Structural Responses and Finite Element Modeling of Hakka Tulou Rammed Earth Structures

NASA Astrophysics Data System (ADS)

Sranislawski, Daniel

Hakka Tulous are rammed earth structures that have survived the effects of aging and natural elements upwards of even over a thousand years. These structures have housed the Hakka people of the Fujian Province, China in natural yet modern housing that has provided benefits over newer building materials. The key building material, rammed earth, which is used for the walls of the Hakka Tulou structures, has provided structural stability along with thermal comfort to the respective inhabitants of the Hakka Tulous. Through material testing and analysis this study has examined how the Tulou structures have maintained their structural stability while also providing thermal comfort. Reports of self healing cracks in the rammed earth walls were also analyzed for their validity in this study. The study has found that although the story of the self healing crack cannot be validated, there is reason to believe that with the existence of lime, some type of autogenous healing could occur on a small scale. The study has also found, through the use of nondestructive testing, that both the internal wooden systems (flooring, roof, and column support) and the rammed earth walls, are still structurally sound. Also, rammed earth's high thermal mass along with the use of sufficient shading has allowed for a delay release of heat energy from the walls of the Tulous, thus providing thermal comfort that can be felt during both night and day temperatures. The Hakka Tulou structures have been found to resist destruction from natural disasters such as strong earthquakes even when more modern construction has not. Through finite element modeling, this study has shown that the high volume of rammed earth used in the construction of the Hakka Tulous helps dissipate lateral force energy into much lower stresses for the rammed earth wall. This absorption of lateral force energy allows the rammed earth structures to survive even the strongest of earthquakes experienced in the region. The Hakka Tulou, if rated by the LEED green building certification program, would earn the highest certification as this rammed earth construction has offered efficient living for hundreds of years. As historic as these rammed earth structures are, they present an environmentally friendly option to structures of the future.

Comparative Study on Cushion Performance Between 3D Printed Kelvin Structure and 3D Printed Lattice Structure

NASA Astrophysics Data System (ADS)

Priyadarshini, Lakshmi

Frequently transported packaging goods are more prone to damage due to impact, jolting or vibration in transit. Fragile goods, for example, glass, ceramics, porcelain are susceptible to mechanical stresses. Hence ancillary materials like cushions play an important role when utilized within package. In this work, an analytical model of a 3D cellular structure is established based on Kelvin model and lattice structure. The research will provide a comparative study between the 3D printed Kelvin unit structure and 3D printed lattice structure. The comparative investigation is based on parameters defining cushion performance such as cushion creep, indentation, and cushion curve analysis. The applications of 3D printing is in rapid prototyping where the study will provide information of which model delivers better form of energy absorption. 3D printed foam will be shown as a cost-effective approach as prototype. The research also investigates about the selection of material for 3D printing process. As cushion development demands flexible material, three-dimensional printing with material having elastomeric properties is required. Further, the concept of cushion design is based on Kelvin model structure and lattice structure. The analytical solution provides the cushion curve analysis with respect to the results observed when load is applied over the cushion. The results are reported on basis of attenuation and amplification curves.

Crosslinking Constraints and Computational Models as Complementary Tools in Modeling the Extracellular Domain of the Glycine Receptor

PubMed Central

Liu, Zhenyu; Szarecka, Agnieszka; Yonkunas, Michael; Speranskiy, Kirill; Kurnikova, Maria; Cascio, Michael

2014-01-01

The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel superfamily, is the major inhibitory neurotransmitter-gated receptor in the spinal cord and brainstem. In these receptors, the extracellular domain binds agonists, antagonists and various other modulatory ligands that act allosterically to modulate receptor function. The structures of homologous receptors and binding proteins provide templates for modeling of the ligand-binding domain of GlyR, but limitations in sequence homology and structure resolution impact on modeling studies. The determination of distance constraints via chemical crosslinking studies coupled with mass spectrometry can provide additional structural information to aid in model refinement, however it is critical to be able to distinguish between intra- and inter-subunit constraints. In this report we model the structure of GlyBP, a structural and functional homolog of the extracellular domain of human homomeric α1 GlyR. We then show that intra- and intersubunit Lys-Lys crosslinks in trypsinized samples of purified monomeric and oligomeric protein bands from SDS-polyacrylamide gels may be identified and differentiated by MALDI-TOF MS studies of limited resolution. Thus, broadly available MS platforms are capable of providing distance constraints that may be utilized in characterizing large complexes that may be less amenable to NMR and crystallographic studies. Systematic studies of state-dependent chemical crosslinking and mass spectrometric identification of crosslinked sites has the potential to complement computational modeling efforts by providing constraints that can validate and refine allosteric models. PMID:25025226

Classification of the Pospiviroidae based on their structural hallmarks.

PubMed

Giguère, Tamara; Perreault, Jean-Pierre

2017-01-01

The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed.

Classification of the Pospiviroidae based on their structural hallmarks

PubMed Central

Giguère, Tamara

2017-01-01

The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed. PMID:28783761

Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.

PubMed

Wang, Juexin; Luttrell, Joseph; Zhang, Ning; Khan, Saad; Shi, NianQing; Wang, Michael X; Kang, Jing-Qiong; Wang, Zheng; Xu, Dong

2016-01-01

Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia. Protein structure prediction and modeling were also applied in nucleotide-gated channels and their interaction interfaces to investigate their roles in brain and heart cells. In molecular mechanism studies of plants, rice salinity tolerance mechanism was studied via structure modeling on crucial proteins identified by systems biology analysis; trait-associated protein-protein interactions were modeled, which sheds some light on the roles of mutations in soybean oil/protein content. In the age of precision medicine, we believe protein structure prediction and modeling will play more and more important roles in investigating biomedical mechanism of diseases and drug design.

Structures, performance, benefit, cost study. [gas turbine engines

NASA Technical Reports Server (NTRS)

Feder, E.

1981-01-01

Aircraft engine structures were studied to identify the advanced structural technologies that would provide the most benefits to future aircraft operations. A series of studies identified engine systems with the greatest potential for improvements. Based on these studies, six advanced generic structural concepts were selected and conceptually designed. The benefits of each concept were quantitatively assessed in terms of thrust specific fuel consumption, weight, cost, maintenance cost, fuel burned and direct operating cost plus interest. The probability of success of each concept was also determined. The concepts were ranked and the three most promising were selected for further study which consisted of identifying and comprehensively outlining the advanced technologies required to develop these concepts for aircraft engine application. Analytic, fabrication, and test technology developments are required. The technology programs outlined emphasize the need to provide basic, fundamental understanding of technology to obtain the benefit goals.

PHYLOGEOGRAPHIC PATTERNS IN LARGE RIVER ECOSYSTEMS: GENETIC STRUCTURE OF SMALLMOUTH BUFFALO (ICTIOBUS BUBALUS) IN THE OHIO RIVER

EPA Science Inventory

Genetic studies on populations of large river fishes provide a potentially useful but underutilized research and assessment tool. Population genetic research on freshwater systems has provided meaningful insight into stock structure, hybridization issues, and gene flow/migration...

Local structure studies of materials using pair distribution function analysis

NASA Astrophysics Data System (ADS)

Peterson, Joseph W.

A collection of pair distribution function studies on various materials is presented in this dissertation. In each case, local structure information of interest pushes the current limits of what these studies can accomplish. The goal is to provide insight into the individual material behaviors as well as to investigate ways to expand the current limits of PDF analysis. Where possible, I provide a framework for how PDF analysis might be applied to a wider set of material phenomena. Throughout the dissertation, I discuss 0 the capabilities of the PDF method to provide information pertaining to a material's structure and properties, ii) current limitations in the conventional approach to PDF analysis, iii) possible solutions to overcome certain limitations in PDF analysis, and iv) suggestions for future work to expand and improve the capabilities PDF analysis.

Effectiveness of structured multidisciplinary rounding in acute care units on length of stay and satisfaction of patients and staff: a quantitative systematic review.

PubMed

Mercedes, Angela; Fairman, Precillia; Hogan, Lisa; Thomas, Rexi; Slyer, Jason T

2016-07-01

Consistent, concise and timely communication between a multidisciplinary team of healthcare providers, patients and families is necessary for the delivery of quality care. Structured multidisciplinary rounding (MDR) using a structured communication tool may positively impact length of stay (LOS) and satisfaction of patients and staff by improving communication, coordination and collaboration among the healthcare team. To evaluate the effectiveness of structured MDR using a structured communication tool in acute care units on LOS and satisfaction of patients and staff. Adult patients admitted to acute care units and healthcare providers who provide direct care for adult patients hospitalized in in-patient acute care units. The implementation of structured MDR utilizing a structured communication tool to enhance and/or guide communication. Quasi-experimental studies and descriptive studies. Length of stay, patient satisfaction and staff satisfaction. The comprehensive search strategy aimed to find relevant published and unpublished quantitative English language studies from the inception of each database searched through June 30, 2015. Databases searched include Cumulative Index to Nursing and Allied Health Literature, PubMed, Excerpta Medica Database, Health Source, Cochrane Central Register of Controlled Trials and Scopus. A search of gray literature was also performed. All reviewers independently evaluated the included studies for methodological quality using critical appraisal tools from the Joanna Briggs Institute (JBI). Data related to the methods, participants, interventions and findings were extracted using a standardized data extraction tool from the JBI. Due to clinical and methodological heterogeneity in the interventions and outcome measures of the included studies, statistical meta-analysis was not possible. Results are presented in narrative form. Eight studies were included, three quasi-experimental studies and five descriptive studies of quality improvement projects. In the three quasi-experimental studies, one had a statistically significant decrease (p = 0.01), one no change (p = 0.1) and one had an increase (p = 0.03) in LOS; in the two descriptive studies, one had a statistically significant decrease (p = 0.02) and the other reported a trend toward reduced LOS. Two studies evaluated patient satisfaction, one showed no change (p = 0.76) and one showed a trend toward increased patient satisfaction at 12 months. Six studies demonstrated an improvement in staff satisfaction (p < 0.05) after implementation of structured MDR. The evidence suggests that MDR utilizing a structured communication tool may have contributed to an improvement in staff satisfaction. There was inconclusive evidence to support the use of structured MDR to improve LOS or patient satisfaction. The use of a structured communication tool during MDR is one means to facilitate communication and collaboration, thus improving satisfaction among the multidisciplinary team. More rigorous research using higher level study designs on larger samples of diverse patient populations is needed to further evaluate the effectiveness of structured MDR on patient care outcomes and satisfaction of patients and providers.

The influence of care provider access to structural empowerment on individualized care in long-term-care facilities.

PubMed

Caspar, Sienna; O'Rourke, Norm

2008-07-01

Implementing management initiatives that enable formal caregivers to provide quality, individualized care to older adults in long-term-care (LTC) facilities is increasingly important given that the number of LTC residents is projected to triple by 2031. The objective of this study was to explore the relationship between care provider access to structural empowerment and the provision of individualized care in LTC. We computed structural equation models separately for registered nurses and licensed practical nurses (n = 242) and care aides (n = 326) to examine the relationship between access to empowerment structures (i.e., informal power, formal power, information, support, resources, opportunity) and the provision of individualized care. We subsequently undertook invariance analyses to determine if the association between empowerment structures and reported provision of individualized care differed between caregiver groups. Access to structural empowerment had a statistically significant, positive association with provision of individualized care for both groups. For registered nurses/licensed practical nurses and care aides, empowerment explained 50% and 45% of observed variance in individualized care, respectively. These notable percentages did not differ significantly between caregiver groups. Of the empowerment structures, support, especially in the form of access to educational opportunities and recognition for a job well done, seems to be particularly significant to care providers. Findings from this study suggest that provision of individualized care in LTC may be enhanced when formal caregivers have appreciable access to empowerment structures.

Comparison of Cellulose Supramolecular Structures Between Nanocrystals of Different Origins

Treesearch

Umesh P. Agarwal; Richard S. Reiner; Christopher G. Hunt; Jeffery Catchmark; E. Johan Foster; Akira Isogai

2015-01-01

In this study, morphologies and supramolecular structures of CNCs from wood-pulp, cotton, bacteria, tunicate, and cladophora were investigated. TEM was used to study the morphological aspects of the nanocrystals whereas Raman spectroscopy provided information on the cellulose molecular structure and its organization within a CNC. Dimensional differences between the...

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.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

When VSEPR Fails: Experimental and Theoretical Investigations of the Behavior of Alkaline-Earth-Metal Acetylides

PubMed Central

Guino-o, Marites A.; Alexander, Jacob S.; McKee, Michael L.; Hope, Håkon; Englich, Ulrich B.

2014-01-01

The synthesis, structural, and spectral characterization as well as a theoretical study of a family of alkaline-earth-metal acetylides provides insights into synthetic access and the structural and bonding characteristics of this group of highly reactive compounds. Based on our earlier communication that reported unusual geometry for a family of triphenylsilyl-substituted alkaline-earth-metal acetylides, we herein present our studies on an expanded family of target derivatives, providing experimental and theoretical data to offer new insights into the intensively debated theme of structural chemistry in heavy alkaline-earth-metal chemistry. PMID:19844925

3D-QSAR study and design of 4-hydroxyamino α-pyranone carboxamide analogues as potential anti-HCV agents

NASA Astrophysics Data System (ADS)

Li, Wenlian; Xiao, Faqi; Zhou, Mingming; Jiang, Xuejin; Liu, Jun; Si, Hongzong; Xie, Meng; Ma, Xiuting; Duan, Yunbo; Zhai, Honglin

2016-09-01

The three dimensional-quantitative structure activity relationship (3D-QSAR) study was performed on a series of 4-hydroxyamino α-pyranone carboxamide analogues using comparative molecular similarity indices analysis (COMSIA). The purpose of the present study was to develop a satisfactory model providing a reliable prediction based on 4-hydroxyamino α-pyranone carboxamide analogues as anti-HCV (hepatitis C virus) inhibitors. The statistical results and the results of validation of this optimum COMSIA model were satisfactory. Furthermore, analysis of the contour maps helped to provide guidelines for finding structural requirement. Therefore, the satisfactory results from this study may provide useful guidelines for drug development of anti-HCV inhibitors.

Population inertia and its sensitivity to changes in vital rates and population structure

USGS Publications Warehouse

Koons, David N.; Holmes, Randall R.; Grand, James B.

2007-01-01

Because the (st)age structure of a population may rarely be stable, studies of transient population dynamics and population momentum are becoming ever more popular. Yet, studies of "population momentum" are restricted in the sense that they describe the inertia of population size resulting from a demographic transition to the stationary population growth rate. Although rarely mentioned, inertia in population size is a general phenomenon and can be produced by any demographic transition or perturbation. Because population size is of central importance in demography, conservation, and management, formulas relating the sensitivity of population inertia to changes in underlying vital rates and population structure could provide much-needed insight into the dynamics of populations with unstable (st)age structure. Here, we derive such formulas, which are readily computable, and provide examples of their potential use in studies of life history and applied arenas of population study. ?? 2007 by the Ecological Society of America.

RNA Structures as Mediators of Neurological Diseases and as Drug Targets.

PubMed

Bernat, Viachaslau; Disney, Matthew D

2015-07-01

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics. Copyright © 2015 Elsevier Inc. All rights reserved.

Multidimensional Knowledge Structures.

ERIC Educational Resources Information Center

Schuh, Kathy L.

Multidimensional knowledge structures, described from a constructivist perspective and aligned with the "Mind as Rhizome" metaphor, provide support for constructivist learning strategies. This qualitative study was conducted to seek empirical support for a description of multidimensional knowledge structures, focusing on the…

Numerical investigation of the aerodynamic and structural characteristics of a corrugated wing

NASA Astrophysics Data System (ADS)

Hord, Kyle

Previous experimental studies on static, bio-inspired corrugated wings have shown that they produce favorable aerodynamic properties such as delayed stall compared to streamlined wings and flat plates at high Reynolds numbers (Re ≥ 4x104). The majority of studies have been carried out with scaled models of dragonfly forewings from the Aeshna Cyanea in either wind tunnels or water channels. In this thesis, the aerodynamics of a corrugated airfoil was studied using computational fluid dynamics methods at a low Reynolds number of 1000. Structural analysis was also performed using the commercial software SolidWorks 2009. The flow field is described by solving the incompressible Navier-Stokes equations on an overlapping grid using the pressure-Poisson method. The equations are discretized in space with second-order accurate central differences. Time integration is achieved through the second-order Crank-Nicolson implicit method. The complex vortex structures that form in the corrugated airfoil valleys and around the corrugated airfoil are studied in detail. Comparisons are made with experimental measurements from corrugated wings and also with simulations of a flat plate. Contrary to the studies at high Reynolds numbers, our study shows that at low Reynolds numbers the wing corrugation does not provide any aerodynamic benefit compared to a smoothed flat plate. Instead, the corrugated profile generates more pressure drag which is only partially offset by the reduction of friction drag, leading to more total drag than the flat plate. Structural analysis shows that the wing corrugation can increase the resistance to bending moments on the wing structure. A smoothed structure has to be three times thicker to provide the same stiffness. It was concluded the corrugated wing has the structural benefit to provide the same resistance to bending moments with a much reduced weight.

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.

Electron crystallography and aquaporins.

PubMed

Schenk, Andreas D; Hite, Richard K; Engel, Andreas; Fujiyoshi, Yoshinori; Walz, Thomas

2010-01-01

Electron crystallography of two-dimensional (2D) crystals can provide information on the structure of membrane proteins at near-atomic resolution. Originally developed and used to determine the structure of bacteriorhodopsin (bR), electron crystallography has recently been applied to elucidate the structure of aquaporins (AQPs), a family of membrane proteins that form pores mostly for water but also other solutes. While electron crystallography has made major contributions to our understanding of the structure and function of AQPs, structural studies on AQPs, in turn, have fostered a number of technical developments in electron crystallography. In this contribution, we summarize the insights electron crystallography has provided into the biology of AQPs, and describe technical advancements in electron crystallography that were driven by structural studies on AQP 2D crystals. In addition, we discuss some of the lessons that were learned from electron crystallographic work on AQPs. Copyright © 2010 Elsevier Inc. All rights reserved.

Structural atlas of dynein motors at atomic resolution.

PubMed

Toda, Akiyuki; Tanaka, Hideaki; Kurisu, Genji

2018-04-01

Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

Conceptual study of the damping of large space structures using large-stroke adaptive stiffness cables

NASA Technical Reports Server (NTRS)

Thorwald, Gregory; Mikulas, Martin M., Jr.

1992-01-01

The concept of a large-stroke adaptive stiffness cable-device for damping control of space structures with large mass is introduced. The cable is used to provide damping in several examples, and its performance is shown through numerical simulation results. Displacement and velocity information of how the structure moves is used to determine when to modify the cable's stiffness in order to provide a damping force.

The relationship between structured and free play in the development of a mentally handicapped child: a case study.

PubMed

Hewson, S; McConkey, R; Jeffree, D

1980-01-01

This case study provides an individual illustration of the work of the Parental Involvement Project. A key feature of the approach used was the structured play situation. Thus, the case study also serves to demonstrate the role of structured play, and its relation to free play, in the development of a young, mentally handicapped child.

Assessment of the structural validity of the domestic violence healthcare providers’ survey questionnaire using a Nigerian sample

PubMed Central

John, Ime A; Lawoko, Stephen

2010-01-01

Abstract: Background: There has been increased advocacy to involve healthcare providers in the prevention of intimate partner violence (IPV) through screening for it in healthcare. Yet, only one in ten providers screen for IPV, suggesting barriers. Understanding the readiness of healthcare providers to screen for IPV is therefore paramount. The Domestic Violence Healthcare Provider Survey Scales (DVHPSS) is a previously validated, comprehensive scale to study readiness of healthcare providers to screen for IPV. However, an understanding of its usefulness in the Sub-Saharan African context remains elusive. The current study undertook to examine the structural validity of the DVHPSS in Nigeria. Methods: Exploratory factor analysis and Cronbach's Alpha were run to reveal the factorial structure and reliability of the instrument/subscales respectively. Established thresholds were used to determine significant factor loadings and alphas coefficient. Results: A six factor model emerged, with 2 factors similar to the original scale, another two differing slightly and a further two factors resulting from a splitting up of the original combination of victim/provider safety to having distinct victim and provider safety subscales. Conclusions: With slight modifications, the DVHPSS can be use to study IPV screening among Nigerian healthcare professionals. Introducing screening protocols could promote better understanding of crucial questions that were lost in the analysis. PMID:21483202

Emerging structural insights into the function of ionotropic glutamate receptors

PubMed Central

Karakas, Erkan; Regan, Michael C.; Furukawa, Hiro

2015-01-01

Summary Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission crucial for brain development and function including learning and memory formation. Recently a wealth of structural studies on iGluRs, including AMPA receptors (AMPARs), kainate receptors, and NMDA receptors (NMDARs) became available.. These studies showed structures of non-NMDARs including AMPAR and kainate receptor in various functional states, thereby providing the first visual sense of how non-NMDAR iGluRs may function in the context of homotetramers. Furthermore, they provided the first view of heterotetrameric NMDAR ion channels, which illuminated the similarities with and differences from non-NMDARs, thus raising a mechanistic distinction between the two groups of iGluRs. Here we review mechanistic insights into iGluR functions gained through structural studies of multiple groups. PMID:25941168

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

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

Li, Qiong; Gluch, Jürgen; Krüger, Peter

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

Workshop on High-Field NMR and Biological Applications

NASA Astrophysics Data System (ADS)

Scientists at the Pacific Northwest Laboratory have been working toward the establishment of a new Molecular Science Research Center (MSRC). The primary scientific thrust of this new research center is in the areas of theoretical chemistry, chemical dynamics, surface and interfacial science, and studies on the structure and interactions of biological macromolecules. The MSRC will provide important new capabilities for studies on the structure of biological macromolecules. The MSRC program includes several types of advanced spectroscopic techniques for molecular structure analysis, and a theory and modeling laboratory for molecular mechanics/dynamics calculations and graphics. It is the goal to closely integrate experimental and theoretical studies on macromolecular structure, and to join these research efforts with those of the molecular biological programs to provide new insights into the structure/function relationships of biological macromolecules. One of the areas of structural biology on which initial efforts in the MSRC will be focused is the application of high field, 2-D NMR to the study of biological macromolecules. First, there is interest in obtaining 3-D structural information on large proteins and oligonucleotides. Second, one of the primary objectives is to closely link theoretical approaches to molecular structure analysis with the results obtained in experimental research using NMR and other spectroscopies.

A space station Structures and Assembly Verification Experiment, SAVE

NASA Technical Reports Server (NTRS)

Russell, R. A.; Raney, J. P.; Deryder, L. J.

1986-01-01

The Space Station structure has been baselined to be a 5 M (16.4 ft) erectable truss. This structure will provide the overall framework to attach laboratory modules and other systems, subsystems and utilities. The assembly of this structure represents a formidable EVA challenge. To validate this capability the Space Station Structures/Dynamics Technical Integration Panel (TIP) met to develop the necessary data for an integrated STS structures flight experiment. As a result of this meeting, the Langley Research Center initiated a joint Langley/Boeing Aerospace Company study which supported the structures/dynamics TIP in developing the preliminary definition and design of a 5 M erectable space station truss and the resources required for a proposed flight experiment. The purpose of the study was to: (1) devise methods of truss assembly by astronauts; (2) define a specific test matrix for dynamic characterization; (3) identify instrumentation and data system requirements; (4) determine the power, propulsion and control requirements for the truss on-orbit for 3 years; (5) study the packaging of the experiment in the orbiter cargo bay; (6) prepare a preliminary cost estimate and schedule for the experiment; and (7) provide a list of potential follow-on experiments using the structure as a free flyer. The results of this three month study are presented.

Advanced transportation system study: Manned launch vehicle concepts for two way transportation system payloads to LEO. Work breakdown structure and work breakdown structure dictionary

NASA Technical Reports Server (NTRS)

Duffy, James B.

1992-01-01

The report describes the work breakdown structure (WBS) and its associated WBS dictionary for task area 1 of contract NAS8-39207, advanced transportation system studies (ATSS). This WBS format is consistent with the preliminary design level of detail employed by both task area 1 and task area 4 in the ATSS study and is intended to provide an estimating structure for parametric cost estimates.

Crystal Structures of Human SIRT[subscript 3] Displaying Substrate-induced Conformational Changes

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

Jin, Lei; Wei, Wentao; Jiang, Yaobin

2009-11-04

SIRT3 is a major mitochondrial NAD{sup +}-dependent protein deacetylase playing important roles in regulating mitochondrial metabolism and energy production and has been linked to the beneficial effects of exercise and caloric restriction. SIRT3 is emerging as a potential therapeutic target to treat metabolic and neurological diseases. We report the first sets of crystal structures of human SIRT3, an apo-structure with no substrate, a structure with a peptide containing acetyl lysine of its natural substrate acetyl-CoA synthetase 2, a reaction intermediate structure trapped by a thioacetyl peptide, and a structure with the dethioacetylated peptide bound. These structures provide insights into themore » conformational changes induced by the two substrates required for the reaction, the acetylated substrate peptide and NAD+. In addition, the binding study by isothermal titration calorimetry suggests that the acetylated peptide is the first substrate to bind to SIRT3, before NAD{sup +}. These structures and biophysical studies provide key insight into the structural and functional relationship of the SIRT3 deacetylation activity.« less

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Reconstitution of Homomeric GluA2flop Receptors in Supported Lipid Membranes

PubMed Central

Baranovic, Jelena; Ramanujan, Chandra S.; Kasai, Nahoko; Midgett, Charles R.; Madden, Dean R.; Torimitsu, Keiichi; Ryan, John F.

2013-01-01

AMPA receptors (AMPARs) are glutamate-gated ion channels ubiquitous in the vertebrate central nervous system, where they mediate fast excitatory neurotransmission and act as molecular determinants of memory formation and learning. Together with detailed analyses of individual AMPAR domains, structural studies of full-length AMPARs by electron microscopy and x-ray crystallography have provided important insights into channel assembly and function. However, the correlation between the structure and functional states of the channel remains ambiguous particularly because these functional states can be assessed only with the receptor bound within an intact lipid bilayer. To provide a basis for investigating AMPAR structure in a membrane environment, we developed an optimized reconstitution protocol using a receptor whose structure has previously been characterized by electron microscopy. Single-channel recordings of reconstituted homomeric GluA2flop receptors recapitulate key electrophysiological parameters of the channels expressed in native cellular membranes. Atomic force microscopy studies of the reconstituted samples provide high-resolution images of membrane-embedded full-length AMPARs at densities comparable to those in postsynaptic membranes. The data demonstrate the effect of protein density on conformational flexibility and dimensions of the receptors and provide the first structural characterization of functional membrane-embedded AMPARs, thus laying the foundation for correlated structure-function analyses of the predominant mediators of excitatory synaptic signals in the brain. PMID:23382380

Terrestrial laser scanning to quantify above-ground biomass of structurally complex coastal wetland vegetation

NASA Astrophysics Data System (ADS)

Owers, Christopher J.; Rogers, Kerrylee; Woodroffe, Colin D.

2018-05-01

Above-ground biomass represents a small yet significant contributor to carbon storage in coastal wetlands. Despite this, above-ground biomass is often poorly quantified, particularly in areas where vegetation structure is complex. Traditional methods for providing accurate estimates involve harvesting vegetation to develop mangrove allometric equations and quantify saltmarsh biomass in quadrats. However broad scale application of these methods may not capture structural variability in vegetation resulting in a loss of detail and estimates with considerable uncertainty. Terrestrial laser scanning (TLS) collects high resolution three-dimensional point clouds capable of providing detailed structural morphology of vegetation. This study demonstrates that TLS is a suitable non-destructive method for estimating biomass of structurally complex coastal wetland vegetation. We compare volumetric models, 3-D surface reconstruction and rasterised volume, and point cloud elevation histogram modelling techniques to estimate biomass. Our results show that current volumetric modelling approaches for estimating TLS-derived biomass are comparable to traditional mangrove allometrics and saltmarsh harvesting. However, volumetric modelling approaches oversimplify vegetation structure by under-utilising the large amount of structural information provided by the point cloud. The point cloud elevation histogram model presented in this study, as an alternative to volumetric modelling, utilises all of the information within the point cloud, as opposed to sub-sampling based on specific criteria. This method is simple but highly effective for both mangrove (r2 = 0.95) and saltmarsh (r2 > 0.92) vegetation. Our results provide evidence that application of TLS in coastal wetlands is an effective non-destructive method to accurately quantify biomass for structurally complex vegetation.

University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

NASA Astrophysics Data System (ADS)

Wu, Ying-Tien

2013-10-01

This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

Finite element study of scaffold architecture design and culture conditions for tissue engineering.

PubMed

Olivares, Andy L; Marsal, Elia; Planell, Josep A; Lacroix, Damien

2009-10-01

Tissue engineering scaffolds provide temporary mechanical support for tissue regeneration and transfer global mechanical load to mechanical stimuli to cells through its architecture. In this study the interactions between scaffold pore morphology, mechanical stimuli developed at the cell microscopic level, and culture conditions applied at the macroscopic scale are studied on two regular scaffold structures. Gyroid and hexagonal scaffolds of 55% and 70% porosity were modeled in a finite element analysis and were submitted to an inlet fluid flow or compressive strain. A mechanoregulation theory based on scaffold shear strain and fluid shear stress was applied for determining the influence of each structures on the mechanical stimuli on initial conditions. Results indicate that the distribution of shear stress induced by fluid perfusion is very dependent on pore distribution within the scaffold. Gyroid architectures provide a better accessibility of the fluid than hexagonal structures. Based on the mechanoregulation theory, the differentiation process in these structures was more sensitive to inlet fluid flow than axial strain of the scaffold. This study provides a computational approach to determine the mechanical stimuli at the cellular level when cells are cultured in a bioreactor and to relate mechanical stimuli with cell differentiation.

Subtractive Structural Modification of Morpho Butterfly Wings.

PubMed

Shen, Qingchen; He, Jiaqing; Ni, Mengtian; Song, Chengyi; Zhou, Lingye; Hu, Hang; Zhang, Ruoxi; Luo, Zhen; Wang, Ge; Tao, Peng; Deng, Tao; Shang, Wen

2015-11-11

Different from studies of butterfly wings through additive modification, this work for the first time studies the property change of butterfly wings through subtractive modification using oxygen plasma etching. The controlled modification of butterfly wings through such subtractive process results in gradual change of the optical properties, and helps the further understanding of structural optimization through natural evolution. The brilliant color of Morpho butterfly wings is originated from the hierarchical nanostructure on the wing scales. Such nanoarchitecture has attracted a lot of research effort, including the study of its optical properties, its potential use in sensing and infrared imaging, and also the use of such structure as template for the fabrication of high-performance photocatalytic materials. The controlled subtractive processes provide a new path to modify such nanoarchitecture and its optical property. Distinct from previous studies on the optical property of the Morpho wing structure, this study provides additional experimental evidence for the origination of the optical property of the natural butterfly wing scales. The study also offers a facile approach to generate new 3D nanostructures using butterfly wings as the templates and may lead to simpler structure models for large-scale man-made structures than those offered by original butterfly wings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Customer-Focused Business Practice Adoption: A Comparison of Private and Public Sector Implementations

DTIC Science & Technology

2004-03-01

Narratives Phenomenologies Ethnographies Grounded Theory Case Studies Mixed Methods Sequential Concurrent Transformative Creswell... ethnographies , grounded theory studies and case studies (Creswell, 2003:18). The methods used in qualitative study provide the framework for...Definition Grounded theory provides a structured

End Effects and Load Diffusion in Composite Structures

NASA Technical Reports Server (NTRS)

Horgan, Cornelius O.; Ambur, D. (Technical Monitor); Nemeth, M. P. (Technical Monitor)

2002-01-01

The research carried out here builds on our previous NASA supported research on the general topic of edge effects and load diffusion in composite structures. Further fundamental solid mechanics studies were carried out to provide a basis for assessing the complicated modeling necessary for large scale structures used by NASA. An understanding of the fundamental mechanisms of load diffusion in composite subcomponents is essential in developing primary composite structures. Specific problems recently considered were focussed on end effects in sandwich structures and for functionally graded materials. Both linear and nonlinear (geometric and material) problems have been addressed. Our goal is the development of readily applicable design formulas for the decay lengths in terms of non-dimensional material and geometric parameters. Analytical models of load diffusion behavior are extremely valuable in building an intuitive base for developing refined modeling strategies and assessing results from finite element analyses. The decay behavior of stresses and other field quantities provides a significant aid towards this process. The analysis is also amenable to parameter study with a large parameter space and should be useful in structural tailoring studies.

Fractual interrelationships in field and seismic data. Final report

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

NONE

1997-01-07

Fractals provide a description of physical patterns over a range of scales in both time and space. Studies presented herein examine the fractal characteristics of various geological variables such as deformed bed-lengths, fold relief, seismic reflection arrival time variations, drainage and topographic patterns, and fracture systems. The studies are also extended to consider the possibility that the fractal characteristics of these variables are interrelated. Fractal interrelationships observed in these studies provide a method for relating variations in the fractal characteristics of seismic reflection events from reservoir intervals to the fractal characteristics of reservoir fracture systems, faults, and fold distributions. Themore » work is motivated by current exploration and development interests to detect fractured reservoirs and to accurately predict flow rates and flow patterns within the fractured reservoir. Accurate prediction requires an understanding of several reservoir properties including the fractal geometry of the reservoir fracture network. Results of these studies provide a method to remotely assess the fractal characteristics of a fractured reservoir, and help guide field development activities. The most significant outgrowth of this research is that the fractal properties of structural relief inferred from seismic data and structural cross sections provide a quantitative means to characterize and compare complex structural patterns. Production from fractured reservoirs is the result of complex structural and stratigraphic controls; hence, the import of fractal characterization to the assessment of fractured reservoirs lies in its potential to quantitatively define interrelationships between subtle structural variation and production. The potential uses are illustrated using seismic data from the Granny Creek oil field in the Appalachian Plateau.« less

Live CLEM imaging to analyze nuclear structures at high resolution.

PubMed

Haraguchi, Tokuko; Osakada, Hiroko; Koujin, Takako

2015-01-01

Fluorescence microscopy (FM) and electron microscopy (EM) are powerful tools for observing molecular components in cells. FM can provide temporal information about cellular proteins and structures in living cells. EM provides nanometer resolution images of cellular structures in fixed cells. We have combined FM and EM to develop a new method of correlative light and electron microscopy (CLEM), called "Live CLEM." In this method, the dynamic behavior of specific molecules of interest is first observed in living cells using fluorescence microscopy (FM) and then cellular structures in the same cell are observed using electron microscopy (EM). Following image acquisition, FM and EM images are compared to enable the fluorescent images to be correlated with the high-resolution images of cellular structures obtained using EM. As this method enables analysis of dynamic events involving specific molecules of interest in the context of specific cellular structures at high resolution, it is useful for the study of nuclear structures including nuclear bodies. Here we describe Live CLEM that can be applied to the study of nuclear structures in mammalian cells.

Emerging structural insights into the function of ionotropic glutamate receptors.

PubMed

Karakas, Erkan; Regan, Michael C; Furukawa, Hiro

2015-06-01

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission crucial for brain development and function, including learning and memory formation. Recently a wealth of structural studies on iGluRs including AMPA receptors (AMPARs), kainate receptors, and NMDA receptors (NMDARs) became available. These studies showed structures of non-NMDARs including AMPAR and kainate receptor in various functional states, thereby providing the first visual sense of how non-NMDAR iGluRs may function in the context of homotetramers. Furthermore, they provided the first view of heterotetrameric NMDAR ion channels, and this illuminated the similarities with and differences from non-NMDARs, thus raising a mechanistic distinction between the two groups of iGluRs. We review mechanistic insights into iGluR functions gained through structural studies of multiple groups. Copyright © 2015 Elsevier Ltd. All rights reserved.

78 FR 46928 - Meeting of the National Commission on the Structure of the Air Force

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... come, first served basis, other opportunities for oral comments will be provided at future meetings... appropriate in light of the results of the study. The comprehensive study of the structure of the U.S. Air...

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Zebra: a web server for bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Evgeny; Takhaveev, Vakil; Svedas, Vytas

2014-01-01

During evolution of proteins from a common ancestor, one functional property can be preserved while others can vary leading to functional diversity. A systematic study of the corresponding adaptive mutations provides a key to one of the most challenging problems of modern structural biology - understanding the impact of amino acid substitutions on protein function. The subfamily-specific positions (SSPs) are conserved within functional subfamilies but are different between them and, therefore, seem to be responsible for functional diversity in protein superfamilies. Consequently, a corresponding method to perform the bioinformatic analysis of sequence and structural data has to be implemented in the common laboratory practice to study the structure-function relationship in proteins and develop novel protein engineering strategies. This paper describes Zebra web server - a powerful remote platform that implements a novel bioinformatic analysis algorithm to study diverse protein families. It is the first application that provides specificity determinants at different levels of functional classification, therefore addressing complex functional diversity of large superfamilies. Statistical analysis is implemented to automatically select a set of highly significant SSPs to be used as hotspots for directed evolution or rational design experiments and analyzed studying the structure-function relationship. Zebra results are provided in two ways - (1) as a single all-in-one parsable text file and (2) as PyMol sessions with structural representation of SSPs. Zebra web server is available at http://biokinet.belozersky.msu.ru/zebra .

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

PubMed

Tavanti, Michele; Porter, Joanne L; Levy, Colin W; Gómez Castellanos, J Rubén; Flitsch, Sabine L; Turner, Nicholas J

2018-07-02

The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes. Copyright © 2018 Elsevier Inc. All rights reserved.

Structural considerations for solar installers : an approach for small, simplified solar installations or retrofits.

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

Richards, Elizabeth H.; Schindel, Kay; Bosiljevac, Tom

2011-12-01

Structural Considerations for Solar Installers provides a comprehensive outline of structural considerations associated with simplified solar installations and recommends a set of best practices installers can follow when assessing such considerations. Information in the manual comes from engineering and solar experts as well as case studies. The objectives of the manual are to ensure safety and structural durability for rooftop solar installations and to potentially accelerate the permitting process by identifying and remedying structural issues prior to installation. The purpose of this document is to provide tools and guidelines for installers to help ensure that residential photovoltaic (PV) power systemsmore » are properly specified and installed with respect to the continuing structural integrity of the building.« less

Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*

PubMed Central

Kaur, Parminder; Kiselar, Janna; Yang, Sichun; Chance, Mark R.

2015-01-01

Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes. PMID:25687570

STI service delivery in British Columbia, Canada; providers' views of their services to youth

PubMed Central

2012-01-01

Background Little is known about service providers’ knowledge, attitudes, and experiences in relation to the assessment, diagnosis, and treatment of individuals seeking care for sexually transmitted infections (STIs), and how they influence the delivery of services. The purpose of this study was to explore the perceptions of STI care providers and the ways they approached their practice. Methods We used a qualitative approach drawing on methods used in thematic analysis. Individual semi-structured in-depth interviews were conducted with 21 service providers delivering STI services in youth clinics, STI clinics, reproductive health clinics, and community public health units in British Columbia (BC), Canada. Results Service providers’ descriptions of their activities and roles were shaped by a number of themes including specialization, scarcity, and maintaining the status quo. The analysis suggests that service providers perceive, at times, the delivery of STI care to be inefficient and inadequate. Conclusion Findings from this study identify deficits in the delivery of STI services in BC. To understand these deficits, more research is needed to examine the larger health care structure within which service providers work, and how this structure not only informs and influences the delivery of services, but also how particular structural barriers impinge on and/or restrict practice. PMID:22863400

Femtosecond laser-induced herringbone patterns

NASA Astrophysics Data System (ADS)

Garcell, Erik M.; Lam, Billy; Guo, Chunlei

2018-06-01

Femtosecond laser-induced herringbone patterns are formed on copper (Cu). These novel periodic structures are created following s-polarized, large incident angle, femtosecond laser pulses. Forming as slanted and axially symmetric laser-induced periodic surface structures along the side walls of ablated channels, the result is a series of v-shaped structures that resemble a herringbone pattern. Fluence mapping, incident angle studies, as well as polarization studies have been conducted and provide a clear understanding of this new structure.

Environmental Enhancements and Navigation Infrastructure: A Study of Existing Practices, Innovative Ideas, Impediments, and Research Needs

DTIC Science & Technology

2011-07-01

velocity/substrate Excavate back channels in river systems Piers & Wharves Design hard structures to facilitate better seaweed recruitment...allows vegetative colonization of areas beneath the structures P Design hard structures to facilitate better seaweed recruitment I Provide

Comparing Factor Structures of Adolescent Psychopathology

ERIC Educational Resources Information Center

Verona, Edelyn; Javdani, Shabnam; Sprague, Jenessa

2011-01-01

Research on the structure of adolescent psychopathology can provide information on broad factors that underlie different forms of maladjustment in youths. Multiple studies from the literature on adult populations suggest that 2 factors, Internalizing and Externalizing, meaningfully comprise the factor structure of adult psychopathology (e.g.,…

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with "high sequence identity." Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells.

PubMed

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U-Ser; Lin, Hao-Wu

2015-09-04

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells

NASA Astrophysics Data System (ADS)

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U.-Ser; Lin, Hao-Wu

2015-09-01

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Studies of midaltitude cyclone structure with SEASAT scanning multichannel microwave radiometer

NASA Technical Reports Server (NTRS)

Katsaros, K. B.

1984-01-01

The data provided by the atmospheric water channels of SEASAT's Scanning Multichannel Microwave Radiometer (SMMR) is used to investigate mesoscale structure at various stages of the development of a midlatitude cyclone. Seasonal and graphic differences in the storms are also studied.

Arginine-based poly(ester amide) nanoparticle platform: From structure-property relationship to nucleic acid delivery.

PubMed

You, Xinru; Gu, Zhipeng; Huang, Jun; Kang, Yang; Chu, Chih-Chang; Wu, Jun

2018-05-25

Many different types of polycations have been vigorously studied for nucleic acid delivery, but a systematical investigation of the structure-property relationships of polycations for nucleic acid delivery is still lacking. In this study, a new library of biodegradable and biocompatible arginine-based poly(ester amide) (Arg-PEA) biomaterials was designed and synthesized with a tunable structure for such a comprehensive structure-property research. Nanoparticle (NP) complexes were formed through the electrostatic interactions between the polycationic Arg-PEAs and anionic nucleic acids. The following structure effects of the Arg-PEAs on the transfection efficiency of nucleic acids were investigated: 1) the linker/spacer length (length effect and odd-even effect); 2) salt type of arginine; 3) the side chain; 4) chain stiffness; 5) molecular weight (MW). The data obtained revealed that a slight change in the Arg-PEA structure could finely tune its physicochemical property such as hydrophobicity, and this could subsequently affect the nanoparticle size and zeta potential, which, in turn, regulate the transfection efficiency and silencing outcomes. A further study of the Arg-PEA/CpG oligodeoxynucleotide NP complexes indicated that the polymer structure could precisily regulate the immune response of CpG, thus providing a new potential nano-immunotherapy strategy. The in vitro data have further confirmed that the Arg-PEA NPs showed a satisfactory delivery performance for a variety of nucleic acids. Therefore, the data from the current study provide comprehensive information about the Arg-PEA structure-transfection property relationship; the tunable property of the library of Arg-PEA biomaterials can be one of the promising candidates for nucleic acid delivery and other biomedical applications. Polycations have being intensive utilized for nucleic acid delivery. However, there has not been elucidated about the relationship between polycation's structure and the physicochemical properties/biological function. In this timely report, an arginine based poly(ester amide) (Arg-PEA) library was prepared with finely tunable structure to systematically investigate the structure-property relationships of polycations for nucleic acid delivery. The results revealed that slight change of Arg-PEA structure could finely tune the physicochemical property (such as hydrophobicity), which subsequently affect the size and zeta potential of Arg-PEA/nucleic acid nanoparticles(NPs), and finally regulate the resulting transfection or silencing outcomes. Further study of Arg-PEA/CpG NPs indicated that the polymer structure could precisely regulate immuno response of CpG, providing new potential nano-immunotherapy strategy. In vitro evaluations confirmed that the NPs showed satisfied delivery performance for a variety types of nucleic acids. Therefore, these studies provide comprehensive information of Arg-PEA structure-property relationship, and the tunable properties of Arg-PEAs make them promising candidates for nucleic acid delivery and other biomedical applications. Overall, we have shown enough significance and novelty in terms of nucleic acid delivery, biomaterials, pharmaceutical science and nanomedicine. Copyright © 2018. Published by Elsevier Ltd.

Identification and Structural Basis of Binding to Host Lung Glycogen by Streptococcal Virulence Factors

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

Lammerts van Bueren,A.; Higgins, M.; Wang, D.

2007-01-01

The ability of pathogenic bacteria to recognize host glycans is often essential to their virulence. Here we report structure-function studies of previously uncharacterized glycogen-binding modules in the surface-anchored pullulanases from Streptococcus pneumoniae (SpuA) and Streptococcus pyogenes (PulA). Multivalent binding to glycogen leads to a strong interaction with alveolar type II cells in mouse lung tissue. X-ray crystal structures of the binding modules reveal a novel fusion of tandem modules into single, bivalent functional domains. In addition to indicating a structural basis for multivalent attachment, the structure of the SpuA modules in complex with carbohydrate provides insight into the molecular basismore » for glycogen specificity. This report provides the first evidence that intracellular lung glycogen may be a novel target of pathogenic streptococci and thus provides a rationale for the identification of the streptococcal {alpha}-glucan-metabolizing machinery as virulence factors.« less

Natural cork agglomerate employed as an environmentally friendly solution for quiet sandwich composites.

PubMed

Sargianis, James; Kim, Hyung-ick; Suhr, Jonghwan

2012-01-01

Carbon fiber-synthetic foam core sandwich composites are widely used for many structural applications due to their superior mechanical performance and low weight. Unfortunately these structures typically have very poor acoustic performance. There is increasingly growing demand in mitigating this noise issue in sandwich composite structures. This study shows that marrying carbon fiber composites with natural cork in a sandwich structure provides a synergistic effect yielding a noise-free sandwich composite structure without the sacrifice of mechanical performance or weight. Moreover the cork-core sandwich composites boast a 250% improvement in damping performance, providing increased durability and lifetime operation. Additionally as the world seeks environmentally friendly materials, the harvesting of cork is a natural, renewable process which reduces subsequent carbon footprints. Such a transition from synthetic foam cores to natural cork cores could provide unprecedented improvements in acoustic and vibrational performance in applications such as aircraft cabins or wind turbine blades.

Infant Brain Structures, Executive Function, and Attention Deficit/Hyperactivity Problems at Preschool Age. A Prospective Study

ERIC Educational Resources Information Center

Ghassabian, Akhgar; Herba, Catherine M.; Roza, Sabine J.; Govaert, Paul; Schenk, Jacqueline J.; Jaddoe, Vincent W.; Hofman, Albert; White, Tonya; Verhulst, Frank C.; Tiemeier, Henning

2013-01-01

Background: Neuroimaging findings have provided evidence for a relation between variations in brain structures and Attention Deficit/Hyperactivity Disorder (ADHD). However, longitudinal neuroimaging studies are typically confined to children who have already been diagnosed with ADHD. In a population-based study, we aimed to characterize the…

Structure, Citizenship, and Professionalism: Exploring Rationale Development as Part of Graduate Education in Social Studies

ERIC Educational Resources Information Center

Hawley, Todd S.; Pifel, A. Robert; Jordan, Adam W.

2012-01-01

This article details an interpretive, qualitative interview study that explored rationales developed by seven social studies graduate students, all experienced teachers, at a large Midwestern university. Interviews revealed three common themes regarding the influence of the rationale development process. The three themes were: providing structure,…

Exploratory and Confirmatory Factor Analyses of the Structured Interview for Disorders of Extreme Stress

ERIC Educational Resources Information Center

Scoboria, Alan; Ford, Julian; Lin, Hsiu-ju; Frisman, Linda

2008-01-01

Two studies were conducted to provide the first empirical examination of the factor structure of a revised version of the clinically derived Structured Interview for Disorders of Extreme Stress, a structured interview designed to assess associated features of posttraumatic stress disorder (PTSD) thought to be related to early onset, interpersonal,…

High-pressure studies with x-rays using diamond anvil cells

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

Shen, Guoyin; Mao, Ho Kwang

2016-11-22

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. Thesemore » HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.« less

High-pressure studies with x-rays using diamond anvil cells

NASA Astrophysics Data System (ADS)

Shen, Guoyin; Mao, Ho Kwang

2017-01-01

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials’ properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.

Grazing-incidence small angle x-ray scattering studies of nanoscale polymer gratings

NASA Astrophysics Data System (ADS)

Doxastakis, Manolis; Suh, Hyo Seon; Chen, Xuanxuan; Rincon Delgadillo, Paulina A.; Wan, Lingshu; Williamson, Lance; Jiang, Zhang; Strzalka, Joseph; Wang, Jin; Chen, Wei; Ferrier, Nicola; Ramirez-Hernandez, Abelardo; de Pablo, Juan J.; Gronheid, Roel; Nealey, Paul

2015-03-01

Grazing-Incidence Small Angle X-ray Scattering (GISAXS) offers the ability to probe large sample areas, providing three-dimensional structural information at high detail in a thin film geometry. In this study we exploit the application of GISAXS to structures formed at one step of the LiNe (Liu-Nealey) flow using chemical patterns for directed self-assembly of block copolymer films. Experiments conducted at the Argonne National Laboratory provided scattering patterns probing film characteristics at both parallel and normal directions to the surface. We demonstrate the application of new computational methods to construct models based on scattering measured. Such analysis allows for extraction of structural characteristics at unprecedented detail.

Review structure of silk by raman spectromicroscopy: from the spinning glands to the fibers.

PubMed

Lefèvre, Thierry; Paquet-Mercier, François; Rioux-Dubé, Jean-François; Pézolet, Michel

2012-06-01

Raman spectroscopy has long been proved to be a useful tool to study the conformation of protein-based materials such as silk. Thanks to recent developments, linearly polarized Raman spectromicroscopy has appeared very efficient to characterize the molecular structure of native single silk fibers and spinning dopes because it can provide information relative to the protein secondary structure, molecular orientation, and amino acid composition. This review will describe recent advances in the study of the structure of silk by Raman spectromicroscopy. A particular emphasis is put on the spider dragline and silkworm cocoon threads, other fibers spun by orb-weaving spiders, the spinning dope contained in their silk glands and the effect of mechanical deformation. Taken together, the results of the literature show that Raman spectromicroscopy is particularly efficient to investigate all aspects of silk structure and production. The data provided can lead to a better understanding of the structure of the silk dope, transformations occurring during the spinning process, and structure and mechanical properties of native fibers. Copyright © 2011 Wiley Periodicals, Inc.

Biochemical and Structural Characterization of the Human TL1A Ectodomain†¶

PubMed Central

Zhan, Chenyang; Yan, Qingrong; Patskovsky, Yury; Li, Zhenhong; Toro, Rafael; Meyer, Amanda; Cheng, Huiyong; Brenowitz, Michael; Nathenson, Stanley G; Almo, Steven C

2009-01-01

TNF-like 1A (TL1A) is a newly described member of the TNF superfamily that is directly implicated in the pathogenesis of autoimmune diseases, including inflammatory bowel disease, atherosclerosis and rheumatoid arthritis. We report the crystal structure of the human TL1A extracellular domain at a resolution of 2.5 Å, which reveals a jelly-roll fold typical of the TNF superfamily. This structural information, in combination with complementary mutagenesis and biochemical characterization, provides insights into the binding interface and the specificity of the interactions between TL1A and the DcR3 and DR3 receptors. These studies suggest that the mode of interaction between TL1A and DcR3 differs from other characterized TNF ligand/receptor complexes. In addition, we have generated functional TL1A mutants with altered disulfide bonding capability that exhibit enhanced solution properties, which will facilitate the production of materials for future cell-based and whole animal studies. In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors. PMID:19522538

Biochemical and Structural Characterization of the Human TL1A Ectodomain

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

Zhan, C.; Yan, Q; Patskovsky, Y

TNF-like 1A (TL1A) is a newly described member of the TNF superfamily that is directly implicated in the pathogenesis of autoimmune diseases, including inflammatory bowel disease, atherosclerosis, and rheumatoid arthritis. We report the crystal structure of the human TL1A extracellular domain at a resolution of 2.5 {angstrom}, which reveals a jelly-roll fold typical of the TNF superfamily. This structural information, in combination with complementary mutagenesis and biochemical characterization, provides insights into the binding interface and the specificity of the interactions between TL1A and the DcR3 and DR3 receptors. These studies suggest that the mode of interaction between TL1A and DcR3more » differs from other characterized TNF ligand/receptor complexes. In addition, we have generated functional TL1A mutants with altered disulfide bonding capability that exhibit enhanced solution properties, which will facilitate the production of materials for future cell-based and whole animal studies. In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors.« less

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K. Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-01

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. PMID:26467476

Structural Genomics of Protein Phosphatases

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

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less

Classification of proteins: available structural space for molecular modeling.

PubMed

Andreeva, Antonina

2012-01-01

The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

Sensitivity to musical structure in the human brain

PubMed Central

McDermott, Josh H.; Norman-Haignere, Sam; Kanwisher, Nancy

2012-01-01

Evidence from brain-damaged patients suggests that regions in the temporal lobes, distinct from those engaged in lower-level auditory analysis, process the pitch and rhythmic structure in music. In contrast, neuroimaging studies targeting the representation of music structure have primarily implicated regions in the inferior frontal cortices. Combining individual-subject fMRI analyses with a scrambling method that manipulated musical structure, we provide evidence of brain regions sensitive to musical structure bilaterally in the temporal lobes, thus reconciling the neuroimaging and patient findings. We further show that these regions are sensitive to the scrambling of both pitch and rhythmic structure but are insensitive to high-level linguistic structure. Our results suggest the existence of brain regions with representations of musical structure that are distinct from high-level linguistic representations and lower-level acoustic representations. These regions provide targets for future research investigating possible neural specialization for music or its associated mental processes. PMID:23019005

Control of Flexible Structures (COFS) Flight Experiment Background and Description

NASA Technical Reports Server (NTRS)

Hanks, B. R.

1985-01-01

A fundamental problem in designing and delivering large space structures to orbit is to provide sufficient structural stiffness and static configuration precision to meet performance requirements. These requirements are directly related to control requirements and the degree of control system sophistication available to supplement the as-built structure. Background and rationale are presented for a research study in structures, structural dynamics, and controls using a relatively large, flexible beam as a focus. This experiment would address fundamental problems applicable to large, flexible space structures in general and would involve a combination of ground tests, flight behavior prediction, and instrumented orbital tests. Intended to be multidisciplinary but basic within each discipline, the experiment should provide improved understanding and confidence in making design trades between structural conservatism and control system sophistication for meeting static shape and dynamic response/stability requirements. Quantitative results should be obtained for use in improving the validity of ground tests for verifying flight performance analyses.

The structure of Turkish trait-descriptive adjectives.

PubMed

Somer, O; Goldberg, L R

1999-03-01

This description of the Turkish lexical project reports some initial findings on the structure of Turkish personality-related variables. In addition, it provides evidence on the effects of target evaluative homogeneity vs. heterogeneity (e.g., samples of well-liked target individuals vs. samples of both liked and disliked targets) on the resulting factor structures, and thus it provides a first test of the conclusions reached by D. Peabody and L. R. Goldberg (1989) using English trait terms. In 2 separate studies, and in 2 types of data sets, clear versions of the Big Five factor structure were found. And both studies replicated and extended the findings of Peabody and Goldberg; virtually orthogonal factors of relatively equal size were found in the homogeneous samples, and a more highly correlated set of factors with relatively large Agreeableness and Conscientiousness dimensions was found in the heterogeneous samples.

LiDAR: Providing structure

USGS Publications Warehouse

Vierling, Lee A.; Martinuzzi, Sebastián; Asner, Gregory P.; Stoker, Jason M.; Johnson, Brian R.

2011-01-01

Since the days of MacArthur, three-dimensional (3-D) structural information on the environment has fundamentally transformed scientific understanding of ecological phenomena (MacArthur and MacArthur 1961). Early data on ecosystem structure were painstakingly laborious to collect. However, as reviewed and reported in recent volumes of Frontiers(eg Vierling et al. 2008; Asner et al.2011), advances in light detection and ranging (LiDAR) remote-sensing technology provide quantitative and repeatable measurements of 3-D ecosystem structure that enable novel ecological insights at scales ranging from the plot, to the landscape, to the globe. Indeed, annual publication of studies using LiDAR to interpret ecological phenomena increased 17-fold during the past decade, with over 180 new studies appearing in 2010 (ISI Web of Science search conducted on 23 Mar 2011: [{lidar AND ecol*} OR {lidar AND fores*} OR {lidar AND plant*}]).

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

Avakian, Harut; Pisano, Silvia

The Deep Inelastic Scattering (DIS) proved to be a great tool in testing of the theory of strong in- teractions. Semi-Inclusive DIS (SIDIS), with detection of an additional hadron allowed first stud- ies of 3D structure of the nucleon, moving the main focus from testing the QCD to understanding of strong interactions and quark gluon dynamics to address a number of puzzles accumulated in recent years. Detection of two hadrons in SIDIS, which is even more complicated, provides ac- cess to details of quark gluon interactions inaccessible in single-hadron SIDIS, providing a new avenue to study the complex nucleon structure.more » Large acceptance of the CLAS detector at Jef- ferson Lab, allowing detection of two hadrons, produced back-to-back (b2b) in the current and target fragmentation regions, provides a unique possibility to study the nucleon structure in target fragmentation region, and correlations of target and current fragmentation regions« less

Word structures of Granada Spanish-speaking preschoolers with typical versus protracted phonological development.

PubMed

Bernhardt, B May; Hanson, R; Perez, D; Ávila, C; Lleó, C; Stemberger, J P; Carballo, G; Mendoza, E; Fresneda, D; Chávez-Peón, M

2015-01-01

Research on children's word structure development is limited. Yet, phonological intervention aims to accelerate the acquisition of both speech-sounds and word structure, such as word length, stress or shapes in CV sequences. Until normative studies and meta-analyses provide in-depth information on this topic, smaller investigations can provide initial benchmarks for clinical purposes. To provide preliminary reference data for word structure development in a variety of Spanish with highly restricted coda use: Granada Spanish (similar to many Hispano-American varieties). To be clinically applicable, such data would need to show differences by age, developmental typicality and word structure complexity. Thus, older typically developing (TD) children were expected to show higher accuracy than younger children and those with protracted phonological development (PPD). Complex or phonologically marked forms (e.g. multisyllabic words, clusters) were expected to be late developing. Participants were 59 children aged 3-5 years in Granada, Spain: 30 TD children, and 29 with PPD and no additional language impairments. Single words were digitally recorded by a native Spanish speaker using a 103-word list and transcribed by native Spanish speakers, with confirmation by a second transcriber team and acoustic analysis. The program Phon 1.5 provided quantitative data. In accordance with expectations, the TD and older age groups had better-established word structures than the younger children and those with PPD. Complexity was also relevant: more structural mismatches occurred in multisyllabic words, initial unstressed syllables and clusters. Heterosyllabic consonant sequences were more accurate than syllable-initial sequences. The most common structural mismatch pattern overall was consonant deletion, with syllable deletion most common in 3-year-olds and children with PPD. The current study provides preliminary reference data for word structure development in a Spanish variety with restricted coda use, both by age and types of word structures. Between ages 3 and 5 years, global measures (whole word match, word shape match) distinguished children with typical versus protracted phonological development. By age 4, children with typical development showed near-mastery of word structures, whereas 4- and 5-year-olds with PPD continued to show syllable deletion and cluster reduction, especially in multisyllabic words. The results underline the relevance of multisyllabic words and words with clusters in Spanish phonological assessment and the utility of word structure data for identification of protracted phonological development. © 2014 Royal College of Speech and Language Therapists.

Discrete shaped strain sensors for intelligent structures

NASA Technical Reports Server (NTRS)

Andersson, Mark S.; Crawley, Edward F.

1992-01-01

Design of discrete, highly distributed sensor systems for intelligent structures has been studied. Data obtained indicate that discrete strain-averaging sensors satisfy the functional requirements for distributed sensing of intelligent structures. Bartlett and Gauss-Hanning sensors, in particular, provide good wavenumber characteristics while meeting the functional requirements. They are characterized by good rolloff rates and positive Fourier transforms for all wavenumbers. For the numerical integration schemes, Simpson's rule is considered to be very simple to implement and consistently provides accurate results for five sensors or more. It is shown that a sensor system that satisfies the functional requirements can be applied to a structure that supports mode shapes with purely sinusoidal curvature.

Structural interpretation of P2X receptor mutagenesis studies on drug action

PubMed Central

Evans, Richard J

2010-01-01

P2X receptors for ATP are ligand gated cation channels that form from the trimeric assembly of subunits with two transmembrane segments, a large extracellular ligand binding loop, and intracellular amino and carboxy termini. The receptors are expressed throughout the body, involved in functions ranging from blood clotting to inflammation, and may provide important targets for novel therapeutics. Mutagenesis based studies have been used to develop an understanding of the molecular basis of their pharmacology with the aim of developing models of the ligand binding site. A crystal structure for the zebra fish P2X4 receptor in the closed agonist unbound state has been published recently, which provides a major advance in our understanding of the receptors. This review gives an overview of mutagenesis studies that have led to the development of a model of the ATP binding site, as well as identifying residues contributing to allosteric regulation and antagonism. These studies are discussed with reference to the crystal to provide a structural interpretation of the molecular basis of drug action. PMID:20977449

Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae)

USDA-ARS?s Scientific Manuscript database

Analyses of genetic structure and phylogenetic relationships illuminate the origin and domestication of modern crops. Despite being an important world-wide vegetable, the genetic structure and domestication of carrot (Daucus carota L.) is poorly understood. We provide the first such study using a la...

Structural Truss Elements and Forces

ERIC Educational Resources Information Center

Troyer, Steve; Griffis, Kurt; Shackelford, Ray

2005-01-01

In the field of construction, most structures are supported by several groups of truss systems working together synergistically. A "truss" is a group of centered and balanced elements combined to carry a common load (Warner, 2003). Trusses provide strength against loads and forces within a structure. Though a complex field of study, structural…

Structural sizing of a solar powered aircraft

NASA Technical Reports Server (NTRS)

Hall, D. W.; Hall, S. A.

1984-01-01

The development of sizing algorithms for very lightweight aircraft structure was studied. Three types of bracing schemes were analyzed and fully cantilevered strut bracing and wire bracing and scaling rules were determined. It is found that wire bracing provides the lightest wing structure for solar high altitude powered platforms.

Employing a Structured Interface to Advance Primary Students' Communicative Competence in a Text-Based Computer Mediated Environment

ERIC Educational Resources Information Center

Chiu, Chiung-Hui; Wu, Chiu-Yi; Hsieh, Sheng-Jieh; Cheng, Hsiao-Wei; Huang, Chung-Kai

2013-01-01

This study investigated whether a structured communication interface fosters primary students' communicative competence in a synchronous typewritten computer-mediated collaborative learning environment. The structured interface provided a set of predetermined utterance patterns for elementary students to use or imitate to develop communicative…

Factors Affecting Teenager Cyber Delinquency

ERIC Educational Resources Information Center

Joo, Young Ju; Lim, Kyu Yon; Cho, Sun Yoo; Jung, Bo Kyung; Choi, Se Bin

2013-01-01

The study aims to investigate structural relationships among teenagers' peer attachment, self-control, academic stress, internet usage time, and cyber delinquency. The data source was the Korea Youth Panel Survey, and the responses from 920 teenagers in the 12th grade provided the study data. Structural equation modeling was used for the analysis.…

A Review of International Telecommunications Industry Issues, Structure, and Regulatory Problems.

ERIC Educational Resources Information Center

Cole, Jack E.; And Others

Industry structure studies prior to 1968 are briefly reviewed, and an overview of industrial and technological developments up to the present is provided through synopses of more recent studies. Areas covered include overseas telephone and record carriers; the creation of the Communications Satellite Corporation; the current regulatory and…

Sexual Minority Women's Satisfaction with Health Care Providers and State-level Structural Support: Investigating the Impact of Lesbian, Gay, Bisexual, and Transgender Nondiscrimination Legislation.

PubMed

Baldwin, Aleta M; Dodge, Brian; Schick, Vanessa; Sanders, Stephanie A; Fortenberry, J Dennis

Structural discrimination is associated with negative health outcomes among sexual minority populations. Recent changes to state-level and national legislation provide both the opportunity and the need to further explore the impact of legislation on the health indicators of sexual minorities. Using an ecosocial theory lens, the present research addresses the relationship between structural support or discrimination and satisfaction with one's health care provider among sexual minority women. Data were drawn from an online survey of sexual minority women's health care experiences. Using the Andersen Behavioral Model of Health Services Utilization to operationalize the variables in our model, we examined the relationship between state-level nondiscrimination legislation and satisfaction with provider-a widely used measure of health care quality-through regression analysis. Participants in structurally supportive states (i.e., those with nondiscrimination legislation) were more likely to disclose their sexual identity to their providers and to report higher satisfaction with their providers. The absence of nondiscrimination legislation was associated negatively with satisfaction with providers. Results of our study show that the external environment in which sexual minority women seek health care, characterized by structural support or lack thereof, is related to perceived quality of health care. Copyright © 2017 Jacobs Institute of Women's Health. Published by Elsevier Inc. All rights reserved.

A Study in Difference: Structures and Cultures in Australian Registered Training Organisations. Full Report

ERIC Educational Resources Information Center

Clayton, Berwyn; Fisher, Thea; Harris, Roger; Bateman, Andrea; Brown, Mike

2008-01-01

This report presents the findings of a study examining organisational culture and structure in ten Australian registered training organisations (RTOs) and is part of a program of research examining the factors which affect and help build the capability of vocational education and training (VET) providers. The study sought to determine: (1) how…

Research on energy stock market associated network structure based on financial indicators

NASA Astrophysics Data System (ADS)

Xi, Xian; An, Haizhong

2018-01-01

A financial market is a complex system consisting of many interacting units. In general, due to the various types of information exchange within the industry, there is a relationship between the stocks that can reveal their clear structural characteristics. Complex network methods are powerful tools for studying the internal structure and function of the stock market, which allows us to better understand the stock market. Applying complex network methodology, a stock associated network model based on financial indicators is created. Accordingly, we set threshold value and use modularity to detect the community network, and we analyze the network structure and community cluster characteristics of different threshold situations. The study finds that the threshold value of 0.7 is the abrupt change point of the network. At the same time, as the threshold value increases, the independence of the community strengthens. This study provides a method of researching stock market based on the financial indicators, exploring the structural similarity of financial indicators of stocks. Also, it provides guidance for investment and corporate financial management.

Structural basis of substrate specificity in the serine proteases.

PubMed Central

Perona, J. J.; Craik, C. S.

1995-01-01

Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in addressing biological function and in establishing a basis for targeted design efforts. Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent to which binding subsites are interdependent, and the roles of polypeptide chain flexibility and distal structural elements in contributing to specificity profiles. The studies also provide a foundation for exploring why specificity modification can be either straightforward or complex, depending on the particular system. PMID:7795518

A systematic review on popularity, application and characteristics of protein secondary structure prediction tools.

PubMed

Kashani-Amin, Elaheh; Tabatabaei-Malazy, Ozra; Sakhteman, Amirhossein; Larijani, Bagher; Ebrahim-Habibi, Azadeh

2018-02-27

Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple secondary structure prediction (SSP) options is challenging. The current study is an insight onto currently favored methods and tools, within various contexts. A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of 209 studies were finally found eligible to extract data. Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating a SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. This study provides a comprehensive insight about the recent usage of SSP tools which could be helpful for selecting a proper tool's choice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Is Structural Subtyping Useful? An Empirical Study

DTIC Science & Technology

2009-12-01

Mellon University Pittsburgh, PA 15213 Abstract Structural subtyping is popular in research languages , but all mainstream object-oriented languages use...nominal subtyping. Since languages with structural subtyping are not in widespread use, the empiri- cal questions of whether and how structural...will provide guidance for language designers who are considering use of this subtyping discipline. Report Documentation Page Form ApprovedOMB No

An overview of STRUCTURE: applications, parameter settings, and supporting software

PubMed Central

Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.

2013-01-01

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071

In vivo study of the effectiveness of quantitative percussion diagnostics as an indicator of the level of the structural pathology of teeth.

PubMed

Sheets, Cherilyn G; Wu, Jean C; Rashad, Samer; Phelan, Michael; Earthman, James C

2016-08-01

Conventional dental diagnostic aids based upon imagery and patient symptoms are at best only partially effective for the detection of fine structural defects such as cracks in teeth. The purpose of this clinical study was to determine whether quantitative percussion diagnostics (QPD) provided knowledge of the structural instability of teeth before restorative work begins. QPD is a mechanics-based methodology that tests the structural integrity of teeth noninvasively. Eight human participants with 60 sites needing restoration were enrolled in an institutional review board-approved clinical study. Comprehensive examinations were performed in each human participant, including QPD testing. Each site was disassembled and microscopically video documented, and the results were recorded on a defect assessment sheet. Each restored site was then tested using QPD. The normal fit error (NFE), which corresponds to the localized defect severity, was correlated with any pretreatment structural pathology. QPD agreed with clinical disassembly in 55 of 60 comparisons (92% agreement). Moreover, the method achieved 98% specificity and 100% sensitivity for detecting structural pathologies found later upon clinical disassembly. Overall, the NFE was found to be highly predictive of advanced structural pathology. The data from the present in vivo study support the hypothesis that QPD can provide the clinician with advance knowledge of the structural instability of teeth before restorative work begins. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Immediate use of prosody and context in predicting a syntactic structure.

PubMed

Nakamura, Chie; Arai, Manabu; Mazuka, Reiko

2012-11-01

Numerous studies have reported an effect of prosodic information on parsing but whether prosody can impact even the initial parsing decision is still not evident. In a visual world eye-tracking experiment, we investigated the influence of contrastive intonation and visual context on processing temporarily ambiguous relative clause sentences in Japanese. Our results showed that listeners used the prosodic cue to make a structural prediction before hearing disambiguating information. Importantly, the effect was limited to cases where the visual scene provided an appropriate context for the prosodic cue, thus eliminating the explanation that listeners have simply associated marked prosodic information with a less frequent structure. Furthermore, the influence of the prosodic information was also evident following disambiguating information, in a way that reflected the initial analysis. The current study demonstrates that prosody, when provided with an appropriate context, influences the initial syntactic analysis and also the subsequent cost at disambiguating information. The results also provide first evidence for pre-head structural prediction driven by prosodic and contextual information with a head-final construction. Copyright © 2012 Elsevier B.V. All rights reserved.

Economic impact of converting an interventional pain medicine physician office-based practice into a provider-based ambulatory pain practice.

PubMed

Grider, Jay S; Findley, Kelley A; Higdon, Courtney; Curtright, Jonathan; Clark, Don P

2014-01-01

One consequence of the shifting economic health care landscape is the growing trend of physician employment and practice acquisition by hospitals. These acquired practices are often converted into hospital- or provider-based clinics. This designation brings the increased services of the hospital, the accreditation of the hospital, and a new billing structure verses the private clinic (the combination of the facility and professional fee billing). One potential concern with moving to a provider-based designation is that this new structure might make the practice less competitive in a marketplace that may still be dominated by private physician office-based practices. The aim of the current study was to evaluate the impact of the provider-based/hospital fee structure on clinical volume. Determine the effect of transition to a hospital- or provider-based practice setting (with concomitant cost implications) on patient volume in the current practice milieu.   Community hospital-based academic interventional pain medicine practice. Economic analysis of effect of change in price structure on clinical volumes. The current study evaluates the effect of a change in designation with price implications on the demand for clinical services that accompany the transition to a hospital-based practice setting from a physician office setting in an academic community hospital. Clinical volumes of both procedures and clinic volumes increased in a mature practice setting following transition to a provider-based designation and the accompanying facility and professional fee structure. Following transition to a provider-based designation clinic visits were increased 24% while procedural volume demand did not change. Single practice entity and single geographic location in southeastern United States. The conversion to a hospital- or provider-based setting does not negatively impact clinical volume and referrals to community-based pain medicine practice. These results imply that factors other than price are a driver of patient choice.  

Expanding the clinical role of community pharmacy: A qualitative ethnographic study of medication reviews in Ontario, Canada.

PubMed

Patton, Sarah J; Miller, Fiona A; Abrahamyan, Lusine; Rac, Valeria E

2018-03-01

Medication reviews by community pharmacists are an increasingly common strategy to improve medication management for chronic conditions, and are part of wider efforts to make more effective use of community-based health professionals. To identify opportunities to optimize the medication review program in Ontario, Canada, we explored how providers and clients interpret and operationalize medication reviews within everyday community pharmacy practice. We conducted a qualitative ethnographic study at four pharmacies in Ontario, Canada, including non-participant observation of provider and client activities and interactions with specific attention to medication reviews, as well as brief ethnographic interviews with providers and clients, and in-depth, semi-structured interviews with providers. We report on 72h of field research, observation of 178 routine pharmacist-client interactions and 29 medication reviews, 62 brief ethnographic interviews with providers and clients, and 7 in-depth, semi-structured interviews with providers. We found that medication reviews were variably conducted across the dimensions of duration, provider type, location, and interaction style, and that local contexts and system-wide developments influence their meaning and practice. Medication reviews are exemplary of policy efforts to enhance the role of community pharmacies within health systems and the scope of practice of pharmacists as healthcare professionals. Our study highlights the importance of the local structure of community pharmacy practice and the clinical aspirations of pharmacists in the delivery of medication reviews. Copyright © 2017 Elsevier B.V. All rights reserved.

Load Diffusion in Composite and Smart Structures

NASA Technical Reports Server (NTRS)

Horgan, C. O.

2003-01-01

The research carried out here builds on our previous NASA supported research on the general topic of edge effects and load diffusion in composite structures. Further fundamental solid mechanics studies were carried out to provide a basis for assessing the complicated modeling necessary for the multi-functional large scale structures used by NASA. An understanding of the fundamental mechanisms of load diffusion in composite subcomponents is essential in developing primary composite structures. Some specific problems recently considered were those of end effects in smart materials and structures, study of the stress response of pressurized linear piezoelectric cylinders for both static and steady rotating configurations, an analysis of the effect of pre-stressing and pre-polarization on the decay of end effects in piezoelectric solids and investigation of constitutive models for hardening rubber-like materials. Our goal in the study of load diffusion is the development of readily applicable results for the decay lengths in terms of non-dimensional material and geometric parameters. Analytical models of load diffusion behavior are extremely valuable in building an intuitive base for developing refined modeling strategies and assessing results from finite element analyses. The decay behavior of stresses and other field quantities provides a significant aid towards this process. The analysis is also amenable to parameter study with a large parameter space and should be useful in structural tailoring studies. Special purpose analytical models of load diffusion behavior are extremely valuable in building an intuitive base for developing refined modeling strategies and in assessing results from general purpose finite element analyses. For example, a rational basis is needed in choosing where to use three-dimensional to two-dimensional transition finite elements in analyzing stiffened plates and shells. The decay behavior of stresses and other field quantities furnished by this research provides a significant aid towards this element transition issue. A priori knowledge of the extent of boundary-layers induced by edge effects is also useful in determination of the instrumentation location in structural verification tests or in material characterization tests.

Comparison of Canadian and Swiss Surgical Training Curricula: Moving on Toward Competency-Based Surgical Education.

PubMed

Hoffmann, Henry; Oertli, Daniel; Mechera, Robert; Dell-Kuster, Salome; Rosenthal, Rachel; Reznick, Richard; MacDonald, Hugh

Quality of surgical training in the era of resident duty-hour restrictions (RDHR) is part of an ongoing debate. Most training elements are provided during surgical service. As exposure to surgical procedures is important but time-consuming, RDHR may affect quality of surgical training. Providing structured training elements may help to compensate for this shortcoming. This binational anonymous questionnaire-based study evaluates frequency, time, and structure of surgical training programs at 2 typical academic teaching hospitals with different RDHR. Departments of Surgery of University of Basel (Basel, Switzerland) and the Queen's University (Kingston, Ontario, Canada). Surgical consultants and residents of the Queen's University Hospital (Kingston, Ontario, Canada) and the University Hospital Basel (Basel, Switzerland) were eligible for this study. Questionnaire response rate was 37% (105/284). Queen's residents work 80 hours per week, receiving 7 hours of formal training (8.8% of workweek). Basel residents work 60 hours per week, including 1 hour of formal training (1.7% of working time). Queen's faculty and residents rated their program as "structured" or "rather structured" in contrast to Basel faculty and residents who rated their programs as "neutral" in structure or "unstructured." Respondents identified specific structured training elements more frequently at Queen's than in Basel. Two-thirds of residents responded that they seek out additional surgical experiences through voluntary extra work. Basel participants articulated a stronger need for improvement of current surgical training. Although Basel residents and consultants in both institutions fear negative influence of RDHR on the training program, this was not the case in Queen's residents. Providing more structured surgical training elements may be advantageous in providing optimal-quality surgical education in an era of work-hour restrictions. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Nanowire modified carbon fibers for enhanced electrical energy storage

NASA Astrophysics Data System (ADS)

Shuvo, Mohammad Arif Ishtiaque; (Bill) Tseng, Tzu-Liang; Ashiqur Rahaman Khan, Md.; Karim, Hasanul; Morton, Philip; Delfin, Diego; Lin, Yirong

2013-09-01

The study of electrochemical super-capacitors has become one of the most attractive topics in both academia and industry as energy storage devices because of their high power density, long life cycles, and high charge/discharge efficiency. Recently, there has been increasing interest in the development of multifunctional structural energy storage devices such as structural super-capacitors for applications in aerospace, automobiles, and portable electronics. These multifunctional structural super-capacitors provide structures combining energy storage and load bearing functionalities, leading to material systems with reduced volume and/or weight. Due to their superior materials properties, carbon fiber composites have been widely used in structural applications for aerospace and automotive industries. Besides, carbon fiber has good electrical conductivity which will provide lower equivalent series resistance; therefore, it can be an excellent candidate for structural energy storage applications. Hence, this paper is focused on performing a pilot study for using nanowire/carbon fiber hybrids as building materials for structural energy storage materials; aiming at enhancing the charge/discharge rate and energy density. This hybrid material combines the high specific surface area of carbon fiber and pseudo-capacitive effect of metal oxide nanowires, which were grown hydrothermally in an aligned fashion on carbon fibers. The aligned nanowire array could provide a higher specific surface area that leads to high electrode-electrolyte contact area thus fast ion diffusion rates. Scanning Electron Microscopy and X-Ray Diffraction measurements are used for the initial characterization of this nanowire/carbon fiber hybrid material system. Electrochemical testing is performed using a potentio-galvanostat. The results show that gold sputtered nanowire carbon fiber hybrid provides 65.9% higher energy density than bare carbon fiber cloth as super-capacitor.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

The impact of structural biology in medicine illustrated with four case studies.

PubMed

Hu, Tiancen; Sprague, Elizabeth R; Fodor, Michelle; Stams, Travis; Clark, Kirk L; Cowan-Jacob, Sandra W

2018-01-01

The contributions of structural biology to drug discovery have expanded over the last 20 years from structure-based ligand optimization to a broad range of clinically relevant topics including the understanding of disease, target discovery, screening for new types of ligands, discovery of new modes of action, addressing clinical challenges such as side effects or resistance, and providing data to support drug registration. This expansion of scope is due to breakthroughs in the technology, which allow structural information to be obtained rapidly and for more complex molecular systems, but also due to the combination of different technologies such as X-ray, NMR, and other biophysical methods, which allows one to get a more complete molecular understanding of disease and ways to treat it. In this review, we provide examples of the types of impact molecular structure information can have in the clinic for both low molecular weight and biologic drug discovery and describe several case studies from our own work to illustrate some of these contributions.

Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.

Multidrug efflux pumps: the structures of prokaryotic ATP-binding cassette transporter efflux pumps and implications for our understanding of eukaryotic P-glycoproteins and homologues.

PubMed

Kerr, Ian D; Jones, Peter M; George, Anthony M

2010-02-01

One of the Holy Grails of ATP-binding cassette transporter research is a structural understanding of drug binding and transport in a eukaryotic multidrug resistance pump. These transporters are front-line mediators of drug resistance in cancers and represent an important therapeutic target in future chemotherapy. Although there has been intensive biochemical research into the human multidrug pumps, their 3D structure at atomic resolution remains unknown. The recent determination of the structure of a mouse P-glycoprotein at subatomic resolution is complemented by structures for a number of prokaryotic homologues. These structures have provided advances into our knowledge of the ATP-binding cassette exporter structure and mechanism, and have provided the template data for a number of homology modelling studies designed to reconcile biochemical data on these clinically important proteins.

Self-organization in suspensions of end-functionalized semiflexible polymers under shear flow

NASA Astrophysics Data System (ADS)

Myung, Jin Suk; Winkler, Roland G.; Gompper, Gerhard

2015-12-01

The nonequilibrium dynamical behavior and structure formation of end-functionalized semiflexible polymer suspensions under flow are investigated by mesoscale hydrodynamic simulations. The hybrid simulation approach combines the multiparticle collision dynamics method for the fluid, which accounts for hydrodynamic interactions, with molecular dynamics simulations for the semiflexible polymers. In equilibrium, various kinds of scaffold-like network structures are observed, depending on polymer flexibility and end-attraction strength. We investigate the flow behavior of the polymer networks under shear and analyze their nonequilibrium structural and rheological properties. The scaffold structure breaks up and densified aggregates are formed at low shear rates, while the structural integrity is completely lost at high shear rates. We provide a detailed analysis of the shear- rate-dependent flow-induced structures. The studies provide a deeper understanding of the formation and deformation of network structures in complex materials.

Study on the conformation changes of Lysozyme induced by Hypocrellin A: The mechanism investigation

NASA Astrophysics Data System (ADS)

Ma, Fei; Huang, He-Yong; Zhou, Lin; Yang, Chao; Zhou, Jia-Hong; Liu, Zheng-Ming

2012-11-01

The interactions between Lysozyme and Hypocrellin A are investigated in details using time-resolved fluorescence, fourier transform infrared spectroscopy (FTIR), circular dichroism spectroscopy (CD), three-dimensional fluorescence spectra, and thermal gravimetric analysis (TGA) techniques. The results of time-resolved fluorescence suggest that the quenching mechanism is static quenching. FTIR and CD spectroscopy provide evidences of the reducing of α-helix after interaction. Hypocrellin A could change the micro-environmental of Lysozyme according to hydrophobic interaction between the aromatic ring and the hydrophobic amino acid residues, and the altered polypeptide backbone structures induce the reduction of α-helical structures. Moreover, TGA study further demonstrates the structure changes of Lysozyme on the effect of Hypocrellin A. This study could provide some important information for the derivatives of HA in pharmacy, pharmacology and biochemistry.

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants.

PubMed

Yang, Xiaofei; Yang, Minglei; Deng, Hongjing; Ding, Yiliang

2018-01-01

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective

PubMed Central

Gupta, Sneha; Biswas, Arijit; Akhter, Mohammad Suhail; Krettler, Christoph; Reinhart, Christoph; Dodt, Johannes; Reuter, Andreas; Philippou, Helen; Ivaskevicius, Vytautas; Oldenburg, Johannes

2016-01-01

The activation and regulation of coagulation Factor XIII (FXIII) protein has been the subject of active research for the past three decades. Although discrete evidence exists on various aspects of FXIII activation and regulation a combinatorial structure/functional view in this regard is lacking. In this study, we present results of a structure/function study of the functional chain of events for FXIII. Our study shows how subtle chronological submolecular changes within calcium binding sites can bring about the detailed transformation of the zymogenic FXIII to its activated form especially in the context of FXIIIA and FXIIIB subunit interactions. We demonstrate what aspects of FXIII are important for the stabilization (first calcium binding site) of its zymogenic form and the possible modes of deactivation (thrombin mediated secondary cleavage) of the activated form. Our study for the first time provides a structural outlook of the FXIIIA2B2 heterotetramer assembly, its association and dissociation. The FXIIIB subunits regulatory role in the overall process has also been elaborated upon. In summary, this study provides detailed structural insight into the mechanisms of FXIII activation and regulation that can be used as a template for the development of future highly specific therapeutic inhibitors targeting FXIII in pathological conditions like thrombosis. PMID:27453290

Word Structures of Granada Spanish-Speaking Preschoolers with Typical versus Protracted Phonological Development

ERIC Educational Resources Information Center

May Bernhardt, B.; Hanson, R.; Perez, D.; Ávila, C.; Lleó, C.; Stemberger, J. P.; Carballo, G.; Mendoza, E.; Fresneda, D.; Chávez-Peón, M.

2015-01-01

Background: Research on children's word structure development is limited. Yet, phonological intervention aims to accelerate the acquisition of both speech-sounds and word structure, such as word length, stress or shapes in CV sequences. Until normative studies and meta-analyses provide in-depth information on this topic, smaller investigations can…

Opportunity Structure for Gambling and Problem Gambling among Employees in the Transport Industry

ERIC Educational Resources Information Center

Revheim, Tevje; Buvik, Kristin

2009-01-01

Working conditions for employees in the transport sector might present an opportunity structure for gambling by providing access to gambling during the workday. This study investigates connections between opportunity structure, gambling during the workday, and gambling problems among employees in the transport sector. Data has been collected from…

Structuralism.

ERIC Educational Resources Information Center

Piaget, Jean

Provided is an overview of the analytical method known as structuralism. The first chapter discusses the three key components of the concept of a structure: the view of a system as a whole instead of so many parts; the study of the transformations in the system; and the fact that these transformations never lead beyond the system but always…

Predictors of Global Quality in Family Child Care Homes: Structural and Belief Characteristics

ERIC Educational Resources Information Center

Hughes-Belding, Kere; Hegland, Susan; Stein, Amanda; Sideris, John; Bryant, Donna

2012-01-01

Research Findings: With a substantial number of young children receiving care in family child care settings, an examination of the characteristics, both structural and attitudinal, that predict program quality is warranted. The current study examines gaps in the research by examining both structural characteristics and provider beliefs that…

Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.

PubMed

da Fonseca, Néli José; Lima Afonso, Marcelo Querino; Pedersolli, Natan Gonçalves; de Oliveira, Lucas Carrijo; Andrade, Dhiego Souto; Bleicher, Lucas

2017-10-28

Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental Tensile Strength Analysis of Woven-Glass/Epoxy Composite Plates with Central Circular Hole

NASA Astrophysics Data System (ADS)

Hadi, Bambang K.; Rofa, Bima K.

2018-04-01

The use of composite materials in aerospace engineering, as well as in maritime structure has increased significantly during the recent years. The extensive use of composite materials in industrial applications should make composite structural engineers and scientists more aware of the advantage and disadvantage of this material and provide them with necessary data and certification process. One of the problems in composite structures is the existence of hole. Hole can not be avoided in actual structures, since it may be the necessity of providing access for maintenance or due to impact damage. The presence of hole will weaken the structures. Therefore, in this paper, the effect of hole on the strength of glass-woven/epoxy composite will be discussed. Extensive tests have been carried out to study the effect of hole-diameter on the tensile strengths of these specimens. The results showed that the bigger the hole-diameter compared to the width of the specimens has weakened the structures further, as expected. Further study should be carried in the future to model it with the finite element and theoretical analysis precisely.

Evaluation of variability in high-resolution protein structures by global distance scoring.

PubMed

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

Organizational Learning from Cross-Cultural Experiences: An Ethnomethodological Case Study Examining the Relative Importance of Social Structure and Cultural Values during Dynamic Interaction

ERIC Educational Resources Information Center

Waldecker, Gary T.

2011-01-01

This study explored how social structure and cultural values dynamically interact in collective learning between two religious organizations cooperating in a joint project. It further explored the enablers of and impediments to collective learning in this context. The study employed the theoretical framework provided by the Organizational Learning…

Elucidation of the structure of retroviral proteases: a reminiscence.

PubMed

Jaskolski, Mariusz; Miller, Maria; Mohana Rao, J K; Gustchina, Alla; Wlodawer, Alexander

2015-11-01

Determinations of only a very few protein structures had consequences comparable to the impact exerted by the structure of the protease encoded by HIV-1, published just over 25 years ago. The structure of this relatively small protein and its cousins from other retroviruses provided a clear target for a spectacularly successful structure-assisted drug design effort that offered new hope for controlling the then-escalating AIDS epidemic. This reminiscence is limited primarily to work conducted at the National Cancer Institute, and is not meant to be a comprehensive history of the field, but is rather an attempt to provide a very personal account of how the structures of this most thoroughly studied crystallographic target were determined. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

System Transformation under the California Mental Health Services Act: Implementation of Full Service Partnerships in Los Angeles County

PubMed Central

Starks, Sarah L.; Arns, Paul G.; Padwa, Howard; Friedman, Jack R.; Marrow, Jocelyn; Meldrum, Marcia L.; Bromley, Elizabeth; Kelly, Erin Lee; Brekke, John; Braslow, Joel T.

2018-01-01

Objective The objective is to evaluate the effect of California’s Mental Health Services Act on the structure, volume, location, and patient-centeredness of Los Angeles County public mental health services. Methods This prospective mixed-methods study (2006-2013) is based in 5 Los Angeles County public mental health clinics, all with usual care and 3 with Full Service Partnerships (FSP): new MHSA-funded programs designed to “do whatever it takes” to provide intensive, recovery-oriented, team-based, integrated services for clients with severe mental illness. Study participants include treatment providers (42 FSP, 130 usual care) and clients (174 FSP, 298 usual care). FSPs were compared to usual care on outpatient services received (claims data) and organizational climate, recovery orientation, and provider-client working alliance (surveys; semi-structured interviews), with regression adjustment for client and provider characteristics. Results FSP clients received significantly more (5,238 vs. 1,643 minutes, p<.001), and more-frequently field-based (22% vs. 2%, p<.001), outpatient services than usual care clients in the first year post-admission. FSP clients reported more recovery-oriented services (RSA-R 3.8 vs. 3.5, p<.001) and better provider-client working alliance (WAI-S 3.8 vs. 3.6, p=.01). FSP providers reported more stress (55.0 vs. 51.3, p<.001) and lower morale (48.1 vs. 49.6, p<.001). Conclusions Los Angeles County’s public mental health system was able to transform service delivery in response to well-funded policy mandates. For providers, a structure emphasizing accountability and patient-centeredness was associated with greater stress, despite smaller caseloads. For clients, service structure and volume created opportunities to build stronger provider-client relationships and address client needs and goals. PMID:28142386

Working and Providing Care: Increasing Student Engagement for Part-Time Community College Students

ERIC Educational Resources Information Center

Leingang, Daniel James

2017-01-01

The purpose of this study was to examine the relationship among external time obligations of work and care giving by part-time students, their participation within structured group learning experiences, and student engagement. The Structured Group Learning Experiences (SGLEs) explored within this study include community college programming…

Do Clinical Clerks Provide Candidates with Adequate Formative Assessment during Objective Structured Clinical Examinations?

ERIC Educational Resources Information Center

Reiter, Harold I.; Rosenfeld, Jack; Nandagopal, Kiruthiga; Eva, Kevin W.

2004-01-01

Context: Various research studies have examined the question of whether expert or non-expert raters, faculty or students, evaluators or standardized patients, give more reliable and valid summative assessments of performance on Objective Structured Clinical Examinations (OSCEs). Less studied has been the question of whether or not non-faculty…

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution.

PubMed Central

Wang, L; Ruffner, D E

1997-01-01

The hammerhead domain is one of the smallest known ribozymes. Like other ribozymes it catalyzes site-specific cleavage of a phosphodiester bond. The hammerhead ribozyme has been the subject of a vast number of biochemical and structural studies aimed at determining the structure and mechanism of cleavage. Recently crystallographic analysis has produced a structure for the hammerhead. As the hammerhead is capable of undergoing cleavage within the crystal, it would appear that the crystal structure is representative of the catalytically active solution structure. However, the crystal structure conflicts with much of the biochemical data and reveals a catalytic metal ion binding site expected to be of very low affinity. Clearly, additional studies are needed to reconcile the discrepancies and provide a clear understanding of the structure and mechanism of the hammerhead ribozyme. Here we demonstrate that a unique crosslink can be induced in the hammerhead with 2-thiocytidine or 4-thiouridine substitution at different locations within the conserved core. Generation of the same crosslink with different modifications at different positions suggests that the structure trapped by the crosslink may be relevant to the catalytically active solution structure of the hammerhead ribozyme. As this crosslink appears to be incompatible with the crystal structure, this provides yet another indication that the active solution and crystal structures may differ significantly. PMID:9336468

STUDIES OF METABOLITE-PROTEIN INTERACTIONS: A REVIEW

PubMed Central

Matsuda, Ryan; Bi, Cong; Anguizola, Jeanethe; Sobansky, Matthew; Rodriquez, Elliot; Badilla, John Vargas; Zheng, Xiwei; Hage, Benjamin; Hage, David S.

2014-01-01

The study of metabolomics can provide valuable information about biochemical pathways and processes at the molecular level. There have been many reports that have examined the structure, identity and concentrations of metabolites in biological systems. However, the binding of metabolites with proteins is also of growing interest. This review examines past reports that have looked at the binding of various types of metabolites with proteins. An overview of the techniques that have been used to characterize and study metabolite-protein binding is first provided. This is followed by examples of studies that have investigated the binding of hormones, fatty acids, drugs or other xenobiotics, and their metabolites with transport proteins and receptors. These examples include reports that have considered the structure of the resulting solute-protein complexes, the nature of the binding sites, the strength of these interactions, the variations in these interactions with solute structure, and the kinetics of these reactions. The possible effects of metabolic diseases on these processes, including the impact of alterations in the structure and function of proteins, are also considered. PMID:24321277

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Structural concepts for very large (400-meter-diameter) solar concentrators

NASA Technical Reports Server (NTRS)

Mikulas, Martin M., Jr.; Hedgepeth, John M.

1989-01-01

A general discussion of various types of large space structures is presented. A brief overview of the history of space structures is presented to provide insight into the current state-of-the art. Finally, the results of a structural study to assess the viability of very large solar concentrators are presented. These results include weight, stiffness, part count, and in-space construction time.

Deformation and Failure of Protein Materials in Physiologically Extreme Conditions and Disease

DTIC Science & Technology

2009-03-01

resonance (NMR) spectroscopy and X- ray crystallography have advanced our ability to identify 3D protein structures57. Site-specific studies using NMR, a... ray crystallography, providing structural and temporal information about mechanisms of deformation and assembly (for example in intermediate...tens of thousands of 3D atomistic protein structures, identifying the structure of numerous proteins from varying species sources60. X- ray

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Structural Image Analysis of the Brain in Neuropsychology Using Magnetic Resonance Imaging (MRI) Techniques.

PubMed

Bigler, Erin D

2015-09-01

Magnetic resonance imaging (MRI) of the brain provides exceptional image quality for visualization and neuroanatomical classification of brain structure. A variety of image analysis techniques provide both qualitative as well as quantitative methods to relate brain structure with neuropsychological outcome and are reviewed herein. Of particular importance are more automated methods that permit analysis of a broad spectrum of anatomical measures including volume, thickness and shape. The challenge for neuropsychology is which metric to use, for which disorder and the timing of when image analysis methods are applied to assess brain structure and pathology. A basic overview is provided as to the anatomical and pathoanatomical relations of different MRI sequences in assessing normal and abnormal findings. Some interpretive guidelines are offered including factors related to similarity and symmetry of typical brain development along with size-normalcy features of brain anatomy related to function. The review concludes with a detailed example of various quantitative techniques applied to analyzing brain structure for neuropsychological outcome studies in traumatic brain injury.

An example of requirements for Advanced Subsonic Civil Transport (ASCT) flight control system using structured techniques

NASA Technical Reports Server (NTRS)

Mclees, Robert E.; Cohen, Gerald C.

1991-01-01

The requirements are presented for an Advanced Subsonic Civil Transport (ASCT) flight control system generated using structured techniques. The requirements definition starts from initially performing a mission analysis to identify the high level control system requirements and functions necessary to satisfy the mission flight. The result of the study is an example set of control system requirements partially represented using a derivative of Yourdon's structured techniques. Also provided is a research focus for studying structured design methodologies and in particular design-for-validation philosophies.

Studying Intermolecular Forces with a Dual Gas Chromatography and Boiling Point Investigation

ERIC Educational Resources Information Center

Cunningham, William Patrick; Xia, Ian; Wickline, Kaitlyn; Huitron, Eric Ivan Garcia; Heo, Jun

2018-01-01

A procedure for the study of structural differences and intermolecular attraction between ethanol and 1-butanol based in laboratory work is described. This study provides comparisons of data retrieved from both a determination of boiling point and gas chromatography traces for the mixture. The methodology reported here should provide instructors…

On the continuum mechanics approach for the analysis of single walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Chaudhry, M. S.; Czekanski, A.

2016-04-01

Today carbon nanotubes have found various applications in structural, thermal and almost every field of engineering. Carbon nanotubes provide great strength, stiffness resilience properties. Evaluating the structural behavior of nanoscale materials is an important task. In order to understand the materialistic behavior of nanotubes, atomistic models provide a basis for continuum mechanics modelling. Although the properties of bulk materials are consistent with the size and depends mainly on the material but the properties when we are in Nano-range, continuously change with the size. Such models start from the modelling of interatomic interaction. Modelling and simulation has advantage of cost saving when compared with the experiments. So in this project our aim is to use a continuum mechanics model of carbon nanotubes from atomistic perspective and analyses some structural behaviors of nanotubes. It is generally recognized that mechanical properties of nanotubes are dependent upon their structural details. The properties of nanotubes vary with the varying with the interatomic distance, angular orientation, radius of the tube and many such parameters. Based on such models one can analyses the variation of young's modulus, strength, deformation behavior, vibration behavior and thermal behavior. In this study some of the structural behaviors of the nanotubes are analyzed with the help of continuum mechanics models. Using the properties derived from the molecular mechanics model a Finite Element Analysis of carbon nanotubes is performed and results are verified. This study provides the insight on continuum mechanics modelling of nanotubes and hence the scope to study the effect of various parameters on some structural behavior of nanotubes.

Weight and structural analysis of four structural concepts for a land mobile satellite system

NASA Technical Reports Server (NTRS)

Ferebee, M. J.; Wright, R. L.; Farmer, J. T.

1982-01-01

The present study is concerned with a Land Mobile Satellite System (LMSS) which can provide mobile communications for commercial and government applications in nonmetropolitan areas of the continental U.S. and Canada as an augmentation to existing and planned terrestrial systems. The satellite system would provide 'narrow band' telecommunications services, thin-route fixed telephone and data services in the 806-890 MHz band, and continuous emergency beacon monitoring in the 406-406.1 MHz band. It is pointed out that a satellite system operating in concert with terrestrial cellular systems could provide truly ubiquitous mobile communications services in the U.S. and Canada. A single shuttle shuttle launch could place the LMSS spacecraft in geosynchronous orbit over the continental U.S. in 1995 with a 10-year lifetime. Attention is given to the structural concepts, a weight analysis, and a structural analysis.

Together and Alone a Study of Interactions between Toddlers and Childcare Providers during Mealtime in Norwegian Childcare Centres

ERIC Educational Resources Information Center

Klette, Trine; Drugli, May Britt; Aandahl, Ann Mari

2018-01-01

The study investigated the quality of interactions between childcare providers and toddlers during a lunch in childcare centres. Meals in childcare centres are semi-structured adult-led situations where the children not only eat, but are also provided with opportunities for implicit learning and interactions. Participants were 13 toddlers aged…

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

PubMed

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-04

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Strategies to curb structural changes of lithium/transition metal oxide cathode materials & the changes' effects on thermal & cycling stability

DOE PAGES

Yu, Xiqian; Hu, Enyuan; Bak, Seongmin; ...

2015-12-07

Structural transformation behaviors of several typical oxide cathode materials during a heating process are reviewed in detail to provide in-depth understanding of the key factors governing the thermal stability of these materials. Furthermore, we also discuss applying the information about heat induced structural evolution in the study of electrochemically induced structural changes. All these discussions are expected to provide valuable insights for designing oxide cathode materials with significantly improved structural stability for safe, long-life lithium ion batteries, as the safety of lithium-ion batteries is a critical issue. As a result, it is widely accepted that the thermal instability of themore » cathodes is one of the most critical factors in thermal runaway and related safety problems.« less

A near term space demonstration program for large structures

NASA Technical Reports Server (NTRS)

Nathan, C. A.

1978-01-01

For applications involving an employment of ultralarge structures in space, it would be necessary to have some form of space fabrication and assembly in connection with launch vehicle payload and volume limitations. The findings of a recently completed NASA sponsored study related to an orbital construction demonstration are reported. It is shown how a relatively small construction facility which is assembled in three shuttle flights can substantially advance space construction know-how and provide the nation with a permanent shuttle tended facility that can further advance large structures technologies and provide a construction capability for deployment of large structural systems envisioned for the late 1980s. The large structures applications identified are related to communications, navigation, earth observation, energy systems, radio astronomy, illumination, space colonization, and space construction.

Structural studies of G protein-coupled receptors.

PubMed

Lu, Mengjie; Wu, Beili

2016-11-01

G protein-coupled receptors (GPCRs) comprise the largest membrane protein family. These receptors sense a variety of signaling molecules, activate multiple intracellular signal pathways, and act as the targets of over 40% of marketed drugs. Recent progress on GPCR structural studies provides invaluable insights into the structure-function relationship of the GPCR superfamily, deepening our understanding about the molecular mechanisms of GPCR signal transduction. Here, we review recent breakthroughs on GPCR structure determination and the structural features of GPCRs, and take the structures of chemokine receptor CCR5 and purinergic receptors P2Y 1 R and P2Y 12 R as examples to discuss the importance of GPCR structures on functional studies and drug discovery. In addition, we discuss the prospect of GPCR structure-based drug discovery. © 2016 IUBMB Life, 68(11):894-903, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism

PubMed Central

Fernandes, Carlos A. H.; Pazin, Wallance M.; Dreyer, Thiago R.; Bicev, Renata N.; Cavalcante, Walter L. G.; Fortes-Dias, Consuelo L.; Ito, Amando S.; Oliveira, Cristiano L. P.; Fernandez, Roberto Morato; Fontes, Marcos R. M.

2017-01-01

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation. PMID:28256632

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism.

PubMed

Fernandes, Carlos A H; Pazin, Wallance M; Dreyer, Thiago R; Bicev, Renata N; Cavalcante, Walter L G; Fortes-Dias, Consuelo L; Ito, Amando S; Oliveira, Cristiano L P; Fernandez, Roberto Morato; Fontes, Marcos R M

2017-03-03

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A 2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation.

Assessing the drivers shaping global patterns of urban vegetation landscape structure.

PubMed

Dobbs, C; Nitschke, C; Kendal, D

2017-08-15

Vegetation is one of the main resources involve in ecosystem functioning and providing ecosystem services in urban areas. Little is known on the landscape structure patterns of vegetation existing in urban areas at the global scale and the drivers of these patterns. We studied the landscape structure of one hundred cities around the globe, and their relation to demography (population), socioeconomic factors (GDP, Gini Index), climate factors (temperature and rain) and topographic characteristics (altitude, variation in altitude). The data revealed that the best descriptors of landscape structure were amount, fragmentation and spatial distribution of vegetation. Populated cities tend to have less, more fragmented, less connected vegetation with a centre of the city with low vegetation cover. Results also provided insights on the influence of socioeconomics at a global scale, as landscape structure was more fragmented in areas that are economically unequal and coming from emergent economies. This study shows the effects of the social system and climate on urban landscape patterns that gives useful insights for the distribution in the provision of ecosystem services in urban areas and therefore the maintenance of human well-being. This information can support local and global policy and planning which is committing our cities to provide accessible and inclusive green space for all urban inhabitants. Copyright © 2017 Elsevier B.V. All rights reserved.

A feasibility study on embedded micro-electromechanical sensors and systems (MEMS) for monitoring highway structures.

DOT National Transportation Integrated Search

2011-06-01

Micro-electromechanical systems (MEMS) provide vast improvements over existing sensing methods in the context of structural health monitoring (SHM) of highway infrastructure systems, including improved system reliability, improved longevity and enhan...

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Evolution of magnetism of Cr nanoclusters on a Au(111) surface

NASA Astrophysics Data System (ADS)

Gotsis, Harry; Kioussis, Nicholas; Papaconstantopoulos, Dimitri

2004-03-01

Advances in low-temperature scanning tunneling microscopy under ultrahigh vacuum have provided new opportunities for investigating the magnetic structures of nanoclusters adsorbed on surfaces. Recent STM studies of Cr trimers on the Au(111) surface suggest a switching between two distinct electronic states. We have carried out ab initio electronic structure calculations to investigate the structural, electronic and magnetic properties of isolated Cr atoms, Cr dimers and trimers in different geometry. We will present results for the evolution of magnetic behavior including noncollinear magnetism and provide insight in the connection between magnetism and geometry.

The prescription opioid epidemic: a review of qualitative studies on the progression from initial use to abuse

PubMed Central

Cicero, Theodore J.; Ellis, Matthew S.

2017-01-01

Most research designed to answer the “why” of the prescription opioid epidemic has relied on structured interviews, which rigidly attempt to capture the complex reasons people use opioids. In contrast this systematic literature review focuses on peer-reviewed studies that have used a qualitative approach to examine the development of an opioid-use disorder from the point of initial exposure. Rather than simply providing a “high,” opioids reportedly relieve psychological/emotional problems or provide an escape from life stressors. As use continues, avoidance of withdrawal sickness becomes an overriding concern, with all other benefits playing minor roles in persistent use. These studies indicate that terms used in structured interviews, such as “nontherapeutic use” or variations thereof, poorly capture the complex range of needs opioids satisfy. Both quantitative/structured studies and more qualitative ones, as well as more focused studies, have an important role in better informing prevention and treatment efforts. PMID:29302223

Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering.

PubMed

Garces, Andrea P; Watowich, Stanley J

2013-10-01

West Nile virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection can cause severe neurological disease and fatality in humans. Efforts are ongoing to develop antiviral drugs that inhibit the WNV protease, a viral enzyme required for polyprotein processing. Unfortunately, little is known about the solution structure of recombinant WNV protease (NS2B-NS3pro) used for antiviral drug discovery and development, although X-ray crystal structures and nuclear magnetic resonance (NMR) studies have provided valuable insights into the interactions between NS2B-NS3pro and peptide-based inhibitors. We completed small-angle X-ray scattering and Fourier transform infrared spectroscopy experiments to determine the solution structure and dynamics of WNV NS2B-NS3pro in the absence of a bound substrate or inhibitor. Importantly, these solution studies suggested that all or most of the NS2B cofactor was highly flexible and formed an ensemble of structures, in contrast to the NS2B tertiary structures observed in crystallographic and NMR studies. The secondary structure of NS2B-NS3pro in solution had high β-content, similar to the secondary structure observed in crystallographic studies. This work provided evidence of the intrinsic flexibility and conformational heterogeneity of the NS2B chain of the WNV protease in the absence of substratelike ligands, which should be considered during antiviral drug discovery and development efforts.

Three-dimensional fluid-structure interaction case study on cubical fluid cavity with flexible bottom

NASA Astrophysics Data System (ADS)

Ghelardi, Stefano; Rizzo, Cesare; Villa, Diego

2017-12-01

In this paper, we report our study on a numerical fluid-structure interaction problem originally presented by Mok et al. (2001) in two dimensions and later studied in three dimensions by Valdés Vazquez (2007), Lombardi (2012), and Trimarchi (2012). We focus on a 3D test case in which we evaluated the sensitivity of several input parameters on the fluid and structural results. In particular, this analysis provides a starting point from which we can look deeper into specific aspects of these simulations and analyze more realistic cases, e.g., in sails design. In this study, using the commercial software ADINA™, we addressed a well-known unsteadiness problem comprising a square box representing the fluid domain with a flexible bottom modeled with structural shell elements. We compared data from previously published work whose authors used the same numerical approach, i.e., a partitioned approach coupling a finite volume solver (for the fluid domain) and a finite element solver (for the solid domain). Specifically, we established several benchmarks and made comparisons with respect to fluid and solid meshes, structural element types, and structural damping, as well as solution algorithms. Moreover, we compared our method with a monolithic finite element solution method. Our comparisons of new and old results provide an outline of best practices for such simulations.

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Contribution to the study of the vasculature of submandibular and sublingual glands and lymph nodes of rats by corrosion cast technique combined with scanning electron microscopy.

PubMed

Rossi-Schneider, Tíssiana Rachel; Verli, Flaviana Dornela; Yurgel, Liliane Soares; De Souza, Maria Antonieta Lopes; Cherubini, Karen

2008-10-01

The study of anatomical structures in their normal state allows the identification of pathological changes that can occur in them. Angiogenesis and the vasculature have been widely studied, mainly because of their association with the development of neoplasms. One of the methods applied for such purposes is the corrosion cast technique, which provides a copy of the vessels with normal as well as pathological structures. The replica of the vasculature provided by this technique allows the three-dimensional analysis of vessels by means of scanning electron microscopy. The aim of the present study was to demonstrate, by means of corrosion casts, the angioarchitecture of the submandibular and sublingual glands and lymph nodes. Scanning electron microscopy showed that the three structures have distinct vascular patterns. The corrosion cast technique can be employed in the study of the angioarchitecture of the submandibular and sublingual glands and lymph nodes, but requires specific precautions. The removal of the structures en bloc and the handling of the replicas with the aid of a stereoscopic magnifier reduce the risk of fractures. (c) 2008 Wiley-Liss, Inc.

Ferrocenylaniline based amide analogs of methoxybenzoic acids: Synthesis, structural characterization and butyrylcholinesterase (BChE) inhibition studies

NASA Astrophysics Data System (ADS)

Altaf, Ataf Ali; Kausar, Samia; Hamayun, Muhammad; Lal, Bhajan; Tahir, Muhammad Nawaz; Badshah, Amin

2017-10-01

Three new ferrocene based amides were synthesized with slight structural difference. The general formula of the amides is C5H5FeC5H4C6H4NHCOC6H4(OCH3). The synthesized compounds were characterized by instrumental techniques like elemental analysis, FTIR and NMR spectroscopy. Structure of the two compounds was also studied by single crystal X-rays diffraction analysis. Structural studies provide the evidence that pMeO (one of the synthesized compounds) is an example of amides having no intermolecular hydrogen bonding in solid structure. In the BChE inhibition assay, compound (oMeO) having strong intermolecular force in the solid structure is less active than the compound (pMeO) with weak intermolecular forces in the solid structure. The docking studies proved that hydrogen bonding between inhibitor and BChE enzyme is of more importance for the activity, rather than intermolecular hydrogen bonding in the solid structure of inhibitor.

Structural interpretation of P2X receptor mutagenesis studies on drug action.

PubMed

Evans, Richard J

2010-11-01

P2X receptors for ATP are ligand gated cation channels that form from the trimeric assembly of subunits with two transmembrane segments, a large extracellular ligand binding loop, and intracellular amino and carboxy termini. The receptors are expressed throughout the body, involved in functions ranging from blood clotting to inflammation, and may provide important targets for novel therapeutics. Mutagenesis based studies have been used to develop an understanding of the molecular basis of their pharmacology with the aim of developing models of the ligand binding site. A crystal structure for the zebra fish P2X4 receptor in the closed agonist unbound state has been published recently, which provides a major advance in our understanding of the receptors. This review gives an overview of mutagenesis studies that have led to the development of a model of the ATP binding site, as well as identifying residues contributing to allosteric regulation and antagonism. These studies are discussed with reference to the crystal to provide a structural interpretation of the molecular basis of drug action. © 2010 The Author. British Journal of Pharmacology © 2010 The British Pharmacological Society.

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.

PubMed

Chattopadhyay, Debasish; Swingle, Mark R; Salter, Edward A; Wood, Eric; D'Arcy, Brandon; Zivanov, Catherine; Abney, Kevin; Musiyenko, Alla; Rusin, Scott F; Kettenbach, Arminja; Yet, Larry; Schroeder, Chad E; Golden, Jennifer E; Dunham, Wade H; Gingras, Anne-Claude; Banerjee, Surajit; Forbes, David; Wierzbicki, Andrzej; Honkanen, Richard E

2016-06-01

Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases. Copyright © 2016 Elsevier Inc. All rights reserved.

Revising the Child and Adolescent Perfectionism Scale: A Test of the Four-Factor Structure in a Chinese Sample

ERIC Educational Resources Information Center

Yang, Hongfei; Hong, Chaoqin; Tao, Xiaodan; Zhu, Lingyi

2015-01-01

This study examined the structure, reliability, and validity of the revised Chinese version of the Child and Adolescent Perfectionism Scale (N = 933). The results confirmed the four-factor structure of the Chinese version of the Child and Adolescent Perfectionism Scale. Implications, limitations, and suggestions for future research are provided.

Using a Semantic Diagram to Structure a Collaborative Problem Solving Process in the Classroom

ERIC Educational Resources Information Center

Cai, Huiying; Lin, Lin; Gu, Xiaoqing

2016-01-01

This study provides an in-depth look into the implementation process of visualization-based tools for structuring collaborative problem solving (CPS) in the classroom. A visualization-based learning platform--the semantic diagram for structuring CPS in a real classroom was designed and implemented. Metafora, the preliminary vehicle of the semantic…

Leisure activities are linked to mental health benefits by providing time structure: comparing employed, unemployed and homemakers

PubMed Central

Goodman, William K; Geiger, Ashley M; Wolf, Jutta M

2017-01-01

Background Unemployment has consistently been linked to negative mental health outcomes, emphasising the need to characterise the underlying mechanisms. The current study aimed at testing whether compared with other employment groups, fewer leisure activities observed in unemployment may contribute to elevated risk for negative mental health via loss of time structure. Methods Depressive symptoms (Center for Epidemiologic Studies Depression), leisure activities (exercise, self-focused, social), and time structure (Time Structure Questionnaire (TSQ)) were assessed cross-sectionally in 406 participants (unemployed=155, employed=140, homemakers=111) recruited through Amazon Mechanical Turk. Results Controlling for gender and age, structural equation modelling revealed time structure partially (employed, homemakers) and fully (unemployed) mediated the relationship between leisure activities and depressive symptoms. With the exception of differential effects for structured routines, all other TSQ factors (sense of purpose, present orientation, effective organisation and persistence) contributed significantly to all models. Conclusions These findings support the idea that especially for the unemployed, leisure activities impose their mental health benefits through increasing individuals’ perception of spending their time effectively. Social leisure activities that provide a sense of daily structure may thereby be a particularly promising low-cost intervention to improve mental health in this population. PMID:27298424

Enabling School Structures, Collegial Trust and Academic Emphasis: Antecedents of professional learning communities

ERIC Educational Resources Information Center

Gray, Julie; Kruse, Sharon; Tarter, C. John

2016-01-01

This study tested the role of enabling school structures, collegial trust and academic emphasis in the development of professional learning communities (PLCs) in a low-income school district. The empirical study was based upon the perceptions of teachers and principals as provided by survey responses (N = 67 schools). While enabling school…

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Nonlinear Polarimetric Microscopy for Biomedical Imaging

NASA Astrophysics Data System (ADS)

Samim, Masood

A framework for the nonlinear optical polarimetry and polarimetric microscopy is developed. Mathematical equations are derived in terms of linear and nonlinear Stokes Mueller formalism, which comprehensively characterize the polarization properties of the incoming and outgoing radiations, and provide structural information about the organization of the investigated materials. The algebraic formalism developed in this thesis simplifies many predictions for a nonlinear polarimetry study and provides an intuitive understanding of various polarization properties for radiations and the intervening medium. For polarimetric microscopy experiments, a custom fast-scanning differential polarization microscope is developed, which is also capable of real-time three-dimensional imaging. The setup is equipped with a pair of high-speed resonant and galvanometric scanning mirrors, and supplemented by advanced adaptive optics and data acquisition modules. The scanning mirrors when combined with the adaptive optics deformable mirror enable fast 3D imaging. Deformable membrane mirrors and genetic algorithm optimization routines are employed to improve the imaging conditions including correcting the optical aberrations, maximizing signal intensities, and minimizing point-spread-functions of the focal volume. A field-programmable-gate array (FPGA) chip is exploited to rapidly acquire and process the multidimensional data. Using the nonlinear optical polarimetry framework and the home-built polarization microscope, a few biologically important tissues are measured and analyzed to gain insight as to their structure and dynamics. The structure and distribution of muscle sarcomere myosins, connective tissue collagen, carbohydrate-rich starch, and fruit fly eye retinal molecules are characterized with revealing polarization studies. In each case, using the theoretical framework, polarization sensitive data are analyzed to decipher the molecular orientations and nonlinear optical susceptibilities. The developed nonlinear optical polarimetric microscopy is applicable to a wide variety of structural studies on ordered materials, and provides a non-invasive possibility to study the structural organization and dynamics within biological samples. For example, the technique is well suited for studies of a muscle contraction, histopathology of collagen structure for cancer tissue diagnostics, investigations of the polysacharide structural organization within a starch granule of a plant, or developmental study of the retina in an eye, among other applications.

Method and apparatus for evaluating structural weakness in polymer matrix composites

DOEpatents

Wachter, E.A.; Fisher, W.G.

1996-01-09

A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image. 6 figs.

Method and apparatus for evaluating structural weakness in polymer matrix composites

DOEpatents

Wachter, Eric A.; Fisher, Walter G.

1996-01-01

A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image.

Characterization of Physical Structure from Measurements of Sound Velocity in Aqueous Solutions of Various Saccharides and Alditols.

NASA Astrophysics Data System (ADS)

Smith, David Eugene

Little basic research has been reported on the physical structure of aqueous solutions of saccharides. Sound velocimeters can be used to study physical structure of solutions, non-destructively. The La Place relationship was used to calculate adiabatic compressibility values for solutions from experimentally determined values for sound velocity and density. Using a sound velocimeter, aqueous solutions of twelve alditols and saccharides were studied at various concentrations and temperatures. Data indicated that over most of the temperature range employed (20 to 70 C) adiabatic compressibility of the solutions was the dominant factor in defining sound velocity through and structural rigidity of solution. As concentration of solute increased, more rigid structures were formed in solution, which caused sound velocity values to increase with increasing concentrations of solute; maximum sound velocity values were obtained at progressively lower temperatures. Analysis of data for sound velocity, density and adiabatic compressibility of various solutions provided partial insight into effects of each solute molecule on structure of solutions. A furanose form in a monosaccharide contributed to a more rigid structure than did a pyranose ring when below 30C. At higher temperatures the pyranose ring provided more rigidity than did the furanose ring. Hydroxyl groups in the equatorial position generally contributed more to rigidity of structure than did OH groups in axial positions. Disaccharides contributed differences from the inherent monosaccharides. A (beta) glycosidic linkage provided more structural rigidity of solution than did a linkage. Among the alditols, mannitol and sorbitol contributed very similar characteristics to solutions. Xylitol, in solution provided less rigidity, density and sound velocity than did mannitol-sorbitol in proportion to the lower molecular weight or xylitol. From the data for velocity of sound through single sugar solutions values for solutions of mixtures of these sugars at concentrations to 0.9m could be calculated with accuracy. Each sugar contributed independently to structure of solution and sound velocity values. At solute concentrations greater than 0.9m, there appeared to be some interaction among mixed solute molecules in solution.

Language Switching in the Production of Phrases

ERIC Educational Resources Information Center

Tarlowski, Andrzej; Wodniecka, Zofia; Marzecova, Anna

2013-01-01

The language switching task has provided a useful insight into how bilinguals produce language. So far, however, the studies using this method have been limited to lexical access. The present study provides empirical evidence on language switching in the production of simple grammar structures. In the reported experiment, Polish-English unbalanced…

Exploring Organizational Characteristics Associated with Practice Changes Following a Mentored Online Educational Module

ERIC Educational Resources Information Center

Rappolt, Susan; Pearce, Kristine; McEwen, Sara; Polatajko, Helene J.

2005-01-01

Introduction: Studies of health professionals' perceptions of barriers to and facilitators of research utilization in clinical practices suggest that structural and resource characteristics of service provider organizations are key determinants of the capacity of individual practitioners to provide evidence-based practices. In this pilot study, we…

Assessment of groundwater potentiality using geophysical techniques in Wadi Allaqi basin, Eastern Desert, Egypt - Case study

NASA Astrophysics Data System (ADS)

Helaly, Ahmad Sobhy

2017-12-01

Electrical resistivity surveying has been carried out for the determination of the thickness and resistivity of layered media in Wadi Allaqi, Eastern Desert, Egypt. That is widely used geophysical tool for the purpose of assessing the groundwater potential and siting the best locations for boreholes in the unconfined Nubian Sandstone aquifers within the study area. This has been done using thirteen 1D Vertical Electrical Sounding (VES) surveys. 1D-VES surveys provide only layered model structures for the subsurface and do not provide comprehensive information for interpreting the structure and extent of subsurface hydro-geological features. The integration of two-dimensional (2D) geophysical techniques for groundwater prospecting has been done to provide a more detailed identification for the subsurface hydro-geological features from which potential sites for successful borehole locations are recognized. In addition, five magnetic profiles were measured for basement depth determination, expected geological structures and thickness of sedimentary succession that could include some basins suitable for groundwater accumulation as groundwater aquifers.

Soil-structure interaction studies for understanding the behavior of integral abutment bridges.

DOT National Transportation Integrated Search

2012-03-01

Integral Abutment Bridges (IAB) are bridges without any joints within the bridge deck or between the : superstructure and the abutments. An IAB provides many advantages during construction and maintenance of : a bridge. Soil-structure interactions at...

A structure-based kinetic model of transcription.

PubMed

Zuo, Yuhong; Steitz, Thomas A

2017-01-01

During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement.

Does service integration improve technical quality of care in low-resource settings? An evaluation of a model integrating HIV care into family planning services in Kenya

PubMed Central

Mutemwa, Richard; Mayhew, Susannah H; Warren, Charlotte E; Abuya, Timothy; Ndwiga, Charity; Kivunaga, Jackline

2017-01-01

Abstract The aim of this study was to investigate association between HIV and family planning integration and technical quality of care. The study focused on technical quality of client–provider consultation sessions. The cross-sectional study observed 366 client–provider consultation sessions and interviewed 37 health care providers in 12 public health facilities in Kenya. Multilevel random intercept and linear regression models were fitted to the matched data to investigate relationships between service integration and technical quality of care as well as associations between facility-level structural and provider factors and technical quality of care. A sensitivity analysis was performed to test for hidden bias. After adjusting for facility-level structural factors, HIV/family planning integration was found to have significant positive effect on technical quality of the consultation session, with average treatment effect 0.44 (95% CI: 0.63–0.82). Three of the 12 structural factors were significantly positively associated with technical quality of consultation session including: availability of family planning commodities (9.64; 95% CI: 5.07–14.21), adequate infrastructure (5.29; 95% CI: 2.89–7.69) and reagents (1.48; 95% CI: 1.02–1.93). Three of the nine provider factors were significantly positively associated with technical quality of consultation session: appropriate provider clinical knowledge (3.14; 95% CI: 1.92–4.36), job satisfaction (2.02; 95% CI: 1.21–2.83) and supervision (1.01; 95% CI: 0.35–1.68), while workload (−0.88; 95% CI: −1.75 to − 0.01) was negatively associated. Technical quality of the client–provider consultation session was also determined by duration of the consultation and type of clinic visit and appeared to depend on whether the clinic visit occurred early or later in the week. Integration of HIV care into family planning services can improve the technical quality of client–provider consultation sessions as measured by both health facility structural and provider factors. PMID:29194543

Does service integration improve technical quality of care in low-resource settings? An evaluation of a model integrating HIV care into family planning services in Kenya.

PubMed

Mutemwa, Richard; Mayhew, Susannah H; Warren, Charlotte E; Abuya, Timothy; Ndwiga, Charity; Kivunaga, Jackline

2017-11-01

The aim of this study was to investigate association between HIV and family planning integration and technical quality of care. The study focused on technical quality of client-provider consultation sessions. The cross-sectional study observed 366 client-provider consultation sessions and interviewed 37 health care providers in 12 public health facilities in Kenya. Multilevel random intercept and linear regression models were fitted to the matched data to investigate relationships between service integration and technical quality of care as well as associations between facility-level structural and provider factors and technical quality of care. A sensitivity analysis was performed to test for hidden bias. After adjusting for facility-level structural factors, HIV/family planning integration was found to have significant positive effect on technical quality of the consultation session, with average treatment effect 0.44 (95% CI: 0.63-0.82). Three of the 12 structural factors were significantly positively associated with technical quality of consultation session including: availability of family planning commodities (9.64; 95% CI: 5.07-14.21), adequate infrastructure (5.29; 95% CI: 2.89-7.69) and reagents (1.48; 95% CI: 1.02-1.93). Three of the nine provider factors were significantly positively associated with technical quality of consultation session: appropriate provider clinical knowledge (3.14; 95% CI: 1.92-4.36), job satisfaction (2.02; 95% CI: 1.21-2.83) and supervision (1.01; 95% CI: 0.35-1.68), while workload (-0.88; 95% CI: -1.75 to - 0.01) was negatively associated. Technical quality of the client-provider consultation session was also determined by duration of the consultation and type of clinic visit and appeared to depend on whether the clinic visit occurred early or later in the week. Integration of HIV care into family planning services can improve the technical quality of client-provider consultation sessions as measured by both health facility structural and provider factors. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Computational investigation of the human SOD1 mutant, Cys146Arg, that directs familial amyotrophic lateral sclerosis.

PubMed

Srinivasan, E; Rajasekaran, R

2017-07-25

The genetic substitution mutation of Cys146Arg in the SOD1 protein is predominantly found in the Japanese population suffering from familial amyotrophic lateral sclerosis (FALS). A complete study of the biophysical aspects of this particular missense mutation through conformational analysis and producing free energy landscapes could provide an insight into the pathogenic mechanism of ALS disease. In this study, we utilized general molecular dynamics simulations along with computational predictions to assess the structural characterization of the protein as well as the conformational preferences of monomeric wild type and mutant SOD1. Our static analysis, accomplished through multiple programs, predicted the deleterious and destabilizing effect of mutant SOD1. Subsequently, comparative molecular dynamic studies performed on the wild type and mutant SOD1 indicated a loss in the protein conformational stability and flexibility. We observed the mutational consequences not only in local but also in long-range variations in the structural properties of the SOD1 protein. Long-range intramolecular protein interactions decrease upon mutation, resulting in less compact structures in the mutant protein rather than in the wild type, suggesting that the mutant structures are less stable than the wild type SOD1. We also presented the free energy landscape to study the collective motion of protein conformations through principal component analysis for the wild type and mutant SOD1. Overall, the study assisted in revealing the cause of the structural destabilization and protein misfolding via structural characterization, secondary structure composition and free energy landscapes. Hence, the computational framework in our study provides a valuable direction for the search for the cure against fatal FALS.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

Anatomical relations of anterior and posterior ankle arthroscopy portals: a cadaveric study.

PubMed

Oliva, Xavier Martin; Méndez López, José Manuel; Monzo Planella, Mariano; Bravo, Alex; Rodrigues-Pinto, Ricardo

2015-04-01

Ankle arthroscopy is an increasingly used technique. Knowledge of the anatomical structures in relation to its portals is paramount to avoid complications. Twenty cadaveric ankles were analysed to assess the distance between relevant neurovascular structures to the anteromedial, anterolateral, posteromedial, and posterolateral arthroscopy portals. The intermediate dorsal branch of the superficial peroneal nerve was the closest structure to any of the portals (4.8 mm from the anterolateral portal), followed by the posterior tibial nerve (7.3 mm from the posteromedial portal). All structures analysed but one (posterior tibial artery) were, at least in one specimen, <5 mm distant from one of the portals. This study provides information on the anatomical relations of ankle arthroscopy portals and relevant neurovascular structures, confirming previous studies identifying the superficial peroneal nerve as the structure at highest risk of injury, but also highlighting some important variations. Techniques to minimise the injury to these structures are discussed.

Computer-Aided Structural Engineering (CASE) Project: State of the Art on Expert Systems Applications in Design, Construction and Maintenance of Structures

DTIC Science & Technology

1989-09-01

OGT, F1EPQRTJTL4, W" - 3^ n"r-- n *ON EXPERT SYSTEMS IN DESIGN, CONSTRUCTION AND’, IWAJNTENANCE-OF STRUCTURES Arockiasamy, Sunghoon Lee Clepartrhent...based expert system applications in the areas of structural design, design standards, and construction planning. This study will aid in the development...of a comprehensive expert system for tvical hydraulic structures. Funding for this report was provided by the US Army Engineer Waterways Experiment

Impact structures in Africa: A review

PubMed Central

Reimold, Wolf Uwe; Koeberl, Christian

2014-01-01

More than 50 years of space and planetary exploration and concomitant studies of terrestrial impact structures have demonstrated that impact cratering has been a fundamental process – an essential part of planetary evolution – ever since the beginning of accretion and has played a major role in planetary evolution throughout the solar system and beyond. This not only pertains to the development of the planets but to evolution of life as well. The terrestrial impact record represents only a small fraction of the bombardment history that Earth experienced throughout its evolution. While remote sensing investigations of planetary surfaces provide essential information about surface evolution and surface processes, they do not provide the information required for understanding the ultra-high strain rate, high-pressure, and high-temperature impact process. Thus, hands-on investigations of rocks from terrestrial impact craters, shock experimentation for pressure and temperature calibration of impact-related deformation of rocks and minerals, as well as parameter studies pertaining to the physics and chemistry of cratering and ejecta formation and emplacement, and laboratory studies of impact-generated lithologies are mandatory tools. These, together with numerical modeling analysis of impact physics, form the backbone of impact cratering studies. Here, we review the current status of knowledge about impact cratering – and provide a detailed account of the African impact record, which has been expanded vastly since a first overview was published in 1994. No less than 19 confirmed impact structures, and one shatter cone occurrence without related impact crater are now known from Africa. In addition, a number of impact glass, tektite and spherule layer occurrences are known. The 49 sites with proposed, but not yet confirmed, possible impact structures contain at least a considerable number of structures that, from available information, hold the promise to be able to expand the African impact record drastically – provided the political conditions for safe ground-truthing will become available. The fact that 28 structures have also been shown to date NOT to be of impact origin further underpins the strong interest in impact in Africa. We hope that this review stimulates the education of students about impact cratering and the fundamental importance of this process for Earth – both for its biological and geological evolution. This work may provide a reference volume for those workers who would like to search for impact craters and their ejecta in Africa. PMID:27065753

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

NASA Technical Reports Server (NTRS)

Alterovitz, Samuel A.; Sekula-Moise, Patricia A.; Sieg, Robert M.; Drotos, Mark N.; Bogner, Nancy A.

1992-01-01

An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

Motion estimation of subcellular structures from fluorescence microscopy images.

PubMed

Vallmitjana, A; Civera-Tregon, A; Hoenicka, J; Palau, F; Benitez, R

2017-07-01

We present an automatic image processing framework to study moving intracellular structures from live cell fluorescence microscopy. The system includes the identification of static and dynamic structures from time-lapse images using data clustering as well as the identification of the trajectory of moving objects with a probabilistic tracking algorithm. The method has been successfully applied to study mitochondrial movement in neurons. The approach provides excellent performance under different experimental conditions and is robust to common sources of noise including experimental, molecular and biological fluctuations.

Modal loss mechanism of micro-structured VCSELs studied using full vector FDTD method.

PubMed

Jo, Du-Ho; Vu, Ngoc Hai; Kim, Jin-Tae; Hwang, In-Kag

2011-09-12

Modal properties of vertical cavity surface-emitting lasers (VCSELs) with holey structures are studied using a finite difference time domain (FDTD) method. We investigate loss behavior with respect to the variation of structural parameters, and explain the loss mechanism of VCSELs. We also propose an effective method to estimate the modal loss based on mode profiles obtained using FDTD simulation. Our results could provide an important guideline for optimization of the microstructures of high-power single-mode VCSELs.

Numbers, systems, people: how interactions influence integration. Insights from case studies of HIV and reproductive health services delivery in Kenya

PubMed Central

Mayhew, Susannah H; Warren, Charlotte E; Collumbien, Martine; Ndwiga, Charity; Mutemwa, Richard; Lut, Irina; Colombini, Manuela; Vassall, Anna

2017-01-01

Abstract Drawing on rich data from the Integra evaluation of integrated HIV and reproductive-health services, we explored the interaction of systems hardware and software factors to explain why some facilities were able to implement and sustain integrated service delivery while others were not. This article draws on detailed mixed-methods data for four case-study facilities offering reproductive-health and HIV services between 2009 and 2013 in Kenya: (i) time-series client flow, tracking service uptake for 8841 clients; (ii) structured questionnaires with 24 providers; (iii) in-depth interviews with 17 providers; (iv) workload and facility data using a periodic activity review and cost-instruments; and (v) contextual data on external activities related to integration in study sites. Overall, our findings suggested that although structural factors like stock-outs, distribution of staffing and workload, rotation of staff can affect how integrated care is provided, all these factors can be influenced by staff themselves: both frontline and management. Facilities where staff displayed agency of decision making, worked as a team to share workload and had management that supported this, showed better integration delivery and staff were able to overcome some structural deficiencies to enable integrated care. Poor-performing facilities had good structural integration, but staff were unable to utilize this because they were poorly organized, unsupported or teams were dysfunctional. Conscientious objection and moralistic attitudes were also barriers. Integra has demonstrated that structural integration is not sufficient for integrated service delivery. Rather, our case studies show that in some cases excellent leadership and peer-teamwork enabled facilities to perform well despite resource shortages. The ability to provide support for staff to work flexibly to deliver integrated services and build resilient health systems to meet changing needs is particularly relevant as health systems face challenges of changing burdens of disease, climate change, epidemic outbreaks and more. PMID:29194544

Cross-Validation of the Implementation Leadership Scale (ILS) in Child Welfare Service Organizations.

PubMed

Finn, Natalie K; Torres, Elisa M; Ehrhart, Mark G; Roesch, Scott C; Aarons, Gregory A

2016-08-01

The Implementation Leadership Scale (ILS) is a brief, pragmatic, and efficient measure that can be used for research or organizational development to assess leader behaviors and actions that actively support effective implementation of evidence-based practices (EBPs). The ILS was originally validated with mental health clinicians. This study validates the ILS factor structure with providers in community-based organizations (CBOs) providing child welfare services. Participants were 214 service providers working in 12 CBOs that provide child welfare services. All participants completed the ILS, reporting on their immediate supervisor. Confirmatory factor analyses were conducted to examine the factor structure of the ILS. Internal consistency reliability and measurement invariance were also examined. Confirmatory factor analyses showed acceptable fit to the hypothesized first- and second-order factor structure. Internal consistency reliability was strong and there was partial measurement invariance for the first-order factor structure when comparing child welfare and mental health samples. The results support the use of the ILS to assess leadership for implementation of EBPs in child welfare organizations. © The Author(s) 2016.

Patient satisfaction constructs.

PubMed

Rahman, Muhammad Sabbir; Osmangani, Aahad M

2015-01-01

The purpose of this paper is to examine the five-factor structure of patients' satisfaction constructs toward private healthcare service providers. This research is a cross-sectional study. A questionnaire-based survey was conducted with previous and current Bangladeshi patients. Exploratory factor analysis was employed to extract the underlying constructs. Five underlying dimensions that play a significant role in structuring the satisfaction perceived by Bangladeshi private healthcare patients are identified in this study. Practical implications - The main contribution of this study is identifying the dimensions of satisfaction perceived by Bangladeshi patients regarding private healthcare service providers. Healthcare managers adopt the five identified underlying construct items in their business practices to improve their respective healthcare efficiency while ensuring overall customer satisfaction.

Comparison of information content of structured and narrative text data sources on the example of medication intensification.

PubMed

Turchin, Alexander; Shubina, Maria; Breydo, Eugene; Pendergrass, Merri L; Einbinder, Jonathan S

2009-01-01

OBJECTIVE To compare information obtained from narrative and structured electronic sources using anti-hypertensive medication intensification as an example clinical issue of interest. DESIGN A retrospective cohort study of 5,634 hypertensive patients with diabetes from 2000 to 2005. MEASUREMENTS The authors determined the fraction of medication intensification events documented in both narrative and structured data in the electronic medical record. The authors analyzed the relationship between provider characteristics and concordance between intensifications in narrative and structured data. As there is no gold standard data source for medication information, the authors clinically validated medication intensification information by assessing the relationship between documented medication intensification and the patients' blood pressure in univariate and multivariate models. RESULTS Overall, 5,627 (30.9%) of 18,185 medication intensification events were documented in both sources. For a medication intensification event documented in narrative notes the probability of a concordant entry in structured records increased by 11% for each study year (p < 0.0001) and decreased by 19% for each decade of provider age (p = 0.035). In a multivariate model that adjusted for patient demographics and intraphysician correlations, an increase of one medication intensification per month documented in either narrative or structured data were associated with a 5-8 mm Hg monthly decrease in systolic and 1.5-4 mm Hg decrease in diastolic blood pressure (p < 0.0001 for all). CONCLUSION Narrative and structured electronic data sources provide complementary information on anti-hypertensive medication intensification. Clinical validity of information in both sources was demonstrated by correlation with changes in blood pressure.

The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study.

PubMed

Gupta, Asmita; Bansal, Manju

2016-10-19

Mechanical unfolding studies on Ribonucleic Acid (RNA) structures are a subject of tremendous interest as they shed light on the principles of higher order assembly of these structures. Pseudoknotting is one of the most elementary ways in which this higher order assembly is achieved as discrete secondary structural units in RNA are brought in close proximity to form a tertiary structure. Using steered molecular dynamics (SMD) simulations, we have studied the unfolding of five RNA pseudoknot structures that differ from each other either by base substitutions in helices or loops. Our SMD simulations reveal the manner in which a biologically functional RNA pseudoknot unfolds and the effect of changes in the primary structure on this unfolding pathway, providing necessary insights into the driving forces behind the functioning of these structures. We observed that an A → C mutation in the loop sequence makes the pseudoknot far more resistant against force induced disruption relative to its wild type structure. In contrast to this, a base-pair substitution GC → AU near the pseudoknot junction region renders it more vulnerable to this disruption. The quantitative estimation of differences in the unfolding paths was carried out using force extension curves, potential of mean force profiles, and the opening of different Watson-Crick and non-Watson-Crick interactions. The results provide a quantified view in which the unfolding paths of the small RNA structures can be used for investigating the programmability of RNA chains for designing RNA switches and aptamers as their biological folding and unfolding could be assessed and manipulated.

Flexible and composite structures for premium pavements. Volume 1, Development of design procedure

DOT National Transportation Integrated Search

1980-11-01

This document provides results of a detailed study to identify flexible and composite structures which will perform as zero-maintenance pavements. To accomplish this, the report identifies the major distress types which have seriously limited the mai...

456th Brookhaven Lecture

ScienceCinema

Allen Orville

2017-12-09

Orville presents “Getting More From Less: Correlated Single-Crystal Spectroscopy and X-ray Crystallography at the NSLS” in which he discusses how researchers can use many different tools and techniques to study atomic structure and electronic structure to provide insights into chemistry.

Structural Analysis of Titan's Tholins by Ultra-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vuitton, V.; Frisari, M.; Thissen, R.; Dutuit, O.; Bonnet, J.-Y.; Quirico, E.; Sciamma O'Brien, E.; Szopa, C.; Carrasco, N.; Somogyi, A.; Smith, M.; Hörst, S. M.; Yelle, R.

2010-04-01

We propose here a systematic ultra-high resolution mass spectrometry and MS/MS study in order to provide a more coherent and complete characterization of the structure of the molecules making up the soluble fraction of the Titan tholins.

Radiosounding in the planned mission to Phobos

NASA Astrophysics Data System (ADS)

Zakharov, A. V.; Eismont, N. A.; Gotlib, V. M.; Smirnov, V. M.; Yushkova, O. V.; Marchuk, V. N.

2017-09-01

The opportunities to study Phobos' internal structure provided by radio methods are considered in this paper. The necessity of these studies is related to solution of the problem of the origin of the Martian moons. Radiosounding is one of the most efficient methods of analyzing the internal structure of small space objects and, in particular, that of Phobos. The new Boomerang project planned according to the Federal Space Program of Russia for 2016—2025 within the Expedition-M program aimed at the exploration of Phobos and delivery of soil samples from its surface to the Earth, as well as the specifics of a ballistic scenario of this expedition, provide a unique opportunity to carry out radioscopy of this space object to discover the internal structure Phobos and to solve the key problem of its origin. The model of Phobos' internal structure, radiosounding ballistic conditions, analysis of optimum frequency range of sounding, and key parameters of the device required for the experiment are considered in this paper. The significance of proposed studies and opportunities for their implementation are discussed.

Hybrid density functional study of structural, bonding, and electronic properties of the manganite series La1-xCaxMnO3 (x =0,1/4,1)

NASA Astrophysics Data System (ADS)

Korotana, R.; Mallia, G.; Gercsi, Z.; Liborio, L.; Harrison, N. M.

2014-05-01

Hybrid-exchange density functional theory calculations are carried out to determine the effects of A-site doping on the electronic and magnetic properties of the manganite series La1-xCaxMnO3. This study focuses on the ground state of an ordered Ca occupancy in a periodic structure. It is shown that the hybrid-exchange functional, Becke three-parameter Lee-Yang-Parr (B3LYP), provides an accurate and consistent description of the electronic structure for LaMnO3, CaMnO3, and La0.75Ca0.25MnO3. We have quantified the relevant structural, magnetic, and electronic energy contributions to the stability of the doped compound. An insight into the exchange coupling mechanism for the low hole density region of the phase diagram, where a polaron (anti-Jahn-Teller) forms, is also provided. This study completes a microscopic description of the lightly doped insulator with an antiferromagnetic-to-ferromagnetic and metal-to-insulator transition.

Dissociation and Alterations in Brain Function and Structure: Implications for Borderline Personality Disorder.

PubMed

Krause-Utz, Annegret; Frost, Rachel; Winter, Dorina; Elzinga, Bernet M

2017-01-01

Dissociation involves disruptions of usually integrated functions of consciousness, perception, memory, identity, and affect (e.g., depersonalization, derealization, numbing, amnesia, and analgesia). While the precise neurobiological underpinnings of dissociation remain elusive, neuroimaging studies in disorders, characterized by high dissociation (e.g., depersonalization/derealization disorder (DDD), dissociative identity disorder (DID), dissociative subtype of posttraumatic stress disorder (D-PTSD)), have provided valuable insight into brain alterations possibly underlying dissociation. Neuroimaging studies in borderline personality disorder (BPD), investigating links between altered brain function/structure and dissociation, are still relatively rare. In this article, we provide an overview of neurobiological models of dissociation, primarily based on research in DDD, DID, and D-PTSD. Based on this background, we review recent neuroimaging studies on associations between dissociation and altered brain function and structure in BPD. These studies are discussed in the context of earlier findings regarding methodological differences and limitations and concerning possible implications for future research and the clinical setting.

EXAMINING THE PREFERENCE FOR SHADE STRUCTURES IN FARMED GREEN SEA TURTLES (CHELONIA MYDAS) AND SHADE'S EFFECT ON GROWTH AND TEMPERATURES.

PubMed

Keller, Martha; Mustin, Walter

2017-03-01

The Cayman Turtle Farm raises thousands of green sea turtles ( Chelonia mydas ) annually under aquaculture conditions. Historically, the turtles have been raised in tanks without routine access to a shade structure. The purpose of this study was to determine the effects of adding a shade structure on curved carapace length (CCL) and weight gain of green sea turtles. In addition, water and cloacal temperatures were compared across treatment groups and shade cover preferences observed. Ninety turtles were split equally into three treatment groups for this 8-wk study. In the first group turtles were kept in tanks in full sun, the second group in half-shaded tanks, and the third group in tanks completely covered with shade cloth. Time-lapse cameras mounted above half-shaded tanks were used to determine turtle shade structure preferences throughout the day. There were no differences in CCL among treatment groups. Significant increases in weights were noted in turtles kept in full sun and half-shaded tanks versus the fully shaded tanks. Significantly higher water and cloacal turtle temperatures were noted in the full-sun tank compared with the half-shaded or completely shaded tanks. A significantly lower number of turtles was observed in the sun in the half-shaded tanks, indicating a possible preference by turtles for a shade structure. Results suggest that providing shade structures for sea turtles results in a significant decrease in both overall water temperature as well as a reduction in maximum high daily temperatures. Results also suggest that turtles exhibit a preference for shade structures when it is provided as an option. From these results, we recommend that a shade structure be provided when housing green sea turtles in outdoor enclosures.

Defense Infrastructure: DOD’s 2013 Facilities Corrosion Study Addressed Reporting Elements

DTIC Science & Technology

2014-03-27

the coating system to metal structures helped prevent corrosion and provided resistance to fire . For the second element, to review a sampling of...noted, was to apply an epoxy coating system to metal structures to prevent corrosion and provide fire resistance. In 2006, DOD applied an epoxy... heat exchange  Fuel distribution  Plumbing  Bridge  Fuel storage  Roof  Building exterior—paint  Generator  Signage  Compressor  Hot water

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE PAGES

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

PubMed

Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

2018-02-01

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

The Structural Changes of Tropical Cyclones Upon Interaction with Vertical Wind Shear

NASA Technical Reports Server (NTRS)

Ritchie, Elizabeth A.

2003-01-01

The Fourth Convection and Moisture Experiment (CAMEX-4) provided a unique opportunity to observe the distributions and document the roles of important atmospheric factors that impact the development of the core asymmetries and core structural changes of tropical cyclones embedded in vertical wind shear. The state-of-the-art instruments flown on the NASA DC-8 and ER-2, in addition to those on the NOAA aircraft, provided a unique set of observations that documented the core structure throughout the depth of the tropical cyclone. These data have been used to conduct a combined observational and modeling study using a state-of-the-art, high- resolution mesoscale model to examine the role of the environmental vertical wind shear in producing tropical cyclone core asymmetries, and the effects on the structure and intensity of tropical cyclones.The scientific objectives of this study were to obtain in situ measurements that would allow documentation of the physical mechanisms that influence the development of the asymmetric convection and its effect on the core structure of the tropical cyclone.

From Nano to Macro: Studying the Hierarchical Structure of the Corneal Extracellular Matrix

PubMed Central

Quantock, Andrew J.; Winkler, Moritz; Parfitt, Geraint J.; Young, Robert D.; Brown, Donald J.; Boote, Craig; Jester, James V.

2014-01-01

In this review, we discuss current methods for studying ocular extracellular matrix (ECM) assembly from the ‘nano’ to the ‘macro’ levels of hierarchical organization. Since collagen is the major structural protein in the eye, providing mechanical strength and controlling ocular shape, the methods presented focus on understanding the molecular assembly of collagen at the nanometer level using x-ray scattering through to the millimeter to centimeter level using nonlinear optical (NLO) imaging of second harmonic generated (SHG) signals. Three-dimensional analysis of ECM structure is also discussed, including electron tomography, serial block face scanning electron microscopy (SBF-SEM) and digital image reconstruction. Techniques to detect non-collagenous structural components of the ECM are also presented, and these include immunoelectron microscopy and staining with cationic dyes. Together, these various approaches are providing new insights into the structural blueprint of the ocular ECM, and in particular that of the cornea, which impacts upon our current understanding of the control of corneal shape, pathogenic mechanisms underlying ectatic disorders of the cornea and the potential for corneal tissue engineering. PMID:25819457

Non Covalent Interactions in Large Diamondoid Dimers in the Gas Phase - a Microwave Study

NASA Astrophysics Data System (ADS)

Perez, Cristobal; Sekutor, Marina; Fokin, Andrey A.; Blomeyer, Sebastian; Vishnevskiy, Yury V.; Mitzel, Norbert W.; Schreiner, Peter R.; Schnell, Melanie

2017-06-01

Accurate structure determination of large molecules still represents an ambitious challenge. Interesting benchmark systems for structure determination are large diamondoid dimers, whose structures are governed by strong intramolecular interactions. Recently, diamondoid dimers with unusually long central C-C bonds (up to 1.71 Å) were synthesized. This long central C-C bond was rationalized by numerous CH...HC-type dispersion attractions between the two halves of the molecule. The thermodynamic stabilization of molecules equipped with bulky groups has provided a conceptually new rationale, since until then it had been assumed that such molecules are highly unstable. We performed a broadband CP-FTMW spectroscopy study in the 2-8 GHz frequency range on oxygen-substituted diamondoid dimers (C_{26}H_{34}O_2, 28 heavy atoms) as well as diadamantyl ether to provide further insight into their structures. The experimental data are compared with results from quantum-chemical calculations and gas-phase electron diffraction. For the ether, we even obtained ^{13}C and ^{18}O isotopologues to generate the full heavy-atom substitution structure.

To Guide or Not to Guide: Issues in the Sequencing of Pedagogical Structure in Computational Model-Based Learning

ERIC Educational Resources Information Center

Jacobson, Michael J.; Kim, Beaumie; Pathak, Suneeta; Zhang, BaoHui

2015-01-01

This research explores issues related to the sequencing of structure that is provided as pedagogical guidance. A study was conducted that involved grade 10 students in Singapore as they learned concepts about electricity using four NetLogo Investigations of Electricity agent-based models. It was found that the low-to-high structure learning…

University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

ERIC Educational Resources Information Center

Wu, Ying-Tien

2013-01-01

This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and…

Factor Structure and Predictive Utility of the 2 x 2 Achievement Goal Model in a Sample of Taiwan Students

ERIC Educational Resources Information Center

Chiang, Yu-Tzu; Yeh, Yu-Chen; Lin, Sunny S. J.; Hwang, Fang-Ming

2011-01-01

This study examined structure and predictive utility of the 2 x 2 achievement goal model among Taiwan pre-university school students (ages 10 to 16) who learned Chinese language arts. The confirmatory factor analyses of Achievement Goal Questionnaire-Chinese version provided good fitting between the factorial and dimensional structures with the…

B-70 Aircraft Study. Volume 1

NASA Technical Reports Server (NTRS)

Johnson, V. T.

1972-01-01

This Phase 2 final report for the B-70 aircraft study contains the data location matrix, which provides a summary of the major cost, schedule, and technical items provided in the report; work breakdown structure; cost definitions; and B-70 program level summary data. The Phase 2 objective was to provide the B-70 aircraft data in accordance with the approved study plan. Several minor modifications to the original plan have been made as the result of the Phase 2 effort.

The functional response of bioactive titania-modified three-dimensional Ti-6Al-4V mesh structure toward providing a favorable pathway for intercellular communication and osteoincorporation.

PubMed

Nune, K C; Misra, R D K; Li, S J; Hao, Y L; Zhang, W

2016-10-01

The objective of the study is to fundamentally elucidate the biological response of 3D printed mesh structures subjected to plasma electrolytic oxidation process through the study of osteoblast functions. The cellular activity of plasma electrolytic-oxidized mesh structure was explored in terms of cell-to-cell communication involving proliferation, synthesis of extracellular and intracellular proteins, and mineralization. Upon plasma electrolytic oxidation of the mesh structure, a thin layer of bioactive titania with pore size 1-3 µm was nucleated on the surface. The combination of microporous bioactive titania and interconnected porous architecture provided the desired pathway for supply of nutrients and oxygen to cells and tissue and a favorable osteogenic microenvironment for tissue on-growth and in-growth, in relation to the unmodified mesh structure. The formation of a confluent layer as envisaged via electron microscopy and quantitative assessment of the expression level of proteins (actin, vinculin, and fibronectin) point toward the determining role of surface-modified mesh structure in modulating osteoblasts functions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2488-2501, 2016. © 2016 Wiley Periodicals, Inc.

The CONNECT project: Combining macro- and micro-structure.

PubMed

Assaf, Yaniv; Alexander, Daniel C; Jones, Derek K; Bizzi, Albero; Behrens, Tim E J; Clark, Chris A; Cohen, Yoram; Dyrby, Tim B; Huppi, Petra S; Knoesche, Thomas R; Lebihan, Denis; Parker, Geoff J M; Poupon, Cyril; Anaby, Debbie; Anwander, Alfred; Bar, Leah; Barazany, Daniel; Blumenfeld-Katzir, Tamar; De-Santis, Silvia; Duclap, Delphine; Figini, Matteo; Fischi, Elda; Guevara, Pamela; Hubbard, Penny; Hofstetter, Shir; Jbabdi, Saad; Kunz, Nicolas; Lazeyras, Francois; Lebois, Alice; Liptrot, Matthew G; Lundell, Henrik; Mangin, Jean-François; Dominguez, David Moreno; Morozov, Darya; Schreiber, Jan; Seunarine, Kiran; Nava, Simone; Poupon, Cyril; Riffert, Till; Sasson, Efrat; Schmitt, Benoit; Shemesh, Noam; Sotiropoulos, Stam N; Tavor, Ido; Zhang, Hui Gary; Zhou, Feng-Lei

2013-10-15

In recent years, diffusion MRI has become an extremely important tool for studying the morphology of living brain tissue, as it provides unique insights into both its macrostructure and microstructure. Recent applications of diffusion MRI aimed to characterize the structural connectome using tractography to infer connectivity between brain regions. In parallel to the development of tractography, additional diffusion MRI based frameworks (CHARMED, AxCaliber, ActiveAx) were developed enabling the extraction of a multitude of micro-structural parameters (axon diameter distribution, mean axonal diameter and axonal density). This unique insight into both tissue microstructure and connectivity has enormous potential value in understanding the structure and organization of the brain as well as providing unique insights to abnormalities that underpin disease states. The CONNECT (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements. This paper summarizes the project and describes the perspective of using micro-structural measures to study the connectome. Copyright © 2013 Elsevier Inc. All rights reserved.

Is the organisation and structure of hospital postnatal care a barrier to quality care? Findings from a state-wide review in Victoria, Australia.

PubMed

McLachlan, Helen L; Forster, Della A; Yelland, Jane; Rayner, Joanne; Lumley, Judith

2008-09-01

to describe the structure and organisation of hospital postnatal care in Victoria, Australia. postal survey sent to all public hospitals in Victoria (n=71) and key-informant interviews with midwives and medical practitioners (n=38). Victoria, Australia. providers of postnatal care in Victorian public hospitals. there is significant diversity across Victoria in the way postnatal units are structured and organised and in the way care is provided. There are differences in numerous practices, including maternal and neonatal observations and the length of time women spend in hospital after giving birth. Although the benefits of continuity of care are recognised by health care providers, continuity is difficult to provide in the postnatal period. Postnatal care is provided in busy, sometimes chaotic environments, with many barriers to providing effective care and few opportunities for women to rest and recover after childbirth. The findings in this study can, in part, be explained by the lack of evidence that has been available to guide early postnatal care. current structures such as standard postnatal documentation (clinical pathways) and fixed length of stay, may inhibit rather than support individualised care for women after childbirth. There is a need to move towards greater flexibility in providing of early postnatal care, including alternative models of service delivery; choice and flexibility in the length of stay after birth; a focus on the individual with far less emphasis on care being structured around organisational requirements; and building an evidence base to guide care.

A hybrid phononic crystal for roof application.

PubMed

Wan, Qingmian; Shao, Rong

2017-11-01

Phononic crystal is a type of acoustic material, and the study of phononic crystals has attracted great attention from national research institutions. Meanwhile, noise reduction in the low-frequency range has always encountered difficulties and troubles in the engineering field. In order to obtain a unique and effective low-frequency noise reduction method, in this paper a low frequency noise attenuation system based on phononic crystal structure is proposed and demonstrated. The finite element simulation of the band gap is consistent with the final test results. The effects of structure parameters on the band gaps were studied by changing the structure parameters and the band gaps can be controlled by suitably tuning structure parameters. The structure and results provide a good support for phononic crystal structures engineering application.

FTIR study of secondary structure of bovine serum albumin and ovalbumin

NASA Astrophysics Data System (ADS)

Abrosimova, K. V.; Shulenina, O. V.; Paston, S. V.

2016-11-01

Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation.

ICCS 2009 Technical Report

ERIC Educational Resources Information Center

Schulz, Wolfram, Ed.; Ainley, John, Ed.; Fraillon, Julian, Ed.

2011-01-01

This report is structured so as to provide technical detail about each aspect of International Civic and Citizenship Education Study (ICCS). The overview is followed by a series of chapters that provide detail about different aspects of ICCS. Chapters, 2, 3, 4, and 5 are concerned with the instruments. Chapter 2 provides information about the…

Build your own soil: exploring microfluidics to create microbial habitat structures

PubMed Central

Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

2018-01-01

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971

Factor Structure of Character Strengths in Youth: Consistency across Ages and Measures

ERIC Educational Resources Information Center

McGrath, Robert E.; Walker, David Ian

2016-01-01

The VIA Classification of Strengths and Virtues attempts to provide a comprehensive model of character based on 24 character strengths. The present study is the largest study to date exploring the structure of the 24 strengths in youth. One sample (N = 23,850) completed the VIA-Youth, a teen measure of the VIA Classification. Based on a random…

Information Technology Governance, Funding and Structure: A Case Analysis of a Public University in Malaysia

ERIC Educational Resources Information Center

Ismail, Noor Azizi

2008-01-01

Purpose: The paper's purpose is to investigate the issues of IT governance, funding and structure of a public university in Malaysia. Design/methodology/approach: The study uses a case study approach, i.e. a series of interviews with users and information services provider of campus information system. Findings: The university lacks a common…

Synthesis, fungicidal activity, structure-activity relationships (SARs) and density functional theory (DFT) studies of novel strobilurin analogues containing arylpyrazole rings.

PubMed

Liu, Yuanyuan; Lv, Kunzhi; Li, Yi; Nan, Qiuli; Xu, Jinyuan

2018-05-18

A series of novel strobilurin analogues (1a-1f, 2a-2e, 3a-3e) containing arylpyrazole rings were synthesized and characterized by NMR spectroscopy. The structures of 1f, 2b and 3b were also determined by single crystal X-ray diffraction analysis. These analogues were collected together with other twenty-eight similar compounds 4a-4f, 5a-5h, 6a-6h and 7a-7f from our previous studies, for in vitro bioassays and thorough structure-activity relationships (SARs) studies. Most compounds exhibited excellent-to-good fungicidal activity against Rhizoctonia solani, especially 5c, 7a, 6c, and 3b with 98.94%, 83.40%, 71.40% and 65.87% inhibition rates at 0.1 μg mL -1 , respectively, better than commercial pyraclostrobin. Comparative molecular field analysis (CoMFA) was employed to study three-dimensional quantitative structure-activity relationships (3D-QSARs). Density functional theory (DFT) calculation was also carried out to provide more information regarding SARs. The present work provided some hints for developing novel strobilurin fungicides.

Patent protection for structural genomics-related inventions.

PubMed

Vinarov, Sara D

2003-01-01

Recently there have been some important developments with respect to the patentability of inventions in the field of structural genomics. The leaders of the European Patent Office (EPO), Japan Patent Office (JPO) and the United States Patent Office (USPTO) came together for a trilateral meeting to conduct a comparative study on protein 3-dimensional (3-D) structure related claims in an effort to come to a mutual understanding about the examination of such inventions. The three patent offices were presented with eight different cases: 1) 3-D structural data of a protein per se; 2) computer-readable storage medium encoded with structural data of a protein; 3) protein defined by its tertiary structure; 4) crystals of known proteins; 5) binding pockets and protein domains; 6) and 7) are both directed to in silico screening methods directed to a specific protein; and 8) pharmacophores. The preliminary conclusions reached at the trilateral meeting provide clarity regarding the types of inventions that may be patentable given a specific set of scientific facts in a patent application. Therefore, the guidance provided by this study will help inventors, attorneys and other patent practitioners who file for patent protection on structural genomics-based inventions both here and abroad comply with the patentability requirements of each office.

Analysis of Soil Structure Turnover with Garnet Particles and X-Ray Microtomography

PubMed Central

Vogel, Hans-Jörg

2016-01-01

Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other. PMID:27453995

An analytical study of double bend achromat lattice.

PubMed

Fakhri, Ali Akbar; Kant, Pradeep; Singh, Gurnam; Ghodke, A D

2015-03-01

In a double bend achromat, Chasman-Green (CG) lattice represents the basic structure for low emittance synchrotron radiation sources. In the basic structure of CG lattice single focussing quadrupole (QF) magnet is used to form an achromat. In this paper, this CG lattice is discussed and an analytical relation is presented, showing the limitation of basic CG lattice to provide the theoretical minimum beam emittance in achromatic condition. To satisfy theoretical minimum beam emittance parameters, achromat having two, three, and four quadrupole structures is presented. In this structure, different arrangements of QF and defocusing quadruple (QD) are used. An analytical approach assuming quadrupoles as thin lenses has been followed for studying these structures. A study of Indus-2 lattice in which QF-QD-QF configuration in the achromat part has been adopted is also presented.

Ab Initio Study of Interfacial Structure Transformation of Amorphous Carbon Catalyzed by Ti, Cr, and W Transition Layers.

PubMed

Li, Xiaowei; Li, Lei; Zhang, Dong; Wang, Aiying

2017-11-29

Amorphous carbon (a-C) films composited with transition layers exhibit the desirable improvement of adhesion strength between films and substrate, but the further understanding on the interfacial structure transformation of a-C structure induced by transition layers is still lacked. In this paper, using ab initio calculations, we comparatively studied the interfacial structure between Ti, Cr, or W transition layers and a-C film from the atomic scale, and demonstrated that the addition of Ti, Cr, or W catalyzed the graphitic transformation of a-C structure at different levels, which provided the theoretical guidance for designing a multilayer nanocomposite film for renewed application.

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

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

Ortiz, Rosario, E-mail: r_oh@ciencias.unam.mx; Kouznetsova, Anna, E-mail: Anna.Kouznetsova@ki.se; Echeverría-Martínez, Olga M., E-mail: omem@ciencias.unam.mx

The synaptonemal complex (SC) is a proteinaceous structure that holds the homologous chromosomes in close proximity while they exchange genetic material in a process known as meiotic recombination. This meiotic recombination leads to genetic variability in sexually reproducing organisms. The ultrastructure of the SC is studied by electron microscopy and it is observed as a tripartite structure. Two lateral elements (LE) separated by a central region (CR) confer its classical tripartite organization. The LEs are the anchoring platform for the replicated homologous chromosomes to properly exchange genetic material with one another. An accurate assembly of the LE is indispensable formore » the proper completion of meiosis. Ultrastructural studies suggested that the LE is organized as a multilayered unit. However, no validation of this model has been previously provided. In this ultrastructural study, by using mice with different genetic backgrounds that affect the LE width, we provide further evidence that support a multilayered organization of the LE. Additionally, we provide data suggesting additional roles of the different cohesin complex components in the structure of the LEs of the SC. - Highlights: • The lateral element of the synaptonemal complex is a multilayered structure. • The width of the lateral element in synaptonemal complex-null mice is different. • Two cohesin complex cores plus one axial element form a wild-type lateral element. • The layers of the lateral element can be analyzed in different null mice models.« less

Specificity of Structural Assessment of Knowledge

ERIC Educational Resources Information Center

Trumpower, David L.; Sharara, Harold; Goldsmith, Timothy E.

2010-01-01

This study examines the specificity of information provided by structural assessment of knowledge (SAK). SAK is a technique which uses the Pathfinder scaling algorithm to transform ratings of concept relatedness into network representations (PFnets) of individuals' knowledge. Inferences about individuals' overall domain knowledge based on the…

Structure of the North American Atlantic Continental Margin.

ERIC Educational Resources Information Center

Klitgord, K. K.; Schlee, J. S.

1986-01-01

Offers explanations on the origin of the North American Atlantic continental margin. Provides an analysis and illustrations of structural and strategraphic elements of cross sections of the Atlantic continental margin. Also explains the operations and applications of seismic-relection profiles in studying ocean areas. (ML)

A structure-based kinetic model of transcription

PubMed Central

Steitz, Thomas A.

2017-01-01

ABSTRACT During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement. PMID:27656764

Sampling considerations for modal analysis with damping

NASA Astrophysics Data System (ADS)

Park, Jae Young; Wakin, Michael B.; Gilbert, Anna C.

2015-03-01

Structural health monitoring (SHM) systems are critical for monitoring aging infrastructure (such as buildings or bridges) in a cost-effective manner. Wireless sensor networks that sample vibration data over time are particularly appealing for SHM applications due to their flexibility and low cost. However, in order to extend the battery life of wireless sensor nodes, it is essential to minimize the amount of vibration data these sensors must collect and transmit. In recent work, we have studied the performance of the Singular Value Decomposition (SVD) applied to the collection of data and provided new finite sample analysis characterizing conditions under which this simple technique{also known as the Proper Orthogonal Decomposition (POD){can correctly estimate the mode shapes of the structure. Specifically, we provided theoretical guarantees on the number and duration of samples required in order to estimate a structure's mode shapes to a desired level of accuracy. In that previous work, however, we considered simplified Multiple-Degree-Of-Freedom (MDOF) systems with no damping. In this paper we consider MDOF systems with proportional damping and show that, with sufficiently light damping, the POD can continue to provide accurate estimates of a structure's mode shapes. We support our discussion with new analytical insight and experimental demonstrations. In particular, we study the tradeoffs between the level of damping, the sampling rate and duration, and the accuracy to which the structure's mode shapes can be estimated.

Payload specialist station study. Volume 3: Program study cost estimates. Part 1: Work breakdown structure

NASA Technical Reports Server (NTRS)

1976-01-01

The work breakdown structure (WBS) for the Payload Specialist Station (PSS) is presented. The WBS is divided into two elements--PSS contractor and mission unique requirements. In accordance with the study ground rules, it is assumed that a single contractor, hereafter referred to as PSS Contractor will perform the following: (1) provide C and D hardware (MFDS and elements of MMSE), except for GFE; (2) identify software requirements; (3) provide GSE and ground test software; and (4) perform systems engineering and integration in support of the Aft Flight Deck (AFD) C and D concept. The PSS Contractor WBS element encompasses a core or standardized PSS concept. Payload peculiar C and D requirements identified by users will originate as a part of the WBS element mission unique requirements; these requirements will be provided to the PSS Contractor for implementation.

Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

PubMed

Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

2016-07-01

Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.

Parametric imaging of collagen structural changes in human osteoarthritic cartilage using optical polarization tractography

NASA Astrophysics Data System (ADS)

Ravanfar, Mohammadreza; Pfeiffer, Ferris M.; Bozynski, Chantelle C.; Wang, Yuanbo; Yao, Gang

2017-12-01

Collagen degeneration is an important pathological feature of osteoarthritis. The purpose of this study is to investigate whether the polarization-sensitive optical coherence tomography (PSOCT)-based optical polarization tractography (OPT) can be useful in imaging collagen structural changes in human osteoarthritic cartilage samples. OPT eliminated the banding artifacts in conventional PSOCT by calculating the depth-resolved local birefringence and fiber orientation. A close comparison between OPT and PSOCT showed that OPT provided improved visualization and characterization of the zonal structure in human cartilage. Experimental results obtained in this study also underlined the importance of knowing the collagen fiber orientation in conventional polarized light microscopy assessment. In addition, parametric OPT imaging was achieved by quantifying the surface roughness, birefringence, and fiber dispersion in the superficial zone of the cartilage. These quantitative parametric images provided complementary information on the structural changes in cartilage, which can be useful for a comprehensive evaluation of collagen damage in osteoarthritic cartilage.

Emergent perversions in the buckling of heterogeneous elastic strips

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

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Structural Insights on the Mycobacterium tuberculosis Proteasomal ATPase Mpa

PubMed Central

Wang, Tao; Li, Hua; Lin, Gang; Tang, Chunyan; Li, Dongyang; Nathan, Carl; Darwin, K. Heran; Li, Huilin

2009-01-01

Summary Proteasome-mediated protein turnover in all domains of life is an energy-dependent process that requires ATPase activity. Mycobacterium tuberculosis (Mtb) was recently shown to possess a ubiquitin-like proteasome pathway that plays an essential role in Mtb resistance to killing by products of host macrophages. Here we report our structural and biochemical investigation of Mpa, the presumptive Mtb proteasomal ATPase. We demonstrate that Mpa binds to the Mtb proteasome in the presence of ATPγS, providing the physical evidence that Mpa is the proteasomal ATPase. X-ray crystallographic determination of the conserved inter-domain showed a five-stranded double β-barrel structure containing a Greek key motif. The structure and mutagenesis indicate a major role of the inter-domain for Mpa hexamerization. Our mutational and functional studies further suggest that the central channel in the Mpa hexamer is involved in protein substrate translocation and degradation. These studies provide insights into how a bacterial proteasomal ATPase interacts with and facilitates protein degradation by the proteasome. PMID:19836337

Emergent perversions in the buckling of heterogeneous elastic strips

DOE PAGES

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin; ...

2016-06-14

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Revealing lithium-silicide phase transformations in nano-structured silicon-based lithium ion batteries via in situ NMR spectroscopy.

PubMed

Ogata, K; Salager, E; Kerr, C J; Fraser, A E; Ducati, C; Morris, A J; Hofmann, S; Grey, C P

2014-01-01

Nano-structured silicon anodes are attractive alternatives to graphitic carbons in rechargeable Li-ion batteries, owing to their extremely high capacities. Despite their advantages, numerous issues remain to be addressed, the most basic being to understand the complex kinetics and thermodynamics that control the reactions and structural rearrangements. Elucidating this necessitates real-time in situ metrologies, which are highly challenging, if the whole electrode structure is studied at an atomistic level for multiple cycles under realistic cycling conditions. Here we report that Si nanowires grown on a conducting carbon-fibre support provide a robust model battery system that can be studied by (7)Li in situ NMR spectroscopy. The method allows the (de)alloying reactions of the amorphous silicides to be followed in the 2nd cycle and beyond. In combination with density-functional theory calculations, the results provide insight into the amorphous and amorphous-to-crystalline lithium-silicide transformations, particularly those at low voltages, which are highly relevant to practical cycling strategies.

Studying neuroanatomy using MRI.

PubMed

Lerch, Jason P; van der Kouwe, André J W; Raznahan, Armin; Paus, Tomáš; Johansen-Berg, Heidi; Miller, Karla L; Smith, Stephen M; Fischl, Bruce; Sotiropoulos, Stamatios N

2017-02-23

The study of neuroanatomy using imaging enables key insights into how our brains function, are shaped by genes and environment, and change with development, aging and disease. Developments in MRI acquisition, image processing and data modeling have been key to these advances. However, MRI provides an indirect measurement of the biological signals we aim to investigate. Thus, artifacts and key questions of correct interpretation can confound the readouts provided by anatomical MRI. In this review we provide an overview of the methods for measuring macro- and mesoscopic structure and for inferring microstructural properties; we also describe key artifacts and confounds that can lead to incorrect conclusions. Ultimately, we believe that, although methods need to improve and caution is required in interpretation, structural MRI continues to have great promise in furthering our understanding of how the brain works.

Barriers of access to care in a managed competition model: lessons from Colombia.

PubMed

Vargas, Ingrid; Vázquez, María Luisa; Mogollón-Pérez, Amparo Susana; Unger, Jean-Pierre

2010-10-29

The health sector reform in Colombia, initiated by Law 100 (1993) that introduced a managed competition model, is generally presented as a successful experience of improving access to care through a health insurance regulated market. The study's objective is to improve our understanding of the factors influencing access to the continuum of care in the Colombian managed competition model, from the social actors' point of view. An exploratory, descriptive-interpretative qualitative study was carried out, based on case studies of four healthcare networks in rural and urban areas. Individual semi-structured interviews were conducted to a three stage theoretical sample: I) cases, II) providers and III) informants: insured and uninsured users (35), health professionals (51), administrative personnel (20), and providers' (18) and insurers' (10) managers. Narrative content analysis was conducted; segmented by cases, informant's groups and themes. Access, particularly to secondary care, is perceived as complex due to four groups of obstacles with synergetic effects: segmented insurance design with insufficient services covered; insurers' managed care and purchasing mechanisms; providers' networks structural and organizational limitations; and, poor living conditions. Insurers' and providers' values based on economic profit permeate all factors. Variations became apparent between the two geographical areas and insurance schemes. In the urban areas barriers related to market functioning predominate, whereas in the rural areas structural deficiencies in health services are linked to insufficient public funding. While financial obstacles are dominant in the subsidized regime, in the contributory scheme supply shortage prevails, related to insufficient private investment. The results show how in the Colombian healthcare system structural and organizational barriers to care access, that are common in developing countries, are widened by both the insurers' use of mechanisms that limit the utilization and the public healthcare providers' change of behavior in a competition environment. They provide evidence to question the promotion of the managed competition model in low and middle-income countries.

Barriers of access to care in a managed competition model: lessons from Colombia

PubMed Central

2010-01-01

Background The health sector reform in Colombia, initiated by Law 100 (1993) that introduced a managed competition model, is generally presented as a successful experience of improving access to care through a health insurance regulated market. The study's objective is to improve our understanding of the factors influencing access to the continuum of care in the Colombian managed competition model, from the social actors' point of view. Methods An exploratory, descriptive-interpretative qualitative study was carried out, based on case studies of four healthcare networks in rural and urban areas. Individual semi-structured interviews were conducted to a three stage theoretical sample: I) cases, II) providers and III) informants: insured and uninsured users (35), health professionals (51), administrative personnel (20), and providers' (18) and insurers' (10) managers. Narrative content analysis was conducted; segmented by cases, informant's groups and themes. Results Access, particularly to secondary care, is perceived as complex due to four groups of obstacles with synergetic effects: segmented insurance design with insufficient services covered; insurers' managed care and purchasing mechanisms; providers' networks structural and organizational limitations; and, poor living conditions. Insurers' and providers' values based on economic profit permeate all factors. Variations became apparent between the two geographical areas and insurance schemes. In the urban areas barriers related to market functioning predominate, whereas in the rural areas structural deficiencies in health services are linked to insufficient public funding. While financial obstacles are dominant in the subsidized regime, in the contributory scheme supply shortage prevails, related to insufficient private investment. Conclusions The results show how in the Colombian healthcare system structural and organizational barriers to care access, that are common in developing countries, are widened by both the insurers' use of mechanisms that limit the utilization and the public healthcare providers' change of behavior in a competition environment. They provide evidence to question the promotion of the managed competition model in low and middle-income countries. PMID:21034481

Understanding protein evolution: from protein physics to Darwinian selection.

PubMed

Zeldovich, Konstantin B; Shakhnovich, Eugene I

2008-01-01

Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

The vector structure of active magnetic fields

NASA Technical Reports Server (NTRS)

Parker, E. N.

1985-01-01

Observations are needed to show the form of the strains introduced into the fields above the surface of the Sun. The longitudinal component alone does not provide the basic information, so that it has been necessary in the past to use the filamentary structure observed in H sub alpha to supplement the longitudinal information. Vector measurements provide the additional essential information to determine the strains, with the filamentary structure available as a check for consistency. It is to be expected, then, that vector measurements will permit a direct mapping of the strains imposed on the magnetic fields of active regions. It will be interesting to study the relation of those strains to the emergence of magnetic flux, flares, eruptive prominences, etc. In particular we may hope to study the relaxation of the strains via the dynamical nonequilibrium.

Aircraft energy efficiency laminar flow control wing design study

NASA Technical Reports Server (NTRS)

Bonner, T. F., Jr.; Pride, J. D., Jr.; Fernald, W. W.

1977-01-01

An engineering design study was performed in which laminar flow control (LFC) was integrated into the wing of a commercial passenger transport aircraft. A baseline aircraft configuration was selected and the wing geometry was defined. The LFC system, with suction slots, ducting, and suction pumps was integrated with the wing structure. The use of standard aluminum technology and advanced superplastic formed diffusion bonded titanium technology was evaluated. The results of the design study show that the LFC system can be integrated with the wing structure to provide a structurally and aerodynamically efficient wing for a commercial transport aircraft.

Solution structure and backbone dynamics of an endopeptidase HycI from Escherichia coli: implications for mechanism of the [NiFe] hydrogenase maturation.

PubMed

Yang, Fan; Hu, Wei; Xu, Huimin; Li, Congmin; Xia, Bin; Jin, Changwen

2007-02-09

[NiFe] hydrogenases are metalloenzymes involved in many biological processes concerning the metabolism of hydrogen. The maturation of the large subunit of these hydrogenases requires the cleavage of a peptide at the C terminus by an endopeptidase before the final formation of the [NiFe] metallocenter. HycI is an endopeptidase of the M52 family and responsible for the C-terminal cleavage of the large subunit of hydrogenase 3 in Escherichia coli. Although extensive studies were performed, the molecular mechanism of recognition and cleavage of hydrogenase 3 remains elusive. Herein, we report the solution structure of E. coli HycI determined by high resolution nuclear magnetic resonance spectroscopy. This is the first solution structure of the apo form of endopeptidase of the M52 family reported thus far. The overall structure is similar to the crystal structure of holo-HybD in the same family. However, significant diversity was observed between the two structures. Especially, HycI shows an open conformation at the putative nickel-binding site, whereas HybD adopts a closed conformation. In addition, we performed backbone dynamic studies to probe the motional properties of the apo form of HycI. Furthermore, the metal ion titration experiments provide insightful information on the substrate recognition and cleavage processes. Taken together, our current structural, biochemical, and dynamic studies extend the knowledge of the M52 family proteins and provide novel insights into the biological function of HycI.

Structural hierarchy of autism spectrum disorder symptoms: an integrative framework.

PubMed

Kim, Hyunsik; Keifer, Cara M; Rodriguez-Seijas, Craig; Eaton, Nicholas R; Lerner, Matthew D; Gadow, Kenneth D

2018-01-01

In an attempt to resolve questions regarding the symptom classification of autism spectrum disorder (ASD), previous research generally aimed to demonstrate superiority of one model over another. Rather than adjudicating which model may be optimal, we propose an alternative approach that integrates competing models using Goldberg's bass-ackwards method, providing a comprehensive understanding of the underlying symptom structure of ASD. The study sample comprised 3,825 individuals, consecutive referrals to a university hospital developmental disabilities specialty clinic or a child psychiatry outpatient clinic. This study analyzed DSM-IV-referenced ASD symptom statements from parent and teacher versions of the Child and Adolescent Symptom Inventory-4R. A series of exploratory structural equation models was conducted in order to produce interpretable latent factors that account for multivariate covariance. Results indicated that ASD symptoms were structured into an interpretable hierarchy across multiple informants. This hierarchy includes five levels; key features of ASD bifurcate into different constructs with increasing specificity. This is the first study to examine an underlying structural hierarchy of ASD symptomatology using the bass-ackwards method. This hierarchy demonstrates how core features of ASD relate at differing levels of resolution, providing a model for conceptualizing ASD heterogeneity and a structure for integrating divergent theories of cognitive processes and behavioral features that define the disorder. These findings suggest that a more coherent and complete understanding of the structure of ASD symptoms may be reflected in a metastructure rather than at one level of resolution. © 2017 Association for Child and Adolescent Mental Health.

Leisure activities are linked to mental health benefits by providing time structure: comparing employed, unemployed and homemakers.

PubMed

Goodman, William K; Geiger, Ashley M; Wolf, Jutta M

2017-01-01

Unemployment has consistently been linked to negative mental health outcomes, emphasising the need to characterise the underlying mechanisms. The current study aimed at testing whether compared with other employment groups, fewer leisure activities observed in unemployment may contribute to elevated risk for negative mental health via loss of time structure. Depressive symptoms (Center for Epidemiologic Studies Depression), leisure activities (exercise, self-focused, social), and time structure (Time Structure Questionnaire (TSQ)) were assessed cross-sectionally in 406 participants (unemployed=155, employed=140, homemakers=111) recruited through Amazon Mechanical Turk. Controlling for gender and age, structural equation modelling revealed time structure partially (employed, homemakers) and fully (unemployed) mediated the relationship between leisure activities and depressive symptoms. With the exception of differential effects for structured routines, all other TSQ factors (sense of purpose, present orientation, effective organisation and persistence) contributed significantly to all models. These findings support the idea that especially for the unemployed, leisure activities impose their mental health benefits through increasing individuals' perception of spending their time effectively. Social leisure activities that provide a sense of daily structure may thereby be a particularly promising low-cost intervention to improve mental health in this population. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors.

PubMed

Xie, Xiang-Qun; Chowdhury, Ananda

2013-01-01

Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design. Copyright © 2013 Elsevier Inc. All rights reserved.

The Theory of Planned Behavior as a Model of Heavy Episodic Drinking Among College Students

PubMed Central

Collins, Susan E.; Carey, Kate B.

2008-01-01

This study provided a simultaneous, confirmatory test of the theory of planned behavior (TPB) in predicting heavy episodic drinking (HED) among college students. It was hypothesized that past HED, drinking attitudes, subjective norms and drinking refusal self-efficacy would predict intention, which would in turn predict future HED. Participants consisted of 131 college drinkers (63% female) who reported having engaged in HED in the previous two weeks. Participants were recruited and completed questionnaires within the context of a larger intervention study (see Collins & Carey, 2005). Latent factor structural equation modeling was used to test the ability of the TPB to predict HED. Chi-square tests and fit indices indicated good fit for the final structural models. Self-efficacy and attitudes but not subjective norms significantly predicted baseline intention, and intention and past HED predicted future HED. Contrary to hypotheses, however, a structural model excluding past HED provided a better fit than a model including it. Although further studies must be conducted before a definitive conclusion is reached, a TPB model excluding past behavior, which is arguably more parsimonious and theory driven, may provide better prediction of HED among college drinkers than a model including past behavior. PMID:18072832

Pathways of information transmission among wild songbirds follow experimentally imposed changes in social foraging structure.

PubMed

Firth, Josh A; Sheldon, Ben C; Farine, Damien R

2016-06-01

Animals regularly use information from others to shape their decisions. Yet, determining how changes in social structure affect information flow and social learning strategies has remained challenging. We manipulated the social structure of a large community of wild songbirds by controlling which individuals could feed together at automated feeding stations (selective feeders). We then provided novel ephemeral food patches freely accessible to all birds and recorded the spread of this new information. We demonstrate that the discovery of new food patches followed the experimentally imposed social structure and that birds disproportionately learnt from those whom they could forage with at the selective feeders. The selective feeders reduced the number of conspecific information sources available and birds subsequently increased their use of information provided by heterospecifics. Our study demonstrates that changes to social systems carry over into pathways of information transfer and that individuals learn from tutors that provide relevant information in other contexts. © 2016 The Authors.

Visualizing polynucleotide polymerase machines at work

PubMed Central

Steitz, Thomas A

2006-01-01

The structures of T7 RNA polymerase (T7 RNAP) captured in the initiation and elongation phases of transcription, that of φ29 DNA polymerase bound to a primer protein and those of the multisubunit RNAPs bound to initiating factors provide insights into how these proteins can initiate RNA synthesis and synthesize 6–10 nucleotides while remaining bound to the site of initiation. Structural insight into the translocation of the product transcript and the separation of the downstream duplex DNA is provided by the structures of the four states of nucleotide incorporation. Single molecule and biochemical studies show a distribution of primer terminus positions that is altered by the binding of NTP and PPi ligands. This article reviews the insights that imaging the structure of polynucleotide polymerases at different steps of the polymerization reaction has provided on the mechanisms of the polymerization reaction. Movies are shown that allow the direct visualization of the conformational changes that the polymerases undergo during the different steps of polymerization. PMID:16900098

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

French, Jarrod B.; Ealick, Steven E.

The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structuralmore » isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K{sub i} of 30 {+-} 2 {micro}m. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.« less

An in vitro recombination-based reverse genetic system for rapid mutagenesis of structural genes of the Japanese encephalitis virus.

PubMed

Du, Ruikun; Wang, Manli; Hu, Zhihong; Wang, Hualin; Deng, Fei

2015-10-01

Japanese encephalitis virus (JEV) is one of the most common pathogens of severe viral encephalitis, which is a severe threat to human health. Despite instability of the JEV genome in bacteria, many strategies have been developed to establish molecular clone systems of JEV, providing convenient tools for studying the virus life cycle and virus-host interactions. In this study, we adapted an In-Fusion enzyme-based in vitro recombination method to construct a reverse genetic system of JEV, thereby providing a rapid approach to introduce mutations into the structural genes. A truncated genome without the structural genes was constructed as the backbone, and the complementary segment containing the structural genes was recombined in vitro, which was then transfected directly into virus-permissive cells. The progeny of the infectious virus was successfully detected in the supernatant of the transfected cells, and showed an identical phenotype to its parental virus. To provide a proof-of-principle, the 12 conserved cysteine residues in the envelope (E) protein of JEV were respectively mutated using this approach, and all mutations resulted in a complete failure to generate infectious virus. However, a leucine-tophenylanine mutation at amino acid 107 of the E protein did not interfere with the production of the infectious virus. These results suggested that all 12 cysteines in the E protein are essential for the JEV life cycle. In summary, a novel reverse genetic system of JEV was established for rapidly introducing mutations into structural genes, which will serve as a useful tool for functional studies.

Protein docking by the interface structure similarity: how much structure is needed?

PubMed

Sinha, Rohita; Kundrotas, Petras J; Vakser, Ilya A

2012-01-01

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Monte Carlo study of the honeycomb structure of anthraquinone molecules on Cu(111)

NASA Astrophysics Data System (ADS)

Kim, Kwangmoo; Einstein, T. L.

2011-06-01

Using Monte Carlo calculations of the two-dimensional (2D) triangular lattice gas model, we demonstrate a mechanism for the spontaneous formation of honeycomb structure of anthraquinone (AQ) molecules on a Cu(111) plane. In our model long-range attractions play an important role, in addition to the long-range repulsions and short-range attractions proposed by Pawin, Wong, Kwon, and Bartels [ScienceSCIEAS0036-807510.1126/science.1129309 313, 961 (2006)]. We provide a global account of the possible combinations of long-range attractive coupling constants which lead to a honeycomb superstructure. We also provide the critical temperature of disruption of the honeycomb structure and compare the critical local coverage rate of AQ’s where the honeycomb structure starts to form with the experimental observations.

Complementary aspects of diffusion imaging and fMRI; I: structure and function.

PubMed

Mulkern, Robert V; Davis, Peter E; Haker, Steven J; Estepar, Raul San Jose; Panych, Lawrence P; Maier, Stephan E; Rivkin, Michael J

2006-05-01

Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function.

The study on the core personality trait words of Chinese medical university students based on social network analysis

PubMed Central

Wu, Ying; Xue, Yunzhen; Xue, Zhanling

2017-01-01

Abstract The medical university students in China whose school work is relatively heavy and educational system is long are a special professional group. Many students have psychological problems more or less. So, to understand their personality characteristics will provide a scientific basis for the intervention of psychological health. We selected top 30 personality trait words according to the order of frequency. Additionally, some methods such as social network analysis (SNA) and visualization technology of mapping knowledge domain were used in this study. Among these core personality trait words Family conscious had the 3 highest centralities and possessed the largest core status and influence. From the analysis of core-peripheral structure, we can see polarized core-perpheral structure was quite obvious. From the analysis of K-plex, there were in total 588 “K-2”K-plexs. From the analysis of Principal Components, we selected the 11 principal components. This study of personality not only can prevent disease, but also provide a scientific basis for students’ psychological healthy education. In addition, we have adopted SNA to pay more attention to the relationship between personality trait words and the connection among personality dimensions. This study may provide the new ideas and methods for the research of personality structure. PMID:28906409

The study on the core personality trait words of Chinese medical university students based on social network analysis.

PubMed

Wu, Ying; Xue, Yunzhen; Xue, Zhanling

2017-09-01

The medical university students in China whose school work is relatively heavy and educational system is long are a special professional group. Many students have psychological problems more or less. So, to understand their personality characteristics will provide a scientific basis for the intervention of psychological health.We selected top 30 personality trait words according to the order of frequency. Additionally, some methods such as social network analysis (SNA) and visualization technology of mapping knowledge domain were used in this study.Among these core personality trait words Family conscious had the 3 highest centralities and possessed the largest core status and influence. From the analysis of core-peripheral structure, we can see polarized core-perpheral structure was quite obvious. From the analysis of K-plex, there were in total 588 "K-2"K-plexs. From the analysis of Principal Components, we selected the 11 principal components.This study of personality not only can prevent disease, but also provide a scientific basis for students' psychological healthy education. In addition, we have adopted SNA to pay more attention to the relationship between personality trait words and the connection among personality dimensions. This study may provide the new ideas and methods for the research of personality structure.

Strategies to curb structural changes of lithium/transition metal oxide cathode materials & the changes’ effects on thermal & cycling stability

NASA Astrophysics Data System (ADS)

Xiqian, Yu; Enyuan, Hu; Seongmin, Bak; Yong-Ning, Zhou; Xiao-Qing, Yang

2016-01-01

Structural transformation behaviors of several typical oxide cathode materials during a heating process are reviewed in detail to provide in-depth understanding of the key factors governing the thermal stability of these materials. We also discuss applying the information about heat induced structural evolution in the study of electrochemically induced structural changes. All these discussions are expected to provide valuable insights for designing oxide cathode materials with significantly improved structural stability for safe, long-life lithium ion batteries, as the safety of lithium-ion batteries is a critical issue; it is widely accepted that the thermal instability of the cathodes is one of the most critical factors in thermal runaway and related safety problems. Project supported by the U.S. Department of Energy, the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Vehicle Technologies (Grant No. DE-SC0012704).

Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

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

Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.

2011-12-22

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformatemore » inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.« less

Structural risk and limits on agency among exotic dancers: HIV risk practices in the exotic dance club.

PubMed

Footer, Katherine H A; Lim, Sahnah; Brantley, Meredith R; Sherman, Susan G

2018-03-01

This paper provides longitudinal examination of women's health and sexual risk trajectories in US exotic dance clubs, which represent an important commercial setting for the economic mainstreaming of sexual services and an important target for public health programmes. Between July 2014 and May 2015, two semi-structured interviews (at baseline and at three months) were conducted with 24 female exotic dancers who had recently started working in in Baltimore City, USA. Results from a constant comparative analysis point to the interrelationship between the structures of the club setting, including the social context, and women's agentic practices concerning their sexual health. Study findings highlight the centrality of the interrelationship between individual- and structural-level experiences in influencing dancers' risk behavior. Findings point to the need for interventions to empower women both individually and collectively so as to provide the foundation for longer-term structural change.

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

Effects of Instruction in Narrative Structure on Childrens' Writing.

ERIC Educational Resources Information Center

Fitzgerald, Jill; Teasley, Alan B.

A study investigated whether direct instruction in story constituents and their interrelationships could enhance children's organization in story writing. It was hypothesized that the special instruction could provide children with an internalized prototype story structure that could serve as a heuristic or planning device for organizing…

Chromosome structure inside the nucleus.

PubMed

Swedlow, J R; Agard, D A; Sedat, J W

1993-06-01

Recent in situ three-dimensional structural studies have provided a new model for the 30 nm chromatin fiber. In addition, research during the past year has revealed some of the molecular complexity of non-histone chromosomal proteins. Still to come is the unification of molecular insights with chromosomal architecture.

Adolescent Social Structure and the Spread of Linguistic Change.

ERIC Educational Resources Information Center

Eckert, Penelope

1988-01-01

Detailed study of Detroit-area adolescents provides explanations for the spread of sound change outward from urban areas and upward through the socioeconomic hierarchy. Social network structure, orientation to the urban area, and phonology are contrasted for the two adolescent social categories, "Jocks" (middle class) and…

Direct solar pumping of semiconductor lasers: A feasibility study

NASA Technical Reports Server (NTRS)

Anderson, Neal G.

1992-01-01

This report describes results of NASA Grant NAG-1-1148, entitled Direct Solar Pumping of Semiconductor Lasers: A Feasibility Study. The goals of this study were to provide a preliminary assessment of the feasibility of pumping semiconductor lasers in space with directly focused sunlight and to identify semiconductor laser structures expected to operate at the lowest possible focusing intensities. It should be emphasized that the structures under consideration would provide direct optical-to-optical conversion of sunlight into laser light in a single crystal, in contrast to a configuration consisting of a solar cell or storage battery electrically pumping a current injection laser. With external modulation, such lasers could perhaps be efficient sources for intersatellite communications. We proposed specifically to develop a theoretical model of semiconductor quantum-well lasers photopumped by a broadband source, test it against existing experimental data where possible, and apply it to estimating solar pumping requirements and identifying optimum structures for operation at low pump intensities. These tasks have been accomplished, as described in this report of our completed project. The report is organized as follows: Some general considerations relevant to the solar-pumped semiconductor laser problem are discussed in Section 2, and the types of structures chosen for specific investigation are described. The details of the laser model we developed for this work are then outlined in Section 3. In Section 4, results of our study are presented, including designs for optimum lattice-matched and strained-layer solar-pumped quantum-well lasers and threshold pumping estimates for these structures. It was hoped at the outset of this work that structures could be identified which could be expected to operate continuously at solar photoexcitation intensities of several thousand suns, and this indeed turned out to be the case as described in this section. Our project is summarized in Section 5, and information on publications resulting from this work is provided in Section 6.

Effects of Marijuana Use on Brain Structure and Function: Neuroimaging Findings from a Neurodevelopmental Perspective

PubMed Central

Brumback, T.; Castro, N.; Jacobus, J.; Tapert, S.

2016-01-01

Marijuana, behind only tobacco and alcohol, is the most popular recreational drug in America with prevalence rates of use rising over the past decade. A wide range of research has highlighted neurocognitive deficits associated with marijuana use, particularly when initiated during childhood or adolescence. Neuroimaging, describing alterations to brain structure and function, has begun to provide a picture of possible mechanisms associated with the deleterious effects of marijuana use. This chapter provides a neurodevelopmental framework from which recent data on brain structural and functional abnormalities associated with marijuana use is reviewed. Based on the current data, we provide aims for future studies to more clearly delineate the effects of marijuana on the developing brain and to define underlying mechanisms of the potential long-term negative consequences of marijuana use. PMID:27503447

Constructing scientific explanations through premise-reasoning-outcome (PRO): an exploratory study to scaffold students in structuring written explanations

NASA Astrophysics Data System (ADS)

Tang, Kok-Sing

2016-06-01

This paper reports on the design and enactment of an instructional strategy aimed to support students in constructing scientific explanations. Informed by the philosophy of science and linguistic studies of science, a new instructional framework called premise-reasoning-outcome (PRO) was conceptualized, developed, and tested over two years in four upper secondary (9th-10th grade) physics and chemistry classrooms. This strategy was conceptualized based on the understanding of the structure of a scientific explanation, which comprises three primary components: (a) premise - accepted knowledge that provides the basis of the explanation, (b) reasoning - logical sequences that follow from the premise, and (c) outcome - the phenomenon to be explained. A study was carried out to examine how the PRO strategy influenced students' written explanations using multiple data sources (e.g. students' writing, lesson observations, focus group discussions). Analysis of students' writing indicates that explanations with a PRO structure were graded better by the teachers. In addition, students reported that the PRO strategy provided a useful organizational structure for writing scientific explanations, although they had some difficulties in identifying and using the structure. With the PRO as a new instructional tool, comparison with other explanation frameworks as well as implications for educational research and practice are discussed.

Developing a short measure of organizational justice: a multisample health professionals study.

PubMed

Elovainio, Marko; Heponiemi, Tarja; Kuusio, Hannamaria; Sinervo, Timo; Hintsa, Taina; Aalto, Anna-Mari

2010-11-01

To develop and test the validity of a short version of the original questionnaire measuring organizational justice. The study samples comprised working physicians (N = 2792) and registered nurses (n = 2137) from the Finnish Health Professionals study. Structural equation modelling was applied to test structural validity, using the justice scales. Furthermore, criterion validity was explored with well-being (sleeping problems) and health indicators (psychological distress/self-rated health). The short version of the organizational justice questionnaire (eight items) provides satisfactory psychometric properties (internal consistency, a good model fit of the data). All scales were associated with an increased risk of sleeping problems and psychological distress, indicating satisfactory criterion validity. This short version of the organizational justice questionnaire provides a useful tool for epidemiological studies focused on health-adverse effects of work environment.

Increasing access to sexual health care for rural and regional young people: Similarities and differences in the views of young people and service providers.

PubMed

Johnston, Karen; Harvey, Caroline; Matich, Paula; Page, Priscilla; Jukka, Clare; Hollins, Jane; Larkins, Sarah

2015-10-01

This study aims to describe the views of sexual health service providers on access issues for young people and consider them together with the views of young people themselves. A cross-sectional mixed-methods study design involving semi-structured interviews with health service providers and an electronic survey with young people. Four towns in rural and regional Queensland, Australia. A total of 32 service providers: 9 sexual health nurses, 8 general practitioners, 6 school-based youth health nurses, 5 sexual health educators, 2 Australian Aboriginal health workers and 2 youth workers. There were 391 young people who participated in the Young People's Survey. Themes generated from interviews with service providers and quantitative data from young people addressing access to sexual and reproductive health (SRH) services for rural and regional young people. Service providers frequently identified structural barriers, confidentiality and lack of awareness of SRH services as barriers for young people seeking SRH care. Young people also reported that structural factors such as transport, cost and service operating hours were important; however, they placed greater value on personal attributes of service providers, particularly welcoming and non-judgemental attitudes. Health service policy and training focused on attitudinal qualities of individual service providers may improve access to SRH services for young people. Selective staff recruitment and professional development are important to increase sensitivity to youth issues. Promotion of non-judgemental and confidential care may also improve access for youth. © 2015 National Rural Health Alliance Inc.

Free-decay time-domain modal identification for large space structures

NASA Technical Reports Server (NTRS)

Kim, Hyoung M.; Vanhorn, David A.; Doiron, Harold H.

1992-01-01

Concept definition studies for the Modal Identification Experiment (MIE), a proposed space flight experiment for the Space Station Freedom (SSF), have demonstrated advantages and compatibility of free-decay time-domain modal identification techniques with the on-orbit operational constraints of large space structures. Since practical experience with modal identification using actual free-decay responses of large space structures is very limited, several numerical and test data reduction studies were conducted. Major issues and solutions were addressed, including closely-spaced modes, wide frequency range of interest, data acquisition errors, sampling delay, excitation limitations, nonlinearities, and unknown disturbances during free-decay data acquisition. The data processing strategies developed in these studies were applied to numerical simulations of the MIE, test data from a deployable truss, and launch vehicle flight data. Results of these studies indicate free-decay time-domain modal identification methods can provide accurate modal parameters necessary to characterize the structural dynamics of large space structures.

A preliminary study of the metabolic stability of a series of benzoxazinone derivatives as potent neuropeptide Y5 antagonists.

PubMed

Dordal, Alberto; Lipkin, Mike; Macritchie, Jackie; Mas, Josep; Port, Adriana; Rose, Sally; Salgado, Leonardo; Savic, Vladimir; Schmidt, Wolfgang; Serafini, Maria Teresa; Spearing, William; Torrens, Antoni; Yeste, Sandra

2005-08-15

The metabolic stability of benzoxazinone derivatives, a potent series of NPY Y5 antagonists, has been investigated. This study resulted in the identification of the structural moieties prone to metabolic transformations and which strongly influenced the in vitro half-life. This provides opportunities to optimize the structure of this new class of NPY Y5 antagonists.

Integrated control-structure design

NASA Technical Reports Server (NTRS)

Hunziker, K. Scott; Kraft, Raymond H.; Bossi, Joseph A.

1991-01-01

A new approach for the design and control of flexible space structures is described. The approach integrates the structure and controller design processes thereby providing extra opportunities for avoiding some of the disastrous effects of control-structures interaction and for discovering new, unexpected avenues of future structural design. A control formulation based on Boyd's implementation of Youla parameterization is employed. Control design parameters are coupled with structural design variables to produce a set of integrated-design variables which are selected through optimization-based methodology. A performance index reflecting spacecraft mission goals and constraints is formulated and optimized with respect to the integrated design variables. Initial studies have been concerned with achieving mission requirements with a lighter, more flexible space structure. Details of the formulation of the integrated-design approach are presented and results are given from a study involving the integrated redesign of a flexible geostationary platform.

Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Schennach, Moritz; Breuker, Kathrin

2015-07-01

The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

Ion spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2015-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level. ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed. Examples of mass property stochastic calculations produced during a recent systems study are provided. This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime, few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed Examples of mass property stochastic calculations produced during a recent systems study are provided This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime,few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Structural covariance of neostriatal and limbic regions in patients with obsessive-compulsive disorder.

PubMed

Subirà, Marta; Cano, Marta; de Wit, Stella J; Alonso, Pino; Cardoner, Narcís; Hoexter, Marcelo Q; Kwon, Jun Soo; Nakamae, Takashi; Lochner, Christine; Sato, João R; Jung, Wi Hoon; Narumoto, Jin; Stein, Dan J; Pujol, Jesus; Mataix-Cols, David; Veltman, Dick J; Menchón, José M; van den Heuvel, Odile A; Soriano-Mas, Carles

2016-03-01

Frontostriatal and frontoamygdalar connectivity alterations in patients with obsessive-compulsive disorder (OCD) have been typically described in functional neuroimaging studies. However, structural covariance, or volumetric correlations across distant brain regions, also provides network-level information. Altered structural covariance has been described in patients with different psychiatric disorders, including OCD, but to our knowledge, alterations within frontostriatal and frontoamygdalar circuits have not been explored. We performed a mega-analysis pooling structural MRI scans from the Obsessive-compulsive Brain Imaging Consortium and assessed whole-brain voxel-wise structural covariance of 4 striatal regions (dorsal and ventral caudate nucleus, and dorsal-caudal and ventral-rostral putamen) and 2 amygdalar nuclei (basolateral and centromedial-superficial). Images were preprocessed with the standard pipeline of voxel-based morphometry studies using Statistical Parametric Mapping software. Our analyses involved 329 patients with OCD and 316 healthy controls. Patients showed increased structural covariance between the left ventral-rostral putamen and the left inferior frontal gyrus/frontal operculum region. This finding had a significant interaction with age; the association held only in the subgroup of older participants. Patients with OCD also showed increased structural covariance between the right centromedial-superficial amygdala and the ventromedial prefrontal cortex. This was a cross-sectional study. Because this is a multisite data set analysis, participant recruitment and image acquisition were performed in different centres. Most patients were taking medication, and treatment protocols differed across centres. Our results provide evidence for structural network-level alterations in patients with OCD involving 2 frontosubcortical circuits of relevance for the disorder and indicate that structural covariance contributes to fully characterizing brain alterations in patients with psychiatric disorders.

Static and Dynamic Magnetic Response in Ferrofluids

DTIC Science & Technology

2007-10-30

much below (dodecane) the carrier fluid freezing temperatures providing interesting regimes to study the relaxation mechanisms associated with the...blocking temperature was just above (hexane) and much below (dodecane) the carrier fluid freezing temperatures providing interesting regimes to study...focused mainly on the following tasks: 1. Chemical synthesis of iron oxide and soft ferrite nanoparticles using co- precipitation, structural and

Correlations and clustering in wholesale electricity markets

DOE PAGES

Cui, Tianyu; Caravelli, Francesco; Ududec, Cozmin

2017-11-24

We study the structure of locational marginal prices in day-ahead and real-time wholesale electricity markets. In particular, we consider the case of two North American markets and show that the price correlations contain information on the locational structure of the grid. We study various clustering methods and introduce a type of correlation function based on event synchronization for spiky time series, and another based on string correlations of location names provided by the markets. As a result, this allows us to reconstruct aspects of the locational structure of the grid.

Correlations and clustering in wholesale electricity markets

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

Cui, Tianyu; Caravelli, Francesco; Ududec, Cozmin

We study the structure of locational marginal prices in day-ahead and real-time wholesale electricity markets. In particular, we consider the case of two North American markets and show that the price correlations contain information on the locational structure of the grid. We study various clustering methods and introduce a type of correlation function based on event synchronization for spiky time series, and another based on string correlations of location names provided by the markets. As a result, this allows us to reconstruct aspects of the locational structure of the grid.

Correlations and clustering in wholesale electricity markets

NASA Astrophysics Data System (ADS)

Cui, Tianyu; Caravelli, Francesco; Ududec, Cozmin

2018-02-01

We study the structure of locational marginal prices in day-ahead and real-time wholesale electricity markets. In particular, we consider the case of two North American markets and show that the price correlations contain information on the locational structure of the grid. We study various clustering methods and introduce a type of correlation function based on event synchronization for spiky time series, and another based on string correlations of location names provided by the markets. This allows us to reconstruct aspects of the locational structure of the grid.

Quantum chemical studies of estrogenic compounds

USDA-ARS?s Scientific Manuscript database

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

Quantum Monte Carlo Studies of Bulk and Few- or Single-Layer Black Phosphorus

NASA Astrophysics Data System (ADS)

Shulenburger, Luke; Baczewski, Andrew; Zhu, Zhen; Guan, Jie; Tomanek, David

2015-03-01

The electronic and optical properties of phosphorus depend strongly on the structural properties of the material. Given the limited experimental information on the structure of phosphorene, it is natural to turn to electronic structure calculations to provide this information. Unfortunately, given phosphorus' propensity to form layered structures bound by van der Waals interactions, standard density functional theory methods provide results of uncertain accuracy. Recently, it has been demonstrated that Quantum Monte Carlo (QMC) methods achieve high accuracy when applied to solids in which van der Waals forces play a significant role. In this talk, we will present QMC results from our recent calculations on black phosphorus, focusing on the structural and energetic properties of monolayers, bilayers and bulk structures. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Hybrid solar cells composed of perovskite and polymer photovoltaic structures

NASA Astrophysics Data System (ADS)

Phaometvarithorn, Apatsanan; Chuangchote, Surawut; Kumnorkaew, Pisist; Wootthikanokkhan, Jatuphorn

2018-06-01

Organic/inorganic lead halide perovskite solar cells have recently attracted much attention in photovoltaic research, due to the devices show promising ways to achieve high efficiencies. The perovskite devices with high efficiencies, however, are typically fabricated in tandem solar cell which is complicated. In this research work, we introduce a solar cell device with the combination of CH3NH3PbI3-xClx perovskite and bulk heterojunction PCDTBT:PC70BM polymer without any tandem structure. The new integrated perovskite/polymer hybrid structure of ITO/PEDOT:PSS/perovskite/PCDTBT:PC70BM/PC70BM/TiOx/Al provides higher power conversion efficiency (PCE) of devices compared with conventional perovskite cell structure. With the optimized PCDTBT:PC70BM thickness of ∼70 nm, the highest PCE of 11.67% is achieved. Variation of conducting donor polymers in this new structure is also preliminary demonstrated. This study provides an attractively innovative structure and a promising design for further development of the new-generation solar cells.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

SFM-FDTD analysis of triangular-lattice AAA structure: Parametric study of the TEM mode

NASA Astrophysics Data System (ADS)

Hamidi, M.; Chemrouk, C.; Belkhir, A.; Kebci, Z.; Ndao, A.; Lamrous, O.; Baida, F. I.

2014-05-01

This theoretical work reports a parametric study of enhanced transmission through annular aperture array (AAA) structure arranged in a triangular lattice. The effect of the incidence angle in addition to the inner and outer radii values on the evolution of the transmission spectra is carried out. To this end, a 3D Finite-Difference Time-Domain code based on the Split Field Method (SFM) is used to calculate the spectral response of the structure for any angle of incidence. In order to work through an orthogonal unit cell which presents the advantage to reduce time and space of computation, special periodic boundary conditions are implemented. This study provides a new modeling of AAA structures useful for producing tunable ultra-compact devices.

Network structure of subway passenger flows

NASA Astrophysics Data System (ADS)

Xu, Q.; Mao, B. H.; Bai, Y.

2016-03-01

The results of transportation infrastructure network analyses have been used to analyze complex networks in a topological context. However, most modeling approaches, including those based on complex network theory, do not fully account for real-life traffic patterns and may provide an incomplete view of network functions. This study utilizes trip data obtained from the Beijing Subway System to characterize individual passenger movement patterns. A directed weighted passenger flow network was constructed from the subway infrastructure network topology by incorporating trip data. The passenger flow networks exhibit several properties that can be characterized by power-law distributions based on flow size, and log-logistic distributions based on the fraction of boarding and departing passengers. The study also characterizes the temporal patterns of in-transit and waiting passengers and provides a hierarchical clustering structure for passenger flows. This hierarchical flow organization varies in the spatial domain. Ten cluster groups were identified, indicating a hierarchical urban polycentric structure composed of large concentrated flows at urban activity centers. These empirical findings provide insights regarding urban human mobility patterns within a large subway network.

Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion

PubMed Central

Bignon, Emmanuelle; Gattuso, Hugo; Morell, Christophe; Dehez, François; Georgakilas, Alexandros G.; Monari, Antonio; Dumont, Elise

2016-01-01

Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions. PMID:27587587

How does vegetation structure influence woodpeckers and secondary cavity nesting birds in African cork oak forest?

NASA Astrophysics Data System (ADS)

Segura, Amalia

2017-08-01

The Great Spotted Woodpecker provides important information about the status of a forest in terms of structure and age. As a primary cavity creator, it provides small-medium size cavities for passerines. However, despite its interest as an ecosystem engineer, studies of this species in Africa are scarce. Here, spatially explicit predictive models were used to investigate how forest structural variables are related to both the Great Spotted Woodpecker and secondary cavity nesting birds in Maamora cork oak forest (northwest Morocco). A positive association between Great Spotted Woodpecker and both dead-tree density and large mature trees (>60 cm dbh) was found. This study area, Maamora, has an old-growth forest structure incorporating a broad range of size and condition of live and dead trees, favouring Great Spotted Woodpecker by providing high availability of foraging and excavating sites. Secondary cavity nesting birds, represented by Great Tit, African Blue Tit, and Hoopoe, were predicted by Great Spotted Woodpecker detections. The findings suggest that the conservation of the Maamora cork oak forest could be key to maintaining these hole-nesting birds. However, this forest is threatened by forestry practises and livestock overgrazing and the challenge is therefore to find sustainable management strategies that ensure conservation while allowing its exploitation.

Stigmatized Attitude of Healthcare Providers: A Barrier for Delivering Health Services to HIV Positive Patients

PubMed Central

Zarei, Nooshin; Joulaei, Hassan; Darabi, Elahe; Fararouei, Mohammad

2015-01-01

Background: Despite the success of developed countries in preventing the spread of HIV/AIDS, the disease is expanding in developing countries where an unfavorable attitude exists among people, health professionals and employees. This study aimed to assess the stigmatized attitude among health care providers toward people living with HIV (PLWHA). Methods: The study is a cross-sectional survey. The data were gathered using a structured questionnaire. The study sample included 575 health care providers of public and private hospitals in Shiraz. The data were gathered using a structured questionnaire in spring 2014. Data analysis was carried out using the Statistical Package for Social Sciences, version 21. Results: The most dominant attitude of the health care providers toward HIV/AIDS patients was related to fear (42.42%). According to the results of this study, there was a significant relationship between stigmatized attitude of the health care providers and their religious beliefs, society stigmatized attitude, and knowledge of transmission routes. The relationship between social stigmatized attitude of health care providers and their knowledge of transmission routes, with their willingness to provide services to patients is significant, as well (P<0.05). 39.6% and 46.2% of the respondents preferred not to provide services to the prostitutes and homosexual patients. Conclusion: Fear of contamination and social stigmatized attitude are the main impediments to dealing with patients and providing services to them. Hence, it seems that creating an effective knowledge about transmission and correcting the socio-cultural beliefs of health providers are two key strategies to tackle this problem. PMID:26448956

Photoreceptor Outer Segment-like Structures in Long-Term 3D Retinas from Human Pluripotent Stem Cells.

PubMed

Wahlin, Karl J; Maruotti, Julien A; Sripathi, Srinivasa R; Ball, John; Angueyra, Juan M; Kim, Catherine; Grebe, Rhonda; Li, Wei; Jones, Bryan W; Zack, Donald J

2017-04-10

The retinal degenerative diseases, which together constitute a leading cause of hereditary blindness worldwide, are largely untreatable. Development of reliable methods to culture complex retinal tissues from human pluripotent stem cells (hPSCs) could offer a means to study human retinal development, provide a platform to investigate the mechanisms of retinal degeneration and screen for neuroprotective compounds, and provide the basis for cell-based therapeutic strategies. In this study, we describe an in vitro method by which hPSCs can be differentiated into 3D retinas with at least some important features reminiscent of a mature retina, including exuberant outgrowth of outer segment-like structures and synaptic ribbons, photoreceptor neurotransmitter expression, and membrane conductances and synaptic vesicle release properties consistent with possible photoreceptor synaptic function. The advanced outer segment-like structures reported here support the notion that 3D retina cups could serve as a model for studying mature photoreceptor development and allow for more robust modeling of retinal degenerative disease in vitro.

The Strengths and Difficulties Questionnaire-Parents for Italian School-Aged Children: Psychometric Properties and Norms.

PubMed

Tobia, Valentina; Marzocchi, Gian Marco

2018-02-01

The Strengths and Difficulties Questionnaire [SDQ; (1)] is a multi-informant instrument for screening developmental psychopathology. This study contributes to the validation of the Italian SDQ-Parent version (SDQ-P), analyzing its factorial structure, providing norms and investigating cross-informant agreement (parents-teachers). The SDQ-P and the SDQ-Teacher version (SDQ-T) were completed for 1917 primary and middle school students. Confirmatory factor analyses were performed to compare two factorial structures: the original five-factor model and the structure obtained in a past Italian study (2). The original model showed the best fit. Significant differences by gender and school grade were found; norms were provided separately for males and females attending 1st-2nd, 3rd-5th and 6th-8th grades. Finally, the analysis of parent-teacher agreement showed correlations ranging from small (prosocial behavior) to large (hyperactivity-inattention). This study offers some reflections on the best way to use this instrument in a community sample.

Advantages and pitfalls in the application of mixed-model association methods.

PubMed

Yang, Jian; Zaitlen, Noah A; Goddard, Michael E; Visscher, Peter M; Price, Alkes L

2014-02-01

Mixed linear models are emerging as a method of choice for conducting genetic association studies in humans and other organisms. The advantages of the mixed-linear-model association (MLMA) method include the prevention of false positive associations due to population or relatedness structure and an increase in power obtained through the application of a correction that is specific to this structure. An underappreciated point is that MLMA can also increase power in studies without sample structure by implicitly conditioning on associated loci other than the candidate locus. Numerous variations on the standard MLMA approach have recently been published, with a focus on reducing computational cost. These advances provide researchers applying MLMA methods with many options to choose from, but we caution that MLMA methods are still subject to potential pitfalls. Here we describe and quantify the advantages and pitfalls of MLMA methods as a function of study design and provide recommendations for the application of these methods in practical settings.

The Role of Industry Training Advisory Bodies. Monograph Series No. 2.

ERIC Educational Resources Information Center

Wooden, Mark

Designed to provide a better understanding of how Industry Training Advisory Bodies (ITABs) operate, a study showed whether current arrangements, incentives, and structures are conducive to ITABs always working in the best interests of their constituents: employers. Semi-structured interviews were conducted with chief executive officers (CEOs) of…

Cognitive Control over Learning: Creating, Clustering, and Generalizing Task-Set Structure

ERIC Educational Resources Information Center

Collins, Anne G. E.; Frank, Michael J.

2013-01-01

Learning and executive functions such as task-switching share common neural substrates, notably prefrontal cortex and basal ganglia. Understanding how they interact requires studying how cognitive control facilitates learning but also how learning provides the (potentially hidden) structure, such as abstract rules or task-sets, needed for…

Long-Term Memory and Learning

ERIC Educational Resources Information Center

Crossland, John

2011-01-01

The English National Curriculum Programmes of Study emphasise the importance of knowledge, understanding and skills, and teachers are well versed in structuring learning in those terms. Research outcomes into how long-term memory is stored and retrieved provide support for structuring learning in this way. Four further messages are added to the…

Structure and pragmatics in informal argument: circularity and question-begging.

PubMed

Brem, Sarah K.

2003-04-01

Most everyday arguments are informal, as contrasted with the formal arguments of logic and mathematics. Whereas formal argument is well understood, the nature of informal argument is more elusive. A recent study by Rips (2002) provides further evidence regarding the roles of structure and pragmatics in informal argument.

Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

USDA-ARS?s Scientific Manuscript database

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

An Examination of Statistical Power in Multigroup Dynamic Structural Equation Models

ERIC Educational Resources Information Center

Prindle, John J.; McArdle, John J.

2012-01-01

This study used statistical simulation to calculate differential statistical power in dynamic structural equation models with groups (as in McArdle & Prindle, 2008). Patterns of between-group differences were simulated to provide insight into how model parameters influence power approximations. Chi-square and root mean square error of…

Reaching Agreement: The Structure & Pragmatics of Critical Care Nurses' Informal Argument

ERIC Educational Resources Information Center

Hagler, Debra A.; Brem, Sarah K.

2008-01-01

The hospital critical care unit provides an authentic, high-stakes setting for studying reasoning, argumentation, and discourse. In particular, it allows examination of structural and pragmatic features of informal collaborative argument created while participants are engaged in familiar, meaningful activities central to their work. The nursing…

A New History, Macrohistory, and Structure in History.

ERIC Educational Resources Information Center

Emerson, Mark F.

Toward the improvement of teaching history and to provide student insights into the study of history, a course involving structure, relevancy, an interdisciplinary approach, and innovation is suggested which advocates analyzing what has happened in the past as a whole, as revealed by the various sciences of archaeology, anthropology, paleontology,…

Adjustable internal structure for reconstructing gradient index profile of crystalline lens.

PubMed

Bahrami, Mehdi; Goncharov, Alexander V; Pierscionek, Barbara K

2014-03-01

Employing advanced technologies in studying the crystalline lens of the eye has improved our understanding of the refractive index gradient of the lens. Reconstructing and studying such a complex structure requires models with adaptable internal geometry that can be altered to simulate geometrical and optical changes of the lens with aging. In this Letter, we introduce an optically well-defined, geometrical structure for modeling the gradient refractive index profile of the crystalline lens with the advantage of an adjustable internal structure that is not available with existing models. The refractive index profile assigned to this rotationally symmetric geometry is calculated numerically, yet it is shown that this does not limit the model. The study provides a basis for developing lens models with sophisticated external and internal structures without the need for analytical solutions to calculate refractive index profiles.

Designing a ticket to ride with the Cognitive Work Analysis Design Toolkit.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G; Jenkins, Daniel P

2015-01-01

Cognitive work analysis has been applied in the design of numerous sociotechnical systems. The process used to translate analysis outputs into design concepts, however, is not always clear. Moreover, structured processes for translating the outputs of ergonomics methods into concrete designs are lacking. This paper introduces the Cognitive Work Analysis Design Toolkit (CWA-DT), a design approach which has been developed specifically to provide a structured means of incorporating cognitive work analysis outputs in design using design principles and values derived from sociotechnical systems theory. This paper outlines the CWA-DT and describes its application in a public transport ticketing design case study. Qualitative and quantitative evaluations of the process provide promising early evidence that the toolkit fulfils the evaluation criteria identified for its success, with opportunities for improvement also highlighted. The Cognitive Work Analysis Design Toolkit has been developed to provide ergonomics practitioners with a structured approach for translating the outputs of cognitive work analysis into design solutions. This paper demonstrates an application of the toolkit and provides evaluation findings.

A structural perspective of the flavivirus life cycle.

PubMed

Mukhopadhyay, Suchetana; Kuhn, Richard J; Rossmann, Michael G

2005-01-01

Dengue, Japanese encephalitis, West Nile and yellow fever belong to the Flavivirus genus, which is a member of the Flaviviridae family. They are human pathogens that cause large epidemics and tens of thousands of deaths annually in many parts of the world. The structural organization of these viruses and their associated structural proteins has provided insight into the molecular transitions that occur during the viral life cycle, such as assembly, budding, maturation and fusion. This review focuses mainly on structural studies of dengue virus.

Stress-strain state of the structure in the service area of underground railway

NASA Astrophysics Data System (ADS)

Barabash, M.; Bashinsky, Y.; Korjakins, A.

2017-10-01

The paper focuses on numerical study how vibration due to underground trains influences the load-bearing building structures. Diagrams of vibration levels for monolithic floor slab depending on frequency are obtained. Levels of vibrations on floor slabs and columns are measured. The simulation of dynamic load from underground railway onto load-bearing building structures is presented as an example with account of load transmission through the soil. Recommendations for generation of design model in dynamic analysis of structure are provided.

Designing food structures for nutrition and health benefits.

PubMed

Norton, Jennifer E; Wallis, Gareth A; Spyropoulos, Fotis; Lillford, Peter J; Norton, Ian T

2014-01-01

In addition to providing specific sensory properties (e.g., flavor or textures), there is a need to produce foods that also provide functionality within the gastrointestinal (GI) tract, over and above simple nutrition. As such, there is a need to understand the physical and chemical processes occurring in the mouth, stomach, small intestine, and large intestine, in addition to the food structure-physiology interactions. In vivo techniques and in vitro models have allowed us to study and simulate these processes, which aids us in the design of food microstructures that can provide functionality within the human body. Furthermore, it is important to be aware of the health or nutritional needs of different groups of consumers when designing food structures, to provide targeted functionality. Examples of three groups of consumers (elderly, obese, and athletes) are given to demonstrate their differing nutritional requirements and the formulation engineering approaches that can be utilized to improve the health of these individuals. Eating is a pleasurable process, but foods of the future will be required to provide much more in terms of functionality for health and nutrition.

G Protein-Coupled Receptor Rhodopsin: A Prospectus

PubMed Central

Filipek, Sławomir; Stenkamp, Ronald E.; Teller, David C.; Palczewski, Krzysztof

2006-01-01

Rhodopsin is a retinal photoreceptor protein of bipartite structure consisting of the transmembrane protein opsin and a light-sensitive chromophore 11-cis-retinal, linked to opsin via a protonated Schiff base. Studies on rhodopsin have unveiled many structural and functional features that are common to a large and pharmacologically important group of proteins from the G protein-coupled receptor (GPCR) superfamily, of which rhodopsin is the best-studied member. In this work, we focus on structural features of rhodopsin as revealed by many biochemical and structural investigations. In particular, the high-resolution structure of bovine rhodopsin provides a template for understanding how GPCRs work. We describe the sensitivity and complexity of rhodopsin that lead to its important role in vision. PMID:12471166

Multifunctional composites for energy storage

NASA Astrophysics Data System (ADS)

Shuvo, Mohammad Arif I.; Karim, Hasanul; Rajib, Md; Delfin, Diego; Lin, Yirong

2014-03-01

Electrochemical super-capacitors have become one of the most important topics in both academia and industry as novel energy storage devices because of their high power density, long life cycles, and high charge/discharge efficiency. Recently, there has been an increasing interest in the development of multifunctional structural energy storage devices such as structural super-capacitors for applications in aerospace, automobiles and portable electronics. These multifunctional structural super-capacitors provide lighter structures combining energy storage and load bearing functionalities. Due to their superior materials properties, carbon fiber composites have been widely used in structural applications for aerospace and automotive industries. Besides, carbon fiber has good electrical conductivity which will provide lower equivalent series resistance; therefore, it can be an excellent candidate for structural energy storage applications. Hence, this paper is focused on performing a pilot study for using nanowire/carbon fiber hybrids as building materials for structural energy storage materials; aiming at enhancing the charge/discharge rate and energy density. This hybrid material combines the high specific surface area of carbon fiber and pseudo-capacitive effect of metal oxide nanowires which were grown hydrothermally in an aligned fashion on carbon fibers. The aligned nanowire array could provide a higher specific surface area that leads to high electrode-electrolyte contact area and fast ion diffusion rates. Scanning Electron Microscopy (SEM) and XRay Diffraction (XRD) measurements were used for the initial characterization of this nanowire/carbon fiber hybrid material system. Electrochemical testing has been performed using a potentio-galvanostat. The results show that gold sputtered nanowire hybrid carbon fiber provides 65.9% better performance than bare carbon fiber cloth as super-capacitor.

Cytotoxic lanostane-type triterpenoids from the fruiting bodies of Ganoderma lucidum and their structure-activity relationships.

PubMed

Chen, Shaodan; Li, Xiangmin; Yong, Tianqiao; Wang, Zhanggen; Su, Jiyan; Jiao, Chunwei; Xie, Yizhen; Yang, Burton B

2017-02-07

We conducted a study of Ganoderma lucidum metabolites and isolated 35 lanostane-type triterpenoids, including 5 new ganoderols (1-5). By spectroscopy, we compared the structures of these compounds with known related compounds in this group. All of the isolated compounds were assayed for their effect against the human breast carcinoma cell line MDA-MB-231 and hepatocellular carcinoma cell line HepG2. Corresponding three-dimensional quantitative structure-activity relationship (3D-QSAR) models were built and analyzed using Discovery Studio. These results provide further evidence for anti-cancer constituents within Ganoderma lucidum, and may provide a theoretical foundation for designing novel therapeutic compounds.

Cognitive control over learning: Creating, clustering and generalizing task-set structure

PubMed Central

Collins, Anne G.E.; Frank, Michael J.

2013-01-01

Executive functions and learning share common neural substrates essential for their expression, notably in prefrontal cortex and basal ganglia. Understanding how they interact requires studying how cognitive control facilitates learning, but also how learning provides the (potentially hidden) structure, such as abstract rules or task-sets, needed for cognitive control. We investigate this question from three complementary angles. First, we develop a new computational “C-TS” (context-task-set) model inspired by non-parametric Bayesian methods, specifying how the learner might infer hidden structure and decide whether to re-use that structure in new situations, or to create new structure. Second, we develop a neurobiologically explicit model to assess potential mechanisms of such interactive structured learning in multiple circuits linking frontal cortex and basal ganglia. We systematically explore the link betweens these levels of modeling across multiple task demands. We find that the network provides an approximate implementation of high level C-TS computations, where manipulations of specific neural mechanisms are well captured by variations in distinct C-TS parameters. Third, this synergism across models yields strong predictions about the nature of human optimal and suboptimal choices and response times during learning. In particular, the models suggest that participants spontaneously build task-set structure into a learning problem when not cued to do so, which predicts positive and negative transfer in subsequent generalization tests. We provide evidence for these predictions in two experiments and show that the C-TS model provides a good quantitative fit to human sequences of choices in this task. These findings implicate a strong tendency to interactively engage cognitive control and learning, resulting in structured abstract representations that afford generalization opportunities, and thus potentially long-term rather than short-term optimality. PMID:23356780

Unraveling protein catalysis through neutron diffraction

NASA Astrophysics Data System (ADS)

Myles, Dean

Neutron scattering and diffraction are exquisitely sensitive to the location, concentration and dynamics of hydrogen atoms in materials and provide a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, non-destructive suite of instruments for biophysical characterization that provide spatial and dynamic information spanning from Angstroms to microns and from picoseconds to microseconds, respectively. Applications range from atomic-resolution analysis of individual hydrogen atoms in enzymes, through to multi-scale analysis of hierarchical structures and assemblies in biological complexes, membranes and in living cells. Here we describe how the precise location of protein and water hydrogen atoms using neutron diffraction provides a more complete description of the atomic and electronic structures of proteins, enabling key questions concerning enzyme reaction mechanisms, molecular recognition and binding and protein-water interactions to be addressed. Current work is focused on understanding how molecular structure and dynamics control function in photosynthetic, cell signaling and DNA repair proteins. We will highlight recent studies that provide detailed understanding of the physiochemical mechanisms through which proteins recognize ligands and catalyze reactions, and help to define and understand the key principles involved.

Assessment of variations in taxonomic diversity, forest structure, and aboveground biomass using remote sensing along an altitudinal gradient in tropical montane forest of Costa Rica

NASA Astrophysics Data System (ADS)

Robinson, C. M.; Saatchi, S. S.; Clark, D.; Fricker, G. A.; Wolf, J.; Gillespie, T. W.; Rovzar, C. M.; Andelman, S.

2012-12-01

This research sought to understand how alpha and beta diversity of plants vary and relate to the three-dimensional vegetation structure and aboveground biomass along environmental gradients in the tropical montane forests of Braulio Carrillo National Park in Costa Rica. There is growing evidence that ecosystem structure plays an important role in defining patterns of species diversity and along with abiotic factors (climate and edaphic) control the phenotypic and functional variations across landscapes. It is well documented that strong subdivisions at local and regional scales are found mainly on geologic or climate gradients. These general determinants of biodiversity are best demonstrated in regions with natural gradients such as tropical montane forests. Altitudinal gradients provide a landscape scale changes through variations in topography, climate, and edaphic conditions on which we tested several theoretical and biological hypotheses regarding drivers of biodiversity. The study was performed by using forest inventory and botanical data from nine 1-ha plots ranging from 100 m to 2800 m above sea level and remote sensing data from airborne lidar and radar sensors to quantify variations in forest structure. In this study we report on the effectiveness of relating patterns of tree taxonomic alpha diversity to three-dimensional structure of a tropical montane forest using lidar and radar observations of forest structure and biomass. We assessed alpha and beta diversity at the species, genus, and family levels utilizing datasets provided by the Terrestrial Ecology Assessment and Monitoring (TEAM) Network. Through the comparison to active remote sensing imagery, our results show that there is a strong relationship between forest 3D-structure, and alpha and beta diversity controlled by variations in abiotic factors along the altitudinal gradient. Using spatial analysis with the aid of remote sensing data, we find distinct patterns along the environmental gradients defining species turnover and changes in functional diversity. The study will provide novel approaches to use detailed spatial information from remote sensing data to study relations between functional and taxonomic dimensions of diversity.

Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

PubMed

Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

2017-01-01

Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

Characterizing Exterior and Interior Tropical Forest Structure Variability with Full-Waveform Airborne LIDAR Data in Lopé, Gabon

NASA Astrophysics Data System (ADS)

Marselis, S.; Tang, H.; Blair, J. B.; Hofton, M. A.; Armston, J.; Dubayah, R.

2017-12-01

Terrestrial ecotones, transition zones between ecological systems, have been identified as important regions to monitor the effects of environmental and human pressures on ecosystems. To observe such changes, the variability in vegetation horizontal and vertical structure must be characterized. The objective of this study is to quantify changes in vegetation structure in a tropical forest-savanna mosaic using airborne waveform lidar data. The study area is located in the northern part of the Lopé National Park in Gabon and is comprised of the vegetation types: savanna, colonizing forest, monodominant Okoumé forest, young Marantaceae forest and mixed Marantaceae forest. The lidar data were collected by the Land Vegetation and Ice Sensor (LVIS) in early March 2016, during the AfriSAR campaign. Metrics derived from the LVIS waveforms were then used to classify the five main vegetation types and characterize observed structural variability within types and across ecotones. Several supervised and unsupervised classification alogrithms, in combination with statistical analysis, were applied. The investigated methods are promising in their use to directly describe the structural variability within and between different vegetation types, map these vegetation types and the extent and location of their transition zones, and to characterize, among other attributes, the sharpness and width of such ecotones. These results provide important information in ecosystem studies as these methods can be used to study changes in vegetation structure, species-specific habitat, or the effects of deforestation and other human and natural pressures on the exterior and interior forest structure. These methods thus provide ample opportunity to assess the vegetation structure in degraded and second growth tropical forests to explore effects of e.g. grazing, logging or fragmentation. From this study we can conclude that lidar waveform remote sensing is highly useful in distinguishing vegetation types and their transition zones which will be increasingly important when assessing the impact of natural and human pressures on the world's tropical forests.

Defining the essential anatomical coverage provided by military body armour against high energy projectiles.

PubMed

Breeze, John; Lewis, E A; Fryer, R; Hepper, A E; Mahoney, Peter F; Clasper, Jon C

2016-08-01

Body armour is a type of equipment worn by military personnel that aims to prevent or reduce the damage caused by ballistic projectiles to structures within the thorax and abdomen. Such injuries remain the leading cause of potentially survivable deaths on the modern battlefield. Recent developments in computer modelling in conjunction with a programme to procure the next generation of UK military body armour has provided the impetus to re-evaluate the optimal anatomical coverage provided by military body armour against high energy projectiles. A systematic review of the literature was undertaken to identify those anatomical structures within the thorax and abdomen that if damaged were highly likely to result in death or significant long-term morbidity. These structures were superimposed upon two designs of ceramic plate used within representative body armour systems using a computerised representation of human anatomy. Those structures requiring essential medical coverage by a plate were demonstrated to be the heart, great vessels, liver and spleen. For the 50th centile male anthropometric model used in this study, the front and rear plates from the Enhanced Combat Body Armour system only provide limited coverage, but do fulfil their original requirement. The plates from the current Mark 4a OSPREY system cover all of the structures identified in this study as requiring coverage except for the abdominal sections of the aorta and inferior vena cava. Further work on sizing of plates is recommended due to its potential to optimise essential medical coverage. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Modeling the Dependency Structure of Integrated Intensity Processes

PubMed Central

Ma, Yong-Ki

2015-01-01

This paper studies an important issue of dependence structure. To model this structure, the intensities within the Cox processes are driven by dependent shot noise processes, where jumps occur simultaneously and their sizes are correlated. The joint survival probability of the integrated intensities is explicitly obtained from the copula with exponential marginal distributions. Subsequently, this result can provide a very useful guide for credit risk management. PMID:26270638

Evolution: Tracing the origins of centrioles, cilia, and flagella.

PubMed

Carvalho-Santos, Zita; Azimzadeh, Juliette; Pereira-Leal, José B; Bettencourt-Dias, Mónica

2011-07-25

Centrioles/basal bodies (CBBs) are microtubule-based cylindrical organelles that nucleate the formation of centrosomes, cilia, and flagella. CBBs, cilia, and flagella are ancestral structures; they are present in all major eukaryotic groups. Despite the conservation of their core structure, there is variability in their architecture, function, and biogenesis. Recent genomic and functional studies have provided insight into the evolution of the structure and function of these organelles.

Is forest structure related to fire severity? Yes, no, and maybe: Methods and insights in quantifying the answer

Treesearch

Theresa Benavidez Jain; Russell T. Graham

2004-01-01

Wildfires in 2000 burned over 500,000 forested ha in the Northern Rocky Mountains. In 2001, National Fire Plan funding became available to evaluate the influence of pre-wildfire forest structure on post wildfire fire severity. Results from this study will provide information on forest structures that are resilient to wildfire. Three years of data (558 plots) have been...

Analysis of composite plates by using mechanics of structure genome and comparison with ANSYS

NASA Astrophysics Data System (ADS)

Zhao, Banghua

Motivated by a recently discovered concept, Structure Genome (SG) which is defined as the smallest mathematical building block of a structure, a new approach named Mechanics of Structure Genome (MSG) to model and analyze composite plates is introduced. MSG is implemented in a general-purpose code named SwiftComp(TM), which provides the constitutive models needed in structural analysis by homogenization and pointwise local fields by dehomogenization. To improve the user friendliness of SwiftComp(TM), a simple graphic user interface (GUI) based on ANSYS Mechanical APDL platform, called ANSYS-SwiftComp GUI is developed, which provides a convenient way to create some common SG models or arbitrary customized SG models in ANSYS and invoke SwiftComp(TM) to perform homogenization and dehomogenization. The global structural analysis can also be handled in ANSYS after homogenization, which could predict the global behavior and provide needed inputs for dehomogenization. To demonstrate the accuracy and efficiency of the MSG approach, several numerical cases are studied and compared using both MSG and ANSYS. In the ANSYS approach, 3D solid element models (ANSYS 3D approach) are used as reference models and the 2D shell element models created by ANSYS Composite PrepPost (ACP approach) are compared with the MSG approach. The results of the MSG approach agree well with the ANSYS 3D approach while being as efficient as the ACP approach. Therefore, the MSG approach provides an efficient and accurate new way to model composite plates.

Investigating buried polymer interfaces using sum frequency generation vibrational spectroscopy

PubMed Central

Chen, Zhan

2010-01-01

This paper reviews recent progress in the studies of buried polymer interfaces using sum frequency generation (SFG) vibrational spectroscopy. Both buried solid/liquid and solid/solid interfaces involving polymeric materials are discussed. SFG studies of polymer/water interfaces show that different polymers exhibit varied surface restructuring behavior in water, indicating the importance of probing polymer/water interfaces in situ. SFG has also been applied to the investigation of interfaces between polymers and other liquids. It has been found that molecular interactions at such polymer/liquid interfaces dictate interfacial polymer structures. The molecular structures of silane molecules, which are widely used as adhesion promoters, have been investigated using SFG at buried polymer/silane and polymer/polymer interfaces, providing molecular-level understanding of polymer adhesion promotion. The molecular structures of polymer/solid interfaces have been examined using SFG with several different experimental geometries. These results have provided molecular-level information about polymer friction, adhesion, interfacial chemical reactions, interfacial electronic properties, and the structure of layer-by-layer deposited polymers. Such research has demonstrated that SFG is a powerful tool to probe buried interfaces involving polymeric materials, which are difficult to study by conventional surface sensitive analytical techniques. PMID:21113334

Chondron curvature mapping in growth plate cartilage under compressive loading.

PubMed

Vendra, Bhavya B; Roan, Esra; Williams, John L

2018-05-18

The physis, or growth plate, is a layer of cartilage responsible for long bone growth. It is organized into reserve, proliferative and hypertrophic zones. Unlike the reserve zone where chondrocytes are randomly arranged, either singly or in pairs, the proliferative and hypertrophic chondrocytes are arranged within tubular structures called chondrons. In previous studies, the strain patterns within the compressed growth plate have been reported to be nonuniform and inhomogeneous, with an apparent random pattern in compressive strains and a localized appearance of tensile strains. In this study we measured structural deformations along the entire lengths of chondrons when the physis was subjected to physiological (20%) and hyper-physiological (30% and 40%) levels of compression. This provided a means to interpret the apparent random strain patterns seen in texture correlation maps in terms of bending deformations of chondron structures and provided a physical explanation for the inhomogeneous and nonuniform strain patterns reported in previous studies. We observed relatively large bending deformations (kinking) of the chondron structures at the interface of the reserve and proliferative zones during compression. Bending in this region may induce dividing cells to align longitudinally to maintain column formation and drive longitudinal growth. Copyright © 2018 Elsevier Ltd. All rights reserved.

Project Ranger Adopter's Guide, 1979.

ERIC Educational Resources Information Center

Douglas, Randi; McCann, Karen, Comp.

Project Ranger is a program providing a combination of classroom study, outdoor survival, and environmental education to students having difficulty adapting to structured learning. The program has three unique features: it tries to reach younger children than most programs for "reluctant learners"; it provides affective counseling…

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures

PubMed Central

Sadan, Maya Bar; Houben, Lothar; Enyashin, Andrey N.; Seifert, Gotthard; Tenne, Reshef

2008-01-01

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS2 nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS2 nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism. PMID:18838681

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Enyashin, Andrey N; Seifert, Gotthard; Tenne, Reshef

2008-10-14

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS(2) nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS(2) nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism.

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring

PubMed Central

Chang, Shu-Wei; Kuo, Shih-Yu; Huang, Ting-Hsuan

2017-01-01

This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future. PMID:29271937

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring.

PubMed

Chang, Shu-Wei; Lin, Tzu-Kang; Kuo, Shih-Yu; Huang, Ting-Hsuan

2017-12-22

This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar

Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS measurements and gas-phase HDX studies at the amino acid residue level, for the first time a drift tube is connected to a linear ion trap (LIT) with electron transfer dissociation (ETD) capability[19, 20]. In this manner CCS and per-residue deuterium uptake measurements for a model peptide carried out successfully[19]. In this study, the gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined. Using ion structures obtained from molecular dynamics (MD) simulation and considering charge-site/exchange-site density the level of the maximum total deuterium uptake for the gas-phase ions is explained. Also a new hydrogen accessibility scoring (HAS) model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) is applied to the in-silico structures to describe the expected HDX behavior for these structures. Further investigation to improve the accuracy of the model is accomplished by a "per-residue" HDX kinetics study of the model peptide [21]. In this study, the ion residence time and the deuterium uptake of each residue is measured at different partial pressures of D2O. Subsequently the contribution each residue to the overall HDX rate of the intact peptide ion is calculated. These rate contributions of the residues exhibit a better fit to HAS than their maximum deuterium uptake. Proteins and peptides with very frequent acidic residue in their sequence provide very poor signal levels when employing positive polarity ESI. Also, the comparison of protonated and deprotonated ions of these biomolecules offers the potential to provide a better structural characterization [22]. Per-residue deuterium uptake values resulting from collision-induced dissociation (CID) of the model peptide KKDDDDIIKIIK were used to investigated the degree of hydrogen deuterium scrambling for deprotonated ions [23]. Remarkably, limited isotopic scrambling was observed in this study of this small model peptide. This data and the per-residue deuterium uptake of the triply-protonated model peptide Acetyl-PAAAAKAAAAKAAAAKAAAAK are exploited to propose a lemma to allocate protonation and deprotonation sites for peptide ions in the gas-phase. Insulin ions, as a small protein model system, are examined to investigate the relation of the maximum deuterium uptake value for each insulin chain to the exposed surface area of each insulin subunit [22]. The results show that the methodology can be applied on the protein complexes to provide information about the exposed surface area of each subunit.

Image-based models of cardiac structure in health and disease

PubMed Central

Vadakkumpadan, Fijoy; Arevalo, Hermenegild; Prassl, Anton J.; Chen, Junjie; Kickinger, Ferdinand; Kohl, Peter; Plank, Gernot; Trayanova, Natalia

2010-01-01

Computational approaches to investigating the electromechanics of healthy and diseased hearts are becoming essential for the comprehensive understanding of cardiac function. In this article, we first present a brief review of existing image-based computational models of cardiac structure. We then provide a detailed explanation of a processing pipeline which we have recently developed for constructing realistic computational models of the heart from high resolution structural and diffusion tensor (DT) magnetic resonance (MR) images acquired ex vivo. The presentation of the pipeline incorporates a review of the methodologies that can be used to reconstruct models of cardiac structure. In this pipeline, the structural image is segmented to reconstruct the ventricles, normal myocardium, and infarct. A finite element mesh is generated from the segmented structural image, and fiber orientations are assigned to the elements based on DTMR data. The methods were applied to construct seven different models of healthy and diseased hearts. These models contain millions of elements, with spatial resolutions in the order of hundreds of microns, providing unprecedented detail in the representation of cardiac structure for simulation studies. PMID:20582162

Coevolution between Male and Female Genitalia in the Drosophila melanogaster Species Subgroup

PubMed Central

Yassin, Amir; Orgogozo, Virginie

2013-01-01

In contrast to male genitalia that typically exhibit patterns of rapid and divergent evolution among internally fertilizing animals, female genitalia have been less well studied and are generally thought to evolve slowly among closely-related species. As a result, few cases of male-female genital coevolution have been documented. In Drosophila, female copulatory structures have been claimed to be mostly invariant compared to male structures. Here, we re-examined male and female genitalia in the nine species of the D. melanogaster subgroup. We describe several new species-specific female genital structures that appear to coevolve with male genital structures, and provide evidence that the coevolving structures contact each other during copulation. Several female structures might be defensive shields against apparently harmful male structures, such as cercal teeth, phallic hooks and spines. Evidence for male-female morphological coevolution in Drosophila has previously been shown at the post-copulatory level (e.g., sperm length and sperm storage organ size), and our results provide support for male-female coevolution at the copulatory level. PMID:23451172

Automated processing of first-pass radionuclide angiocardiography by factor analysis of dynamic structures.

PubMed

Cavailloles, F; Bazin, J P; Capderou, A; Valette, H; Herbert, J L; Di Paola, R

1987-05-01

A method for automatic processing of cardiac first-pass radionuclide study is presented. This technique, factor analysis of dynamic structures (FADS) provides an automatic separation of anatomical structures according to their different temporal behaviour, even if they are superimposed. FADS has been applied to 76 studies. A description of factor patterns obtained in various pathological categories is presented. FADS provides easy diagnosis of shunts and tricuspid insufficiency. Quantitative information derived from the factors (cardiac output and mean transit time) were compared to those obtained by the region of interest method. Using FADS, a higher correlation with cardiac catheterization was found for cardiac output calculation. Thus compared to the ROI method, FADS presents obvious advantages: a good separation of overlapping cardiac chambers is obtained; this operator independant method provides more objective and reproducible results. A number of parameters of the cardio-pulmonary function can be assessed by first-pass radionuclide angiocardiography (RNA) [1,2]. Usually, they are calculated using time-activity curves (TAC) from regions of interest (ROI) drawn on the cardiac chambers and the lungs. This method has two main drawbacks: (1) the lack of inter and intra-observers reproducibility; (2) the problem of crosstalk which affects the evaluation of the cardio-pulmonary performance. The crosstalk on planar imaging is due to anatomical superimposition of the cardiac chambers and lungs. The activity measured in any ROI is the sum of the activity in several organs and 'decontamination' of the TAC cannot easily be performed using the ROI method [3]. Factor analysis of dynamic structures (FADS) [4,5] can solve the two problems mentioned above. It provides an automatic separation of anatomical structures according to their different temporal behaviour, even if they are superimposed. The resulting factors are estimates of the time evolution of the activity in each structure (underlying physiological components), and the associated factor images are estimates of the spatial distribution of each factor. The aim of this study was to assess the reliability of FADS in first pass RNA and compare the results to those obtained by the ROI method which is generally considered as the routine procedure.

Structural versus dynamical origins of mean-field behavior in a self-organized critical model of neuronal avalanches

NASA Astrophysics Data System (ADS)

Moosavi, S. Amin; Montakhab, Afshin

2015-11-01

Critical dynamics of cortical neurons have been intensively studied over the past decade. Neuronal avalanches provide the main experimental as well as theoretical tools to consider criticality in such systems. Experimental studies show that critical neuronal avalanches show mean-field behavior. There are structural as well as recently proposed [Phys. Rev. E 89, 052139 (2014), 10.1103/PhysRevE.89.052139] dynamical mechanisms that can lead to mean-field behavior. In this work we consider a simple model of neuronal dynamics based on threshold self-organized critical models with synaptic noise. We investigate the role of high-average connectivity, random long-range connections, as well as synaptic noise in achieving mean-field behavior. We employ finite-size scaling in order to extract critical exponents with good accuracy. We conclude that relevant structural mechanisms responsible for mean-field behavior cannot be justified in realistic models of the cortex. However, strong dynamical noise, which can have realistic justifications, always leads to mean-field behavior regardless of the underlying structure. Our work provides a different (dynamical) origin than the conventionally accepted (structural) mechanisms for mean-field behavior in neuronal avalanches.

Flutter Analysis for Turbomachinery Using Volterra Series

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing; Yao, Weigang

2014-01-01

The objective of this paper is to describe an accurate and efficient reduced order modeling method for aeroelastic (AE) analysis and for determining the flutter boundary. Without losing accuracy, we develop a reduced order model based on the Volterra series to achieve significant savings in computational cost. The aerodynamic force is provided by a high-fidelity solution from the Reynolds-averaged Navier-Stokes (RANS) equations; the structural mode shapes are determined from the finite element analysis. The fluid-structure coupling is then modeled by the state-space formulation with the structural displacement as input and the aerodynamic force as output, which in turn acts as an external force to the aeroelastic displacement equation for providing the structural deformation. NASA's rotor 67 blade is used to study its aeroelastic characteristics under the designated operating condition. First, the CFD results are validated against measured data available for the steady state condition. Then, the accuracy of the developed reduced order model is compared with the full-order solutions. Finally the aeroelastic solutions of the blade are computed and a flutter boundary is identified, suggesting that the rotor, with the material property chosen for the study, is structurally stable at the operating condition, free of encountering flutter.

Stability and kinetics of G-quadruplex structures

PubMed Central

Lane, Andrew N.; Chaires, J. Brad; Gray, Robert D.; Trent, John O.

2008-01-01

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence. PMID:18718931

Development of ultralight, super-elastic, hierarchical metallic meta-structures with i3DP technology

NASA Astrophysics Data System (ADS)

Zhang, Dongxing; Xiao, Junfeng; Moorlag, Carolyn; Guo, Qiuquan; Yang, Jun

2017-11-01

Lightweight and mechanically robust materials show promising applications in thermal insulation, energy absorption, and battery catalyst supports. This study demonstrates an effective method for creation of ultralight metallic structures based on initiator-integrated 3D printing technology (i3DP), which provides a possible platform to design the materials with the best geometric parameters and desired mechanical performance. In this study, ultralight Ni foams with 3D interconnected hollow tubes were fabricated, consisting of hierarchical features spanning three scale orders ranging from submicron to centimeter. The resultant materials can achieve an ultralight density of as low as 5.1 mg cm-3 and nearly recover after significant compression up to 50%. Due to a high compression ratio, the hierarchical structure exhibits superior properties in terms of energy absorption and mechanical efficiency. The relationship of structural parameters and mechanical response was established. The ability of achieving ultralight density <10 mg cm-3 and the stable \\bar{E}˜ {\\bar{ρ }}2 scaling through all range of relative density, indicates an advantage over the previous stochastic metal foams. Overall, this initiator-integrated 3D printing approach provides metallic structures with substantial benefits from the hierarchical design and fabrication flexibility to ultralight applications.

Studies of Tidal and Planetary Wave Variability in the Middle Atmosphere using UARS and Correlative MF Radar Data

NASA Technical Reports Server (NTRS)

Fritts, David C.

1996-01-01

The goals of this research effort have been to use MF radar and UARS/HRDI wind measurements for correlative studies of large-scale atmospheric dynamics, focusing specifically on the tidal and various planetary wave structures occurring in the middle atmosphere. We believed that the two data sets together would provide the potential for much more comprehensive studies than either by itself, since they jointly would allow the removal of ambiguities in wave structure that are difficult to resolve with either data set alone. The joint data were to be used for studies of wave structure, variability, and the coupling of these motions to mean and higher-frequency motions.

Socio-Cognitive Phenotypes Differentially Modulate Large-Scale Structural Covariance Networks.

PubMed

Valk, Sofie L; Bernhardt, Boris C; Böckler, Anne; Trautwein, Fynn-Mathis; Kanske, Philipp; Singer, Tania

2017-02-01

Functional neuroimaging studies have suggested the existence of 2 largely distinct social cognition networks, one for theory of mind (taking others' cognitive perspective) and another for empathy (sharing others' affective states). To address whether these networks can also be dissociated at the level of brain structure, we combined behavioral phenotyping across multiple socio-cognitive tasks with 3-Tesla MRI cortical thickness and structural covariance analysis in 270 healthy adults, recruited across 2 sites. Regional thickness mapping only provided partial support for divergent substrates, highlighting that individual differences in empathy relate to left insular-opercular thickness while no correlation between thickness and mentalizing scores was found. Conversely, structural covariance analysis showed clearly divergent network modulations by socio-cognitive and -affective phenotypes. Specifically, individual differences in theory of mind related to structural integration between temporo-parietal and dorsomedial prefrontal regions while empathy modulated the strength of dorsal anterior insula networks. Findings were robust across both recruitment sites, suggesting generalizability. At the level of structural network embedding, our study provides a double dissociation between empathy and mentalizing. Moreover, our findings suggest that structural substrates of higher-order social cognition are reflected rather in interregional networks than in the the local anatomical markup of specific regions per se. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

PubMed Central

Mustoe, Anthony M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2014-01-01

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. PMID:25217593

Factor Structure of the Center for Epidemiologic Studies-Depression Scale (CES-D) Among Older Men and Women Who Provide Care to Persons with Dementia

ERIC Educational Resources Information Center

O'Rourke, Norm

2005-01-01

The Center for Epidemiologic Studies?Depression Scale (CES-D) is among the most widely used depression screening measures. Existing research suggests a higher order factor structure of responses among older adults (factors labeled as Depressive Affect, Absence of Well-being, Somatic Symptoms, and Interpersonal Affect each loading on a 2nd-order…

Intercomparison of vertical structure of storms revealed by ground-based (NMQ) and spaceborne radars (CloudSat-CPR and TRMM-PR).

PubMed

Fall, Veronica M; Cao, Qing; Hong, Yang

2013-01-01

Spaceborne radars provide great opportunities to investigate the vertical structure of clouds and precipitation. Two typical spaceborne radars for such a study are the W-band Cloud Profiling Radar (CPR) and Ku-band Precipitation Radar (PR), which are onboard NASA's CloudSat and TRMM satellites, respectively. Compared to S-band ground-based radars, they have distinct scattering characteristics for different hydrometeors in clouds and precipitation. The combination of spaceborne and ground-based radar observations can help in the identification of hydrometeors and improve the radar-based quantitative precipitation estimation (QPE). This study analyzes the vertical structure of the 18 January, 2009 storm using data from the CloudSat CPR, TRMM PR, and a NEXRAD-based National Mosaic and Multisensor QPE (NMQ) system. Microphysics above, within, and below the melting layer are studied through an intercomparison of multifrequency measurements. Hydrometeors' type and their radar scattering characteristics are analyzed. Additionally, the study of the vertical profile of reflectivity (VPR) reveals the brightband properties in the cold-season precipitation and its effect on the radar-based QPE. In all, the joint analysis of spaceborne and ground-based radar data increases the understanding of the vertical structure of storm systems and provides a good insight into the microphysical modeling for weather forecasts.

Intercomparison of Vertical Structure of Storms Revealed by Ground-Based (NMQ) and Spaceborne Radars (CloudSat-CPR and TRMM-PR)

PubMed Central

Fall, Veronica M.; Hong, Yang

2013-01-01

Spaceborne radars provide great opportunities to investigate the vertical structure of clouds and precipitation. Two typical spaceborne radars for such a study are the W-band Cloud Profiling Radar (CPR) and Ku-band Precipitation Radar (PR), which are onboard NASA's CloudSat and TRMM satellites, respectively. Compared to S-band ground-based radars, they have distinct scattering characteristics for different hydrometeors in clouds and precipitation. The combination of spaceborne and ground-based radar observations can help in the identification of hydrometeors and improve the radar-based quantitative precipitation estimation (QPE). This study analyzes the vertical structure of the 18 January, 2009 storm using data from the CloudSat CPR, TRMM PR, and a NEXRAD-based National Mosaic and Multisensor QPE (NMQ) system. Microphysics above, within, and below the melting layer are studied through an intercomparison of multifrequency measurements. Hydrometeors' type and their radar scattering characteristics are analyzed. Additionally, the study of the vertical profile of reflectivity (VPR) reveals the brightband properties in the cold-season precipitation and its effect on the radar-based QPE. In all, the joint analysis of spaceborne and ground-based radar data increases the understanding of the vertical structure of storm systems and provides a good insight into the microphysical modeling for weather forecasts. PMID:24459424

Structure-activity relationship study of spider polyamine toxins as inhibitors of ionotropic glutamate receptors.

PubMed

Xiong, Xiao-Feng; Poulsen, Mette H; Hussein, Rama A; Nørager, Niels G; Strømgaard, Kristian

2014-12-01

The spider polyamine toxins Joro spider toxin-3 (JSTX-3) and Nephila polyamine toxins-1 and -8 (NPTX-1 and NPTX-8) are isolated from the venom of the orb-weaver spider Nephila clavata (Joro spider). They share a high degree of structural resemblance, their aromatic head groups being the only difference, and were recently found to be very potent open-channel blockers of ionotropic glutamate (iGlu) receptors. In this study we designed and synthesized a collection of 24 analogues of these toxins using a recently developed solid-phase synthetic methodology. Systematic variation in two regions of the toxins and subsequent evaluation of biological activity at AMPA and NMDA subtypes of iGlu receptors provided succinct information on structure-activity relationships. In particular, one set of analogues were found to display exquisite selectivity and potency for AMPA receptors relative to the natural products. Thus, this systematic SAR study has provided new pharmacological tools for studies of iGlu receptors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photothermal technique in cell microscopy studies

NASA Astrophysics Data System (ADS)

Lapotko, Dmitry; Chebot'ko, Igor; Kutchinsky, Georgy; Cherenkevitch, Sergey

1995-01-01

Photothermal (PT) method is applied for a cell imaging and quantitative studies. The techniques for cell monitoring, imaging and cell viability test are developed. The method and experimental set up for optical and PT-image acquisition and analysis is described. Dual- pulsed laser set up combined with phase contrast illumination of a sample provides visualization of temperature field or absorption structure of a sample with spatial resolution 0.5 micrometers . The experimental optics, hardware and software are designed using the modular principle, so the whole set up can be adjusted for various experiments: PT-response monitoring or photothermal spectroscopy studies. Sensitivity of PT-method provides the imaging of the structural elements of live (non-stained) white blood cells. The results of experiments with normal and subnormal blood cells (red blood cells, lymphocytes, neutrophyles and lymphoblasts) are reported. Obtained PT-images are different from optical analogs and deliver additional information about cell structure. The quantitative analysis of images was used for cell population comparative diagnostic. The viability test for red blood cell differentiation is described. During the study of neutrophyles in norma and sarcoidosis disease the differences in PT-images of cells were found.

Providers' Reported and Actual Use of Coaching Strategies in Natural Environments

ERIC Educational Resources Information Center

Salisbury, Christine; Cambray-Engstrom, Elizabeth; Woods, Juliann

2012-01-01

This case study examined the agreement between reported and actual use of coaching strategies based on home visit data collected on a diverse sample of providers and families. Paired videotape and contact note data of and from providers during home visits were collected over a six month period and analyzed using structured protocols. Results of…

Modeling the Structure of Partnership between Researchers and Front-Line Service Providers: Strengthening Collaborative Public Health Research

ERIC Educational Resources Information Center

Pinto, Rogério M.; Wall, Melanie M.; Spector, Anya Y.

2014-01-01

Partnerships between HIV researchers and service providers are essential for reducing the gap between research and practice. Community-Based Participatory Research principles guided this cross-sectional study, combining 40 in-depth interviews with surveys of 141 providers in 24 social service agencies in New York City. We generated the…

CCProf: exploring conformational change profile of proteins

PubMed Central

Chang, Che-Wei; Chou, Chai-Wei; Chang, Darby Tien-Hao

2016-01-01

In many biological processes, proteins have important interactions with various molecules such as proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions. This work presents the CCProf platform, which provides conformational changes of entire proteins, named conformational change profile (CCP) in the context. CCProf aims to be a platform where users can study potential causes of novel conformational changes. It provides 10 biological features, including conformational change, potential binding target site, secondary structure, conservation, disorder propensity, hydropathy propensity, sequence domain, structural domain, phosphorylation site and catalytic site. All these information are integrated into a well-aligned view, so that researchers can capture important relevance between different biological features visually. The CCProf contains 986 187 protein structure pairs for 3123 proteins. In addition, CCProf provides a 3D view in which users can see the protein structures before and after conformational changes as well as binding targets that induce conformational changes. All information (e.g. CCP, binding targets and protein structures) shown in CCProf, including intermediate data are available for download to expedite further analyses. Database URL: http://zoro.ee.ncku.edu.tw/ccprof/ PMID:27016699

Cellular Electron Cryotomography: Toward Structural Biology In Situ.

PubMed

Oikonomou, Catherine M; Jensen, Grant J

2017-06-20

Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.

Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2

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

Samanta, Dibyendu; Guo, Haisu; Rubinstein, Rotem

In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells. Here we report the crystal structure of the human TIGITmore » ectodomain, which exhibits the classic two-layer β-sandwich topology observed in other immunoglobulin super family (IgSF) members. Biophysical studies indicate that TIGIT is monomeric in solution but can form a dimer at high concentrations, consistent with the observation of a canonical immunoglobulin-like dimer interface in the crystalline state. Based on existing structural data, we present a model of the TIGIT:nectin-2 complex and utilized complementary biochemical studies to map the nectin-binding interface on TIGIT. Our data provide important structural and biochemical determinants responsible for the recognition of nectin-2 by TIGIT. Defining the TIGIT:nectin-2 binding interface provides the basis for rational manipulation of this molecular interaction for the development of immunotherapeutic reagents in autoimmunity and cancer.« less

Job Knowledge Test Design: A Cognitively-Oriented Approach

DTIC Science & Technology

1993-07-01

protocol analyses and related methods. We employed a plan-goal graph representation to capture the knowledge content and goal structure of the studied task...between job knowledge and hands-on performance from previous studies was .38. For the subset of Marines in this sample who had recently been examined...the job knowledge test provided similar results to conventional, total number correct scoring. Conclusion The evidence provided by this study supports

Engineered control of enzyme structural dynamics and function.

PubMed

Boehr, David D; D'Amico, Rebecca N; O'Rourke, Kathleen F

2018-04-01

Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine. © 2018 The Protein Society.

3D Documentation and BIM Modeling of Cultural Heritage Structures Using UAVs: The Case of the Foinikaria Church

NASA Astrophysics Data System (ADS)

Themistocleous, K.; Agapiou, A.; Hadjimitsis, D.

2016-10-01

The documentation of architectural cultural heritage sites has traditionally been expensive and labor-intensive. New innovative technologies, such as Unmanned Aerial Vehicles (UAVs), provide an affordable, reliable and straightforward method of capturing cultural heritage sites, thereby providing a more efficient and sustainable approach to documentation of cultural heritage structures. In this study, hundreds of images of the Panagia Chryseleousa church in Foinikaria, Cyprus were taken using a UAV with an attached high resolution camera. The images were processed to generate an accurate digital 3D model by using Structure in Motion techniques. Building Information Model (BIM) was then used to generate drawings of the church. The methodology described in the paper provides an accurate, simple and cost-effective method of documenting cultural heritage sites and generating digital 3D models using novel techniques and innovative methods.

Proteoglycomics: Recent Progress and Future Challenges

PubMed Central

Ly, Mellisa; Laremore, Tatiana N.

2010-01-01

Abstract Proteoglycomics is a systematic study of structure, expression, and function of proteoglycans, a posttranslationally modified subset of a proteome. Although relying on the established technologies of proteomics and glycomics, proteoglycomics research requires unique approaches for elucidating structure–function relationships of both proteoglycan components, glycosaminoglycan chain, and core protein. This review discusses our current understanding of structure and function of proteoglycans, major players in the development, normal physiology, and disease. A brief outline of the proteoglycomic sample preparation and analysis is provided along with examples of several recent proteoglycomic studies. Unique challenges in the characterization of glycosaminoglycan component of proteoglycans are discussed, with emphasis on the many analytical tools used and the types of information they provide. PMID:20450439

Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

Ultrastructural Mapping of the Zebrafish Gastrointestinal System as a Basis for Experimental Drug Studies

PubMed Central

Shami, Gerald J.; Morsch, Marco; Chung, Roger S.; Braet, Filip

2016-01-01

Research in the field of gastroenterology is increasingly focused on the use of alternative nonrodent model organisms to provide new experimental tools to study chronic diseases. The zebrafish is a particularly valuable experimental platform to explore organ and cell structure-function relationships under relevant biological and pathobiological settings. This is due to its optical transparency and its close-to-human genetic makeup. To-date, the structure-function properties of the GIS of the zebrafish are relatively unexplored and limited to histology and fluorescent microscopy. Occasionally those studies include EM of a given subcellular process but lack the required full histological picture. In this work, we employed a novel combined biomolecular imaging approach in order to cross-correlate 3D ultrastructure over different length scales (optical-, X-ray micro-CT, and high-resolution EM). Our correlated imaging studies and subsequent data modelling provide to our knowledge the first detailed 3D picture of the zebrafish larvae GIS. Our results provide unequivocally a limit of confidence for studying various digestive disorders and drug delivery pathways in the zebrafish. PMID:27340669

Ultrastructural Mapping of the Zebrafish Gastrointestinal System as a Basis for Experimental Drug Studies.

PubMed

Cheng, Delfine; Shami, Gerald J; Morsch, Marco; Chung, Roger S; Braet, Filip

2016-01-01

Research in the field of gastroenterology is increasingly focused on the use of alternative nonrodent model organisms to provide new experimental tools to study chronic diseases. The zebrafish is a particularly valuable experimental platform to explore organ and cell structure-function relationships under relevant biological and pathobiological settings. This is due to its optical transparency and its close-to-human genetic makeup. To-date, the structure-function properties of the GIS of the zebrafish are relatively unexplored and limited to histology and fluorescent microscopy. Occasionally those studies include EM of a given subcellular process but lack the required full histological picture. In this work, we employed a novel combined biomolecular imaging approach in order to cross-correlate 3D ultrastructure over different length scales (optical-, X-ray micro-CT, and high-resolution EM). Our correlated imaging studies and subsequent data modelling provide to our knowledge the first detailed 3D picture of the zebrafish larvae GIS. Our results provide unequivocally a limit of confidence for studying various digestive disorders and drug delivery pathways in the zebrafish.

Estimate of the size and demographic structure of the owned dog and cat population living in Veneto region (north-eastern Italy).

PubMed

Capello, Katia; Bortolotti, Laura; Lanari, Manuela; Baioni, Elisa; Mutinelli, Franco; Vascellari, Marta

2015-01-01

The knowledge of the size and demographic structure of animal populations is a necessary prerequisite for any population-based epidemiological study, especially to ascertain and interpret prevalence data, to implement surveillance plans in controlling zoonotic diseases and, moreover, to provide accurate estimates of tumours incidence data obtained by population-based registries. The main purpose of this study was to provide an accurate estimate of the size and structure of the canine population in Veneto region (north-eastern Italy), using the Lincoln-Petersen version of the capture-recapture methodology. The Regional Canine Demographic Registry (BAC) and a sample survey of households of Veneto Region were the capture and recapture sources, respectively. The secondary purpose was to estimate the size and structure of the feline population in the same region, using the same survey applied for dog population. A sample of 2465 randomly selected households was drawn and submitted to a questionnaire using the CATI technique, in order to obtain information about the ownership of dogs and cats. If the dog was declared to be identified, owner's information was used to recapture the dog in the BAC. The study was conducted in Veneto Region during 2011, when the dog population recorded in the BAC was 605,537. Overall, 616 households declared to possess at least one dog (25%), with a total of 805 dogs and an average per household of 1.3. The capture-recapture analysis showed that 574 dogs (71.3%, 95% CI: 68.04-74.40%) had been recaptured in both sources, providing a dog population estimate of 849,229 (95% CI: 814,747-889,394), 40% higher than that registered in the BAC. Concerning cats, 455 of 2465 (18%, 95% CI: 17-20%) households declared to possess at least one cat at the time of the telephone interview, with a total of 816 cats. The mean number of cats per household was equal to 1.8, providing an estimate of the cat population in Veneto region equal to 663,433 (95% CI: 626,585-737,159). The estimate of the size and structure of owned canine and feline populations in Veneto region provide useful data to perform epidemiological studies and monitoring plans in this area. Copyright © 2014 Elsevier B.V. All rights reserved.

High-resolution cryo-EM proteasome structures in drug development

PubMed Central

da Fonseca, Paula C. A.

2017-01-01

With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein–ligand inter­actions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein–ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites. Subsequently, the cryo-EM structure of the Plasmodium falciparum 20S proteasome, with a new prototype specific inhibitor bound, revealed the molecular basis for the ligand specificity towards the parasite complex, which provides a framework to guide the development of highly needed new-generation antimalarials. Here, the cryo-EM analysis of the ligand-bound human and P. falciparum 20S proteasomes is reviewed, and a complete description of the methods used for structure determination is provided, including the strategy to overcome the bias orientation of the human 20S proteasome on electron-microscope grids and details of the icr3d software used for three-dimensional reconstruction. PMID:28580914

Prospects for quantifying structure, floristic composition and species richness of tropical forests

USGS Publications Warehouse

Gillespie, T.W.; Brock, J.; Wright, C.W.

2004-01-01

Airborne spectral and light detection and ranging (lidar) sensors have been used to quantify biophysical characteristics of tropical forests. Lidar sensors have provided high-resolution data on forest height, canopy topography, volume, and gap size; and provided estimates on number of strata in a forest, successional status of forests, and above-ground biomass. Spectral sensors have provided data on vegetation types, foliar biochemistry content of forest canopies, tree and canopy phenology, and spectral signatures for selected tree species. A number of advances are theoretically possible with individual and combined spectral and lidar sensors for the study of forest structure, floristic composition and species richness. Delineating individual canopies of over-storey trees with small footprint lidar and discrimination of tree architectural types with waveform distributions is possible and would provide scientists with a new method to study tropical forest structure. Combined spectral and lidar data can be used to identify selected tree species and identify the successional status of tropical forest fragments in order to rank forest patches by levels of species richness. It should be possible in the near future to quantify selected patterns of tropical forests at a higher resolution than can currently be undertaken in the field or from space. ?? 2004 Taylor and Francis Ltd.

Structural Challenges of Providing Palliative Care for Patients with Breast Cancer

PubMed Central

Khoshnazar, Tahereh Alsadat Khoubbin; Rassouli, Maryam; Akbari, Mohammad Esmaeil; Lotfi-Kashani, Farah; Momenzadeh, Syrus; Haghighat, Shahpar; Sajjadi, Moosa

2016-01-01

Introduction: To establish a palliative care system (PCS) in Iran, it is necessary to identify the potential barriers. Aim: This study aims to highlight the views of stakeholders to know the challenges of providing palliative care for women with breast cancer. Materials and Methods: Semi-structured in-depth interviews are used with purposeful sampling conducted in Tehran, Iran; from January to June 2015. Twenty participants were included in the study: nine patients with breast cancer and ten health-care providers. The interviews were analyzed using qualitative directed content analysis based on Donabedian model. Data credibility was examined using the criteria of Lincoln and Guba. Results: Based on the pattern of Avedis Donabedian model, two main categories were identified: (1) palliative care services in the health system still remain undefined and (2) lack of adequate care providers. The subcategories emerged from the main categories are: (1) Inexistent home care, (2) specialized palliative care being in high demand, lack of: (a) Rehabilitation program and guidelines, (b) treatment/training protocols, (c) inefficient insurance and out-of-pocket costs, (d) patient referral system, (e) nontransparency of job description, and (f) weakness of teamwork. Discussion: The findings of the study identify views and perceptions of patients as well as the health professionals around the challenges of providing palliative care. To establish a structured PCS, we need to meet the challenges and remove perceived barriers to, including but not limited to, building up knowledge and awareness of health professionals, educating professional, and developing updated, well-defined, and standard treatment protocols, tailored to local conditions. PMID:27803569

Structural and Biochemical Characterization of Spa47 Provides Mechanistic Insight into Type III Secretion System ATPase Activation and Shigella Virulence Regulation.

PubMed

Burgess, Jamie L; Burgess, R Alan; Morales, Yalemi; Bouvang, Jenna M; Johnson, Sean J; Dickenson, Nicholas E

2016-12-09

Like many Gram-negative pathogens, Shigella rely on a complex type III secretion system (T3SS) to inject effector proteins into host cells, take over host functions, and ultimately establish infection. Despite these critical roles, the energetics and regulatory mechanisms controlling the T3SS and pathogen virulence remain largely unclear. In this study, we present a series of high resolution crystal structures of Spa47 and use the structures to model an activated Spa47 oligomer, finding that ATP hydrolysis may be supported by specific side chain contributions from adjacent protomers within the complex. Follow-up mutagenesis experiments targeting the predicted active site residues validate the oligomeric model and determined that each of the tested residues are essential for Spa47 ATPase activity, although they are not directly responsible for stable oligomer formation. Although N-terminal domain truncation was necessary for crystal formation, it resulted in strictly monomeric Spa47 that is unable to hydrolyze ATP, despite maintaining the canonical ATPase core structure and active site residues. Coupled with studies of ATPase inactive full-length Spa47 point mutants, we find that Spa47 oligomerization and ATP hydrolysis are needed for complete T3SS apparatus formation, a proper translocator secretion profile, and Shigella virulence. This work represents the first structure-function characterization of Spa47, uniquely complementing the multitude of included Shigella T3SS phenotype assays and providing a more complete understanding of T3SS ATPase-mediated pathogen virulence. Additionally, these findings provide a strong platform for follow-up studies evaluating regulation of Spa47 oligomerization in vivo as a much needed means of treating and perhaps preventing shigellosis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and Biochemical Characterization of Spa47 Provides Mechanistic Insight into Type III Secretion System ATPase Activation and Shigella Virulence Regulation*

PubMed Central

Burgess, Jamie L.; Burgess, R. Alan; Morales, Yalemi; Bouvang, Jenna M.; Johnson, Sean J.; Dickenson, Nicholas E.

2016-01-01

Like many Gram-negative pathogens, Shigella rely on a complex type III secretion system (T3SS) to inject effector proteins into host cells, take over host functions, and ultimately establish infection. Despite these critical roles, the energetics and regulatory mechanisms controlling the T3SS and pathogen virulence remain largely unclear. In this study, we present a series of high resolution crystal structures of Spa47 and use the structures to model an activated Spa47 oligomer, finding that ATP hydrolysis may be supported by specific side chain contributions from adjacent protomers within the complex. Follow-up mutagenesis experiments targeting the predicted active site residues validate the oligomeric model and determined that each of the tested residues are essential for Spa47 ATPase activity, although they are not directly responsible for stable oligomer formation. Although N-terminal domain truncation was necessary for crystal formation, it resulted in strictly monomeric Spa47 that is unable to hydrolyze ATP, despite maintaining the canonical ATPase core structure and active site residues. Coupled with studies of ATPase inactive full-length Spa47 point mutants, we find that Spa47 oligomerization and ATP hydrolysis are needed for complete T3SS apparatus formation, a proper translocator secretion profile, and Shigella virulence. This work represents the first structure-function characterization of Spa47, uniquely complementing the multitude of included Shigella T3SS phenotype assays and providing a more complete understanding of T3SS ATPase-mediated pathogen virulence. Additionally, these findings provide a strong platform for follow-up studies evaluating regulation of Spa47 oligomerization in vivo as a much needed means of treating and perhaps preventing shigellosis. PMID:27770024

Structural direction of hybrid organic-inorganic materials: Synthesis of vanadium oxyfluoride, copper vanadate, and copper molybdate solid state materials through solvuthermal and solution methods

NASA Astrophysics Data System (ADS)

Deburgomaster, Paul

The vast structural complexity of inorganic oxides with structure directing organocations, nitrogen containing ligands and organophosphonate ligands was explored. The hydrothermal reaction conditions utilized herein include the variables of temperature, pH, fill volume and stoichiometry. The systems studied included: (1) the complex materials rendered from reactions of organoamine cations on the structure of vanadium oxides, oxyfluorides and fluorides. As with other systems, the influence of the mineralizer HF was not limited to pH as fluorine incorporation was not uncommon. In specific cases this coincided with reduction of vanadium sites. (2) The copper-organonitrogen ligand/vanadium oxide/aromatic phosphonate system has been studied. The rigid aromatic di- and tri-phosphonate tethers have provided a series of materials which are structurally distinct from the previously investigated aliphatic series. The inclusion of copper-coordinated nitrogen bi- and tri-dentate ligands also provided structural diversity. Product composition was highly influenced by the HF/V ratio. A similar study was conducted with the ligand 1,4-carboxy-phenylphosphonic acid. (3) The preparation of a series of bimetallic organic-inorganic hybrid materials of the M(II)/VxOy/organonitrogen ligand class was further evidence of the utility of thermodynamically driven hydrothermal synthesis. (4) While decomposition of the spherical Keplerate molybdenum clusters is encountered under hydrothermal conditions, this highly soluble form of molybdate was investigated for the development of hybrid organic-inorganic room temperature solution synthesis.

Gene-Transformation-Induced Changes in Chemical Functional Group Features and Molecular Structure Conformation in Alfalfa Plants Co-Expressing Lc-bHLH and C1-MYB Transcriptive Flavanoid Regulatory Genes: Effects of Single-Gene and Two-Gene Insertion.

PubMed

Heendeniya, Ravindra G; Yu, Peiqiang

2017-03-20

Alfalfa ( Medicago sativa L.) genotypes transformed with Lc-bHLH and Lc transcription genes were developed with the intention of stimulating proanthocyanidin synthesis in the aerial parts of the plant. To our knowledge, there are no studies on the effect of single-gene and two-gene transformation on chemical functional groups and molecular structure changes in these plants. The objective of this study was to use advanced molecular spectroscopy with multivariate chemometrics to determine chemical functional group intensity and molecular structure changes in alfalfa plants when co-expressing Lc-bHLH and C1-MYB transcriptive flavanoid regulatory genes in comparison with non-transgenic (NT) and AC Grazeland (ACGL) genotypes. The results showed that compared to NT genotype, the presence of double genes ( Lc and C1 ) increased ratios of both the area and peak height of protein structural Amide I/II and the height ratio of α-helix to β-sheet. In carbohydrate-related spectral analysis, the double gene-transformed alfalfa genotypes exhibited lower peak heights at 1370, 1240, 1153, and 1020 cm -1 compared to the NT genotype. Furthermore, the effect of double gene transformation on carbohydrate molecular structure was clearly revealed in the principal component analysis of the spectra. In conclusion, single or double transformation of Lc and C1 genes resulted in changing functional groups and molecular structure related to proteins and carbohydrates compared to the NT alfalfa genotype. The current study provided molecular structural information on the transgenic alfalfa plants and provided an insight into the impact of transgenes on protein and carbohydrate properties and their molecular structure's changes.

Numbers, systems, people: how interactions influence integration. Insights from case studies of HIV and reproductive health services delivery in Kenya.

PubMed

Mayhew, Susannah H; Sweeney, Sedona; Warren, Charlotte E; Collumbien, Martine; Ndwiga, Charity; Mutemwa, Richard; Lut, Irina; Colombini, Manuela; Vassall, Anna

2017-11-01

Drawing on rich data from the Integra evaluation of integrated HIV and reproductive-health services, we explored the interaction of systems hardware and software factors to explain why some facilities were able to implement and sustain integrated service delivery while others were not. This article draws on detailed mixed-methods data for four case-study facilities offering reproductive-health and HIV services between 2009 and 2013 in Kenya: (i) time-series client flow, tracking service uptake for 8841 clients; (ii) structured questionnaires with 24 providers; (iii) in-depth interviews with 17 providers; (iv) workload and facility data using a periodic activity review and cost-instruments; and (v) contextual data on external activities related to integration in study sites. Overall, our findings suggested that although structural factors like stock-outs, distribution of staffing and workload, rotation of staff can affect how integrated care is provided, all these factors can be influenced by staff themselves: both frontline and management. Facilities where staff displayed agency of decision making, worked as a team to share workload and had management that supported this, showed better integration delivery and staff were able to overcome some structural deficiencies to enable integrated care. Poor-performing facilities had good structural integration, but staff were unable to utilize this because they were poorly organized, unsupported or teams were dysfunctional. Conscientious objection and moralistic attitudes were also barriers.Integra has demonstrated that structural integration is not sufficient for integrated service delivery. Rather, our case studies show that in some cases excellent leadership and peer-teamwork enabled facilities to perform well despite resource shortages. The ability to provide support for staff to work flexibly to deliver integrated services and build resilient health systems to meet changing needs is particularly relevant as health systems face challenges of changing burdens of disease, climate change, epidemic outbreaks and more. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Seismic isolation systems with distinct multiple frequencies

DOEpatents

Wu, Ting-shu; Seidensticker, Ralph W.

1990-01-01

A method and apparatus for isolating a building or other structure from smic vibratory motion which provides increased assurance that large horizontal motion of the structure will not occur than is provided by other isolation systems. Increased assurance that large horizontal motion will not occur is achieved by providing for change of the natural frequency of the support and structure system in response to displacement of the structure beyond a predetermined value. The natural frequency of the support and structure system may be achieved by providing for engaging and disengaging of the structure and some supporting members in response to motion of the supported structure.

The evolution of structured illumination microscopy in studies of HIV.

PubMed

Marno, Kelly; Al'Zoubi, Lara; Pearson, Matthew; Posch, Markus; McKnight, Áine; Wheeler, Ann P

2015-10-15

The resolution limit of conventional light microscopy has proven to be limiting for many biological structures such as viruses including Human immunodeficiency virus (HIV). Individual HIV virions are impossible to study using confocal microscopy as they are well below the 200 nm resolution limit of conventional light microscopes. Structured illumination microscopy (SIM) allows a twofold enhancement in image resolution compared to standard widefield illumination and so provides an excellent tool for study of HIV. Viral capsids (CAs) vary between 110 and 146 nm so this study challenges the performance of SIM microscopes. SIM microscopy was first developed in 2000, commercialised in 2007 and rapidly developed. Here we present the changes in capabilities of the SIM microscopes for study of HIV localisation as the instrumentation for structured illumination microscopy has evolved over the past 8 years. Copyright © 2015. Published by Elsevier Inc.

SCIS Teacher's Handbook.

ERIC Educational Resources Information Center

Karplus, Robert, Comp.; Lawson, Chester A., Comp.

This teacher's handbook provides information about the philosophy, rationale, and teaching strategies of the Science Curriculum Improvement Study (SCIS) program, as well as information about the SCIS physical and life science sequences to provide teachers with an understanding of the program's overall content and structure. Much of the material in…

Building a model of the blue cone pigment based on the wild type rhodopsin structure with QM/MM methods.

PubMed

Frähmcke, Jan S; Wanko, Marius; Elstner, Marcus

2012-03-15

Understanding the mechanism of color tuning of the retinal chromophore by its host protein became one of the key issues in the research on rhodopsins. While early mutation studies addressed its genetic origin, recent studies advanced to investigate its structural origin, based on X-ray crystallographic structures. For the human cone pigments, no crystal structures have been produced, and homology models were employed to elucidate the origin of its blue-shifted absorption. In this theoretical study, we take a different route to establish a structural model for human blue. Starting from the well-resolved structure of bovine rhodopsin, we derive multiple mutant models by stepwise mutation and equilibration using molecular dynamics simulations in a hybrid quantum mechanics/molecular mechanics framework. Our 30fold mutant reproduces the experimental UV-vis absorption shift of 0.45 eV and provides new insights about both structural and genetic factors that affect the excitation energy. Electrostatic effects of individual amino acids and collaborative structural effects are analyzed using semiempirical (OM2/MRCI) and ab initio (SORCI) multireference approaches. © 2012 American Chemical Society

Communication and Organization in Software Development: An Empirical Study

NASA Technical Reports Server (NTRS)

Seaman, Carolyn B.; Basili, Victor R.

1996-01-01

The empirical study described in this paper addresses the issue of communication among members of a software development organization. The independent variables are various attributes of organizational structure. The dependent variable is the effort spent on sharing information which is required by the software development process in use. The research questions upon which the study is based ask whether or not these attributes of organizational structure have an effect on the amount of communication effort expended. In addition, there are a number of blocking variables which have been identified. These are used to account for factors other than organizational structure which may have an effect on communication effort. The study uses both quantitative and qualitative methods for data collection and analysis. These methods include participant observation, structured interviews, and graphical data presentation. The results of this study indicate that several attributes of organizational structure do affect communication effort, but not in a simple, straightforward way. In particular, the distances between communicators in the reporting structure of the organization, as well as in the physical layout of offices, affects how quickly they can share needed information, especially during meetings. These results provide a better understanding of how organizational structure helps or hinders communication in software development.

Deterioration of concrete structures in coastal environment due to carbonation.

PubMed

Balaji, K V G D; Gopalaraju, S S S V; Trilochan, Jena

2010-07-01

Failure of existing concrete structures takes place due to lack of durability, and not due to less structural strength. One of the important aspects of durability is carbonation depth. The rate of carbonation in concrete is influenced by both its physical properties and exposure conditions. Rebar corrodes when carbonation reaches to a depth of concrete cover provided. In the present work, various concrete structures with different life periods and exposed to different weather conditions have been considered to study the carbonation effect. It is observed that the effect of carbonation is more in the structures located near to the sea coast and on windward face of the structure.

Combined loading criterial influence on structural performance

NASA Technical Reports Server (NTRS)

Kuchta, B. J.; Sealey, D. M.; Howell, L. J.

1972-01-01

An investigation was conducted to determine the influence of combined loading criteria on the space shuttle structural performance. The study consisted of four primary phases: Phase (1) The determination of the sensitivity of structural weight to various loading parameters associated with the space shuttle. Phase (2) The determination of the sensitivity of structural weight to various levels of loading parameter variability and probability. Phase (3) The determination of shuttle mission loading parameters variability and probability as a function of design evolution and the identification of those loading parameters where inadequate data exists. Phase (4) The determination of rational methods of combining both deterministic time varying and probabilistic loading parameters to provide realistic design criteria. The study results are presented.

Examining clinicians’ experiences providing sexual health services for LGBTQ youth: considering social and structural determinants of health in clinical practice

PubMed Central

Knight, R. E.; Shoveller, J. A.; Carson, A. M.; Contreras-Whitney, J. G.

2014-01-01

Although barriers related to lesbian, gay, bisexual, transgender and queer (LGBTQ) youth’s experiences accessing sexual health services have been examined in detail, research into the experiences and perceptions of clinicians providing these services has been conspicuously absent. The aim of this article is to explore the perceptions and experiences of clinicians providing sexual health services for LGBTQ youth. Drawing on in-depth, semi-structured interviews, this study examines 24 clinicians’ experiences providing sexual health services to LGBTQ youth in five communities in British Columbia, Canada. Our findings reveal how many clinicians provide services to LGBTQ youth with a lack of cultural competency—either implicitly (e.g. by describing heteronormative practices) or explicitly (e.g. by expressing frustration that they had not been sufficiently provided with appropriate training related to LGBTQ youth sexual health). Institutional norms and values were identified as the dominant barriers in the effective provision of LGBTQ-tailored services. Many clinicians find themselves unprepared to provide culturally competent sexual health services that have both the capacity to address individual-level issues (e.g. promoting condom use) while considering (and adapting services to) the broader socio-cultural and structural conditions that can render LGBTQ youth socially vulnerable. PMID:24412811

Extracting nursing practice patterns from structured labor and delivery data sets.

PubMed

Hall, Eric S; Thornton, Sidney N

2007-10-11

This study was designed to demonstrate the feasibility of a computerized care process model that provides real-time case profiling and outcome forecasting. A methodology was defined for extracting nursing practice patterns from structured point-of-care data collected using the labor and delivery information system at Intermountain Healthcare. Data collected during January 2006 were retrieved from Intermountain Healthcare's enterprise data warehouse for use in the study. The knowledge discovery in databases process provided a framework for data analysis including data selection, preprocessing, data-mining, and evaluation. Development of an interactive data-mining tool and construction of a data model for stratification of patient records into profiles supported the goals of the study. Five benefits of the practice pattern extraction capability, which extend to other clinical domains, are listed with supporting examples.

A Visual Evaluation Study of Graph Sampling Techniques

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

Zhang, Fangyan; Zhang, Song; Wong, Pak C.

2017-01-29

We evaluate a dozen prevailing graph-sampling techniques with an ultimate goal to better visualize and understand big and complex graphs that exhibit different properties and structures. The evaluation uses eight benchmark datasets with four different graph types collected from Stanford Network Analysis Platform and NetworkX to give a comprehensive comparison of various types of graphs. The study provides a practical guideline for visualizing big graphs of different sizes and structures. The paper discusses results and important observations from the study.

Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

ERIC Educational Resources Information Center

Li, Spencer D.

2011-01-01

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

Using Structural Equation Models with Latent Variables to Study Student Growth and Development.

ERIC Educational Resources Information Center

Pike, Gary R.

1991-01-01

Analysis of data on freshman-to-senior developmental gains in 722 University of Tennessee-Knoxville students provides evidence of the advantages of structural equation modeling with latent variables and suggests that the group differences identified by traditional analysis of variance and covariance techniques may be an artifact of measurement…

Using the Community of Inquiry Framework to Scaffold Online Tutoring

ERIC Educational Resources Information Center

Feng, Xiaoying; Xie, Jingjing; Liu, Yue

2017-01-01

Tutoring involves providing learners with a suitable level of structure and guidance to support their learning. This study reports on an exploration of how to design such structure and guidance (i.e., learning scaffolds) in the Chinese online educational context, and in so doing, answer the following two questions: (a) What scaffolding strategies…

Italian Sign Language (LIS) Poetry: Iconic Properties and Structural Regularities.

ERIC Educational Resources Information Center

Russo, Tommaso; Giuranna, Rosaria; Pizzuto, Elena

2001-01-01

Explores and describes from a crosslinguistic perspective, some of the major structural irregularities that characterize poetry in Italian Sign Language and distinguish poetic from nonpoetic texts. Reviews findings of previous studies of signed language poetry, and points out issues that need to be clarified to provide a more accurate description…

A Hierarchy of Medicine: Health Strategies of Elder Khmer Refugees in the United States

ERIC Educational Resources Information Center

Lewis, Denise C.

2007-01-01

This study addresses ways Khmer refugee elders utilize traditional herbal medicine with Western biomedicine in the treatment and prevention of illnesses. Methods include semi-structured and informal interviews with elders and family members, semi-structured interviews with local health care providers and Khmer physicians, and participant…

Situational Meanings and Functions of Korean Speech Styles

ERIC Educational Resources Information Center

Yoon, Sangseok

2010-01-01

This study aims to provide a perspective which allows honorifics to be seen beyond the frame of politeness and/or formality in social structures. Korean school grammar explains honorifics as linguistic forms that reflect relative social positional difference (e.g., K-H. Lee, 2010), and has assumed that social structure and language use have a…

Income Tax Reform and Agriculture: A Symposium.

ERIC Educational Resources Information Center

Economic Research Service (USDA), Washington, DC.

Five papers are provided from a symposium organized to present several economic studies relating to income tax structure and reform in agriculture. "Toward an Optimal Income Tax Policy for Southern and U.S. Agriculture" (Harold F. Breimyer) is a structured argument for comprehensive tax reform that increases the equity of the income tax…

Fitting Meta-Analytic Structural Equation Models with Complex Datasets

ERIC Educational Resources Information Center

Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

2016-01-01

A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

Dynamics of Representational Change: Entropy, Action, and Cognition

ERIC Educational Resources Information Center

Stephen, Damian G.; Dixon, James A.; Isenhower, Robert W.

2009-01-01

Explaining how the cognitive system can create new structures has been a major challenge for cognitive science. Self-organization from the theory of nonlinear dynamics offers an account of this remarkable phenomenon. Two studies provide an initial test of the hypothesis that the emergence of new cognitive structure follows the same universal…

Situational and Structural Variation in Youth Perceptions of Maternal Guilt Induction

ERIC Educational Resources Information Center

Rote, Wendy M.; Smetana, Judith G.

2017-01-01

Parental induction of empathy-related guilt plays an important role in children's moral development. However, guilt induction can also be psychologically controlling and detrimental for youth adjustment. This study provided a more nuanced view of parental guilt induction by examining how the nature of a child's misdeed and the structure and…

Discussion Tool Effects on Collaborative Learning and Social Network Structure

ERIC Educational Resources Information Center

Tomsic, Astrid; Suthers, Daniel D.

2006-01-01

This study investigated the social network structure of booking officers at the Honolulu Police Department and how the introduction of an online discussion tool affected knowledge about operation of a booking module. Baseline data provided evidence for collaboration among officers in the same district using e-mail, telephone and face-to-face media…

Structural dynamics of tropical moist forest gaps

Treesearch

Maria O. Hunter; Michael Keller; Douglas Morton; Bruce Cook; Michael Lefsky; Mark Ducey; Scott Saleska; Raimundo Cosme de Oliveira; Juliana Schietti

2015-01-01

Gap phase dynamics are the dominant mode of forest turnover in tropical forests. However, gap processes are infrequently studied at the landscape scale. Airborne lidar data offer detailed information on three-dimensional forest structure, providing a means to characterize fine-scale (1 m) processes in tropical forests over large areas. Lidar-based estimates of forest...

French Interrogative Structures: A New Pedagogical Norm for the 21st-Century Classroom

ERIC Educational Resources Information Center

Antes, Theresa A.

2016-01-01

This study investigated interrogative structures most frequently used by native speakers of French, in an attempt to reconcile differences between language forms taught in the French as a foreign language classroom and those that are encountered in authentic input. Radio, television, and magazine interviews provided multiple examples of…

Social Influences, School Motivation and Gender Differences: An Application of the Expectancy-Value Theory

ERIC Educational Resources Information Center

Fan, Weihua

2011-01-01

The present study examined the structural relations of social influences, task values, ability beliefs, educational expectation and academic engagement for both boys and girls. The structural equation modelling analyses provided nationally representative evidence of gender differences in: (1) the links from teacher-student relationship and peer…

Exploration of Nursing Faculty Members' Lived Experiences of Objective Structured Clinical Examination (OSCE) in Undergraduate Nursing Education

ERIC Educational Resources Information Center

Obizoba, Cordelia O.

2014-01-01

The purpose of this phenomenological study was to gain an understanding of nursing faculty members' lived experiences of Objective Structured Clinical Examination (OSCE) in undergraduate nursing education. As owners of their programs' curriculum, nursing faculties are charged with the responsibility of providing needed knowledge, skills, and…

Parent Participation in School Governance: A Legal Analysis of Experiences in South Africa and Kentucky

ERIC Educational Resources Information Center

Bathon, Justin; Beckmann, Johan; Bjork, Lars G.

2011-01-01

This comparative study on the educational governance systems of South Africa and the Commonwealth of Kentucky examines legal evidence from judicial decisions and administrative law to understand similarities in how school-based governance structures have been developed. We found that although school-level governance structures may provide greater…

System Transformation Under the California Mental Health Services Act: Implementation of Full-Service Partnerships in L.A. County.

PubMed

Starks, Sarah L; Arns, Paul G; Padwa, Howard; Friedman, Jack R; Marrow, Jocelyn; Meldrum, Marcia L; Bromley, Elizabeth; Kelly, Erin L; Brekke, John S; Braslow, Joel T

2017-06-01

The study evaluated the effect of California's Mental Health Services Act (MHSA) on the structure, volume, location, and patient centeredness of Los Angeles County public mental health services. This prospective mixed-methods study (2006-2013) was based in five Los Angeles County public mental health clinics, all with usual care and three with full-service partnerships (FSPs). FSPs are MHSA-funded programs designed to "do whatever it takes" to provide intensive, recovery-oriented, team-based, integrated services for clients with severe mental illness. FSPs were compared with usual care on outpatient services received (claims data) and on organizational climate, recovery orientation, and provider-client working alliance (surveys and semistructured interviews), with regression adjustment for client and provider characteristics. In the first year after admission, FSP clients (N=174) received significantly more outpatient services than did usual care clients (N=298) (5,238 versus 1,643 minutes, p<.001), and a larger proportion of these services were field based (22% versus 2%, p<.001). Compared with usual care clients, FSP clients reported more recovery-oriented services (p<.001) and a better provider-client working alliance (p=.01). Compared with usual care providers (N=130), FSP providers (N=42) reported more stress (p<.001) and lower morale (p<.001). Los Angeles County's public mental health system was able to transform service delivery in response to well-funded policy mandates. For providers, a structure emphasizing accountability and patient centeredness was associated with greater stress, despite smaller caseloads. For clients, service structure and volume created opportunities to build stronger provider-client relationships and address their needs and goals.

Simulations of CYP51A from Aspergillus fumigatus in a model bilayer provide insights into triazole drug resistance.

PubMed

Nash, Anthony; Rhodes, Johanna

2018-04-01

Azole antifungal drugs target CYP51A in Aspergillus fumigatus by binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole antifungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, predominantly conferring resistance to itraconazole, although cross-resistance has been reported in conjunction with other mutations. In this study, we create a homology model of CYP51A using a recently published crystal structure of the paralog protein CYP51B. The derived structures, wild type, and L98H mutant are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighboring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set of dynamics of the A. fumigatus Lanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance.

Modeling Protein Expression and Protein Signaling Pathways

PubMed Central

Telesca, Donatello; Müller, Peter; Kornblau, Steven M.; Suchard, Marc A.; Ji, Yuan

2015-01-01

High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case, inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The proposed approach exploits available expert knowledge about the target pathway to define an informative prior on the hidden conditional dependence structure. An important feature of this prior is that it provides an instrument to explicitly anchor the model space to a set of interactions of interest, favoring a local search approach to model determination. We apply our model to reverse-phase protein array data from a study on acute myeloid leukemia. Our inference identifies relevant subpathways in relation to the unfolding of the biological process under study. PMID:26246646

Medical student storytelling on an institutional blog: a case study analysis.

PubMed

Becker, Katherine A; Freberg, Karen

2014-05-01

Despite the proclivity and proliferation of blogs on the Internet, the use of blogs at medical institutions is not well documented. In examining the structured stories that medical students share with the digital community, we may better understand how students use institutional blogs to discuss their medical school experiences while maintaining their role as a medical student ambassador for the program. We conducted a case study to analyze the stories within 309 medical student blogs from one medical institution in the United States. In an attempt to communicate their experiences to different benefactors, student bloggers engaged in structured and personal storytelling. Structured stories offered medical school advice to prospective students, while personal stories embodied features of a personal diary where students recounted significant milestones, talked about personal relationships and engaged in emotional reflection and disclosure. Institutional blogs may provide social marketing for medical institutions, as students strategically framed their experiences to reflect a positive attitude about the medical institution and focused on providing advice to prospective students. Although these structured stories limit complete disclosure, students may still achieve benefits by engaging in emotional disclosure and personal reflection.

Classification of mathematics deficiency using shape and scale analysis of 3D brain structures

NASA Astrophysics Data System (ADS)

Kurtek, Sebastian; Klassen, Eric; Gore, John C.; Ding, Zhaohua; Srivastava, Anuj

2011-03-01

We investigate the use of a recent technique for shape analysis of brain substructures in identifying learning disabilities in third-grade children. This Riemannian technique provides a quantification of differences in shapes of parameterized surfaces, using a distance that is invariant to rigid motions and re-parameterizations. Additionally, it provides an optimal registration across surfaces for improved matching and comparisons. We utilize an efficient gradient based method to obtain the optimal re-parameterizations of surfaces. In this study we consider 20 different substructures in the human brain and correlate the differences in their shapes with abnormalities manifested in deficiency of mathematical skills in 106 subjects. The selection of these structures is motivated in part by the past links between their shapes and cognitive skills, albeit in broader contexts. We have studied the use of both individual substructures and multiple structures jointly for disease classification. Using a leave-one-out nearest neighbor classifier, we obtained a 62.3% classification rate based on the shape of the left hippocampus. The use of multiple structures resulted in an improved classification rate of 71.4%.

Study on Topology Optimization Design, Manufacturability, and Performance Evaluation of Ti-6Al-4V Porous Structures Fabricated by Selective Laser Melting (SLM)

PubMed Central

Xu, Yangli; Zhang, Dongyun; Zhou, Yan; Wang, Weidong; Cao, Xuanyang

2017-01-01

The combination of topology optimization (TOP) and selective laser melting (SLM) provides the possibility of fabricating the complex, lightweight and high performance geometries overcoming the traditional manufacturing “bottleneck”. This paper evaluates the biomechanical properties of porous structures with porosity from 40% to 80% and unit cell size from 2 to 8 mm, which are designed by TOP and manufactured by SLM. During manufacturability exploration, three typical structures including spiral structure, arched bridge structure and structures with thin walls and small holes are abstracted and investigated, analyzing their manufacturing limits and forming reason. The property tests show that dynamic elastic modulus and compressive strength of porous structures decreases with increases of porosity (constant unit cell size) or unit cell size (constant porosity). Based on the Gibson-Ashby model, three failure models are proposed to describe their compressive behavior, and the structural parameter λ is used to evaluate the stability of the porous structure. Finally, a numerical model for the correlation between porous structural parameters (unit cell size and porosity) and elastic modulus is established, which provides a theoretical reference for matching the elastic modulus of human bones from different age, gender and skeletal sites during innovative medical implant design and manufacturing. PMID:28880229

Study on Topology Optimization Design, Manufacturability, and Performance Evaluation of Ti-6Al-4V Porous Structures Fabricated by Selective Laser Melting (SLM).

PubMed

Xu, Yangli; Zhang, Dongyun; Zhou, Yan; Wang, Weidong; Cao, Xuanyang

2017-09-07

The combination of topology optimization (TOP) and selective laser melting (SLM) provides the possibility of fabricating the complex, lightweight and high performance geometries overcoming the traditional manufacturing "bottleneck". This paper evaluates the biomechanical properties of porous structures with porosity from 40% to 80% and unit cell size from 2 to 8 mm, which are designed by TOP and manufactured by SLM. During manufacturability exploration, three typical structures including spiral structure, arched bridge structure and structures with thin walls and small holes are abstracted and investigated, analyzing their manufacturing limits and forming reason. The property tests show that dynamic elastic modulus and compressive strength of porous structures decreases with increases of porosity (constant unit cell size) or unit cell size (constant porosity). Based on the Gibson-Ashby model, three failure models are proposed to describe their compressive behavior, and the structural parameter λ is used to evaluate the stability of the porous structure. Finally, a numerical model for the correlation between porous structural parameters (unit cell size and porosity) and elastic modulus is established, which provides a theoretical reference for matching the elastic modulus of human bones from different age, gender and skeletal sites during innovative medical implant design and manufacturing.

Reanalysis, compatibility and correlation in analysis of modified antenna structures

NASA Technical Reports Server (NTRS)

Levy, R.

1989-01-01

A simple computational procedure is synthesized to process changes in the microwave-antenna pathlength-error measure when there are changes in the antenna structure model. The procedure employs structural modification reanalysis methods combined with new extensions of correlation analysis to provide the revised rms pathlength error. Mainframe finite-element-method processing of the structure model is required only for the initial unmodified structure, and elementary postprocessor computations develop and deal with the effects of the changes. Several illustrative computational examples are included. The procedure adapts readily to processing spectra of changes for parameter studies or sensitivity analyses.

High-pressure behavior of methylammonium lead iodide (MAPbI3) hybrid perovskite

NASA Astrophysics Data System (ADS)

Capitani, Francesco; Marini, Carlo; Caramazza, Simone; Postorino, Paolo; Garbarino, Gaston; Hanfland, Michael; Pisanu, Ambra; Quadrelli, Paolo; Malavasi, Lorenzo

2016-05-01

In this paper we provide an accurate high-pressure structural and optical study of the MAPbI3 hybrid perovskite. Structural data show the presence of a phase transition toward an orthorhombic structure around 0.3 GPa followed by full amorphization of the system above 3 GPa. After releasing the pressure, the system keeps the high-pressure orthorhombic phase. The occurrence of these structural transitions is further confirmed by pressure induced variations of the photoluminescence signal at high pressure. These variations clearly indicate that the bandgap value and the electronic structure of MAPI change across the phase transition.

RSRE: RNA structural robustness evaluator

PubMed Central

Shu, Wenjie; Zheng, Zhiqiang; Wang, Shengqi

2007-01-01

Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous studies in recent years. Although structural robustness has been explored in several types of RNA molecules, the origins of robustness are still controversial. Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems. The RNA structural robustness evaluator (RSRE) web server presented here provides a freely available online tool to quantitatively evaluate the structural robustness of RNA based on the widely accepted definition of neutrality. Several classical structure comparison methods are employed; five randomization methods are implemented to generate control sequences; sub-optimal predicted structures can be optionally utilized to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate analysis. The RSRE will be helpful in the wide exploration of RNA structural robustness and will catalyze our understanding of RNA evolution. The RSRE web server is freely available at http://biosrv1.bmi.ac.cn/RSRE/ or http://biotech.bmi.ac.cn/RSRE/. PMID:17567615

Angle-resolved photoemission spectroscopy studies of metallic surface and interface states of oxide insulators

NASA Astrophysics Data System (ADS)

Plumb, Nicholas C.; Radović, Milan

2017-11-01

Over the last decade, conducting states embedded in insulating transition metal oxides (TMOs) have served as gateways to discovering and probing surprising phenomena that can emerge in complex oxides, while also opening opportunities for engineering advanced devices. These states are commonly realized at thin film interfaces, such as the well-known case of LaAlO3 (LAO) grown on SrTiO3 (STO). In recent years, the use of angle-resolved photoemission spectroscopy (ARPES) to investigate the k-space electronic structure of such materials led to the discovery that metallic states can also be formed on the bare surfaces of certain TMOs. In this topical review, we report on recent studies of low-dimensional metallic states confined at insulating oxide surfaces and interfaces as seen from the perspective of ARPES, which provides a direct view of the occupied band structure. While offering a fairly broad survey of progress in the field, we draw particular attention to STO, whose surface is so far the best-studied, and whose electronic structure is probably of the most immediate interest, given the ubiquitous use of STO substrates as the basis for conducting oxide interfaces. The ARPES studies provide crucial insights into the electronic band structure, orbital character, dimensionality/confinement, spin structure, and collective excitations in STO surfaces and related oxide surface/interface systems. The obtained knowledge increases our understanding of these complex materials and gives new perspectives on how to manipulate their properties.

Crustal structure of the coastal and marine San Francisco Bay region, California

USGS Publications Warehouse

Parsons, Tom

2002-01-01

In summary, these studies were carried out in an environment where background information on faults in the San Francisco Bay region was sought. Much of the structural information presented here comes from experiments of a style unlikely to be conducted by the USGS in the near future. Together, the chapters in this volume provide a structural framework for a major part of a complex strike-slip fault system.

Optical study on the dependence of breast tissue composition and structure on subject anamnesis

NASA Astrophysics Data System (ADS)

Taroni, Paola; Quarto, Giovanna; Pifferi, Antonio; Abbate, Francesca; Balestreri, Nicola; Menna, Simona; Cassano, Enrico; Cubeddu, Rinaldo

2015-07-01

Time domain multi-wavelength (635 to 1060 nm) optical mammography was performed on 200 subjects to estimate their average breast tissue composition in terms of oxy- and deoxy-hemoglobin, water, lipid and collagen, and structural information, as provided by scattering parameters (amplitude and power). Significant (and often marked) dependence of tissue composition and structure on age, menopausal status, body mass index, and use of oral contraceptives was demonstrated.

Final Scientific/Technical Report

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

Reeder, Richard; Phillips, Brian

A variety of calcifying organisms produce a transient or metastable amorphous calcium carbonate (ACC) precursor phase that is assembled and subsequently transformed into a crystalline biomineral, typically calcite or aragonite. The complex shapes, hierarchical structures, and unique physical properties of the biominerals that result from this calcification pathway have stimulated interest in adapting these concepts for the design and creation of bio-inspired functional materials in the laboratory. ACC also forms as a reactive precursor in diverse inorganic systems and is likely to play a much broader role in calcium carbonate formation. Knowledge of the structure, composition, and behavior of thismore » metastable phase is critical for establishing a structural and mechanistic framework for calcium carbonate formation and its role in biogeochemical processes, including carbon cycling. Minor additives, such as magnesium, phosphorus, and organic macromolecules, are known to play important roles in controlling ACC stability, transformation kinetics, and selection of final crystalline polymorph. Molecular water also occurs in many types of ACC and is thought to play a structural role in its stability and transformation behavior. One of the major challenges that remain unresolved is identification of the structural basis for the role of these minor additives and molecular water. The absence of long-range order in ACC, and other amorphous phases, has posed a challenge for study by techniques commonly used for crystalline solids. Preliminary studies in our group show that the combination of two techniques, synchrotron X-ray-based pair distribution function (PDF) analysis and nuclear magnetic resonance (NMR) spectroscopy can provide entirely new insight to structural properties of synthetic ACC over length scales that are most relevant for understanding its transformation properties. Building on preliminary experiments, we propose a systematic study of synthesis, structure, and transformation behavior in abiotic systems. The work will specifically address the influence of phosphate as a minor additive. PDF analysis will utilize total X-ray scattering data collected at synchrotron facilities optimized for this method and will provide direct characterization of the short- and intermediate-range structure of ACC synthesized under controlled conditions. Parallel computational work using reverse Monte Carlo methods will allow structural models to be constructed for a more complete analysis of PDF results. NMR spectroscopy, using a variety of single- and double-resonance techniques, will provide information on H and CO3 components, including dynamical properties, and their relationship to stabilizing additives. PDF and NMR results will be complemented by parallel studies using X-ray absorption and FT-IR spectroscopy to allow direct comparison to previous studies. These techniques will be used to follow the transformation of different ACC samples, with specific additives, to crystalline phases under controlled condition (e.g., relative humidity). This work will provide the structural and mechanistic basis for understanding ACC stability, its transformation behavior, and the factors that govern polymorph selection. This new insight will directly benefit researchers in diverse fields, as well as adding to the framework of knowledge for understanding and controlling calcium carbonate formation in natural and engineered systems.« less

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Single versus double-row repair of the rotator cuff: does double-row repair with improved anatomical and biomechanical characteristics lead to better clinical outcome?

PubMed

Pauly, Stephan; Gerhardt, Christian; Chen, Jianhai; Scheibel, Markus

2010-12-01

Several techniques for arthroscopic repair of rotator cuff defects have been introduced over the past years. Besides established techniques such as single-row repairs, new techniques such as double-row reconstructions have gained increasing interest. The present article therefore provides an overview of the currently available literature on both repair techniques with respect to several anatomical, biomechanical, clinical and structural endpoints. Systematic literature review of biomechanical, clinical and radiographic studies investigating or comparing single- and double-row techniques. These results were evaluated and compared to provide an overview on benefits and drawbacks of the respective repair type. Reconstructions of the tendon-to-bone unit for full-thickness tears in either single- or double-row technique differ with respect to several endpoints. Double-row repair techniques provide more anatomical reconstructions of the footprint and superior initial biomechanical characteristics when compared to single-row repair. With regard to clinical results, no significant differences were found while radiological data suggest a better structural tendon integrity following double-row fixation. Presently published clinical studies cannot emphasize a clearly superior technique at this time. Available biomechanical studies are in favour of double-row repair. Radiographic studies suggest a beneficial effect of double-row reconstruction on structural integrity of the reattached tendon or reduced recurrent defect rates, respectively.

Segmental structure in banded mongoose calls.

PubMed

Fitch, W Tecumseh

2012-12-03

In complex animal vocalizations, such as bird or whale song, a great variety of songs can be produced via rearrangements of a smaller set of 'syllables', known as 'phonological syntax' or 'phonocoding' However, food or alarm calls, which function as referential signals, were previously thought to lack such combinatorial structure. A new study of calls in the banded mongoose Mungos mungo provides the first evidence of phonocoding at the level of single calls. The first portion of the call provides cues to the identity of the caller, and the second part encodes its current activity. This provides the first example known in animals of something akin to the consonants and vowels of human speech.

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

PubMed

Emperador, Agustí; Orozco, Modesto

2017-03-14

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

Nondestructive cryomicro-CT imaging enables structural and molecular analysis of human lung tissue.

PubMed

Vasilescu, Dragoş M; Phillion, André B; Tanabe, Naoya; Kinose, Daisuke; Paige, David F; Kantrowitz, Jacob J; Liu, Gang; Liu, Hanqiao; Fishbane, Nick; Verleden, Stijn E; Vanaudenaerde, Bart M; Lenburg, Marc; Stevenson, Christopher S; Spira, Avrum; Cooper, Joel D; Hackett, Tillie-Louise; Hogg, James C

2017-01-01

Micro-computed tomography (CT) enables three-dimensional (3D) imaging of complex soft tissue structures, but current protocols used to achieve this goal preclude cellular and molecular phenotyping of the tissue. Here we describe a radiolucent cryostage that permits micro-CT imaging of unfixed frozen human lung samples at an isotropic voxel size of (11 µm) 3 under conditions where the sample is maintained frozen at -30°C during imaging. The cryostage was tested for thermal stability to maintain samples frozen up to 8 h. This report describes the methods used to choose the materials required for cryostage construction and demonstrates that whole genome mRNA integrity and expression are not compromised by exposure to micro-CT radiation and that the tissue can be used for immunohistochemistry. The new cryostage provides a novel method enabling integration of 3D tissue structure with cellular and molecular analysis to facilitate the identification of molecular determinants of disease. The described micro-CT cryostage provides a novel way to study the three-dimensional lung structure preserved without the effects of fixatives while enabling subsequent studies of the cellular matrix composition and gene expression. This approach will, for the first time, enable researchers to study structural changes of lung tissues that occur with disease and correlate them with changes in gene or protein signatures. Copyright © 2017 the American Physiological Society.

[Structures and processes in outpatient neurorehabilitation].

PubMed

Pöppl, Dominik; Deck, R; Kringler, W; Reuther, P

2014-06-01

Quality of structures, processes and outcome are commonly accepted as dimensions of quality management and quality assurance. Data of structures and processes are not published to date for German outpatient neurorehabilitation. Rehabilitative care and service providers are legally bound to apply concepts of quality management and quality assurance. The service providers pass recommendations, which have to be implemented by outpatient neurorehabilitation centres. Data analysis of existing structures and processes in outpatient neurorehabilitation centres are embedded as a part of a long-term multicentres outcome study. 22 outpatient neurorehabilitation centres participated in an online survey with 227 items using the google tool "Docs" between September and December 2011. Following issues were asked: general information about the centres (e. g. date of establishment, number of therapy places, kind of patients, responsible organization), utility supply contracts with service providers, local cooperation and networking, staff and equipment and appliances, treatment concepts, processes of therapy (e. g. individual and group therapy, frequency, concentration, planning), team processes, goals and team development, quality management and documentation. In the meantime outpatient centres of neurorehabilitation are well-established as care providers and commonly accepted by service providers. However a comprehensive availability does not exist. The results show comparable structures of the centres, what is mostly determined by the service provider audited regulatory framework. Different concepts result in different processes. There are a lot of hints with respect to different concepts in form and content to implement the legally obligated mandate. In general their work with context -factors is still a frequently unused potential. It can be countered by the therapeutic inclusion of the social and environmental living conditions of the patients. © Georg Thieme Verlag KG Stuttgart · New York.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

PubMed

Keates, Tracy; Cooper, Christopher D O; Savitsky, Pavel; Allerston, Charles K; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-06-15

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. Copyright © 2011 Elsevier B.V. All rights reserved.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

PubMed Central

Keates, Tracy; Cooper, Christopher D.O.; Savitsky, Pavel; Allerston, Charles K.; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A.; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-01-01

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. PMID:22027370

The neuronal porosome complex in health and disease

PubMed Central

Naik, Akshata R; Lewis, Kenneth T

2015-01-01

Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse. PMID:26264442

Functional and Structural Brain Changes Associated with Methamphetamine Abuse

PubMed Central

Jan, Reem K.; Kydd, Rob R.; Russell, Bruce R.

2012-01-01

Methamphetamine (MA) is a potent psychostimulant drug whose abuse has become a global epidemic in recent years. Firstly, this review article briefly discusses the epidemiology and clinical pharmacology of methamphetamine dependence. Secondly, the article reviews relevant animal literature modeling methamphetamine dependence and discusses possible mechanisms of methamphetamine-induced neurotoxicity. Thirdly, it provides a critical review of functional and structural neuroimaging studies in human MA abusers; including positron emission tomography (PET) and functional and structural magnetic resonance imaging (MRI). The effect of abstinence from methamphetamine, both short- and long-term within the context of these studies is also reviewed. PMID:24961256

A methodology for choosing candidate materials for the fabrication of planetary space suit structures

NASA Technical Reports Server (NTRS)

Jacobs, Gilda

1990-01-01

A study of space suit structures and materials is under way at NASA Ames Research Center, Moffett Field, CA. The study was initiated by the need for a generation of lightweight space suits to be used in future planetary Exploration Missions. This paper provides a brief description of the Lunar and Mars environments and reviews what has been done in the past in the design and development of fabric, metal, and composite suit components in order to establish criteria for comparison of promising candidate materials and space suit structures. Environmental factors and mission scenarios will present challenging material and structural requirements; thus, a program is planned to outline the methodology used to identify materials and processes for producing candidate space suit structures which meet those requirements.

Reliability-based structural optimization: A proposed analytical-experimental study

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson; Nikolaidis, Efstratios

1993-01-01

An analytical and experimental study for assessing the potential of reliability-based structural optimization is proposed and described. In the study, competing designs obtained by deterministic and reliability-based optimization are compared. The experimental portion of the study is practical because the structure selected is a modular, actively and passively controlled truss that consists of many identical members, and because the competing designs are compared in terms of their dynamic performance and are not destroyed if failure occurs. The analytical portion of this study is illustrated on a 10-bar truss example. In the illustrative example, it is shown that reliability-based optimization can yield a design that is superior to an alternative design obtained by deterministic optimization. These analytical results provide motivation for the proposed study, which is underway.

Cross-cultural evidence for the two-facet structure of pride.

PubMed

Shi, Yan; Chung, Joanne M; Cheng, Joey T; Tracy, Jessica L; Robins, Richard W; Chen, Xiao; Zheng, Yong

2015-04-01

Across six studies conducted in Mainland China and South Korea, the present research extended prior findings showing that pride is comprised of two distinct conceptual and experiential facets in the U.S.: a pro-social, achievement-oriented "authentic pride", and an arrogant, self-aggrandizing "hubristic pride". This same two-facet structure emerged in Chinese participants' semantic conceptualizations of pride (Study 1), Chinese and Koreans' dispositional tendencies to experience pride (Studies 2, 3a, and 3b), Chinese and Koreans' momentary pride experiences (Studies 3a, 3b, and 5), and Americans' pride experiences using descriptors derived indigenously in Korea (Study 4). Together, these studies provide the first evidence that the two-facet structure of pride generalizes to cultures with highly divergent views of pride and self-enhancement processes from North America.

Parametric and Non-Parametric Vibration-Based Structural Identification Under Earthquake Excitation

NASA Astrophysics Data System (ADS)

Pentaris, Fragkiskos P.; Fouskitakis, George N.

2014-05-01

The problem of modal identification in civil structures is of crucial importance, and thus has been receiving increasing attention in recent years. Vibration-based methods are quite promising as they are capable of identifying the structure's global characteristics, they are relatively easy to implement and they tend to be time effective and less expensive than most alternatives [1]. This paper focuses on the off-line structural/modal identification of civil (concrete) structures subjected to low-level earthquake excitations, under which, they remain within their linear operating regime. Earthquakes and their details are recorded and provided by the seismological network of Crete [2], which 'monitors' the broad region of south Hellenic arc, an active seismic region which functions as a natural laboratory for earthquake engineering of this kind. A sufficient number of seismic events are analyzed in order to reveal the modal characteristics of the structures under study, that consist of the two concrete buildings of the School of Applied Sciences, Technological Education Institute of Crete, located in Chania, Crete, Hellas. Both buildings are equipped with high-sensitivity and accuracy seismographs - providing acceleration measurements - established at the basement (structure's foundation) presently considered as the ground's acceleration (excitation) and at all levels (ground floor, 1st floor, 2nd floor and terrace). Further details regarding the instrumentation setup and data acquisition may be found in [3]. The present study invokes stochastic, both non-parametric (frequency-based) and parametric methods for structural/modal identification (natural frequencies and/or damping ratios). Non-parametric methods include Welch-based spectrum and Frequency response Function (FrF) estimation, while parametric methods, include AutoRegressive (AR), AutoRegressive with eXogeneous input (ARX) and Autoregressive Moving-Average with eXogeneous input (ARMAX) models[4, 5]. Preliminary results indicate that parametric methods are capable of sufficiently providing the structural/modal characteristics such as natural frequencies and damping ratios. The study also aims - at a further level of investigation - to provide a reliable statistically-based methodology for structural health monitoring after major seismic events which potentially cause harming consequences in structures. Acknowledgments This work was supported by the State Scholarships Foundation of Hellas. References [1] J. S. Sakellariou and S. D. Fassois, "Stochastic output error vibration-based damage detection and assessment in structures under earthquake excitation," Journal of Sound and Vibration, vol. 297, pp. 1048-1067, 2006. [2] G. Hloupis, I. Papadopoulos, J. P. Makris, and F. Vallianatos, "The South Aegean seismological network - HSNC," Adv. Geosci., vol. 34, pp. 15-21, 2013. [3] F. P. Pentaris, J. Stonham, and J. P. Makris, "A review of the state-of-the-art of wireless SHM systems and an experimental set-up towards an improved design," presented at the EUROCON, 2013 IEEE, Zagreb, 2013. [4] S. D. Fassois, "Parametric Identification of Vibrating Structures," in Encyclopedia of Vibration, S. G. Braun, D. J. Ewins, and S. S. Rao, Eds., ed London: Academic Press, London, 2001. [5] S. D. Fassois and J. S. Sakellariou, "Time-series methods for fault detection and identification in vibrating structures," Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 365, pp. 411-448, February 15 2007.

Research and Evaluations of the Health Aspects of Disasters, Part VI: Interventional Research and the Disaster Logic Model.

PubMed

Birnbaum, Marvin L; Daily, Elaine K; O'Rourke, Ann P; Kushner, Jennifer

2016-04-01

Disaster-related interventions are actions or responses undertaken during any phase of a disaster to change the current status of an affected community or a Societal System. Interventional disaster research aims to evaluate the results of such interventions in order to develop standards and best practices in Disaster Health that can be applied to disaster risk reduction. Considering interventions as production functions (transformation processes) structures the analyses and cataloguing of interventions/responses that are implemented prior to, during, or following a disaster or other emergency. Since currently it is not possible to do randomized, controlled studies of disasters, in order to validate the derived standards and best practices, the results of the studies must be compared and synthesized with results from other studies (ie, systematic reviews). Such reviews will be facilitated by the selected studies being structured using accepted frameworks. A logic model is a graphic representation of the transformation processes of a program [project] that shows the intended relationships between investments and results. Logic models are used to describe a program and its theory of change, and they provide a method for the analyzing and evaluating interventions. The Disaster Logic Model (DLM) is an adaptation of a logic model used for the evaluation of educational programs and provides the structure required for the analysis of disaster-related interventions. It incorporates a(n): definition of the current functional status of a community or Societal System, identification of needs, definition of goals, selection of objectives, implementation of the intervention(s), and evaluation of the effects, outcomes, costs, and impacts of the interventions. It is useful for determining the value of an intervention and it also provides the structure for analyzing the processes used in providing the intervention according to the Relief/Recovery and Risk-Reduction Frameworks.

SES Multi-Purpose Ship Study. Transport Application. Volume 1. Technical Summary.

DTIC Science & Technology

1980-07-01

suitability for marine applications. Aluminum provides the lightest structure but the material cost is high, fabrication relatively difficult, the structure...and its application in Mili- tary Transportb and was prepared by the staff of the Navy’s Surface Effect Ship Acquisition Proje~~he study report...manu- facture of large surface effect craft, and a wealth of corporate knowledge and * expertise residing in the U.S. Navy Surface Effect Ships

Hydrolytic degradation of N,N‧-ethylenedimaleimide: Crystal structures of key intermediates and proposed mechanisms

NASA Astrophysics Data System (ADS)

Tan, Xue-Jie; Cheng, Shuang-Shuang; Shi, Yan; Xing, Dian-Xiang; Liu, Yun; Li, Hui; Feng, Wen-Quan; Yang, Jian-Bo

2016-12-01

Maleimide groups are used extensively in bioconjugation reactions, but limited mechanistic studies are available regarding their hydrolysis reactions. In this paper, five single-crystal structures related with the reaction of four-step hydrolytic degradation of N,N‧-ethylenedimaleimide have been investigated. On the basis of experimental results, the reaction mechanisms without or with water catalysis are proposed, which could provide some enlightenment into the study of similar hydrolytic degradations.

System analysis study of space platform and station accommodations for life sciences research facilities. Volume 2: Study results. Appendix E: Work breakdown structure and dictionary

NASA Technical Reports Server (NTRS)

Wiley, Lowell F.

1985-01-01

A work breakdown structure for the Space Station Life Sciences Research Facility (LSRF) is presented up to level 5. The purpose is to provide the framework for task planning and control and to serve as a basis for budgeting, task assignment, cost collection and report, and contractual performance measurement and tracking of the Full Scale Development Phase tasks.

The suite of small-angle neutron scattering instruments at Oak Ridge National Laboratory

DOE PAGES

Heller, William T.; Cuneo, Matthew J.; Debeer-Schmitt, Lisa M.; ...

2018-02-21

Oak Ridge National Laboratory is home to the High Flux Isotope Reactor (HFIR), a high-flux research reactor, and the Spallation Neutron Source (SNS), the world's most intense source of pulsed neutron beams. The unique co-localization of these two sources provided an opportunity to develop a suite of complementary small-angle neutron scattering instruments for studies of large-scale structures: the GP-SANS and Bio-SANS instruments at the HFIR and the EQ-SANS and TOF-USANS instruments at the SNS. This article provides an overview of the capabilities of the suite of instruments, with specific emphasis on how they complement each other. As a result, amore » description of the plans for future developments including greater integration of the suite into a single point of entry for neutron scattering studies of large-scale structures is also provided.« less

The suite of small-angle neutron scattering instruments at Oak Ridge National Laboratory

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

Heller, William T.; Cuneo, Matthew J.; Debeer-Schmitt, Lisa M.

Oak Ridge National Laboratory is home to the High Flux Isotope Reactor (HFIR), a high-flux research reactor, and the Spallation Neutron Source (SNS), the world's most intense source of pulsed neutron beams. The unique co-localization of these two sources provided an opportunity to develop a suite of complementary small-angle neutron scattering instruments for studies of large-scale structures: the GP-SANS and Bio-SANS instruments at the HFIR and the EQ-SANS and TOF-USANS instruments at the SNS. This article provides an overview of the capabilities of the suite of instruments, with specific emphasis on how they complement each other. As a result, amore » description of the plans for future developments including greater integration of the suite into a single point of entry for neutron scattering studies of large-scale structures is also provided.« less

GPACC program cost work breakdown structure-dictionary. General purpose aft cargo carrier study, volume 3

NASA Technical Reports Server (NTRS)

1985-01-01

The results of detailed cost estimates and economic analysis performed on the updated Model 101 configuration of the general purpose Aft Cargo Carrier (ACC) are given. The objective of this economic analysis is to provide the National Aeronautics and Space Administration (NASA) with information on the economics of using the ACC on the Space Transportation System (STS). The detailed cost estimates for the ACC are presented by a work breakdown structure (WBS) to ensure that all elements of cost are considered in the economic analysis and related subsystem trades. Costs reported by WBS provide NASA with a basis for comparing competing designs and provide detailed cost information that can be used to forecast phase C/D planning for new projects or programs derived from preliminary conceptual design studies. The scope covers all STS and STS/ACC launch vehicle cost impacts for delivering payloads to a 160 NM low Earth orbit (LEO).

DACC program cost and work breakdown structure-dictionary. General purpose aft cargo carrier study, volume 2

NASA Technical Reports Server (NTRS)

1985-01-01

Results of detailed cost estimates and economic analysis performed on the updated 201 configuration of the dedicated Aft Cargo Carrier (DACC) are given. The objective of this economic analysis is to provide the National Aeronautics and Space Administration (NASA) with information on the economics of using the DACC on the Space Transportation System (STS). The detailed cost estimates for the DACC are presented by a work breakdown structure (WBS) to ensure that all elements of cost are considered in the economic analysis and related subsystem trades. Costs reported by WBS provide NASA with a basis for comparing competing designs and provide detailed cost information that can be used to forecast phase C/D planning for new projects or programs derived from preliminary conceptual design studies. The scope covers all STS and STS/DACC launch vehicle cost impacts for delivering an orbital transfer vehicle to a 120 NM low Earth orbit (LEO).

Comparative study of the pentamodal property of four potential pentamode microstructures

NASA Astrophysics Data System (ADS)

Huang, Yan; Lu, Xuegang; Liang, Gongying; Xu, Zhuo

2017-03-01

In this paper, a numerical comparative study is presented on the pentamodal property of four potential pentamode microstructures (three based on simple cubic and one on body-centered cubic structures) based on phonon band calculations. The finite-element method is employed to calculate the band structures, and the two essential factors of the ratio of bulk modulus B to shear modulus G and the single-mode band gap (SBG) are analyzed to quantitatively evaluate the pentamodal property. The results show that all four structures possess a higher B/G ratio than traditional materials. One of the simple cubic structures exhibits the incomplete SBG, while the three other structures exhibit complete SBG to decouple the compression and shear waves in all propagation directions. Further parametric analyses are presented investigating the effects of geometrical and material parameters on the pentamodal property of these structures. This study provides guidelines for the future design of novel pentamode microstructures possessing a high B/G ratio and a low-frequency broadband SBG.

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.

Blueprints for a Collaborative Classroom.

ERIC Educational Resources Information Center

1997

This book provides guidelines and suggested activities for collaborative learning for elementary grade students with a variety of abilities and disabilities. It is based on experiences at the Developmental Studies Center (Oakland, California). Activities are presented as blueprint formats that provide a comprehensive set of structures which can be…

The Basic Structure of Community Early Intervention Programs for Children with Autism: Provider Descriptions

PubMed Central

Stahmer, Aubyn C.

2007-01-01

Autism researchers have identified a set of common effective practice elements for early intervention (EI) (e.g., intensive programming). The current study examined the reported about use of common elements of effective interventions in community EI settings. Eighty EI providers reported about their programs. The majority of participants reported using common effective elements, however, the depth and quality of the use of these elements was highly variable. Taking community program structure into account in future research will facilitate the development of methodologies, which immediately fit into the context of community programming rather than requiring program adaptation for use in the real world. Recommendations for using current community program structure to improve use of evidence-based practices are discussed. PMID:17086438

Probing the structure of the stable Xe isotopes with inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Peters, Erin E.; Ross, Timothy J.; Crider, Benjamin P.; Yates, Steven W.

2018-05-01

The stable isotopes of xenon, which have attracted interest for a number of reasons, span a transitional region that evolves from γ-soft structures for the lighter mass isotopes to nearly spherical 136Xe with a closed neutron shell. The nature of this transition, which is gradual, is not well understood. To provide detailed spectroscopic information on the Xe isotopes, we have studied 130,132,134,136Xe at the University of Kentucky Accelerator Laboratory using inelastic neutron scattering and γ-ray detection. These measurements yielded γ-ray angular distributions, branching ratios, multipole mixing ratios, and level lifetimes (from the Doppler-shift attenuation method), which allowed the determination of reduced transition probabilities and provided insight into the structure of these nuclei.

Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure.

PubMed

Christoph, J; Griebel, L; Leb, I; Engel, I; Köpcke, F; Toddenroth, D; Prokosch, H-U; Laufer, J; Marquardt, K; Sedlmayr, M

2015-01-01

The secondary use of clinical data provides large opportunities for clinical and translational research as well as quality assurance projects. For such purposes, it is necessary to provide a flexible and scalable infrastructure that is compliant with privacy requirements. The major goals of the cloud4health project are to define such an architecture, to implement a technical prototype that fulfills these requirements and to evaluate it with three use cases. The architecture provides components for multiple data provider sites such as hospitals to extract free text as well as structured data from local sources and de-identify such data for further anonymous or pseudonymous processing. Free text documentation is analyzed and transformed into structured information by text-mining services, which are provided within a cloud-computing environment. Thus, newly gained annotations can be integrated along with the already available structured data items and the resulting data sets can be uploaded to a central study portal for further analysis. Based on the architecture design, a prototype has been implemented and is under evaluation in three clinical use cases. Data from several hundred patients provided by a University Hospital and a private hospital chain have already been processed. Cloud4health has shown how existing components for secondary use of structured data can be complemented with text-mining in a privacy compliant manner. The cloud-computing paradigm allows a flexible and dynamically adaptable service provision that facilitates the adoption of services by data providers without own investments in respective hardware resources and software tools.

Chinese Teachers' Perceptions of the Roles and Functions of School Psychological Service Providers in Beijing

ERIC Educational Resources Information Center

Wang, Cixin; Ni, Hong; Ding, Yi; Yi, Chunli

2015-01-01

This study used a semi-structured interview with 94 teachers from 92 elementary and secondary schools in Beijing, China, to explore their perceptions of the roles, training, and challenges of school psychological service providers (SPs) as well as teachers' satisfaction with the services provided by SPs. Results indicated that the SP to student…

Impact of conversion to mixed-oxide fuels on reactor structural components

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

Yahr, G.T.

1997-04-01

The use of mixed-oxide (MOX) fuel to replace conventional uranium fuel in commercial light-water power reactors will result in an increase in the neutron flux. The impact of the higher flux on the structural integrity of reactor structural components must be evaluated. This report briefly reviews the effects of radiation on the mechanical properties of metals. Aging degradation studies and reactor operating experience provide a basis for determining the areas where conversion to MOX fuels has the potential to impact the structural integrity of reactor components.

Ferroelectric tunnel junctions with multi-quantum well structures

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

Ma, Zhijun; Zhang, Tianjin, E-mail: zhangtj@hubu.edu.cn; Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Hubei University, Wuhan 430062

Ferroelectric tunnel junctions (FTJs) with multi-quantum well structures are proposed and the tunneling electroresistance (TER) effect is investigated theoretically. Compared with conventional FTJs with monolayer ferroelectric barriers, FTJs with single-well structures provide TER ratio improvements of one order of magnitude, while FTJs with optimized multi-well structures can enhance this improvement by another order of magnitude. It is believed that the increased resonant tunneling strength combined with appropriate asymmetry in these FTJs contributes to the improvement. These studies may help to fabricate FTJs with large TER ratio experimentally and put them into practice.

Insights into Fanconi Anaemia from the structure of human FANCE

PubMed Central

Nookala, Ravi K.; Hussain, Shobbir; Pellegrini, Luca

2007-01-01

Fanconi Anaemia (FA) is a cancer predisposition disorder characterized by spontaneous chromosome breakage and high cellular sensitivity to genotoxic agents. In response to DNA damage, a multi-subunit assembly of FA proteins, the FA core complex, monoubiquitinates the downstream FANCD2 protein. The FANCE protein plays an essential role in the FA process of DNA repair as the FANCD2-binding component of the FA core complex. Here we report a crystallographic and biological study of human FANCE. The first structure of a FA protein reveals the presence of a repeated helical motif that provides a template for the structural rationalization of other proteins defective in Fanconi Anaemia. The portion of FANCE defined by our crystallographic analysis is sufficient for interaction with FANCD2, yielding structural information into the mode of FANCD2 recruitment to the FA core complex. Disease-associated mutations disrupt the FANCE–FANCD2 interaction, providing structural insight into the molecular mechanisms of FA pathogenesis. PMID:17308347

Structured Therapeutic Games for Nonoffending Caregivers of Children Who Have Experienced Sexual Abuse.

PubMed

Springer, Craig I; Colorado, Giselle; Misurell, Justin R

2015-01-01

Game-based cognitive-behavioral therapy group model for nonoffending caregivers utilizes structured therapeutic games to assist parents following child sexual abuse. Game-based cognitive-behavioral therapy group model is a manualized group treatment approach that integrates evidence-based cognitive-behavioral therapy components with structured play therapy to teach parenting and coping skills, provide psychoeducation, and process trauma. Structured therapeutic games were designed to allow nonoffending caregivers to process their children's abuse experiences and learn skills necessary to overcome trauma in a nonthreatening, fun, and engaging manner. The implementation of these techniques allow clinicians to address a variety of psychosocial difficulties that are commonly found among nonoffending caregivers of children who have experienced sexual abuse. In addition, structured therapeutic games help caregivers develop strengths and abilities that they can use to help their children cope with abuse and trauma and facilitates the development of positive posttraumatic growth. Techniques and procedures for treatment delivery along with a description of core components and therapeutic modules are discussed. An illustrative case study is provided.

Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

PubMed

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

PubMed

Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.

PubMed

Hoffman, J I; Kowalski, G J; Klimova, A; Eberhart-Phillips, L J; Staniland, I J; Baylis, A M M

2016-07-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

PubMed Central

Hoffman, J. I.; Kowalski, G. J.; Klimova, A.; Staniland, I. J.; Baylis, A. M. M.

2016-01-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations. PMID:27493782

Empowerment and performance of managers and subordinates in elderly care: A longitudinal and multilevel study.

PubMed

Hagerman, Heidi; Högberg, Hans; Skytt, Bernice; Wadensten, Barbro; Engström, Maria

2017-11-01

To investigate relationships between first-line managers' ratings of structural and psychological empowerment, and the subordinates' ratings of structural empowerment, as well as their ratings of the managers' leadership-management performance. Work situations in elderly care are complex. To date, few studies have used a longitudinal, correlational and multilevel design to study the working life of subordinates and managers. In five Swedish municipalities, questionnaires were answered twice during 2010-12 by 56 first-line managers and 769 subordinates working in nursing homes or home-help services. First-line managers' empowerment at Time 1 partially predicted subordinate's structural empowerment and ratings of their managers' leadership-management performance at Time 2. Changes over time partially revealed that the more access managers had to structural empowerment, i.e. increase over time, the higher the ratings were for structural empowerment and managerial leadership-management performance among subordinates. Findings strengthen research and theoretical suggestions linking first-line managers' structural empowerment to their subordinates' structural empowerment and ratings of their manager's leadership-management performance. Managers with high access to structural empowerment are more likely to provide subordinates access to structural empowerment. © 2017 The Authors. Journal of Nursing Management Published by John Wiley & Sons Ltd.

CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana

PubMed Central

2012-01-01

Background The cytochrome P450 (CYP) superfamily enables terrestrial plants to adapt to harsh environments. CYPs are key enzymes involved in a wide range of metabolic pathways. It is particularly useful to be able to analyse the three-dimensional (3D) structure when investigating the interactions between CYPs and their substrates. However, only two plant CYP structures have been resolved. In addition, no currently available databases contain structural information on plant CYPs and ligands. Fortunately, the 3D structure of CYPs is highly conserved and this has made it possible to obtain structural information from template-based modelling (TBM). Description The CYP Structure Interface (CYPSI) is a platform for CYP studies. CYPSI integrated the 3D structures for 266 A. thaliana CYPs predicted by three TBM methods: BMCD, which we developed specifically for CYP TBM; and two well-known web-servers, MUSTER and I-TASSER. After careful template selection and optimization, the models built by BMCD were accurate enough for practical application, which we demonstrated using a docking example aimed at searching for the CYPs responsible for ABA 8′-hydroxylation. CYPSI also provides extensive resources for A. thaliana CYP structure and function studies, including 400 PDB entries for solved CYPs, 48 metabolic pathways associated with A. thaliana CYPs, 232 reported CYP ligands and 18 A. thaliana CYPs docked with ligands (61 complexes in total). In addition, CYPSI also includes the ability to search for similar sequences and chemicals. Conclusions CYPSI provides comprehensive structure and function information for A. thaliana CYPs, which should facilitate investigations into the interactions between CYPs and their substrates. CYPSI has a user-friendly interface, which is available at http://bioinfo.cau.edu.cn/CYPSI. PMID:23256889

Fuzzy Edge Connectivity of Graphical Fuzzy State Space Model in Multi-connected System

NASA Astrophysics Data System (ADS)

Harish, Noor Ainy; Ismail, Razidah; Ahmad, Tahir

2010-11-01

Structured networks of interacting components illustrate complex structure in a direct or intuitive way. Graph theory provides a mathematical modeling for studying interconnection among elements in natural and man-made systems. On the other hand, directed graph is useful to define and interpret the interconnection structure underlying the dynamics of the interacting subsystem. Fuzzy theory provides important tools in dealing various aspects of complexity, imprecision and fuzziness of the network structure of a multi-connected system. Initial development for systems of Fuzzy State Space Model (FSSM) and a fuzzy algorithm approach were introduced with the purpose of solving the inverse problems in multivariable system. In this paper, fuzzy algorithm is adapted in order to determine the fuzzy edge connectivity between subsystems, in particular interconnected system of Graphical Representation of FSSM. This new approach will simplify the schematic diagram of interconnection of subsystems in a multi-connected system.

Velocity-depth ambiguity and the seismic structure of large igneous provinces: a case study from the Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Korenaga, Jun

2011-05-01

The seismic structure of large igneous provinces provides unique constraints on the nature of their parental mantle, allowing us to investigate past mantle dynamics from present crustal structure. To exploit this crust-mantle connection, however, it is prerequisite to quantify the uncertainty of a crustal velocity model, as it could suffer from considerable velocity-depth ambiguity. In this contribution, a practical strategy is suggested to estimate the model uncertainty by explicitly exploring the degree of velocity-depth ambiguity in the model space. In addition, wide-angle seismic data collected over the Ontong Java Plateau are revisited to provide a worked example of the new approach. My analysis indicates that the crustal structure of this gigantic plateau is difficult to reconcile with the melting of a pyrolitic mantle, pointing to the possibility of large-scale compositional heterogeneity in the convecting mantle.

Music and language perception: expectations, structural integration, and cognitive sequencing.

PubMed

Tillmann, Barbara

2012-10-01

Music can be described as sequences of events that are structured in pitch and time. Studying music processing provides insight into how complex event sequences are learned, perceived, and represented by the brain. Given the temporal nature of sound, expectations, structural integration, and cognitive sequencing are central in music perception (i.e., which sounds are most likely to come next and at what moment should they occur?). This paper focuses on similarities in music and language cognition research, showing that music cognition research provides insight into the understanding of not only music processing but also language processing and the processing of other structured stimuli. The hypothesis of shared resources between music and language processing and of domain-general dynamic attention has motivated the development of research to test music as a means to stimulate sensory, cognitive, and motor processes. Copyright © 2012 Cognitive Science Society, Inc.

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

Wojcik, Roza; Webb, Ian K.; Deng, Liulin

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

Acoustic Emission Measurement with Fiber Bragg Gratings for Structure Health Monitoring

NASA Technical Reports Server (NTRS)

Banks, Curtis E.; Walker, James L.; Russell, Sam; Roth, Don; Mabry, Nehemiah; Wilson, Melissa

2010-01-01

Structural Health monitoring (SHM) is a way of detecting and assessing damage to large scale structures. Sensors used in SHM for aerospace structures provide real time data on new and propagating damage. One type of sensor that is typically used is an acoustic emission (AE) sensor that detects the acoustic emissions given off from a material cracking or breaking. The use of fiber Bragg grating (FBG) sensors to provide acoustic emission data for damage detection is studied. In this research, FBG sensors are used to detect acoustic emissions of a material during a tensile test. FBG sensors were placed as a strain sensor (oriented parallel to applied force) and as an AE sensor (oriented perpendicular to applied force). A traditional AE transducer was used to collect AE data to compare with the FBG data. Preliminary results show that AE with FBGs can be a viable alternative to traditional AE sensors.

Classification of Chemicals Based On Structured Toxicity ...

EPA Pesticide Factsheets

Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-based classifications of chemicals were performed as a model application of ToxRefDB. These endpoints will ultimately provide the anchoring toxicity information for the development of predictive models and biological signatures utilizing in vitro assay data. Utilizing query and structured data mining approaches, toxicity profiles were uniformly generated for greater than 300 chemicals. Based on observation rate, species concordance and regulatory relevance, individual and aggregated effects have been selected to classify the chemicals providing a set of predictable endpoints. ToxRefDB exhibits the utility of transforming unstructured toxicity data into structured data and, furthermore, into computable outputs, and serves as a model for applying such data to address modern toxicological problems.

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

PubMed

Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

2009-10-01

Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

Atomic force microscopy of RNA: State of the art and recent advancements.

PubMed

Schön, Peter

2018-01-01

The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-resolution study of the 3D collagen fibrillary matrix of Achilles tendons without tissue labelling and dehydrating.

PubMed

Wu, Jian-Ping; Swift, Benjamin John; Becker, Thomas; Squelch, Andrew; Wang, Allan; Zheng, Yong-Chang; Zhao, Xuelin; Xu, Jiake; Xue, Wei; Zheng, Minghao; Lloyd, David; Kirk, Thomas Brett

2017-06-01

Knowledge of the collagen structure of an Achilles tendon is critical to comprehend the physiology, biomechanics, homeostasis and remodelling of the tissue. Despite intensive studies, there are still uncertainties regarding the microstructure. The majority of studies have examined the longitudinally arranged collagen fibrils as they are primarily attributed to the principal tensile strength of the tendon. Few studies have considered the structural integrity of the entire three-dimensional (3D) collagen meshwork, and how the longitudinal collagen fibrils are integrated as a strong unit in a 3D domain to provide the tendons with the essential tensile properties. Using second harmonic generation imaging, a 3D imaging technique was developed and used to study the 3D collagen matrix in the midportion of Achilles tendons without tissue labelling and dehydration. Therefore, the 3D collagen structure is presented in a condition closely representative of the in vivo status. Atomic force microscopy studies have confirmed that second harmonic generation reveals the internal collagen matrix of tendons in 3D at a fibril level. Achilles tendons primarily contain longitudinal collagen fibrils that braid spatially into a dense rope-like collagen meshwork and are encapsulated or wound tightly by the oblique collagen fibrils emanating from the epitenon region. The arrangement of the collagen fibrils provides the longitudinal fibrils with essential structural integrity and endows the tendon with the unique mechanical function for withstanding tensile stresses. A novel 3D microscopic method has been developed to examine the 3D collagen microstructure of tendons without tissue dehydrating and labelling. The study also provides new knowledge about the collagen microstructure in an Achilles tendon, which enables understanding of the function of the tissue. The knowledge may be important for applying surgical and tissue engineering techniques to tendon reconstruction. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Structural Basis for Iloprost as a Dual Peroxisome Proliferator-activated Receptor [alpha/delta] Agonist

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

Jin, Lihua; Lin, Shengchen; Rong, Hui

2012-03-15

Iloprost is a prostacyclin analog that has been used to treat many vascular conditions. Peroxisome proliferator-activated receptors (PPARs) are ligand-regulated transcription factors with various important biological effects such as metabolic and cardiovascular physiology. Here, we report the crystal structures of the PPAR{alpha} ligand-binding domain and PPAR{delta} ligand-binding domain bound to iloprost, thus providing unambiguous evidence for the direct interaction between iloprost and PPARs and a structural basis for the recognition of PPAR{alpha}/{delta} by this prostacyclin analog. In addition to conserved contacts for all PPAR{alpha} ligands, iloprost also initiates several specific interactions with PPARs using its unique structural groups. Structural andmore » functional studies of receptor-ligand interactions reveal strong functional correlations of the iloprost-PPAR{alpha}/{delta} interactions as well as the molecular basis of PPAR subtype selectivity toward iloprost ligand. As such, the structural mechanism may provide a more rational template for designing novel compounds targeting PPARs with more favorable pharmacologic impact based on existing iloprost drugs.« less

Vibration isolation by exploring bio-inspired structural nonlinearity.

PubMed

Wu, Zhijing; Jing, Xingjian; Bian, Jing; Li, Fengming; Allen, Robert

2015-10-08

Inspired by the limb structures of animals/insects in motion vibration control, a bio-inspired limb-like structure (LLS) is systematically studied for understanding and exploring its advantageous nonlinear function in passive vibration isolation. The bio-inspired system consists of asymmetric articulations (of different rod lengths) with inside vertical and horizontal springs (as animal muscle) of different linear stiffness. Mathematical modeling and analysis of the proposed LLS reveal that, (a) the system has very beneficial nonlinear stiffness which can provide flexible quasi-zero, zero and/or negative stiffness, and these nonlinear stiffness properties are adjustable or designable with structure parameters; (b) the asymmetric rod-length ratio and spring-stiffness ratio present very beneficial factors for tuning system equivalent stiffness; (c) the system loading capacity is also adjustable with the structure parameters which presents another flexible benefit in application. Experiments and comparisons with existing quasi-zero-stiffness isolators validate the advantageous features above, and some discussions are also given about how to select structural parameters for practical applications. The results would provide an innovative bio-inspired solution to passive vibration control in various engineering practice.

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.

PubMed

Sicoli, Giuseppe; Mathis, Gérald; Aci-Sèche, Samia; Saint-Pierre, Christine; Boulard, Yves; Gasparutto, Didier; Gambarelli, Serge

2009-06-01

Double electron-electron resonance (DEER) was applied to determine nanometre spin-spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes' positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids.

Breaking Boundaries: Complementary and Alternative Medicine Provider Framing of Preventive Care.

PubMed

Agarwal, Vinita

2017-11-01

This textual examination extends understandings of how complementary and alternative medicine (CAM) providers constitute preventive care in their discourse by identifying the frame of breaking boundaries referencing relational, structural, and philosophical orientations in their practice with their clients. Analysis of semistructured, in-depth interviews with CAM providers ( n = 17) reveals that the frame of breaking boundaries was comprised of three themes: finding one's own strength; I don't prescribe, so I'm exploring; and ground yourself, and have an escape route. The themes describe preventive care by identifying how CAM providers negotiate their relational positionality in connecting with clients, structural positionality within the field of health care, and philosophical positionality within the ontological understandings that guide how health is defined and conceptualized. The study contributes toward enhancing diverse understandings of constituting preventive care in practice and suggests pragmatic implications for addressing biomedical provider communication with their patients seeking CAM care alongside conventional treatments.

Effects of using structured templates for recalling chemistry experiments.

PubMed

Willoughby, Cerys; Logothetis, Thomas A; Frey, Jeremy G

2016-01-01

The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help researchers to remember to record particular aspects of their experiment, but they may also constrain the information that is recorded by encouraging them to record only what is asked for. It is therefore unknown whether using structured templates for capturing experiment records will have positive or negative effects on the quality and usefulness of the records for assessment and future use. In this paper we report on the results of a set of studies investigating the effects of different template designs on the recording of experiments by undergraduate students and academic researchers. The results indicate that using structured templates to write up experiments does make a significant difference to the information that is recalled and recorded. These differences have both positive and negative effects, with templates prompting the capture of specific information that is otherwise forgotten, but also apparently losing some of the personal elements of the experiment experience such as observations and explanations. Other unexpected effects were seen with templates that can change the information that is captured, but also interfere with the way an experiment is conducted. Our results showed that using structured templates can improve the completeness of the experiment context information captured but can also cause a loss of personal elements of the experiment experience when compared with allowing the researcher to structure their own record. The results suggest that interfaces for recording information about chemistry experiments, whether paper-based questionnaires or templates in Electronic Laboratory Notebooks, can be an effective way to improve the quality of experiment write-ups, but that care needs to be taken to ensure that the correct cues are provided.Graphical abstractScientists have traditionally recorded their research in paper notebooks, a format that provides great flexibility for capturing information. In contrast, Electronic Laboratory Notebooks frequently make use of forms or structured templates for capturing experiment records. Structured templates can provide cues that can improve record quality by increasing the amount of information captured and encouraging consistency. However, using the wrong cues can lead to a loss of personal elements of the experiment experience and frustrate users. This image shows two participants from one of our studies recording their experiment using a computer-based template.

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof-of-concept and roadmap for future studies

PubMed Central

Anttila, Verneri; Hibar, Derrek P; van Hulzen, Kimm J E; Arias-Vasquez, Alejandro; Smoller, Jordan W; Nichols, Thomas E; Neale, Michael C; McIntosh, Andrew M; Lee, Phil; McMahon, Francis J; Meyer-Lindenberg, Andreas; Mattheisen, Manuel; Andreassen, Ole A; Gruber, Oliver; Sachdev, Perminder S; Roiz-Santiañez, Roberto; Saykin, Andrew J; Ehrlich, Stefan; Mather, Karen A; Turner, Jessica A; Schwarz, Emanuel; Thalamuthu, Anbupalam; Shugart, Yin Yao; Ho, Yvonne YW; Martin, Nicholas G; Wright, Margaret J

2016-01-01

Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between schizophrenia cases and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. The current study provides proof-of-concept (albeit based on a limited set of structural brain measures), and defines a roadmap for future studies investigating the genetic covariance between structural/functional brain phenotypes and risk for psychiatric disorders. PMID:26854805

Ion Spectral Structures Observed by the Van Allen Probes and Cluster

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

2014-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

Problems and Processes in Medical Encounters: The CASES method of dialogue analysis

PubMed Central

Laws, M. Barton; Taubin, Tatiana; Bezreh, Tanya; Lee, Yoojin; Beach, Mary Catherine; Wilson, Ira B.

2013-01-01

Objective To develop methods to reliably capture structural and dynamic temporal features of clinical interactions. Methods Observational study of 50 audio-recorded routine outpatient visits to HIV specialty clinics, using innovative analytic methods. The Comprehensive Analysis of the Structure of Encounters System (CASES) uses transcripts coded for speech acts, then imposes larger-scale structural elements: threads – the problems or issues addressed; and processes within threads –basic tasks of clinical care labeled Presentation, Information, Resolution (decision making) and Engagement (interpersonal exchange). Threads are also coded for the nature of resolution. Results 61% of utterances are in presentation processes. Provider verbal dominance is greatest in information and resolution processes, which also contain a high proportion of provider directives. About half of threads result in no action or decision. Information flows predominantly from patient to provider in presentation processes, and from provider to patient in information processes. Engagement is rare. Conclusions In this data, resolution is provider centered; more time for patient participation in resolution, or interpersonal engagement, would have to come from presentation. Practice Implications Awareness of the use of time in clinical encounters, and the interaction processes associated with various tasks, may help make clinical communication more efficient and effective. PMID:23391684

Problems and processes in medical encounters: the cases method of dialogue analysis.

PubMed

Laws, M Barton; Taubin, Tatiana; Bezreh, Tanya; Lee, Yoojin; Beach, Mary Catherine; Wilson, Ira B

2013-05-01

To develop methods to reliably capture structural and dynamic temporal features of clinical interactions. Observational study of 50 audio-recorded routine outpatient visits to HIV specialty clinics, using innovative analytic methods. The comprehensive analysis of the structure of encounters system (CASES) uses transcripts coded for speech acts, then imposes larger-scale structural elements: threads--the problems or issues addressed; and processes within threads--basic tasks of clinical care labeled presentation, information, resolution (decision making) and Engagement (interpersonal exchange). Threads are also coded for the nature of resolution. 61% of utterances are in presentation processes. Provider verbal dominance is greatest in information and resolution processes, which also contain a high proportion of provider directives. About half of threads result in no action or decision. Information flows predominantly from patient to provider in presentation processes, and from provider to patient in information processes. Engagement is rare. In this data, resolution is provider centered; more time for patient participation in resolution, or interpersonal engagement, would have to come from presentation. Awareness of the use of time in clinical encounters, and the interaction processes associated with various tasks, may help make clinical communication more efficient and effective. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Ground Vibration Testing Options for Space Launch Vehicles

NASA Technical Reports Server (NTRS)

Patterson, Alan; Smith, Robert K.; Goggin, David; Newsom, Jerry

2011-01-01

New NASA launch vehicles will require development of robust systems in a fiscally-constrained environment. NASA, Department of Defense (DoD), and commercial space companies routinely conduct ground vibration tests as an essential part of math model validation and launch vehicle certification. Although ground vibration testing must be a part of the integrated test planning process, more affordable approaches must also be considered. A study evaluated several ground vibration test options for the NASA Constellation Program flight test vehicles, Orion-1 and Orion-2, which concluded that more affordable ground vibration test options are available. The motivation for ground vibration testing is supported by historical examples from NASA and DoD. The approach used in the present study employed surveys of ground vibration test subject-matter experts that provided data to qualitatively rank six test options. Twenty-five experts from NASA, DoD, and industry provided scoring and comments for this study. The current study determined that both element-level modal tests and integrated vehicle modal tests have technical merits. Both have been successful in validating structural dynamic math models of launch vehicles. However, element-level testing has less overall cost and schedule risk as compared to integrated vehicle testing. Future NASA launch vehicle development programs should anticipate that some structural dynamics testing will be necessary. Analysis alone will be inadequate to certify a crew-capable launch vehicle. At a minimum, component and element structural dynamic tests are recommended for new vehicle elements. Three viable structural dynamic test options were identified. Modal testing of the new vehicle elements and an integrated vehicle test on the mobile launcher provided the optimal trade between technical, cost, and schedule.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Foundational Approaches in Science Teaching (FAST)--A Structured "Inquiry" Oriented Junior Science Curriculum

ERIC Educational Resources Information Center

Dekkers, John; Rouse, Fae

1977-01-01

Provides a detailed description of the three-year Foundational Approaches in Science Education curriculum developed at the University of Hawaii. The program utilizes a spiral approach with topics in ecology, physical science and relational study. Sample units and implementation suggestions are provided. (CP)

Extended X-ray Absorption Fine Structure Study of Bond Constraints in Ge-Sb-Te Alloys

DTIC Science & Technology

2011-02-07

Ray Absorption Spectroscopy, or EXAFS. Using the spectroscopic capabilities provided by the MCAT line at the Advanced Photon Source at Argonne...Absorption Spectroscopy, or EXAFS. Using the spectroscopic capabilities provided by the MCAT line at the Advanced Photon Source at Argonne National

Australian Communication Scholarship: 1970-beyond 2000.

ERIC Educational Resources Information Center

Irwin, Harry

The development of Australian communication studies has closely followed capitalization upon the opportunities provided by major structural changes in the higher education system in the early 1970s and the late 1980s as well as those provided by disciplinary development and student demand. Before 1970, little in the way of communication studies…

Effectiveness of Problem-Based Learning in Introductory Business Courses

ERIC Educational Resources Information Center

Hartman, Katherine B.; Moberg, Christopher R.; Lambert, Jamie M.

2013-01-01

Problem-based learning (PBL) is an instructional approach that provides learners with opportunities to identify solutions to ill-structured, real-world problems. Previous research provides evidence to support claims about the positive effects of PBL on cognitive skill development and knowledge retention. This study contributes to existing…

Study of the correlation parameters of the surface structure of disordered semiconductors by the two-dimensional DFA and average mutual information methods

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

Alpatov, A. V.; Vikhrov, S. P.; Rybina, N. V., E-mail: pgnv@mail.ru

The processes of self-organization of the surface structure of hydrogenated amorphous silicon are studied by the methods of fluctuation analysis and average mutual information on the basis of atomic-force-microscopy images of the surface. It is found that all of the structures can be characterized by a correlation vector and represented as a superposition of harmonic components and noise. It is shown that, under variations in the technological parameters of the production of a-Si:H films, the correlation properties of their structure vary as well. As the substrate temperature is increased, the formation of structural irregularities becomes less efficient; in this case,more » the length of the correlation vector and the degree of structural ordering increase. It is shown that the procedure based on the method of fluctuation analysis in combination with the method of average mutual information provides a means for studying the self-organization processes in any structures on different length scales.« less

Subsidies to target specialist outreach services into more remote locations: a national cross-sectional study.

PubMed

O'Sullivan, Belinda G; McGrail, Matthew R; Stoelwinder, Johannes U

2017-07-01

Objective Targeting rural outreach services to areas of highest relative need is challenging because of the higher costs it imposes on health workers to travel longer distances. This paper studied whether subsidies have the potential to support the provision of specialist outreach services into more remote locations. Methods National data about subsidies for medical specialist outreach providers as part of the Wave 7 Medicine in Australia: Balancing Employment and Life (MABEL) Survey in 2014. Results Nearly half received subsidies: 19% (n=110) from a formal policy, namely the Australian Government Rural Health Outreach Fund (RHOF), and 27% (n=154) from other sources. Subsidised specialists travelled for longer and visited more remote locations relative to the non-subsidised group. In addition, compared with non-subsidised specialists, RHOF-subsidised specialists worked in priority areas and provided equally regular services they intended to continue, despite visiting more remote locations. Conclusion This suggests the RHOF, although limited to one in five specialist outreach providers, is important to increase targeted and stable outreach services in areas of highest relative need. Other subsidies also play a role in facilitating remote service distribution, but may need to be more structured to promote regular, sustained outreach practice. What is known about this topic? There are no studies describing subsidies for specialist doctors to undertake rural outreach work and whether subsidies, including formal and structured subsidies via the Australian Government RHOF, support targeted outreach services compared with no financial support. What does this paper add? Using national data from Australia, we describe subsidisation among specialist outreach providers and show that specialists subsidised via the RHOF or another source are more likely to provide remote outreach services. What are the implications for practitioners? Subsidised specialist outreach providers are more likely to provide remote outreach services. The RHOF, as a formally structured comprehensive subsidy, further targets the provision of priority services into such locations on a regular, ongoing basis.

Structure formation of 5083 alloy during friction stir welding

NASA Astrophysics Data System (ADS)

Zaikina, A. A.; Kolubaev, A. V.; Sizova, O. V.; Ivanov, K. V.; Filippov, A. V.; Kolubaev, E. A.

2017-12-01

This paper provides a comparative study of structures obtained by friction stir welding and sliding friction of 5083 Al alloy. Optical and electron microscopy reveals identical fine-grained structures with a grain size of ˜5 µm both in the weld nugget zone and subsurface layer in friction independently of the initial grain size of the alloy. It has been suggested that the grain boundary sliding is responsible for the specific material flow pattern in both techniques considered.

Comparison and Analysis of Steel Frame Based on High Strength Column and Normal Strength Column

NASA Astrophysics Data System (ADS)

Liu, Taiyu; An, Yuwei

2018-01-01

The anti-seismic performance of high strength steel has restricted its industrialization in civil buildings. In order to study the influence of high strength steel column on frame structure, three models are designed through MIDAS/GEN finite element software. By comparing the seismic performance and economic performance of the three models, the three different structures are comprehensively evaluated to provide some references for the development of high strength steel in steel structure.

Micromachined silicon acoustic delay line with improved structural stability and acoustic directivity for real-time photoacoustic tomography

NASA Astrophysics Data System (ADS)

Cho, Young; Kumar, Akhil; Xu, Song; Zou, Jun

2017-03-01

Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. However, as its length increases to provide longer delay time, the delay line becomes more vulnerable to structural instability due to reduced mechanical stiffness. In addition, the small cross-section area of the delay line results in a large acoustic acceptance angle and therefore poor directivity. To address these two issues, this paper reports the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, a new tapered design for the input terminal of the delay line was also investigate to improve its acoustic directivity by reducing the acoustic acceptance angle. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

Genetic dyslexia risk variant is related to neural connectivity patterns underlying phonological awareness in children.

PubMed

Skeide, Michael A; Kirsten, Holger; Kraft, Indra; Schaadt, Gesa; Müller, Bent; Neef, Nicole; Brauer, Jens; Wilcke, Arndt; Emmrich, Frank; Boltze, Johannes; Friederici, Angela D

2015-09-01

Phonological awareness is the best-validated predictor of reading and spelling skill and therefore highly relevant for developmental dyslexia. Prior imaging genetics studies link several dyslexia risk genes to either brain-functional or brain-structural factors of phonological deficits. However, coherent evidence for genetic associations with both functional and structural neural phenotypes underlying variation in phonological awareness has not yet been provided. Here we demonstrate that rs11100040, a reported modifier of SLC2A3, is related to the functional connectivity of left fronto-temporal phonological processing areas at resting state in a sample of 9- to 12-year-old children. Furthermore, we provide evidence that rs11100040 is related to the fractional anisotropy of the arcuate fasciculus, which forms the structural connection between these areas. This structural connectivity phenotype is associated with phonological awareness, which is in turn associated with the individual retrospective risk scores in an early dyslexia screening as well as to spelling. These results suggest a link between a dyslexia risk genotype and a functional as well as a structural neural phenotype, which is associated with a phonological awareness phenotype. The present study goes beyond previous work by integrating genetic, brain-functional and brain-structural aspects of phonological awareness within a single approach. These combined findings might be another step towards a multimodal biomarker for developmental dyslexia. Copyright © 2015 Elsevier Inc. All rights reserved.

Study of structural change in volcanic and geothermal areas using seismic tomography

NASA Astrophysics Data System (ADS)

Mhana, Najwa; Foulger, Gillian; Julian, Bruce; peirce, Christine

2014-05-01

Long Valley caldera is a large silicic volcano. It has been in a state of volcanic and seismic unrest since 1978. Farther escalation of this unrest could pose a threat to the 5,000 residents and the tens of thousands of tourists who visit the area. We have studied the crustal structure beneath 28 km X 16 km area using seismic tomography. We performed tomographic inversions for the years 2009 and 2010 with a view to differencing it with the 1997 result to look for structural changes with time and whether repeat tomography is a capable of determining the changes in structure in volcanic and geothermal reservoirs. Thus, it might provide a useful tool to monitoring physical changes in volcanoes and exploited geothermal reservoirs. Up to 600 earthquakes, selected from the best-quality events, were used for the inversion. The inversions were performed using program simulps12 [Thurber, 1983]. Our initial results show that changes in both V p and V s were consistent with the migration of CO2 into the upper 2 km or so. Our ongoing work will also invert pairs of years simultaneously using a new program, tomo4d [Julian and Foulger, 2010]. This program inverts for the differences in structure between two epochs so it can provide a more reliable measure of structural change than simply differencing the results of individual years.

"They're younger… it's harder." Primary providers' perspectives on hypertension management in young adults: a multicenter qualitative study.

PubMed

Johnson, Heather M; Warner, Ryan C; Bartels, Christie M; LaMantia, Jamie N

2017-01-03

Young adults (18-39 year-olds) have the lowest hypertension control rates among adults with hypertension in the United States. Unique barriers to hypertension management in young adults with primary care access compared to older adults have not been evaluated. Understanding these differences will inform the development of hypertension interventions tailored to young adults. The goals of this multicenter study were to explore primary care providers' perspectives on barriers to diagnosing, treating, and controlling hypertension among young adults with regular primary care. Primary care providers (physicians and advanced practice providers) actively managing young adults with uncontrolled hypertension were recruited by the Wisconsin Research & Education Network (WREN), a statewide practice-based research network. Semi-structured qualitative interviews were conducted in three diverse Midwestern clinical practices (academic, rural, and urban clinics) using a semi-structured interview guide, and content analysis was performed. Primary care providers identified unique barriers across standard hypertension healthcare delivery practices for young adults. Altered self-identity, greater blood pressure variability, and unintended consequences of medication initiation were critical hypertension control barriers among young adults. Gender differences among young adults were also noted as barriers to hypertension follow-up and antihypertensive medication initiation. Tailored interventions addressing the unique barriers of young adults are needed to improve population hypertension control. Augmenting traditional clinic structure to support the "health identity" of young adults and self-management skills are promising next steps to improve hypertension healthcare delivery.

Structure Elucidation of New Acetylated Saponins, Lessoniosides A, B, C, D, and E, and Non-Acetylated Saponins, Lessoniosides F and G, from the Viscera of the Sea Cucumber Holothuria lessoni

PubMed Central

Bahrami, Yadollah; Franco, Christopher M. M.

2015-01-01

Sea cucumbers produce numerous compounds with a wide range of chemical structural diversity. Among these, saponins are the most diverse and include sulfated, non-sulfated, acetylated and methylated congeners with different aglycone and sugar moieties. In this study, MALDI and ESI tandem mass spectrometry, in the positive ion mode, were used to elucidate the structure of new saponins extracted from the viscera of H. lessoni. Fragmentation of the aglycone provided structural information on the presence of the acetyl group. The presence of the O-acetyl group was confirmed by observing the mass transition of 60 u corresponding to the loss of a molecule of acetic acid. Ion fingerprints from the glycosidic cleavage provided information on the mass of the aglycone (core), and the sequence and type of monosaccharides that constitute the sugar moiety. The tandem mass spectra of the saponin precursor ions [M + Na]+ provided a wealth of detailed structural information on the glycosidic bond cleavages. As a result, and in conjunction with existing literature, we characterized the structure of five new acetylated saponins, Lessoniosides A–E, along with two non-acetylated saponins Lessoniosides F and G at m/z 1477.7, which are promising candidates for future drug development. The presented strategy allows a rapid, reliable and complete analysis of native saponins. PMID:25603350

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

PubMed

Kuzmanic, Antonija; Zagrovic, Bojan

2010-03-03

Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, (1/2), is directly related to average B-factors () and (1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.