion. We analyzed 37 humic fractions with respect to their isotopic composition, structural characteristics, and properties responsible for stimulating plant root parameters. We showed that regardless of the source of origin of the carbon (C3 or C4), soil-extracted HSs and humic acids (HAs) are structurally similar to each other. The more labile and functionalized HS fraction is responsible for root emission, whereas the more recalcitrant and less functionalized HA fraction is related to root growth. Labile structures promote root stimulation at lower concentrations, while recalcitrant structures require higher concentrations to promote a similar stimulus. These findings show that lability and recalcitrance, which are derived properties of humic fractions, are related to the type and intensity of their bioactivity. In summary, the comparison of humic fractions allowed a better understanding of the relationship between the source of origin of plant carbon and the structure, properties, and type and intensity of the bioactivity of HSs in plants. In this study, scientific concepts are unified and the basis for the agronomic use of HSs is established. PMID:26862010

Ecological Models of Sexual Satisfaction among Lesbian/Bisexual and Heterosexual Women

PubMed Central

Henderson, Alison W.; Simoni, Jane M.

2014-01-01

Sexual satisfaction is an integral component of sexual health and well-being, yet we know little about which factors contribute to it among lesbian/bisexual women. To examine a proposed ecological model of sexual satisfaction, we conducted an internet survey of married heterosexual women and lesbian/bisexual women in committed same-sex relationships. Structural equation modeling included five final latent variables for heterosexual women and seven final latent variables for lesbian/bisexual women. Overall, results indicated that, for both groups of women, a similar constellation of factors (depressive symptoms, relationship satisfaction, sexual functioning, and social support) was related to sexual satisfaction. In lesbian/bisexual women, internalized homophobia was an additional factor. Contrary to expectations, the presence of children in the home and a history of childhood sexual abuse did not contribute significantly to the model for either group. Findings support the idea that gender socialization may influence sexual satisfaction more than socialization around sexual orientation. Additionally, given that for both groups of women relationship satisfaction explained a substantial amount of variance in sexual satisfaction, sexual concerns may be better addressed at the relationship than the individual level. PMID:18574685

Predicting athletes' functional and dysfunctional emotions: The role of the motivational climate and motivation regulations.

PubMed

Ruiz, Montse C; Haapanen, Saara; Tolvanen, Asko; Robazza, Claudio; Duda, Joan L

2017-08-01

This study examined the relationships between perceptions of the motivational climate, motivation regulations, and the intensity and functionality levels of athletes' pleasant and unpleasant emotional states. Specifically, we examined the hypothesised mediational role of motivation regulations in the climate-emotion relationship. We also tested a sequence in which emotions were assumed to be predicted by the motivational climate dimensions and then served as antecedents to variability in motivation regulations. Participants (N = 494) completed a multi-section questionnaire assessing targeted variables. Structural equation modelling (SEM) revealed that a perceived task-involving climate was a positive predictor of autonomous motivation and of the impact of functional anger, and a negative predictor of the intensity of anxiety and dysfunctional anger. Autonomous motivation was a partial mediator of perceptions of a task-involving climate and the impact of functional anger. An ego-involving climate was a positive predictor of controlled motivation, and of the intensity and impact of functional anger and the intensity of dysfunctional anger. Controlled motivation partially mediated the relationship between an ego-involving climate and the intensity of dysfunctional anger. Good fit to the data also emerged for the motivational climate, emotional states, and motivation regulations sequence. Findings provide support for the consideration of hedonic tone and functionality distinctions in the assessment of athletes' emotional states.

Maternal Emotion Regulation and Adolescent Behaviors: The Mediating Role of Family Functioning and Parenting.

PubMed

Crandall, AliceAnn; Ghazarian, Sharon R; Day, Randal D; Riley, Anne W

2016-11-01

Prior research links poor maternal emotion regulation to maladaptive parenting and child behaviors, but little research is available on these relationships during the adolescent period. We use structural equation modeling to assess the influence of poor maternal emotion regulation, measured as emotional reactivity and distancing, on adolescent behaviors (measured as aggression and prosocial behaviors) among 478 adolescents (53 % female; baseline age 10-13 years) and their mothers over a 5 year period. We also tested the possible mediating roles of family functioning and parenting behaviors between maternal emotion regulation and adolescent behaviors. Results indicated that higher baseline maternal emotional distancing and reactivity were not directly predictive of adolescents' behaviors, but they were indirectly related through family functioning and parenting. Specifically, indulgent parenting mediated the relationship between maternal emotional reactivity and adolescent aggression. Maternal-reported family functioning significantly mediated the relationship between maternal emotional distancing and adolescent aggression. Family functioning also mediated the relationship between emotional distancing and regulation parenting. The results imply that poor maternal emotion regulation during their child's early adolescence leads to more maladaptive parenting and problematic behaviors during the later adolescent period. However, healthy family processes may ameliorate the negative impact of low maternal emotion regulation on parenting and adolescent behavioral outcomes. The implications for future research and interventions to improve parenting and adolescent outcomes are discussed.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

An Exponentiation Method for XML Element Retrieval

PubMed Central

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP. PMID:24696643

The relationship between change in apathy and changes in cognition and functional outcomes in currently non-depressed SSRI-treated patients with major depressive disorder.

PubMed

Rothschild, Anthony J; Raskin, Joel; Wang, Chia-Ning; Marangell, Lauren B; Fava, Maurizio

2014-01-01

Apathy in the context of treated major depressive disorder (MDD) is a frequently observed phenomenon in clinical practice. This study aimed to assess the validity of the Rothschild Scale for Antidepressant Tachyphylaxis® (RSAT) and the Massachusetts General Hospital Cognitive and Physical Functioning Questionnaire (CPFQ) for measuring apathy, and to assess the relationship between apathy and possible contributing factors, in patients with MDD and residual apathy in the absence of depressed mood. The underlying structure and validity of the RSAT and CPFQ were assessed via factor analysis and correlation with the Apathy Evaluation Scale-Clinician rated version (AES-C) in 483 patients who had previously responded to treatment with a selective serotonin reuptake inhibitor. The relationship between apathy and contributing variables was investigated via structural equation modeling. Correlation and regression analyses were conducted to examine the relationship between the Sheehan Disability Scale (SDS) and the RSAT, CPFQ, and AES-C. The RSAT and CPFQ were validated with the AES-C with respect to energy and motivation. The latent variable "Energy and Interest", based on the energy, motivation, and interest items (RSAT and CPFQ), was a major contributing factor to apathy. Improvements in function (SDS) were significantly correlated with, and predicted by, improvements in apathy and cognitive and physical functioning (assessed by the RSAT, CPFQ, and AES-C). These analyses provide further information on apathy and its assessment in the context of treated MDD. A better understanding of apathy will aid further investigation of this phenomenon and, ultimately, determination of the most appropriate approach for its clinical management. © 2013.

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model

PubMed Central

Gordon, J.A.; Freedman, B.R.; Zuskov, A.; Iozzo, R.V.; Birk, D.E.; Soslowsky, L.J.

2015-01-01

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn−/−) and biglycan-null (Bgn−/−) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. PMID:25888014

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model.

PubMed

Gordon, J A; Freedman, B R; Zuskov, A; Iozzo, R V; Birk, D E; Soslowsky, L J

2015-07-16

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn(-/-)) and biglycan-null (Bgn(-/-)) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Animal Structures and Functions, Science (Experimental): 5314.13.

ERIC Educational Resources Information Center

Silver, Barbara A.

This unit of instruction was designed to introduce the student to the relationship between structure and function in the animal kingdom, with emphasis given to: (1) the evolution of physiological systems in the major animal phyla, (2) the complementarity of structure and function, and (3) the concept of homeostasis. The booklet lists the relevant…

Developmental Sex Differences in the Relation of Neuroanatomical Connectivity to Intelligence

ERIC Educational Resources Information Center

Schmithorst, Vincent J.

2009-01-01

Recent neuroimaging research has shown sex-related differences in the relationship between brain structure and cognitive function. Anatomical studies have shown a greater reliance for cognitive function on white matter structure in adult females, and a greater reliance on gray matter structure in adult males. Functional neuroimaging studies have…

Large-eddy simulations of surface roughness parameter sensitivity to canopy-structure characteristics

DOE PAGES

Maurer, K. D.; Bohrer, G.; Kenny, W. T.; ...

2015-04-30

Surface roughness parameters, namely the roughness length and displacement height, are an integral input used to model surface fluxes. However, most models assume these parameters to be a fixed property of plant functional type and disregard the governing structural heterogeneity and dynamics. In this study, we use large-eddy simulations to explore, in silico, the effects of canopy-structure characteristics on surface roughness parameters. We performed a virtual experiment to test the sensitivity of resolved surface roughness to four axes of canopy structure: (1) leaf area index, (2) the vertical profile of leaf density, (3) canopy height, and (4) canopy gap fraction.more » We found roughness parameters to be highly variable, but uncovered positive relationships between displacement height and maximum canopy height, aerodynamic canopy height and maximum canopy height and leaf area index, and eddy-penetration depth and gap fraction. We also found negative relationships between aerodynamic canopy height and gap fraction, as well as between eddy-penetration depth and maximum canopy height and leaf area index. We generalized our model results into a virtual "biometric" parameterization that relates roughness length and displacement height to canopy height, leaf area index, and gap fraction. Using a decade of wind and canopy-structure observations in a site in Michigan, we tested the effectiveness of our model-driven biometric parameterization approach in predicting the friction velocity over heterogeneous and disturbed canopies. We compared the accuracy of these predictions with the friction-velocity predictions obtained from the common simple approximation related to canopy height, the values calculated with large-eddy simulations of the explicit canopy structure as measured by airborne and ground-based lidar, two other parameterization approaches that utilize varying canopy-structure inputs, and the annual and decadal means of the surface roughness parameters at the site from meteorological observations. We found that the classical representation of constant roughness parameters (in space and time) as a fraction of canopy height performed relatively well. Nonetheless, of the approaches we tested, most of the empirical approaches that incorporate seasonal and interannual variation of roughness length and displacement height as a function of the dynamics of canopy structure produced more precise and less biased estimates for friction velocity than models with temporally invariable parameters.« less

Large-eddy simulations of surface roughness parameter sensitivity to canopy-structure characteristics

NASA Astrophysics Data System (ADS)

Maurer, K. D.; Bohrer, G.; Kenny, W. T.; Ivanov, V. Y.

2015-04-01

Surface roughness parameters, namely the roughness length and displacement height, are an integral input used to model surface fluxes. However, most models assume these parameters to be a fixed property of plant functional type and disregard the governing structural heterogeneity and dynamics. In this study, we use large-eddy simulations to explore, in silico, the effects of canopy-structure characteristics on surface roughness parameters. We performed a virtual experiment to test the sensitivity of resolved surface roughness to four axes of canopy structure: (1) leaf area index, (2) the vertical profile of leaf density, (3) canopy height, and (4) canopy gap fraction. We found roughness parameters to be highly variable, but uncovered positive relationships between displacement height and maximum canopy height, aerodynamic canopy height and maximum canopy height and leaf area index, and eddy-penetration depth and gap fraction. We also found negative relationships between aerodynamic canopy height and gap fraction, as well as between eddy-penetration depth and maximum canopy height and leaf area index. We generalized our model results into a virtual "biometric" parameterization that relates roughness length and displacement height to canopy height, leaf area index, and gap fraction. Using a decade of wind and canopy-structure observations in a site in Michigan, we tested the effectiveness of our model-driven biometric parameterization approach in predicting the friction velocity over heterogeneous and disturbed canopies. We compared the accuracy of these predictions with the friction-velocity predictions obtained from the common simple approximation related to canopy height, the values calculated with large-eddy simulations of the explicit canopy structure as measured by airborne and ground-based lidar, two other parameterization approaches that utilize varying canopy-structure inputs, and the annual and decadal means of the surface roughness parameters at the site from meteorological observations. We found that the classical representation of constant roughness parameters (in space and time) as a fraction of canopy height performed relatively well. Nonetheless, of the approaches we tested, most of the empirical approaches that incorporate seasonal and interannual variation of roughness length and displacement height as a function of the dynamics of canopy structure produced more precise and less biased estimates for friction velocity than models with temporally invariable parameters.

Eye model for the ground squirrel

NASA Astrophysics Data System (ADS)

Sussman, Dafna; Chou, B. Ralph; Lakshminarayanan, Vasudevan

2011-11-01

This paper presents an anatomically-correct eye model for the ground squirrel, a diurnal, highly-developed mammal with high visual acuity. This model can assist in understanding the relationship between ocular structural development and its corresponding function. The eye model is constructed based on anatomical measurements of thicknesses and indices of refraction of the various ocular media. The model then derives the gradient index distribution of the crystalline lens using a ray tracing method with a Monte Carlo optimization. Results indicate a diffraction-limited ocular behaviour, implying the visual acuity of the ground squirrel is more likely to be limited by photoreceptor density and diffraction effects, than by ocular geometry.

Computational modeling of the structure-function relationship in human placental terminal villi.

PubMed

Plitman Mayo, R; Olsthoorn, J; Charnock-Jones, D S; Burton, G J; Oyen, M L

2016-12-08

Placental oxygen transport takes place at the final branches of the villous tree and is dictated by the relative arrangement of the maternal and fetal circulations. Modeling techniques have failed to accurately assess the structure-function relationship in the terminal villi due to the geometrical complexity. Three-dimensional blood flow and oxygen transport was modeled in four terminal villi reconstructed from confocal image stacks. The blood flow was analyzed along the center lines of capillary segments and the effect of the variability in capillary diameter, tortuosity and branching was investigated. Additionally, a validation study was performed to corroborate the simulation results. The results show how capillary variations impact motion of the fetal blood, and how their bends and dilatations can decelerate the flow by up to 80%. Vortical flow is also demonstrated not to develop in the fetal capillaries. The different geometries are shown to dictate the transport of gases with differences of over 100% in the oxygen flux between samples. Capillary variations are key for efficient oxygen uptake by the fetus; they allow the blood to decelerate where the villous membrane is thinnest allowing for a better oxygenation, but also by reducing the vessel diameter they carry the oxygenated blood away fast. The methodology employed herein could become a platform to simulate complicated in-vivo and in-vitro scenarios of pregnancy complications. Copyright © 2016 Elsevier Ltd. All rights reserved.

From functional architecture to functional connectomics.

PubMed

Reid, R Clay

2012-07-26

"Receptive Fields, Binocular Interaction and Functional Architecture in the Cat's Visual Cortex" by Hubel and Wiesel (1962) reported several important discoveries: orientation columns, the distinct structures of simple and complex receptive fields, and binocular integration. But perhaps the paper's greatest influence came from the concept of functional architecture (the complex relationship between in vivo physiology and the spatial arrangement of neurons) and several models of functionally specific connectivity. They thus identified two distinct concepts, topographic specificity and functional specificity, which together with cell-type specificity constitute the major determinants of nonrandom cortical connectivity. Orientation columns are iconic examples of topographic specificity, whereby axons within a column connect with cells of a single orientation preference. Hubel and Wiesel also saw the need for functional specificity at a finer scale in their model of thalamic inputs to simple cells, verified in the 1990s. The difficult but potentially more important question of functional specificity between cortical neurons is only now becoming tractable with new experimental techniques. Copyright © 2012 Elsevier Inc. All rights reserved.

Brain Events Underlying Episodic Memory Changes in Aging: A Longitudinal Investigation of Structural and Functional Connectivity.

PubMed

Fjell, Anders M; Sneve, Markus H; Storsve, Andreas B; Grydeland, Håkon; Yendiki, Anastasia; Walhovd, Kristine B

2016-03-01

Episodic memories are established and maintained by close interplay between hippocampus and other cortical regions, but degradation of a fronto-striatal network has been suggested to be a driving force of memory decline in aging. We wanted to directly address how changes in hippocampal-cortical versus striatal-cortical networks over time impact episodic memory with age. We followed 119 healthy participants (20-83 years) for 3.5 years with repeated tests of episodic verbal memory and magnetic resonance imaging for quantification of functional and structural connectivity and regional brain atrophy. While hippocampal-cortical functional connectivity predicted memory change in young, changes in cortico-striatal functional connectivity were related to change in recall in older adults. Within each age group, effects of functional and structural connectivity were anatomically closely aligned. Interestingly, the relationship between functional connectivity and memory was strongest in the age ranges where the rate of reduction of the relevant brain structure was lowest, implying selective impacts of the different brain events on memory. Together, these findings suggest a partly sequential and partly simultaneous model of brain events underlying cognitive changes in aging, where different functional and structural events are more or less important in various time windows, dismissing a simple uni-factorial view on neurocognitive aging. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Purpose-driven biomaterials research in liver-tissue engineering.

PubMed

Ananthanarayanan, Abhishek; Narmada, Balakrishnan Chakrapani; Mo, Xuejun; McMillian, Michael; Yu, Hanry

2011-03-01

Bottom-up engineering of microscale tissue ("microtissue") constructs to recapitulate partially the complex structure-function relationships of liver parenchyma has been realized through the development of sophisticated biomaterial scaffolds, liver-cell sources, and in vitro culture techniques. With regard to in vivo applications, the long-lived stem/progenitor cell constructs can improve cell engraftment, whereas the short-lived, but highly functional hepatocyte constructs stimulate host liver regeneration. With regard to in vitro applications, microtissue constructs are being adapted or custom-engineered into cell-based assays for testing acute, chronic and idiosyncratic toxicities of drugs or pathogens. Systems-level methods and computational models that represent quantitative relationships between biomaterial scaffolds, cells and microtissue constructs will further enable their rational design for optimal integration into specific biomedical applications. Copyright © 2010 Elsevier Ltd. All rights reserved.

Modulation of hemoglobin dynamics by an allosteric effector

DOE PAGES

Lal, Jyotsana; Maccarini, Marco; Fouquet, Peter; ...

2016-12-15

Hemoglobin (Hb) is an extensively studied paradigm of proteins that alter their function in response to allosteric effectors. Models of its action have been used as prototypes for structure-function relationships in many proteins, and models for the molecular basis of its function have been deeply studied and extensively argued. Recent reports suggest that dynamics may play an important role in its function. Relatively little is known about the slow, correlated motions of hemoglobin subunits in various structural states because experimental and computational strategies for their characterization are challenging. Allosteric effectors such as inositol hexaphosphate (IHP) bind to both deoxy-Hb andmore » HbCO, albeit at different sites, leading to a lowered oxygen affinity. The manner in which these effectors impact oxygen binding is unclear and may involve changes in structure, dynamics or both. Here we use neutron spin echo (NSE) measurements accompanied by wideangle x-ray scattering (WAXS) to show that binding of IHP to HbCO results in an increase in the rate of coordinated motions of Hb subunits relative to one another with little if any change in large scale structure. This increase of large-scale dynamics seems to be coupled with a decrease in the average magnitude of higher frequency modes of individual residues. Furthermore, these observations indicate that enhanced dynamic motions contribute to the functional changes induced by IHP and suggest that they may be responsible for the lowered oxygen affinity triggered by these effectors.« less

On the role of structure-dynamic relationship in determining the excess entropy of mixing and chemical ordering in binary square-well liquid alloys

NASA Astrophysics Data System (ADS)

Lalneihpuii, R.; Shrivastava, Ruchi; Mishra, Raj Kumar

2018-05-01

Using statistical mechanical model with square-well (SW) interatomic potential within the frame work of mean spherical approximation, we determine the composition dependent microscopic correlation functions, interdiffusion coefficients, surface tension and chemical ordering in Ag-Cu melts. Further Dzugutov universal scaling law of normalized diffusion is verified with SW potential in binary mixtures. We find that the excess entropy scaling law is valid for SW binary melts. The partial and total structure factors in the attractive and repulsive regions of the interacting potential are evaluated and then Fourier transformed to get partial and total radial distribution functions. A good agreement between theoretical and experimental values for total structure factor and the reduced radial distribution function are observed, which consolidates our model calculations. The well-known Bhatia-Thornton correlation functions are also computed for Ag-Cu melts. The concentration-concentration correlations in the long wavelength limit in liquid Ag-Cu alloys have been analytically derived through the long wavelength limit of partial correlation functions and apply it to demonstrate the chemical ordering and interdiffusion coefficients in binary liquid alloys. We also investigate the concentration dependent viscosity coefficients and surface tension using the computed diffusion data in these alloys. Our computed results for structure, transport and surface properties of liquid Ag-Cu alloys obtained with square-well interatomic interaction are fully consistent with their corresponding experimental values.

Beyond the Central Dogma: Model-Based Learning of How Genes Determine Phenotypes

PubMed Central

Reinagel, Adam; Bray Speth, Elena

2016-01-01

In an introductory biology course, we implemented a learner-centered, model-based pedagogy that frequently engaged students in building conceptual models to explain how genes determine phenotypes. Model-building tasks were incorporated within case studies and aimed at eliciting students’ understanding of 1) the origin of variation in a population and 2) how genes/alleles determine phenotypes. Guided by theory on hierarchical development of systems-thinking skills, we scaffolded instruction and assessment so that students would first focus on articulating isolated relationships between pairs of molecular genetics structures and then integrate these relationships into an explanatory network. We analyzed models students generated on two exams to assess whether students’ learning of molecular genetics progressed along the theoretical hierarchical sequence of systems-thinking skills acquisition. With repeated practice, peer discussion, and instructor feedback over the course of the semester, students’ models became more accurate, better contextualized, and more meaningful. At the end of the semester, however, more than 25% of students still struggled to describe phenotype as an output of protein function. We therefore recommend that 1) practices like modeling, which require connecting genes to phenotypes; and 2) well-developed case studies highlighting proteins and their functions, take center stage in molecular genetics instruction. PMID:26903496

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Contribution of hydrophobic effect to the sorption of phenanthrene, 9-phenanthrol and 9, 10-phenanthrenequinone on carbon nanotubes.

PubMed

Peng, Hongbo; Zhang, Di; Pan, Bo; Peng, Jinhui

2017-02-01

Polycyclic aromatic hydrocarbons (PAHs), with diverse sources and acute toxicity, are categorized as priority pollutants. Previous studies have stated that the hydrophobic effect controls PAH sorption, but no study has been conducted to quantify the exact contribution of the hydrophobic effect. Considering the well-defined structure of carbon nanotubes and their stable chemical composition in organic solvents, three multi-walled carbon nanotubes (MWCNTs) were selected as a model adsorbent. Phenanthrene (PHE) and its degradation intermediates 9-phenanthrol (PTR) and 9, 10-phenanthrenequinone (PQN) were used as model adsorbates. To quantify the contribution of the hydrophobic effect for these three chemicals, the effect of organic solvent (methanol and hexadecane) was investigated. Adsorption isotherms for PHE, PTR and PQN were well fitted by the Freundlich isotherm model. A positive relationship between adsorption affinities of these three chemicals and specific surface area (SSA) was observed in hexadecane but not in water or methanol. Other factors should be included other than SSA. Adsorption of PQN on MWCNTs with oxygen functional groups was higher than that on pristine MWCNTs due to π-π EDA interactions. The contribution of hydrophobic effect was 50%-85% for PHE, suggesting that hydrophobic effect was the predominant mechanism. This contribution was lower than 30% for PTR/PQN on functionalized MWCNTs. Hydrogen bonds control the adsorption of PTR, and π-π bonding interactions control PQN sorption after screening out the hydrophobic effect in hexadecane. Hydrophobic effect is the control mechanism for nonpolar chemicals, while functional groups of CNTs and solvent types control the adsorption of polar compounds. Extended work on quantifying the relationship between chemical structure and the contribution of the hydrophobic effect will provide a useful technique for PAH fate modeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intrinsic motivation as a mediator of relationships between symptoms and functioning among individuals with schizophrenia spectrum disorders in a diverse urban community.

PubMed

Yamada, Ann-Marie; Lee, Karen K; Dinh, Tam Q; Barrio, Concepción; Brekke, John S

2010-01-01

This study investigated intrinsic motivation as a mediator of the relationship between clinical symptoms and functioning. The mediation model was tested with a sample of 166 adults with schizophrenia spectrum disorders attending psychosocial rehabilitation programs in a diverse urban community. Ethnic minority status was examined as a moderator of the mediation model. Motivation was measured using items reflecting intrapsychic drive. Symptoms were assessed with the expanded Brief Psychiatric Rating Scale and functioning with the Role Functioning Scale. Motivation was a significant mediator of the relationship between functioning and all symptom scores; fully mediating the relationship between functioning and negative, disorganized, and global symptoms, and partially mediating the relationship between positive symptoms and functioning. Motivation scores between ethnic minority and nonminority individuals differed significantly (p < 0.05), but no moderation effect was indicated. The strong mediation effect schizophrenia of motivation on the symptoms-functioning relationship supports future work to translate findings into effective recovery-oriented services.

Intrinsic Motivation as a Mediator of Relationships Between Symptoms and Functioning Among Individuals With Schizophrenia Spectrum Disorders in a Diverse Urban Community

PubMed Central

Yamada, Ann-Marie; Lee, Karen K.; Dinh, Tam Q.; Barrio, Concepción; Brekke, John S.

2010-01-01

This study investigated intrinsic motivation as a mediator of the relationship between clinical symptoms and functioning. The mediation model was tested with a sample of 166 adults with schizophrenia spectrum disorders attending psychosocial rehabilitation programs in a diverse urban community. Ethnic minority status was examined as a moderator of the mediation model. Motivation was measured using items reflecting intrapsychic drive. Symptoms were assessed with the expanded Brief Psychiatric Rating Scale and functioning with the Role Functioning Scale. Motivation was a significant mediator of the relationship between functioning and all symptom scores; fully mediating the relationship between functioning and negative, disorganized, and global symptoms, and partially mediating the relationship between positive symptoms and functioning. Motivation scores between ethnic minority and nonminority individuals differed significantly (p < 0.05), but no moderation effect was indicated. The strong mediation effect schizophrenia of motivation on the symptoms-functioning relationship supports future work to translate findings into effective recovery-oriented services. PMID:20061866

Social class shapes the form and function of relationships and selves.

PubMed

Carey, Rebecca M; Markus, Hazel Rose

2017-12-01

Social class shapes relational realities, which in turn situate and structure different selves and their associated psychological tendencies. We first briefly review how higher class contexts tend to foster independent models of self and lower class contexts tend to foster interdependent models of self. We then consider how these independent and interdependent models of self are situated in and adapted to different social class-driven relational realities. We review research demonstrating that in lower social class contexts, social networks tend to be small, dense, homogenous and strongly connected. Ties in these networks provide the bonding capital that is key for survival and that promotes the interdependence between self and other(s). In higher social class contexts, social networks tend to be large, far-reaching, diverse and loosely connected. Ties in these networks provide the bridging capital that is key for achieving personal goals and that promotes an independence of self from other. We conclude that understanding and addressing issues tied to social class and inequality requires understanding the form and function of relationships across class contexts. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways

PubMed Central

Boucher, Benjamin; Lee, Anna Y.; Hallett, Michael; Jenna, Sarah

2016-01-01

A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution. PMID:26871911

Modality-Spanning Deficits in Attention-Deficit/Hyperactivity Disorder in Functional Networks, Gray Matter, and White Matter

PubMed Central

Kessler, Daniel; Angstadt, Michael; Welsh, Robert C.

2014-01-01

Previous neuroimaging investigations in attention-deficit/hyperactivity disorder (ADHD) have separately identified distributed structural and functional deficits, but interconnections between these deficits have not been explored. To unite these modalities in a common model, we used joint independent component analysis, a multivariate, multimodal method that identifies cohesive components that span modalities. Based on recent network models of ADHD, we hypothesized that altered relationships between large-scale networks, in particular, default mode network (DMN) and task-positive networks (TPNs), would co-occur with structural abnormalities in cognitive regulation regions. For 756 human participants in the ADHD-200 sample, we produced gray and white matter volume maps with voxel-based morphometry, as well as whole-brain functional connectomes. Joint independent component analysis was performed, and the resulting transmodal components were tested for differential expression in ADHD versus healthy controls. Four components showed greater expression in ADHD. Consistent with our a priori hypothesis, we observed reduced DMN-TPN segregation co-occurring with structural abnormalities in dorsolateral prefrontal cortex and anterior cingulate cortex, two important cognitive control regions. We also observed altered intranetwork connectivity in DMN, dorsal attention network, and visual network, with co-occurring distributed structural deficits. There was strong evidence of spatial correspondence across modalities: For all four components, the impact of the respective component on gray matter at a region strongly predicted the impact on functional connectivity at that region. Overall, our results demonstrate that ADHD involves multiple, cohesive modality spanning deficits, each one of which exhibits strong spatial overlap in the pattern of structural and functional alterations. PMID:25505309

Depression and pain impair daily functioning and quality of life in patients with major depressive disorder.

PubMed

Lin, Ching-Hua; Yen, Yung-Chieh; Chen, Ming-Chao; Chen, Cheng-Chung

2014-09-01

Depression and pain frequently occur together. The objective of this study was to investigate the effects of depression and pain on the impairment of daily functioning and quality of life (QOL) of depressed patients. We enrolled 131 acutely ill inpatients with major depressive disorder. Depression, pain, and daily functioning were assessed using the 17-item Hamilton Depression Rating Scale, the Short-Form 36 (SF-36) Body Pain Index, and the Work and Social Adjustment Scale. Health-related QOL was assessed using three primary domains of the SF-36: social functioning, vitality, and general health perceptions. Pearson׳s correlation and structural equation modeling were used to examine relationships among the study variables. Five models were proposed. In all, 129 patients completed all the measures. Model 5, both depression and pain impaired daily functioning and QOL, was the most fitted structural equation model (χ(2)=9.2, df=8, p=0.33, GFI=0.98, AGFI=0.94, TLI=0.99, CFI=0.99, RMSEA=0.03). The correlation between pain and depression was weak (r=-0.27, z=-2.95, p=0.003). This was a cross-sectional study with a small sample size. Depression and pain exert a direct influence on the impairment of daily functioning and QOL of depressed patients; this impairment could be expected regardless of increased pain, depression, or both pain and depression. Pain had a somewhat separate entity from depression. Copyright © 2014. Published by Elsevier B.V.

Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity.

PubMed

Rutsdottir, Gudrun; Härmark, Johan; Weide, Yoran; Hebert, Hans; Rasmussen, Morten I; Wernersson, Sven; Respondek, Michal; Akke, Mikael; Højrup, Peter; Koeck, Philip J B; Söderberg, Christopher A G; Emanuelsson, Cecilia

2017-05-12

Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended I X V X I motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the I X V X I motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Cross-sectional and longitudinal relationship between neuroticism and cognitive ability in advanced old age: the moderating role of severe sensory impairment.

PubMed

Wettstein, Markus; Kuźma, Elżbieta; Wahl, Hans-Werner; Heyl, Vera

2016-09-01

Gaining a comprehensive picture of the network of constructs in which cognitive functioning is embedded is crucial across the full lifespan. With respect to personality, previous findings support a relationship between neuroticism and cognitive abilities. However, findings regarding old age are inconsistent. In particular, little is known about potentially moderating variables which might explain some of the inconsistency. Our aim was to examine the moderating effect of severe sensory impairment on cross-sectional and longitudinal associations between neuroticism and cognitive functioning. The study sample consisted of 121 visually impaired (VI), 116 hearing impaired (HI), and 150 sensory unimpaired older adults (UI). Mean age was 82.50 years (SD = 4.71 years). Neuroticism was assessed by the NEO Five Factor Inventory, and multiple established tests were used for the assessment of cognitive performance (e.g., subtests of the revised Wechsler Adult Intelligence Scale). Bivariate correlations and multi-group structural equation models indicated stronger relationships between cognitive abilities and neuroticism in both sensory impaired groups (VI and HI) compared to UI older individuals. This relationship was attenuated but still significant in both sensory impaired groups when controlling for age, education and health (number of chronic conditions). In cross-lagged panel models, higher baseline neuroticism was significantly associated with lower cognitive performance four years later in VI and HI individuals. Our results suggest that sensory impairment moderates both cross-sectional and longitudinal associations between neuroticism and cognitive function in advanced old age.

Structural and Functional Neuroimaging of Visual Hallucinations in Lewy Body Disease: A Systematic Literature Review

PubMed Central

Cagnin, Annachiara; Bandmann, Oliver; Venneri, Annalena

2017-01-01

Patients with Lewy body disease (LBD) frequently experience visual hallucinations (VH), well-formed images perceived without the presence of real stimuli. The structural and functional brain mechanisms underlying VH in LBD are still unclear. The present review summarises the current literature on the neural correlates of VH in LBD, namely Parkinson’s disease (PD), and dementia with Lewy bodies (DLB). Following a systematic literature search, 56 neuroimaging studies of VH in PD and DLB were critically reviewed and evaluated for quality assessment. The main structural neuroimaging results on VH in LBD revealed grey matter loss in frontal areas in patients with dementia, and parietal and occipito-temporal regions in PD without dementia. Parietal and temporal hypometabolism was also reported in hallucinating PD patients. Disrupted functional connectivity was detected especially in the default mode network and fronto-parietal regions. However, evidence on structural and functional connectivity is still limited and requires further investigation. The current literature is in line with integrative models of VH suggesting a role of attention and perception deficits in the development of VH. However, despite the close relationship between VH and cognitive impairment, its associations with brain structure and function have been explored only by a limited number of studies. PMID:28714891

The relationship between sociosexuality and aspects of body image in men and women: a structural equation modeling approach.

PubMed

Rammsayer, Thomas H; Troche, Stefan J

2013-10-01

The present study investigated the association between individual differences in sociosexual orientation and four aspects of body image in 156 male and 136 female students. While men were characterized by a less restricted sociosexual orientation, higher self-perceived physical attractiveness, and more pronounced self-rated physical assertiveness, women placed more emphasis on accentuation of body presentation. Structural equation modeling revealed significant positive relationships between sociosexual attitudes and physical attractiveness and accentuation of body presentation as well as between sociosexual behavior and physical attractiveness for the total sample. When introducing sex as a grouping variable, the attitudinal and behavioral components of sociosexuality were reliably related to both physical attractiveness and accentuation of body presentation as two aspects of body image in men, but not in women. Furthermore, our findings suggest that accentuation of body presentation represents a goal-directed behavior in men to increase the likelihood of having uncommitted sex but serves additional functions widely unrelated to unrestrictive sociosexual behavior in women.