Structure formation in fibrous materials based on poly-3-hydroxybutyrate for traumatology

NASA Astrophysics Data System (ADS)

Olkhov, A. A.; Sklyanchuk, E. D.; Staroverova, O. V.; Abbasov, T. A.; Guryev, V. V.; Akatov, V. S.; Fadeyeva, I. S.; Fesenko, N. I.; Filatov, Yu. N.; Iordanskii, A. L.

2015-10-01

The paper reviews the structure formation of fibrous materials based on poly-3-hydroxybutyrate depending on parameters of electrospinning and characteristics of polymer solution. Fiber structure was studied by DSC, ESR and SEM. The molecular weight affects the diameter and uniformity of the fiber. An electromechanical impact leads to an orientation of crystalline structure in the fiber. The design of an artificial bioresorbable implant based on nano- and microfibers of poly-3-hydroxybutyrate is created. Dynamics of growth of mesenchymal stem cells on poly-3-hydroxybutyrate scaffolds is studied. Successful field tests of implants of the Achilles tendon in Wistar rats are conducted.

Uncertainty of large-area estimates of indicators of forest structural gamma diversity: A study based on national forest inventory data

Treesearch

Susanne Winter; Andreas Böck; Ronald E. McRoberts

2012-01-01

Tree diameter and height are commonly measured forest structural variables, and indicators based on them are candidates for assessing forest diversity. We conducted our study on the uncertainty of estimates for mostly large geographic scales for four indicators of forest structural gamma diversity: mean tree diameter, mean tree height, and standard deviations of tree...

Modelling the Somatic Electrical Response of Hippocampal Pyramidal Neurons

DTIC Science & Technology

1989-09-01

postulated in the present study, and b) an approximation of the electrotonic structure of the cell that is derived in this thesis , based on data for the...the literature or postulated in the present study, and b) an approximation of the electrotonic structure of the cell that is derived in this thesis ...postulated in the present study, and b) an approximation of the electrotonic structure of the cell that is derived in this thesis , based on data for

Web-Based Text Structure Strategy Instruction Improves Seventh Graders' Content Area Reading Comprehension

ERIC Educational Resources Information Center

Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Puiwa

2017-01-01

Reading comprehension in the content areas is a challenge for many middle grade students. Text structure-based instruction has yielded positive outcomes in reading comprehension at all grade levels in small and large studies. The text structure strategy delivered via the web, called Intelligent Tutoring System for the Text Structure Strategy…

NASA-UVa Light Aerospace Alloy and Structures Technology Program: Aluminum-Based Materials for High Speed Aircraft

NASA Technical Reports Server (NTRS)

Starke, E. A., Jr. (Editor)

1996-01-01

This report is concerned with 'Aluminum-Based Materials for High Speed Aircraft' which was initiated to identify the technology needs associated with advanced, low-cost aluminum base materials for use as primary structural materials. Using a reference baseline aircraft, these materials concept will be further developed and evaluated both technically and economically to determine the most attractive combinations of designs, materials, and manufacturing techniques for major structural sections of an HSCT. Once this has been accomplished, the baseline aircraft will be resized, if applicable, and performance objectives and economic evaluations made to determine aircraft operating costs. The two primary objectives of this study are: (1) to identify the most promising aluminum-based materials with respect to major structural use on the HSCT and to further develop those materials, and (2) to assess these materials through detailed trade and evaluation studies with respect to their structural efficiency on the HSCT.

Air Force Nuclear Enterprise Organization: A Case Study

DTIC Science & Technology

2016-09-15

will improve the performance of the AFNE. Based on analysis of commercial and industrial business models, what organizational structure , or...Business Dictionary 2015). Organizational structures will be developed based on decisions made with regards to design. The core of an...work flows. Based on design parameter decisions, senior leaders will establish an organizational structure that includes the layout of the

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

PubMed

Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

2017-06-01

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Development of biocomposed material based on zirconium oxide for regeneration of bone tissue

NASA Astrophysics Data System (ADS)

Lytkin, Ivan; Buyakov, Ales; Kurzina, Irina

2017-11-01

Porous ceramic materials based on magnesium oxide stabilized zirconia were studied. The pore structure and thin crystalline structure were studied. The porosity of some of the materials studied was obtained by conducting a pore-forming additive, UHMWPE. It is shown that after impregnation with polylactide, the residual porosity varies from 22.5 to 5.9%. The average pore size was 2 µm. X-Ray diffraction analysis showed that the fine crystal structure of the ceramic is mainly represented by baddeleyite.

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.

Joint representation of consistent structural and functional profiles for identification of common cortical landmarks.

PubMed

Zhang, Shu; Zhao, Yu; Jiang, Xi; Shen, Dinggang; Liu, Tianming

2018-06-01

In the brain mapping field, there have been significant interests in representation of structural/functional profiles to establish structural/functional landmark correspondences across individuals and populations. For example, from the structural perspective, our previous studies have identified hundreds of consistent DICCCOL (dense individualized and common connectivity-based cortical landmarks) landmarks across individuals and populations, each of which possess consistent DTI-derived fiber connection patterns. From the functional perspective, a large collection of well-characterized HAFNI (holistic atlases of functional networks and interactions) networks based on sparse representation of whole-brain fMRI signals have been identified in our prior studies. However, due to the remarkable variability of structural and functional architectures in the human brain, it is challenging for earlier studies to jointly represent the connectome-scale structural and functional profiles for establishing a common cortical architecture which can comprehensively encode both structural and functional characteristics across individuals. To address this challenge, we propose an effective computational framework to jointly represent the structural and functional profiles for identification of consistent and common cortical landmarks with both structural and functional correspondences across different brains based on DTI and fMRI data. Experimental results demonstrate that 55 structurally and functionally common cortical landmarks can be successfully identified.

Evaluation of Road Performance Based on International Roughness Index and Falling Weight Deflectometer

NASA Astrophysics Data System (ADS)

Hasanuddin; Setyawan, A.; Yulianto, B.

2018-03-01

Assessment to the performance of road pavement is deemed necessary to improve the management quality of road maintenance and rehabilitation. This research to evaluate the road base on functional and structural and recommendations handling done. Assessing the pavement performance is conducted with functional and structural evaluation. Functional evaluation of pavement is based on the value of IRI (International Roughness Index) which among others is derived from reading NAASRA for analysis and recommended road handling. Meanwhile, structural evaluation of pavement is done by analyzing deflection value based on FWD (Falling Weight Deflectometer) data resulting in SN (Structural Number) value. The analysis will result in SN eff (Structural Number Effective) and SN f (Structural Number Future) value obtained from comparing SN eff to SN f value that leads to SCI (Structural Condition Index) value. SCI value implies the possible recommendation for handling pavement. The study done to Simpang Tuan-Batas Kota Jambi road segment was based on functional analysis. The study indicated that the road segment split into 12 segments in which segment 1, 3, 5, 7, 9, and 11 were of regular maintenance, segment 2, 4, 8, 10, 12 belonged to periodic maintenance, and segment 6 was of rehabilitation. The structural analysis resulted in 8 segments consisting of segment 1 and 2 recommended for regular maintenance, segment 3, 4, 5, and 7 for functional overlay, and 6 and 8 were of structural overlay.

Significance of Shear Wall in Multi-Storey Structure With Seismic Analysis

NASA Astrophysics Data System (ADS)

Bongilwar, Rajat; Harne, V. R.; Chopade, Aditya

2018-03-01

In past decades, shear walls are one of the most appropriate and important structural component in multi-storied building. Therefore, it would be very interesting to study the structural response and their systems in multi-storied structure. Shear walls contribute the stiffness and strength during earthquakes which are often neglected during design of structure and construction. This study shows the effect of shear walls which significantly affect the vulnerability of structures. In order to test this hypothesis, G+8 storey building was considered with and without shear walls and analyzed for various parameters like base shear, storey drift ratio, lateral displacement, bending moment and shear force. Significance of shear wall has been studied with the help of two models. First model is without shear wall i.e. bare frame and other another model is with shear wall considering opening also in it. For modeling and analysis of both the models, FEM based software ETABS 2016 were used. The analysis of all models was done using Equivalent static method. The comparison of results has been done based on same parameters like base shear, storey drift ratio, lateral displacement, bending moment and shear force.

Reservoir and Source Rock Identification Based on Geologycal, Geophysics and Petrophysics Analysis Study Case: South Sumatra Basin

NASA Astrophysics Data System (ADS)

Anggit Maulana, Hiska; Haris, Abdul

2018-05-01

Reservoir and source rock Identification has been performed to deliniate the reservoir distribution of Talangakar Formation South Sumatra Basin. This study is based on integrated geophysical, geological and petrophysical data. The aims of study to determine the characteristics of the reservoir and source rock, to differentiate reservoir and source rock in same Talangakar formation, to find out the distribution of net pay reservoir and source rock layers. The method of geophysical included seismic data interpretation using time and depth structures map, post-stack inversion, interval velocity, geological interpretations included the analysis of structures and faults, and petrophysical processing is interpret data log wells that penetrating Talangakar formation containing hydrocarbons (oil and gas). Based on seismic interpretation perform subsurface mapping on Layer A and Layer I to determine the development of structures in the Regional Research. Based on the geological interpretation, trapping in the form of regional research is anticline structure on southwest-northeast trending and bounded by normal faults on the southwest-southeast regional research structure. Based on petrophysical analysis, the main reservoir in the field of research, is a layer 1,375 m of depth and a thickness 2 to 8.3 meters.

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

Pair distribution function study and mechanical behavior of as-cast and structurally relaxed Zr-based bulk metallic glasses

NASA Astrophysics Data System (ADS)

Fan, Cang; Liaw, P. K.; Wilson, T. W.; Choo, H.; Gao, Y. F.; Liu, C. T.; Proffen, Th.; Richardson, J. W.

2006-12-01

Contrary to reported results on structural relaxation inducing brittleness in amorphous alloys, the authors found that structural relaxation actually caused an increase in the strength of Zr55Cu35Al10 bulk metallic glass (BMG) without changing the plasticity. Three dimensional models were rebuilt for the as-cast and structurally relaxed BMGs by reverse Monte Carlo (RMC) simulations based on the pair distribution function (PDF) measured by neutron scattering. Only a small portion of the atom pairs was found to change to more dense packing. The concept of free volume was defined based on the PDF and RMC studies, and the mechanism of mechanical behavior was discussed.

The influence of affective and cognitive arguments on message judgement and attitude change: The moderating effects of meta-bases and structural bases.

PubMed

Keer, Mario; van den Putte, Bas; Neijens, Peter; de Wit, John

2013-01-01

This study investigated whether the efficacy of affective vs. cognitive persuasive messages was moderated by (1) individuals' subjective assessments of whether their attitudes were based on affect or cognition (i.e. meta-bases) and (2) the degree individuals' attitudes were correlated with affect and cognition (i.e. structural bases). Participants (N = 97) were randomly exposed to a message containing either affective or cognitive arguments discouraging binge drinking. The results demonstrated that meta-bases and not structural bases moderated the influence of argument type on message judgement. Affective (cognitive) messages were judged more positively when individuals' meta-bases were more affective (cognitive). In contrast, structural bases and not meta-bases moderated the influence of argument type on attitude and intention change following exposure to the message. Surprisingly, change was greater among individuals who read a message that mismatched their structural attitude base. Affective messages were more effective as attitudes were more cognition-based, and vice versa. Thus, although individuals prefer messages that match their meta-base, attitude and intention change regarding binge drinking are best established by mismatching their structural base.

Plant-based Food and Feed Protein Structure Changes Induced by Gene-transformation heating and bio-ethanol processing: A Synchrotron-based Molecular Structure and Nutrition Research Program

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

P Yu

Unlike traditional 'wet' analytical methods which during processing for analysis often result in destruction or alteration of the intrinsic protein structures, advanced synchrotron radiation-based Fourier transform infrared microspectroscopy has been developed as a rapid and nondestructive and bioanalytical technique. This cutting-edge synchrotron-based bioanalytical technology, taking advantages of synchrotron light brightness (million times brighter than sun), is capable of exploring the molecular chemistry or structure of a biological tissue without destruction inherent structures at ultra-spatial resolutions. In this article, a novel approach is introduced to show the potential of the advanced synchrotron-based analytical technology, which can be used to study plant-basedmore » food or feed protein molecular structure in relation to nutrient utilization and availability. Recent progress was reported on using synchrotron-based bioanalytical technique synchrotron radiation-based Fourier transform infrared microspectroscopy and diffused reflectance infrared Fourier transform spectroscopy to detect the effects of gene-transformation (Application 1), autoclaving (Application 2), and bio-ethanol processing (Application 3) on plant-based food and feed protein structure changes on a molecular basis. The synchrotron-based technology provides a new approach for plant-based protein structure research at ultra-spatial resolutions at cellular and molecular levels.« less

Teaching mathematical word problem solving: the quality of evidence for strategy instruction priming the problem structure.

PubMed

Jitendra, Asha K; Petersen-Brown, Shawna; Lein, Amy E; Zaslofsky, Anne F; Kunkel, Amy K; Jung, Pyung-Gang; Egan, Andrea M

2015-01-01

This study examined the quality of the research base related to strategy instruction priming the underlying mathematical problem structure for students with learning disabilities and those at risk for mathematics difficulties. We evaluated the quality of methodological rigor of 18 group research studies using the criteria proposed by Gersten et al. and 10 single case design (SCD) research studies using criteria suggested by Horner et al. and the What Works Clearinghouse. Results indicated that 14 group design studies met the criteria for high-quality or acceptable research, whereas SCD studies did not meet the standards for an evidence-based practice. Based on these findings, strategy instruction priming the mathematics problem structure is considered an evidence-based practice using only group design methodological criteria. Implications for future research and for practice are discussed. © Hammill Institute on Disabilities 2013.

Deformable complex network for refining low-resolution X-ray structures

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

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

Structure, Intent and Conformance Monitoring in ATC

NASA Technical Reports Server (NTRS)

Reynolds, Tom G.; Histon, Jonathan M.; Davison, Hayley J.; Hansman, R. John

2004-01-01

Infield studies of current Air Traffic Control operations it is found that controllers rely on underlying airspace structure to reduce the complexity of the planning and conformance monitoring tasks. The structure appears to influence the controller's working mental model through abstractions that reduce the apparent cognitive complexity. These structure-based abstractions are useful for the controller's key tasks of planning, implementing, monitoring, and evaluating tactical situations. In addition, the structure-based abstractions appear to be important in the maintenance of Situation Awareness. The process of conformance monitoring is analyzed in more detail and an approach to conformance monitoring which utilizes both the structure-based abstractions and intent is presented.

Issues in Implementing a Structured Problem-Based Learning Strategy in a Volcano Unit: A Case Study

ERIC Educational Resources Information Center

Lee, Hyunju; Bae, Sungah

2008-01-01

The purpose of this study was to understand how an 8th grade science class used a structured problem-based learning (PBL) strategy to study volcanoes and to discuss some of the issues that science teachers might encounter when designing and implementing the PBL strategy. This study took place at Collins Middle School, which is located in a…

Analysis and sizing of Mars aerobrake structure

NASA Technical Reports Server (NTRS)

Raju, I. S.; Craft, W. J.

1993-01-01

A cone-sphere aeroshell structure for aerobraking into Martian atmosphere is studied. Using this structural configuration, a space frame load-bearing structure is proposed. To generate this structure efficiently and to perform a variety of studies of several configurations, a mesh generator that utilizes only a few configurational parameters is developed. A finite element analysis program that analyzes space frame structures was developed. A sizing algorithm that arrives at a minimum mass configuration was developed and integrated into the finite element analysis program. A typical 135-ft-diam aerobrake configuration was analyzed and sized. The minimum mass obtained in this study using high modulus graphite/epoxy composite material members is compared with the masses obtained from two other aerobrake structures using lightweight erectable tetrahedral truss and part-spherical truss configurations. Excellent agreement for the minimum mass was obtained with the three different aerobrake structures. Also, the minimum mass using the present structure was obtained when the supports were not at the base but at about 75 percent of the base diameter.

Novel Hybrid Virtual Screening Protocol Based on Molecular Docking and Structure-Based Pharmacophore for Discovery of Methionyl-tRNA Synthetase Inhibitors as Antibacterial Agents

PubMed Central

Liu, Chi; He, Gu; Jiang, Qinglin; Han, Bo; Peng, Cheng

2013-01-01

Methione tRNA synthetase (MetRS) is an essential enzyme involved in protein biosynthesis in all living organisms and is a potential antibacterial target. In the current study, the structure-based pharmacophore (SBP)-guided method has been suggested to generate a comprehensive pharmacophore of MetRS based on fourteen crystal structures of MetRS-inhibitor complexes. In this investigation, a hybrid protocol of a virtual screening method, comprised of pharmacophore model-based virtual screening (PBVS), rigid and flexible docking-based virtual screenings (DBVS), is used for retrieving new MetRS inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen the Specs (202,408 compounds) database, a structurally diverse chemical database. Fifteen hit compounds were selected from the final hits and shifted to experimental studies. These results may provide important information for further research of novel MetRS inhibitors as antibacterial agents. PMID:23839093

An optimum organizational structure for a large earth-orbiting multidisciplinary space base. Ph.D. Thesis - Fla. State Univ., 1973

NASA Technical Reports Server (NTRS)

Ragusa, J. M.

1975-01-01

An optimum hypothetical organizational structure was studied for a large earth-orbiting, multidisciplinary research and applications space base manned by a crew of technologists. Because such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than with the empirical testing of the model. The essential finding of this research was that a four-level project type total matrix model will optimize the efficiency and effectiveness of space base technologists.

An optimum organizational structure for a large earth-orbiting multidisciplinary Space Base

NASA Technical Reports Server (NTRS)

Ragusa, J. M.

1973-01-01

The purpose of this exploratory study was to identify an optimum hypothetical organizational structure for a large earth-orbiting multidisciplinary research and applications (R&A) Space Base manned by a mixed crew of technologists. Since such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than the empirical testing of it. The essential finding of this research was that a four-level project type 'total matrix' model will optimize the efficiency and effectiveness of Space Base technologists.

Structural Design of Ares V Interstage Composite Structure

NASA Technical Reports Server (NTRS)

Sleigh, David W.; Sreekantamurthy, Thammaiah; Kosareo, Daniel N.; Martin, Robert A.; Johnson, Theodore F.

2011-01-01

Preliminary and detailed design studies were performed to mature composite structural design concepts for the Ares V Interstage structure as a part of NASA s Advanced Composite Technologies Project. Aluminum honeycomb sandwich and hat-stiffened composite panel structural concepts were considered. The structural design and analysis studies were performed using HyperSizer design sizing software and MSC Nastran finite element analysis software. System-level design trade studies were carried out to predict weight and margins of safety for composite honeycomb-core sandwich and composite hat-stiffened skin design concepts. Details of both preliminary and detailed design studies are presented in the paper. For the range of loads and geometry considered in this work, the hat-stiffened designs were found to be approximately 11-16 percent lighter than the sandwich designs. A down-select process was used to choose the most favorable structural concept based on a set of figures of merit, and the honeycomb sandwich design was selected as the best concept based on advantages in manufacturing cost.

pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

PubMed

Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

2009-11-23

Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

Analysis of population structure and genetic history of cattle breeds based on high-density SNP data

USDA-ARS?s Scientific Manuscript database

Advances in single nucleotide polymorphism (SNP) genotyping microarrays have facilitated a new understanding of population structure and evolutionary history for several species. Most existing studies in livestock were based on low density SNP arrays. The first wave of low density SNP studies on cat...

Size-Expanded yDNA bases: An Ab Initio Study

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

Fuentes-Cabrera, Miguel A; Sumpter, Bobby G; Lipkowski, Pawel

2006-01-01

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount ofmore » experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.« less

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

NASA Astrophysics Data System (ADS)

Nagy, Julia; Eilert, Tobias; Michaelis, Jens

2018-03-01

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

Ultra-Small-Angle X-ray Scattering – X-ray Photon Correlation Spectroscopy Studies of Incipient Structural Changes in Amorphous Calcium Phosphate Based Dental Composites

PubMed Central

Zhang, F.; Allen, A.J.; Levine, L.E.; Espinal, L.; Antonucci, J.M.; Skrtic, D.; O’Donnell, J.N.R.; Ilavsky, J.

2012-01-01

The local structural changes in amorphous calcium phosphate (ACP) based dental composites were studied under isothermal conditions using both static, bulk measurement techniques and a recently developed methodology based on combined ultra-small angle X-ray scattering – X-ray photon correlation spectroscopy (USAXS-XPCS), which permits a dynamic approach. While results from conventional bulk measurements do not show clear signs of structural change, USAXS-XPCS results reveal unambiguous evidence for local structural variations on a similar time scale to that of water loss in the ACP fillers. A thermal-expansion based simulation indicates that thermal behavior alone does not account for the observed dynamics. Together, these results suggest that changes in the water content of ACP affect the composite morphology due to changes in ACP structure that occur without an amorphous-to-crystalline conversion. It is also noted that biomedical materials research could benefit greatly from USAXS-XPCS, a dynamic approach. PMID:22374649

Aircraft propeller induced structure-borne noise

NASA Technical Reports Server (NTRS)

Unruh, James F.

1989-01-01

A laboratory-based test apparatus employing components typical of aircraft construction was developed that would allow the study of structure-borne noise transmission due to propeller induced wake/vortex excitation of in-wake structural appendages. The test apparatus was employed to evaluate several aircraft installation effects (power plant placement, engine/nacelle mass loading, and wing/fuselage attachment methods) and several structural response modifications for structure-borne noise control (the use of wing blocking mass/fuel, wing damping treaments, and tuned mechanical dampers). Most important was the development of in-flight structure-borne noise transmission detection techniques using a combination of ground-based frequency response function testing and in-flight structural response measurement. Propeller wake/vortex excitation simulation techniques for improved ground-based testing were also developed to support the in-flight structure-borne noise transmission detection development.

Prevention of falls, malnutrition and pressure ulcers among older persons - nursing staff's experiences of a structured preventive care process.

PubMed

Lannering, Christina; Ernsth Bravell, Marie; Johansson, Linda

2017-05-01

A structured and systematic care process for preventive work, aimed to reduce falls, pressure ulcers and malnutrition among older people, has been developed in Sweden. The process involves risk assessment, team-based interventions and evaluation of results. Since development, this structured work process has become web-based and has been implemented in a national quality registry called 'Senior Alert' and used countrywide. The aim of this study was to describe nursing staff's experience of preventive work by using the structured preventive care process as outlined by Senior Alert. Eight focus group interviews were conducted during 2015 including staff from nursing homes and home-based nursing care in three municipalities. The interview material was subjected to qualitative content analysis. In this study, both positive and negative opinions were expressed about the process. The systematic and structured work flow seemed to only partly facilitate care providers to improve care quality by making better clinical assessments, performing team-based planned interventions and learning from results. Participants described lack of reliability in the assessments and varying opinions about the structure. Furthermore, organisational structures limited the preventive work. © 2016 John Wiley & Sons Ltd.

A comparative study of theoretical graph models for characterizing structural networks of human brain.

PubMed

Li, Xiaojin; Hu, Xintao; Jin, Changfeng; Han, Junwei; Liu, Tianming; Guo, Lei; Hao, Wei; Li, Lingjiang

2013-01-01

Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network.

An unsupervised two-stage clustering approach for forest structure classification based on X-band InSAR data - A case study in complex temperate forest stands

NASA Astrophysics Data System (ADS)

Abdullahi, Sahra; Schardt, Mathias; Pretzsch, Hans

2017-05-01

Forest structure at stand level plays a key role for sustainable forest management, since the biodiversity, productivity, growth and stability of the forest can be positively influenced by managing its structural diversity. In contrast to field-based measurements, remote sensing techniques offer a cost-efficient opportunity to collect area-wide information about forest stand structure with high spatial and temporal resolution. Especially Interferometric Synthetic Aperture Radar (InSAR), which facilitates worldwide acquisition of 3d information independent from weather conditions and illumination, is convenient to capture forest stand structure. This study purposes an unsupervised two-stage clustering approach for forest structure classification based on height information derived from interferometric X-band SAR data which was performed in complex temperate forest stands of Traunstein forest (South Germany). In particular, a four dimensional input data set composed of first-order height statistics was non-linearly projected on a two-dimensional Self-Organizing Map, spatially ordered according to similarity (based on the Euclidean distance) in the first stage and classified using the k-means algorithm in the second stage. The study demonstrated that X-band InSAR data exhibits considerable capabilities for forest structure classification. Moreover, the unsupervised classification approach achieved meaningful and reasonable results by means of comparison to aerial imagery and LiDAR data.

Experimental study on Statistical Damage Detection of RC Structures based on Wavelet Packet Analysis

NASA Astrophysics Data System (ADS)

Zhu, X. Q.; Law, S. S.; Jayawardhan, M.

2011-07-01

A novel damage indicator based on wavelet packet transform is developed in this study for structural health monitoring. The response signal of a structure under an impact load is normalized and then decomposed into wavelet packet components. Energies of these wavelet packet components are then calculated to obtain the energy distribution. A statistical indicator is developed to describe the damage extent of the structure. This approach is applied to the test results from simply supported reinforced concrete beams in the laboratory. Cases with single damage are created from static loading, and accelerations of the structure from under impact loads are analyzed. Results show that the method can be used for the damage monitoring and assessment of the structure.

Theoretical Background and Prognostic Modeling for Benchmarking SHM Sensors for Composite Structures

DTIC Science & Technology

2010-10-01

minimum flaw size can be detected by the existing SHM based monitoring methods. Sandwich panels with foam , WebCore and honeycomb structures were...Whether it be hat stiffened, corrugated sandwich, honeycomb sandwich, or foam filled sandwich, all composite structures have one basic handicap in...based monitoring methods. Sandwich panels with foam , WebCore and honeycomb structures were considered for use in this study. Eigenmode frequency

Formal Transformations from Graphically-Based Object-Oriented Representations to Theory-Based Specifications

DTIC Science & Technology

1996-06-01

for Software Synthesis." KBSE 󈨡. IEEE, 1993. 51. Kang, Kyo C., et al. Feature-Oriented Domain Analysis ( FODA ) Feasibility Study. Technical Report...and usefulness in domain analysis and modeling. Rumbaugh uses three distinct views to describe a domain: (1) the object model describes structural...Gibbons describe a methodology where Structured Analysis is used to build a hierarchical system structure chart. This structure chart is then translated

The microdopant effects of surfactant elements on structure-phase transitions during the rapid quenched crystallization of Fe-C-based melts

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Belyakova, R. M.; Rigmant, L. K.

2008-02-01

The nature of microdopant effects of surfactant Te and H2 reagents on structure-phase transitions in rapidly quenched and crystallized eutectic Fe-C-based melts were studied by experimental and computer methods. On the base of results of statistic-geometrical analysis the new information about the structure changes in multi-scaling systems -from meso- to nano-ones were obtained.

Evaluating MEDEVAC Force Structure Requirements Using an Updated Army Scenario, Total Army Analysis Admission Data, Monte Carlo Simulation, and Theater Structure.

PubMed

Fulton, Lawrence; Kerr, Bernie; Inglis, James M; Brooks, Matthew; Bastian, Nathaniel D

2015-07-01

In this study, we re-evaluate air ambulance requirements (rules of allocation) and planning considerations based on an Army-approved, Theater Army Analysis scenario. A previous study using workload only estimated a requirement of 0.4 to 0.6 aircraft per admission, a significant bolus over existence-based rules. In this updated study, we estimate requirements for Phase III (major combat operations) using a simulation grounded in previously published work and Phase IV (stability operations) based on four rules of allocation: unit existence rules, workload factors, theater structure (geography), and manual input. This study improves upon previous work by including the new air ambulance mission requirements of Department of Defense 51001.1, Roles and Functions of the Services, by expanding the analysis over two phases, and by considering unit rotation requirements known as Army Force Generation based on Department of Defense policy. The recommendations of this study are intended to inform future planning factors and already provided decision support to the Army Aviation Branch in determining force structure requirements. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

ZnSe based semiconductor core-shell structures: From preparation to application

NASA Astrophysics Data System (ADS)

Sun, Chengcheng; Gu, Yarong; Wen, Weijia; Zhao, Lijuan

2018-07-01

Inorganic core-shell semiconductor materials have attracted increasing interest in recent years because of the unique structure, stable chemical properties and high performance in devices. With special properties such as a direct band-gap and excellent photoelectrical characteristics, ZnSe based semiconductor core-shell structures are promising materials for applications in such fields as photocatalysts, light-emitting diodes, solar cells, photodetectors, biomedical science and so on. However, few reviews on ZnSe based semiconductor core-shell structures have been reported so far. Therefore this manuscript mainly focuses on the research activities on ZnSe based semiconductor core-shell composites including various preparation methods and the applications of these core-shell structures, especially in photocatalysts, light emitting, solar cells and photodetectors. The possibilities and limitations of studies on ZnSe based semiconductor core-shell composites are also highlighted.

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

PubMed Central

Brender, Jeffrey R.; Czajka, Jeff; Marsh, David; Gray, Felicia; Cierpicki, Tomasz; Zhang, Yang

2013-01-01

Computational protein design is a reverse procedure of protein folding and structure prediction, where constructing structures from evolutionarily related proteins has been demonstrated to be the most reliable method for protein 3-dimensional structure prediction. Following this spirit, we developed a novel method to design new protein sequences based on evolutionarily related protein families. For a given target structure, a set of proteins having similar fold are identified from the PDB library by structural alignments. A structural profile is then constructed from the protein templates and used to guide the conformational search of amino acid sequence space, where physicochemical packing is accommodated by single-sequence based solvation, torsion angle, and secondary structure predictions. The method was tested on a computational folding experiment based on a large set of 87 protein structures covering different fold classes, which showed that the evolution-based design significantly enhances the foldability and biological functionality of the designed sequences compared to the traditional physics-based force field methods. Without using homologous proteins, the designed sequences can be folded with an average root-mean-square-deviation of 2.1 Å to the target. As a case study, the method is extended to redesign all 243 structurally resolved proteins in the pathogenic bacteria Mycobacterium tuberculosis, which is the second leading cause of death from infectious disease. On a smaller scale, five sequences were randomly selected from the design pool and subjected to experimental validation. The results showed that all the designed proteins are soluble with distinct secondary structure and three have well ordered tertiary structure, as demonstrated by circular dichroism and NMR spectroscopy. Together, these results demonstrate a new avenue in computational protein design that uses knowledge of evolutionary conservation from protein structural families to engineer new protein molecules of improved fold stability and biological functionality. PMID:24204234

Low Cost Large Core Vehicle Structures Assessment

NASA Technical Reports Server (NTRS)

Hahn, Steven E.

1998-01-01

Boeing Information, Space, and Defense Systems executed a Low Cost Large Core Vehicle Structures Assessment (LCLCVSA) under contract to NASA Marshall Space Flight Center (MSFC) between November 1997 and March 1998. NASA is interested in a low-cost launch vehicle, code named Magnum, to place heavy payloads into low earth orbit for missions such as a manned mission to Mars, a Next Generation Space Telescope, a lunar-based telescope, the Air Force's proposed space based laser, and large commercial satellites. In this study, structural concepts with the potential to reduce fabrication costs were evaluated in application to the Magnum Launch Vehicle (MLV) and the Liquid Fly Back Booster (LFBB) shuttle upgrade program. Seventeen concepts were qualitatively evaluated to select four concepts for more in-depth study. The four structural concepts selected were: an aluminum-lithium monocoque structure, an aluminum-lithium machined isogrid structure, a unitized composite sandwich structure, and a unitized composite grid structure. These were compared against a baseline concept based on the Space Shuttle External Tank (ET) construction. It was found that unitized composite structures offer significant cost and weight benefits to MLV structures. The limited study of application to LFBB structures indicated lower, but still significant benefits. Technology and facilities development roadmaps to prepare the approaches studied for application to MLV and LFBB were constructed. It was found that the cost and schedule to develop these approaches were in line with both MLV and LFBB development schedules. Current Government and Boeing programs which address elements of the development of the technologies identified are underway. It is recommended that NASA devote resources in a timely fashion to address the specific elements related to MLV and LFBB structures.

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…

Lightweight composites for modular panelized construction

NASA Astrophysics Data System (ADS)

Vaidya, Amol S.

Rapid advances in construction materials technology have enabled civil engineers to achieve impressive gains in the safety, economy, and functionality of structures built to serve the common needs of society. Modular building systems is a fast-growing modern, form of construction gaining recognition for its increased efficiency and ability to apply modern technology to the needs of the market place. In the modular construction technique, a single structural panel can perform a number of functions such as providing thermal insulation, vibration damping, and structural strength. These multifunctional panels can be prefabricated in a manufacturing facility and then transferred to the construction site. A system that uses prefabricated panels for construction is called a "panelized construction system". This study focuses on the development of pre-cast, lightweight, multifunctional sandwich composite panels to be used for panelized construction. Two thermoplastic composite panels are proposed in this study, namely Composite Structural Insulated Panels (CSIPs) for exterior walls, floors and roofs, and Open Core Sandwich composite for multifunctional interior walls of a structure. Special manufacturing techniques are developed for manufacturing these panels. The structural behavior of these panels is analyzed based on various building design codes. Detailed descriptions of the design, cost analysis, manufacturing, finite element modeling and structural testing of these proposed panels are included in this study in the of form five peer-reviewed journal articles. The structural testing of the proposed panels involved in this study included flexural testing, axial compression testing, and low and high velocity impact testing. Based on the current study, the proposed CSIP wall and floor panels were found satisfactory, based on building design codes ASCE-7-05 and ACI-318-05. Joining techniques are proposed in this study for connecting the precast panels on the construction site. Keywords: Modular panelized construction, sandwich composites, composite structural insulated panels (CSIPs).

Evaluating structural connectomics in relation to different Q-space sampling techniques.

PubMed

Rodrigues, Paulo; Prats-Galino, Alberto; Gallardo-Pujol, David; Villoslada, Pablo; Falcon, Carles; Prckovska, Vesna

2013-01-01

Brain networks are becoming forefront research in neuroscience. Network-based analysis on the functional and structural connectomes can lead to powerful imaging markers for brain diseases. However, constructing the structural connectome can be based upon different acquisition and reconstruction techniques whose information content and mutual differences has not yet been properly studied in a unified framework. The variations of the structural connectome if not properly understood can lead to dangerous conclusions when performing these type of studies. In this work we present evaluation of the structural connectome by analysing and comparing graph-based measures on real data acquired by the three most important Diffusion Weighted Imaging techniques: DTI, HARDI and DSI. We thus come to several important conclusions demonstrating that even though the different techniques demonstrate differences in the anatomy of the reconstructed fibers the respective connectomes show variations of 20%.

Biophysics of cadherin adhesion.

PubMed

Leckband, Deborah; Sivasankar, Sanjeevi

2012-01-01

Since the identification of cadherins and the publication of the first crystal structures, the mechanism of cadherin adhesion, and the underlying structural basis have been studied with a number of different experimental techniques, different classical cadherin subtypes, and cadherin fragments. Earlier studies based on biophysical measurements and structure determinations resulted in seemingly contradictory findings regarding cadherin adhesion. However, recent experimental data increasingly reveal parallels between structures, solution binding data, and adhesion-based biophysical measurements that are beginning to both reconcile apparent differences and generate a more comprehensive model of cadherin-mediated cell adhesion. This chapter summarizes the functional, structural, and biophysical findings relevant to cadherin junction assembly and adhesion. We emphasize emerging parallels between findings obtained with different experimental approaches. Although none of the current models accounts for all of the available experimental and structural data, this chapter discusses possible origins of apparent discrepancies, highlights remaining gaps in current knowledge, and proposes challenges for further study.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facilitating Interactions through Structured Web-Based Bulletin Boards: A Quasi-Experimental Study on Promoting Learners' Critical Thinking Skills

ERIC Educational Resources Information Center

Yang, Ya-Ting C.; Newby, Timothy; Bill, Robert

2008-01-01

This experimental study investigated the effectiveness of structured Web-Based Bulletin Board (WBB) discussions in improving the critical thinking (CT) skills of learners involved in veterinary distance learning, as well as their attitudes toward learning via WBBs. The two dependent variables were learners' CT skills and their attitudes toward…

Research Study in the Cost of Housing, Volume 3.

ERIC Educational Resources Information Center

New York State Div. of Housing and Community Renewal, Albany.

The results of a study based on experiments conducted in multistory fireproof structures of public housing projects, and in a mock-up simulating all conditions of a fireproof structure, are reported. The findings are based on tests conducted during several winter seasons, none of which deviated markedly from the norm in New York City. The…

Single-subject structural networks with closed-form rotation invariant matching mprove power in developmental studies of the cortex.

PubMed

Kandel, Benjamin M; Wang, Danny J J; Gee, James C; Avants, Brian B

2014-01-01

Although much attention has recently been focused on single-subject functional networks, using methods such as resting-state functional MRI, methods for constructing single-subject structural networks are in their infancy. Single-subject cortical networks aim to describe the self-similarity across the cortical structure, possibly signifying convergent developmental pathways. Previous methods for constructing single-subject cortical networks have used patch-based correlations and distance metrics based on curvature and thickness. We present here a method for constructing similarity-based cortical structural networks that utilizes a rotation-invariant representation of structure. The resulting graph metrics are closely linked to age and indicate an increasing degree of closeness throughout development in nearly all brain regions, perhaps corresponding to a more regular structure as the brain matures. The derived graph metrics demonstrate a four-fold increase in power for detecting age as compared to cortical thickness. This proof of concept study indicates that the proposed metric may be useful in identifying biologically relevant cortical patterns.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

[Advances in studies on the structure of farmland shelterbelt ecosystem].

PubMed

Li, Chunping; Guan, Wenbin; Fan, Zhiping; Su, Fanxin; Wang, Xilin

2003-11-01

The ecological function of farmland shelterbelt system is determined by its structure. The spatio-temporal structure is a key aspect in related researches, which is very necessary to study the integrity, stability and durability of shelterbelt modules. In this article, the researches on the structure of farmland shelterbelt ecosystem were reviewed from the four scales of tree structure, shelterbelt structure, shelterbelts network and landscape structure. The principles, methods and productions of each scale were summarized, and the prospects were also discussed. Dynamic simulation of tree growth process in shelterbelts could be conducted by the theory of form and quality structure of tree and by fractal graphics, which were helpful to study the mechanism of individual trees and belts based on photosynthetic and transpiration mechanism of individual trees. The mechanism model of shelterbelt porosity should be conducted, so that, the sustainable yield model of shelterbelt management could be established, and the optimized model of shelterbelt networks with multi-special and multi-hierarchical structure could also be formed. Evaluating the reasonability, stability and durability of shelterbelt landscape based on the theories and methods of landscape ecology was an important task in the future studies.

Local-structure change rendered by electronic localization-delocalization transition in cerium-based metallic glasses

NASA Astrophysics Data System (ADS)

Luo, Qiang; Schwarz, Björn; Swarbrick, Janine C.; Bednarčik, Jozef; Zhu, Yingcai; Tang, Meibo; Zheng, Lirong; Li, Ran; Shen, Jun; Eckert, Jürgen

2018-02-01

With increasing temperature, metallic glasses (MGs) undergo first glass transition without pronounced structural change and then crystallization with distinct variation in structure and properties. The present study shows a structural change of short-range order induced by an electron-delocalization transition, along with an unusual large-volume shrinkage in Ce-based MGs. An f -electron localization-delocalization transition with thermal hysteresis is observed from the temperature dependence of x-ray absorption spectroscopy and resonant inelastic x-ray scattering spectra, indicating an inheritance of the 4 f configuration of pure Ce. However, the delocalization transition becomes broadened due to the local structural heterogeneity and related fluctuation of 4 f levels in the Ce-based MGs. The amorphous structure regulated 4 f delocalization of Ce leads to bond shortening and abnormal structure change of the topological and chemical short-range orders. Due to the hierarchical bonding nature, the structure should change in a similar manner on different length scales (but not isostructurally like the Ce metal) in Ce-based MGs.

Rapid identification of Keap1-Nrf2 small-molecule inhibitors through structure-based virtual screening and hit-based substructure search.

PubMed

Zhuang, Chunlin; Narayanapillai, Sreekanth; Zhang, Wannian; Sham, Yuk Yin; Xing, Chengguo

2014-02-13

In this study, rapid structure-based virtual screening and hit-based substructure search were utilized to identify small molecules that disrupt the interaction of Keap1-Nrf2. Special emphasis was placed toward maximizing the exploration of chemical diversity of the initial hits while economically establishing informative structure-activity relationship (SAR) of novel scaffolds. Our most potent noncovalent inhibitor exhibits three times improved cellular activation in Nrf2 activation than the most active noncovalent Keap1 inhibitor known to date.

Salmonella Typhimurium and Staphylococcus aureus dynamics in/on variable (micro)structures of fish-based model systems at suboptimal temperatures.

PubMed

Baka, Maria; Verheyen, Davy; Cornette, Nicolas; Vercruyssen, Stijn; Van Impe, Jan F

2017-01-02

The limited knowledge concerning the influence of food (micro)structure on microbial dynamics decreases the accuracy of the developed predictive models, as most studies have mainly been based on experimental data obtained in liquid microbiological media or in/on real foods. The use of model systems has a great potential when studying this complex factor. Apart from the variability in (micro)structural properties, model systems vary in compositional aspects, as a consequence of their (micro)structural variation. In this study, different experimental food model systems, with compositional and physicochemical properties similar to fish patés, are developed to study the influence of food (micro)structure on microbial dynamics. The microbiological safety of fish products is of major importance given the numerous cases of salmonellosis and infections attributed to staphylococcus toxins. The model systems understudy represent food (micro)structures of liquids, aqueous gels, emulsions and gelled emulsions. The growth/inactivation dynamics and a modelling approach of combined growth and inactivation of Salmonella Typhimurium and Staphylococcus aureus, related to fish products, are investigated in/on these model systems at temperatures relevant to fish products' common storage (4°C) and to abuse storage temperatures (8 and 12°C). ComBase (http://www.combase.cc/) predictions compared with the maximum specific growth rate (μ max ) values estimated by the Baranyi and Roberts model in the current study indicated that the (micro)structure influences the microbial dynamics. Overall, ComBase overestimated microbial growth at the same pH, a w and storage temperature. Finally, the storage temperature had also an influence on how much each model system affected the microbial dynamics. Copyright © 2016. Published by Elsevier B.V.

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.

A determinant-based criterion for working correlation structure selection in generalized estimating equations.

PubMed

Jaman, Ajmery; Latif, Mahbub A H M; Bari, Wasimul; Wahed, Abdus S

2016-05-20

In generalized estimating equations (GEE), the correlation between the repeated observations on a subject is specified with a working correlation matrix. Correct specification of the working correlation structure ensures efficient estimators of the regression coefficients. Among the criteria used, in practice, for selecting working correlation structure, Rotnitzky-Jewell, Quasi Information Criterion (QIC) and Correlation Information Criterion (CIC) are based on the fact that if the assumed working correlation structure is correct then the model-based (naive) and the sandwich (robust) covariance estimators of the regression coefficient estimators should be close to each other. The sandwich covariance estimator, used in defining the Rotnitzky-Jewell, QIC and CIC criteria, is biased downward and has a larger variability than the corresponding model-based covariance estimator. Motivated by this fact, a new criterion is proposed in this paper based on the bias-corrected sandwich covariance estimator for selecting an appropriate working correlation structure in GEE. A comparison of the proposed and the competing criteria is shown using simulation studies with correlated binary responses. The results revealed that the proposed criterion generally performs better than the competing criteria. An example of selecting the appropriate working correlation structure has also been shown using the data from Madras Schizophrenia Study. Copyright © 2015 John Wiley & Sons, Ltd.

Arguments, Contradictions, Resistances, and Conceptual Change in Students' Understanding of Atomic Structure.

ERIC Educational Resources Information Center

Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo

2002-01-01

Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…

Influence of Structure and Interaction on Student Achievement and Satisfaction in Web-Based Distance Learning

ERIC Educational Resources Information Center

Lee, Hye-Jung; Rha, Ilju

2009-01-01

This study examines the influence of instructional design and management style on student achievement and satisfaction in a web-based distance learning environment. From the literature review, two major instructional design and management styles in web-based distance education were conceptualized as structure and interpersonal interaction. To…

Structure and function of seed storage proteins in faba bean (Vicia faba L.).

PubMed

Liu, Yujiao; Wu, Xuexia; Hou, Wanwei; Li, Ping; Sha, Weichao; Tian, Yingying

2017-05-01

The protein subunit is the most important basic unit of protein, and its study can unravel the structure and function of seed storage proteins in faba bean. In this study, we identified six specific protein subunits in Faba bean (cv. Qinghai 13) combining liquid chromatography (LC), liquid chromatography-electronic spray ionization mass (LC-ESI-MS/MS) and bio-information technology. The results suggested a diversity of seed storage proteins in faba bean, and a total of 16 proteins (four GroEL molecular chaperones and 12 plant-specific proteins) were identified from 97-, 96-, 64-, 47-, 42-, and 38-kD-specific protein subunits in faba bean based on the peptide sequence. We also analyzed the composition and abundance of the amino acids, the physicochemical characteristics, secondary structure, three-dimensional structure, transmembrane domain, and possible subcellular localization of these identified proteins in faba bean seed, and finally predicted function and structure. The three-dimensional structures were generated based on homologous modeling, and the protein function was analyzed based on the annotation from the non-redundant protein database (NR database, NCBI) and function analysis of optimal modeling. The objective of this study was to identify the seed storage proteins in faba bean and confirm the structure and function of these proteins. Our results can be useful for the study of protein nutrition and achieve breeding goals for optimal protein quality in faba bean.

Structural invariance of multiple intelligences, based on the level of execution.

PubMed

Almeida, Leandro S; Prieto, María Dolores; Ferreira, Arístides; Ferrando, Mercedes; Ferrandiz, Carmen; Bermejo, Rosario; Hernández, Daniel

2011-11-01

The independence of multiple intelligences (MI) of Gardner's theory has been debated since its conception. This article examines whether the one- factor structure of the MI theory tested in previous studies is invariant for low and high ability students. Two hundred ninety-four children (aged 5 to 7) participated in this study. A set of Gardner's Multiple Intelligence assessment tasks based on the Spectrum Project was used. To analyze the invariance of a general dimension of intelligence, the different models of behaviours were studied in samples of participants with different performance on the Spectrum Project tasks with Multi-Group Confirmatory Factor Analysis (MGCFA). Results suggest an absence of structural invariance in Gardner's tasks. Exploratory analyses suggest a three-factor structure for individuals with higher performance levels and a two-factor structure for individuals with lower performance levels.

Towards fully automated structure-based function prediction in structural genomics: a case study.

PubMed

Watson, James D; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A; Thornton, Janet M

2007-04-13

As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.

Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

NASA Astrophysics Data System (ADS)

Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.

2009-11-01

Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

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…

Enhancement of Performance and Mechanism Studies of All-Solution Processed Small-Molecule based Solar Cells with an Inverted Structure.

PubMed

Long, Guankui; Wu, Bo; Yang, Xuan; Kan, Bin; Zhou, Ye-Cheng; Chen, Li-Chuan; Wan, Xiangjian; Zhang, Hao-Li; Sum, Tze Chien; Chen, Yongsheng

2015-09-30

Both solution-processed polymers and small molecule based solar cells have achieved PCEs over 9% with the conventional device structure. However, for the practical applications of photovoltaic technology, further enhancement of both device performance and stability are urgently required, particularly for the inverted structure devices, since this architecture will probably be most promising for the possible coming commercialization. In this work, we have fabricated both conventional and inverted structure devices using the same small molecular donor/acceptor materials and compared the performance of both device structures, and found that the inverted structure based device gave significantly improved performance, the highest PCE so far for inverted structure based device using small molecules as the donor. Furthermore, the inverted device shows a remarkable stability with almost no obvious degradation after three months. Systematic device physics and charge generation dynamics studies, including optical simulation, light-intensity-dependent current-voltage experiments, photocurrent density-effective voltage analyses, transient absorption measurements, and electrical simulations, indicate that the significantly enhanced performance using inverted device is ascribed to the increasing of Jsc compared to the conventional device, which in turn is mainly attributed to the increased absorption of photons in the active layers, rather than the reduced nongeminate recombination.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy.

PubMed

Zhang, Hang; Xu, Qingyan

2017-10-27

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter ( d w ), the spiral pitch ( h b ) and the spiral diameter ( h s ), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy

PubMed Central

Zhang, Hang; Xu, Qingyan

2017-01-01

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter (dw), the spiral pitch (hb) and the spiral diameter (hs), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure. PMID:29077067

Deflection-Based Aircraft Structural Loads Estimation with Comparison to Flight

NASA Technical Reports Server (NTRS)

Lizotte, Andrew M.; Lokos, William A.

2005-01-01

Traditional techniques in structural load measurement entail the correlation of a known load with strain-gage output from the individual components of a structure or machine. The use of strain gages has proved successful and is considered the standard approach for load measurement. However, remotely measuring aerodynamic loads using deflection measurement systems to determine aeroelastic deformation as a substitute to strain gages may yield lower testing costs while improving aircraft performance through reduced instrumentation weight. With a reliable strain and structural deformation measurement system this technique was examined. The objective of this study was to explore the utility of a deflection-based load estimation, using the active aeroelastic wing F/A-18 aircraft. Calibration data from ground tests performed on the aircraft were used to derive left wing-root and wing-fold bending-moment and torque load equations based on strain gages, however, for this study, point deflections were used to derive deflection-based load equations. Comparisons between the strain-gage and deflection-based methods are presented. Flight data from the phase-1 active aeroelastic wing flight program were used to validate the deflection-based load estimation method. Flight validation revealed a strong bending-moment correlation and slightly weaker torque correlation. Development of current techniques, and future studies are discussed.

Deflection-Based Structural Loads Estimation From the Active Aeroelastic Wing F/A-18 Aircraft

NASA Technical Reports Server (NTRS)

Lizotte, Andrew M.; Lokos, William A.

2005-01-01

Traditional techniques in structural load measurement entail the correlation of a known load with strain-gage output from the individual components of a structure or machine. The use of strain gages has proved successful and is considered the standard approach for load measurement. However, remotely measuring aerodynamic loads using deflection measurement systems to determine aeroelastic deformation as a substitute to strain gages may yield lower testing costs while improving aircraft performance through reduced instrumentation weight. This technique was examined using a reliable strain and structural deformation measurement system. The objective of this study was to explore the utility of a deflection-based load estimation, using the active aeroelastic wing F/A-18 aircraft. Calibration data from ground tests performed on the aircraft were used to derive left wing-root and wing-fold bending-moment and torque load equations based on strain gages, however, for this study, point deflections were used to derive deflection-based load equations. Comparisons between the strain-gage and deflection-based methods are presented. Flight data from the phase-1 active aeroelastic wing flight program were used to validate the deflection-based load estimation method. Flight validation revealed a strong bending-moment correlation and slightly weaker torque correlation. Development of current techniques, and future studies are discussed.

Ligand-based and structure-based approaches in identifying ideal pharmacophore against c-Jun N-terminal kinase-3.

PubMed

Kumar, B V S Suneel; Kotla, Rohith; Buddiga, Revanth; Roy, Jyoti; Singh, Sardar Shamshair; Gundla, Rambabu; Ravikumar, Muttineni; Sarma, Jagarlapudi A R P

2011-01-01

Structure and ligand based pharmacophore modeling and docking studies carried out using diversified set of c-Jun N-terminal kinase-3 (JNK3) inhibitors are presented in this paper. Ligand based pharmacophore model (LBPM) was developed for 106 inhibitors of JNK3 using a training set of 21 compounds to reveal structural and chemical features necessary for these molecules to inhibit JNK3. Hypo1 consisted of two hydrogen bond acceptors (HBA), one hydrogen bond donor (HBD), and a hydrophobic (HY) feature with a correlation coefficient (r²) of 0.950. This pharmacophore model was validated using test set containing 85 inhibitors and had a good r² of 0.846. All the molecules were docked using Glide software and interestingly, all the docked conformations showed hydrogen bond interactions with important hinge region amino acids (Gln155 and Met149)and these interactions were compared with Hypo1 features. The results of ligand based pharmacophore model (LBPM)and docking studies are validated each other. The structure based pharmacophore model (SBPM) studies have identified additional features, two hydrogen bond donors and one hydrogen bond acceptor. The combination of these methodologies is useful in designing ideal pharmacophore which provides a powerful tool for the discovery of novel and selective JNK3 inhibitors.

Output-Based Structural Damage Detection by Using Correlation Analysis Together with Transmissibility

PubMed Central

Cao, Hongyou; Liu, Quanmin; Wahab, Magd Abdel

2017-01-01

Output-based structural damage detection is becoming increasingly appealing due to its potential in real engineering applications without any restriction regarding excitation measurements. A new transmissibility-based damage detection approach is presented in this study by combining transmissibility with correlation analysis in order to strengthen its performance in discriminating damaged from undamaged scenarios. From this perspective, damage detection strategies are hereafter established by constructing damage-sensitive indicators from a derived transmissibility. A cantilever beam is numerically analyzed to verify the feasibility of the proposed damage detection procedure, and an ASCE (American Society of Civil Engineers) benchmark is henceforth used in the validation for its application in engineering structures. The results of both studies reveal a good performance of the proposed methodology in identifying damaged states from intact states. The comparison between the proposed indicator and the existing indicator also affirms its applicability in damage detection, which might be adopted in further structural health monitoring systems as a discrimination criterion. This study contributed an alternative criterion for transmissibility-based damage detection in addition to the conventional ones. PMID:28773218

Followers are not enough: a multifaceted approach to community detection in online social networks.

PubMed

Darmon, David; Omodei, Elisa; Garland, Joshua

2015-01-01

In online social media networks, individuals often have hundreds or even thousands of connections, which link these users not only to friends, associates, and colleagues, but also to news outlets, celebrities, and organizations. In these complex social networks, a 'community' as studied in the social network literature, can have very different meaning depending on the property of the network under study. Taking into account the multifaceted nature of these networks, we claim that community detection in online social networks should also be multifaceted in order to capture all of the different and valuable viewpoints of 'community.' In this paper we focus on three types of communities beyond follower-based structural communities: activity-based, topic-based, and interaction-based. We analyze a Twitter dataset using three different weightings of the structural network meant to highlight these three community types, and then infer the communities associated with these weightings. We show that interesting insights can be obtained about the complex community structure present in social networks by studying when and how these four community types give rise to similar as well as completely distinct community structure.

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…

Family Structure Transitions and Early Childhood Development in Taiwan: Evidence from a Population-Based Birth Cohort Study

ERIC Educational Resources Information Center

Wu, Jennifer Chun-Li; Chiang, Tung-liang

2015-01-01

Taiwan has over the past three decades been experiencing demographic changes that may pose important concerns for children's quality of life. This study examines the relationships and potential pathways between family structure transitions and early childhood development. Our analysis is based on 19,499 children from the 2005 birth cohort who…

A Study of the Effects of Competitive Team-Based Learning and Structured Academic Controversy on the Language Proficiency of Iranian EFL College Seniors

ERIC Educational Resources Information Center

Hosseini, Seyed Mohammad Hassan

2012-01-01

This paper presents reports on an experimental study which intended to look into and compare the possible effects of this researcher's instructional innovation, Competitive Team-Based Learning (CTBL), with Structured Academic Controversy (SAC) -- the most popular method of Cooperative Learning (CL) -- on language proficiency of Iranian EFL college…

Problem-Based Learning: Using Ill-Structured Problems in Biology Project Work

ERIC Educational Resources Information Center

Chin, Christine; Chia, Li-Gek

2006-01-01

This case study involved year 9 students carrying out project work in biology via problem-based learning. The purpose of the study was to (a) find out how students approach and work through ill-structured problems, (b) identify some issues and challenges related to the use of such problems, and (c) offer some practical suggestions on the…

Perceived Social Relationships and Science Learning Outcomes for Taiwanese Eighth Graders: Structural Equation Modeling with a Complex Sampling Consideration

ERIC Educational Resources Information Center

Jen, Tsung-Hau; Lee, Che-Di; Chien, Chin-Lung; Hsu, Ying-Shao; Chen, Kuan-Ming

2013-01-01

Based on the Trends in International Mathematics and Science Study 2007 study and a follow-up national survey, data for 3,901 Taiwanese grade 8 students were analyzed using structural equation modeling to confirm a social-relation-based affection-driven model (SRAM). SRAM hypothesized relationships among students' perceived social relationships in…

A Fundamental Approach to Developing Aluminium based Bulk Amorphous Alloys based on Stable Liquid Metal Structures and Electronic Equilibrium - 154041

DTIC Science & Technology

2017-03-28

AFRL-AFOSR-JP-TR-2017-0027 A Fundamental Approach to Developing Aluminium-based Bulk Amorphous Alloys based on Stable Liquid -Metal Structures and...to 16 Dec 2016 4.  TITLE AND SUBTITLE A Fundamental Approach to Developing Aluminium-based Bulk Amorphous Alloys based on Stable Liquid -Metal...including Al, Cu, Ni, Zr, Mg, Pd, Ga , Ca. Many new Al-based amorphous alloys were found within the numerous alloy systems studied in this project, and

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

PubMed

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

2009-07-01

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

Electromechanical impedance-based health diagnosis for tendon and anchorage zone in a nuclear containment structure

NASA Astrophysics Data System (ADS)

Min, Jiyoung; Shim, Hyojin; Yun, Chung-Bang

2012-04-01

For a nuclear containment structure, the structural health monitoring is essential because of its high potential risk and grave social impact. In particular, the tendon and anchorage zone are to be monitored because they are under high tensile or compressive stress. In this paper, a method to monitor the tendon force and the condition of the anchorage zone is presented by using the impedance-based health diagnosis system. First, numerical simulations were conducted for cases with various loose tensile forces on the tendon as well as damages on the bearing plate and concrete structure. Then, experimental studies were carried out on a scaled model of the anchorage system. The relationship between the loose tensile force and the impedance-based damage index was analyzed by a regression analysis. When a structure gets damaged, the damage index increases so that the status of damage can be identified. The results of the numerical and experimental studies indicate a big potential of the proposed impedance-based method for monitoring the tendon and anchorage system.

Mobile communications satellite antenna flight experiment definition

NASA Technical Reports Server (NTRS)

Freeland, Robert E.

1987-01-01

Results of a NASA-sponsored study to determine the technical feasibility and cost of a Shuttle-based flight experiment specifically intended for the MSAT commercial user community are presented. The experiment will include demonstrations of technology in the areas of radio frequency, sensing and control, and structures. The results of the structural subsystem study summarized here include experiment objective and technical approach, experiment structural description, structure/environment interactions, structural characterization, thermal characterization, structural measurement system, and experiment functional description.

Atomistic full-quantum transport model for zigzag graphene nanoribbon-based structures: Complex energy-band method

NASA Astrophysics Data System (ADS)

Chen, Chun-Nan; Luo, Win-Jet; Shyu, Feng-Lin; Chung, Hsien-Ching; Lin, Chiun-Yan; Wu, Jhao-Ying

2018-01-01

Using a non-equilibrium Green’s function framework in combination with the complex energy-band method, an atomistic full-quantum model for solving quantum transport problems for a zigzag-edge graphene nanoribbon (zGNR) structure is proposed. For transport calculations, the mathematical expressions from the theory for zGNR-based device structures are derived in detail. The transport properties of zGNR-based devices are calculated and studied in detail using the proposed method.

Cortical Thinning and Altered Cortico-Cortical Structural Covariance of the Default Mode Network in Patients with Persistent Insomnia Symptoms.

PubMed

Suh, Sooyeon; Kim, Hosung; Dang-Vu, Thien Thanh; Joo, Eunyeon; Shin, Chol

2016-01-01

Recent studies have suggested that structural abnormalities in insomnia may be linked with alterations in the default-mode network (DMN). This study compared cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia (PI) and good sleepers (GS). The current study used a clinical subsample from the longitudinal community-based Korean Genome and Epidemiology Study (KoGES). Cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia symptoms (PIS; n = 57) were compared to good sleepers (GS; n = 40). All participants underwent MRI acquisition. Based on literature review, we selected cortical regions corresponding to the DMN. A seed-based structural covariance analysis measured cortical thickness correlation between each seed region of the DMN and other cortical areas. Association of cortical thickness and covariance with sleep quality and neuropsychological assessments were further assessed. Compared to GS, cortical thinning was found in PIS in the anterior cingulate cortex, precentral cortex, and lateral prefrontal cortex. Decreased structural connectivity between anterior and posterior regions of the DMN was observed in the PIS group. Decreased structural covariance within the DMN was associated with higher PSQI scores. Cortical thinning in the lateral frontal lobe was related to poor performance in executive function in PIS. Disrupted structural covariance network in PIS might reflect malfunctioning of antero-posterior disconnection of the DMN during the wake to sleep transition that is commonly found during normal sleep. The observed structural network alteration may further implicate commonly observed sustained sleep difficulties and cognitive impairment in insomnia. © 2016 Associated Professional Sleep Societies, LLC.

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

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.

Thienoacene-based organic semiconductors.

PubMed

Takimiya, Kazuo; Shinamura, Shoji; Osaka, Itaru; Miyazaki, Eigo

2011-10-11

Thienoacenes consist of fused thiophene rings in a ladder-type molecular structure and have been intensively studied as potential organic semiconductors for organic field-effect transistors (OFETs) in the last decade. They are reviewed here. Despite their simple and similar molecular structures, the hitherto reported properties of thienoacene-based OFETs are rather diverse. This Review focuses on four classes of thienoacenes, which are classified in terms of their chemical structures, and elucidates the molecular electronic structure of each class. The packing structures of thienoacenes and the thus-estimated solid-state electronic structures are correlated to their carrier transport properties in OFET devices. With this perspective of the molecular structures of thienoacenes and their carrier transport properties in OFET devices, the structure-property relationships in thienoacene-based organic semiconductors are discussed. The discussion provides insight into new molecular design strategies for the development of superior organic semiconductors. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structures performance, benefit, cost-study

NASA Technical Reports Server (NTRS)

Woike, O. G.; Salemme, C.; Stearns, E.; Oritz, P.; Roberts, M. L.; Baughman, J. L.; Johnston, R. P.; Demel, H. F.; Stabrylla, R. G.; Coffinberry, G. A.

1981-01-01

New technology concepts and structural analysis development needs which could lead to improved life cycle cost for future high-bypass turbofans were studied. The NASA-GE energy efficient engine technology is used as a base to assess the concept benefits. Recommended programs are identified for attaining these generic structural and other beneficial technologies.

Self-Study and Evaluation Guide/Revised 1979. Section C-1: Function and Structure.

ERIC Educational Resources Information Center

National Accreditation Council for Agencies Serving the Blind and Visually Handicapped, New York, NY.

The self study guide designed for accreditation of programs serving the blind and visually handicapped covers function and structure standards, standards address five areas: basic characteristics of the organization (legal base, planning, consumer rights), governing authority, the Chief administrator, basic administrative structure (fees for…

First principles and experimental study of the electronic structure and phase stability of bulk thallium bromide

NASA Astrophysics Data System (ADS)

Smith, Holland M.; Zhou, Yuzhi; Ciampi, Guido; Kim, Hadong; Cirignano, Leonard J.; Shah, Kanai S.; Haller, E. E.; Chrzan, D. C.

2013-08-01

We apply state-of-art first principle calculations to study the polymorphism and electronic structure of three previously reported phases of TlBr. The calculated band structures of NaCl-structure phase and orthorhombic-structure phase have different features than that of commonly observed CsCl-structure phase. We further interpret photoluminescence spectra based on our calculations. Several peaks close to calculated band gap values of the NaCl-structure phase and the orthorhombic-structure phase are found in unpolished TlBr samples.

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.

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

Scaffolding Online Argumentation during Problem Solving

ERIC Educational Resources Information Center

Oh, S.; Jonassen, D. H.

2007-01-01

In this study, constraint-based argumentation scaffolding was proposed to facilitate online argumentation performance and ill-structured problem solving during online discussions. In addition, epistemological beliefs were presumed to play a role in solving ill-structured diagnosis-solution problems. Constraint-based discussion boards were…

Smartphone based hemispherical photography for canopy structure measurement

NASA Astrophysics Data System (ADS)

Wan, Xuefen; Cui, Jian; Jiang, Xueqin; Zhang, Jingwen; Yang, Yi; Zheng, Tao

2018-01-01

The canopy is the most direct and active interface layer of the interaction between plant and environment, and has important influence on energy exchange, biodiversity, ecosystem matter and climate change. The measurement about canopy structure of plant is an important foundation to analyze the pattern, process and operation mechanism of forest ecosystem. Through the study of canopy structure of plant, solar radiation, ambient wind speed, air temperature and humidity, soil evaporation, soil temperature and other forest environmental climate characteristics can be evaluated. Because of its accuracy and effectiveness, canopy structure measurement based on hemispherical photography has been widely studied. However, the traditional method of canopy structure hemispherical photogrammetry based on SLR camera and fisheye lens. This method is expensive and difficult to be used in some low-cost occasions. In recent years, smartphone technology has been developing rapidly. The smartphone not only has excellent image acquisition ability, but also has the considerable computational processing ability. In addition, the gyroscope and positioning function on the smartphone will also help to measure the structure of the canopy. In this paper, we present a smartphone based hemispherical photography system. The system consists of smart phones, low-cost fisheye lenses and PMMA adapters. We designed an Android based App to obtain the canopy hemisphere images through low-cost fisheye lenses and provide horizontal collimation information. In addition, the App will add the acquisition location tag obtained by GPS and auxiliary positioning method in hemisphere image information after the canopy structure hemisphere image acquisition. The system was tested in the urban forest after it was completed. The test results show that the smartphone based hemispherical photography system can effectively collect the high-resolution canopy structure image of the plant.

Optical-fiber strain sensors with asymmetric etched structures.

PubMed

Vaziri, M; Chen, C L

1993-11-01

Optical-fiber strain gauges with asymmetric etched structures have been analyzed, fabricated, and tested. These sensors are very sensitive with a gauge factor as high as 170 and a flat frequency response to at least 2.7 kHz. The gauge factor depends on the asymmetry of the etched structures and the number of etched sections. To understand the physical principles involved, researchers have used structural analysis programs based on a finite-element method to analyze fibers with asymmetric etched structures under tensile stress. The results show that lateral bends are induced on the etched fibers when they are stretched axially. To relate the lateral bending to the optical attenuation, we have also employed a ray-tracing technique to investigate the dependence of the attenuation on the structural deformation. Based on the structural analysis and the ray-tracing study parameters affecting the sensitivity have been studied. These results agree with the results of experimental investigations.

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.

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

PubMed

Ohtana, Yuki; Abdullah, Azian Azamimi; Altaf-Ul-Amin, Md; Huang, Ming; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Horai, Hisayuki; Nakamura, Yukiko; Morita Hirai, Aki; Lange, Klaus W; Kibinge, Nelson K; Katsuragi, Tetsuo; Shirai, Tsuyoshi; Kanaya, Shigehiko

2014-12-01

Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bottom-up Formation of Carbon-Based Structures with Multilevel Hierarchy from MOF-Guest Polyhedra.

PubMed

Wang, Tiesheng; Kim, Hyun-Kyung; Liu, Yingjun; Li, Weiwei; Griffiths, James T; Wu, Yue; Laha, Sourav; Fong, Kara D; Podjaski, Filip; Yun, Chao; Kumar, R Vasant; Lotsch, Bettina V; Cheetham, Anthony K; Smoukov, Stoyan K

2018-05-16

Three-dimensional carbon-based structures have proven useful for tailoring material properties in structural mechanical and energy storage applications. One approach to obtain them has been by carbonization of selected metal-organic frameworks (MOFs) with catalytic metals, but this is not applicable to most common MOF structures. Here, we present a strategy to transform common MOFs, by guest inclusions and high-temperature MOF-guest interactions, into complex carbon-based, diatom-like, hierarchical structures (named for the morphological similarities with the naturally existing diatomaceous species). As an example, we introduce metal salt guests into HKUST-1-type MOFs to generate a family of carbon-based nano-diatoms with two to four levels of structural hierarchy. We report control of the morphology by simple changes in the chemistry of the MOF and guest, with implications for the formation mechanisms. We demonstrate that one of these structures has unique advantages as a fast-charging lithium-ion battery anode. The tunability of composition should enable further studies of reaction mechanisms and result in the growth of a myriad of unprecedented carbon-based structures from the enormous variety of currently available MOF-guest candidates.

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

PubMed Central

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

2017-01-01

Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

Lactose-modified DNA tile nanostructures as drug carriers.

PubMed

Akkus Sut, Pinar; Tunc, Cansu Umran; Culha, Mustafa

2016-09-01

DNA hybridization allows the preparation of nanoscale DNA structures with desired shape and size. DNA structures using simple base pairing can be used for the delivery of drug molecules into the cells. Since DNA carries multiple negative charges, their cellular uptake efficiency is low. Thus, the modification of the DNA structures with molecules that may enhance the cellular internalization may be an option. The objective of this study is to construct DNA-based nanocarrier system and to investigate the cellular uptake of DNA tile with/without lactose modification. Doxorubicin was intercalated to DNA tile and cellular uptake of drug-loaded DNA-based carrier with/without lactose modification was investigated in vitro. HeLa, BT-474, and MDA-MB-231 cancer cells were used for cellular uptake studies and cytotoxicity assays. Using fluorescence spectroscopy, flow cytometry, and confocal microscopy, cellular uptake behavior of DNA tile was investigated. The cytotoxicity of DNA tile structures was determined with WST-1 assay. The results show that modification with lactose effectively increases the intracellular uptake of doxorubicin loaded DNA tile structure by cancer cells compared with the unmodified DNA tile. The findings of this study suggest that DNA-based nanostructures modified with carbohydrates can be used as suitable multifunctional nanocarriers with simple chemical modifications.

Contrastive Numerical Investigations on Thermo-Structural Behaviors in Mass Concrete with Various Cements

PubMed Central

Zhou, Wei; Feng, Chuqiao; Liu, Xinghong; Liu, Shuhua; Zhang, Chao; Yuan, Wei

2016-01-01

This work is a contrastive investigation of numerical simulations to improve the comprehension of thermo-structural coupled phenomena of mass concrete structures during construction. The finite element (FE) analysis of thermo-structural behaviors is used to investigate the applicability of supersulfated cement (SSC) in mass concrete structures. A multi-scale framework based on a homogenization scheme is adopted in the parameter studies to describe the nonlinear concrete behaviors. Based on the experimental data of hydration heat evolution rate and quantity of SSC and fly ash Portland cement, the hydration properties of various cements are studied. Simulations are run on a concrete dam section with a conventional method and a chemo-thermo-mechanical coupled method. The results show that SSC is more suitable for mass concrete structures from the standpoint of temperature control and crack prevention. PMID:28773517

Contrastive Numerical Investigations on Thermo-Structural Behaviors in Mass Concrete with Various Cements.

PubMed

Zhou, Wei; Feng, Chuqiao; Liu, Xinghong; Liu, Shuhua; Zhang, Chao; Yuan, Wei

2016-05-20

This work is a contrastive investigation of numerical simulations to improve the comprehension of thermo-structural coupled phenomena of mass concrete structures during construction. The finite element (FE) analysis of thermo-structural behaviors is used to investigate the applicability of supersulfated cement (SSC) in mass concrete structures. A multi-scale framework based on a homogenization scheme is adopted in the parameter studies to describe the nonlinear concrete behaviors. Based on the experimental data of hydration heat evolution rate and quantity of SSC and fly ash Portland cement, the hydration properties of various cements are studied. Simulations are run on a concrete dam section with a conventional method and a chemo-thermo-mechanical coupled method. The results show that SSC is more suitable for mass concrete structures from the standpoint of temperature control and crack prevention.

Lymph Node Metastases Optical Molecular Diagnostic and Radiation Therapy

DTIC Science & Technology

2017-03-01

because most imaging is based upon structures and not molecular functions. The one tool commonly used for metastases imaging is nuclear medicine...imaging, which is that micro metastases cannot be visualized at a relevant stage., largely because most imaging is based upon structures and not...evaluate the limits on structural , metabolic and immunologic probes for molecular imaging, and (4) to complete studies on metastatic breast cancer

Development of self-powered strain sensor using mechano-luminescent ZnS:Cu and mechano-optoelectronic P3HT

NASA Astrophysics Data System (ADS)

Pulliam, Elias; Hoover, George; Tiparti, Dhruv; Ryu, Donghyeon

2017-04-01

Aerospace structural systems are prone to structural damage during their use by vibration, impact, material degradation, and other factors. Due to the harsh environments in which aerospace structures operate, aerospace structures are susceptible to various types of damage and often their structural integrity is jeopardized unless damage onset is detected in timely manner. Yet, current state-of-the-art sensor technologies are still limited for structural health monitoring (SHM) of aerospace structures due to their high power consumption, need for large form factor design, and manageable integration into aerospace structures. This study proposes a design of multilayered self-powered strain sensor by coupling mechano-luminescent (ML) property of copper-doped zinc sulfide (ZnS:Cu) and mechano-optoelectronic (MO) property of poly(3-hexylthiophene) (P3HT). One functional layer of the self-powered strain sensor is ZnS:Cu-based elastomeric composites that emit light in response to mechanical deformation. Another functional layer is P3HT-based thin films that generate direct current (DC) under light illumination and DC magnitude changes with applied strain. First, ML light emission characteristics of ZnS:Cu-based composites are studied under cyclic tensile strain with two various maximum strain up to 10% and 15% at various loading frequencies from 5 Hz to 20 Hz. Second, piezo-optical properties of P3HT-based thin films are investigated by acquiring light absorption of the thin films at various strains from 0% to 2% tensile strain. Last, micro-mechanical properties of the P3HT-based thin films are characterized using nanoindentation.

Receptor-based 3D-QSAR in Drug Design: Methods and Applications in Kinase Studies.

PubMed

Fang, Cheng; Xiao, Zhiyan

2016-01-01

Receptor-based 3D-QSAR strategy represents a superior integration of structure-based drug design (SBDD) and three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. It combines the accurate prediction of ligand poses by the SBDD approach with the good predictability and interpretability of statistical models derived from the 3D-QSAR approach. Extensive efforts have been devoted to the development of receptor-based 3D-QSAR methods and two alternative approaches have been exploited. One associates with computing the binding interactions between a receptor and a ligand to generate structure-based descriptors for QSAR analyses. The other concerns the application of various docking protocols to generate optimal ligand poses so as to provide reliable molecular alignments for the conventional 3D-QSAR operations. This review highlights new concepts and methodologies recently developed in the field of receptorbased 3D-QSAR, and in particular, covers its application in kinase studies.

The feasibility of accommodating physically handicapped individuals on pedestrian over and undercrossing structures

DOT National Transportation Integrated Search

1980-09-01

The objective of this study was to determine the feasibility of accommodating the physically handicapped on over- and undercrossing structures. Based upon the evaluation of 124 crossing structures, 86 percent of these structures had at least one majo...

The effects of liquid-phase oxidation of multiwall carbon nanotubes on their surface characteristics

NASA Astrophysics Data System (ADS)

Burmistrov, I. N.; Muratov, D. S.; Ilinykh, I. A.; Kolesnikov, E. A.; Godymchuk, A. Yu; Kuznetsov, D. V.

2016-01-01

The development of new sorbents based on nanostructured carbon materials recently became a perspective field of research. Main topic of current study is to investigate the effect of different regimes of multiwall carbon nanotubes (MWCNT) surface modification process on their structural characteristics. MWCNT samples were treated with nitric acid at high temperature. Structural properties were studied using low temperature nitrogen adsorption and acid-base back titration methods. The study showed that diluted nitric acid does not affect MWCNT structure. Concentrated nitric acid treatment leads to formation of 2.8 carboxylic groups per 1 nm2 of the sample surface.

Advanced thermally stable jet fuels. Technical progress report, January 1995--March 1995

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

Schobert, H.H.; Eser, S.; Song, C.

Quantitative structure-property relationships have been applied to study the thermal stability of pure hydrocarbons typical of jet fuel components. A simple method of chemical structure description in terms of Benson groups was tested in searching for structure-property relationships for the hydrocarbons tested experimentally in this program. Molecular connectivity as a structure-based approach to chemical structure-property relationship analysis was also tested. Further development of both the experimental data base and computational methods will be necessary. Thermal decomposition studies, using glass tube reactors, were extended to two additional model compounds: n-decane and n-dodecane. Efforts on refining the deposit growth measurement and characterizationmore » of suspended matter in stressed fuels have lead to improvements in the analysis of stressed fuels. Catalytic hydrogenation and dehydrogenation studies utilizing a molybdenum sulfide catalyst are also described.« less

Feasibility Study on 3-D Printing of Metallic Structural Materials with Robotized Laser-Based Metal Additive Manufacturing

NASA Astrophysics Data System (ADS)

Ding, Yaoyu; Kovacevic, Radovan

2016-07-01

Metallic structural materials continue to open new avenues in achieving exotic mechanical properties that are naturally unavailable. They hold great potential in developing novel products in diverse industries such as the automotive, aerospace, biomedical, oil and gas, and defense. Currently, the use of metallic structural materials in industry is still limited because of difficulties in their manufacturing. This article studied the feasibility of printing metallic structural materials with robotized laser-based metal additive manufacturing (RLMAM). In this study, two metallic structural materials characterized by an enlarged positive Poisson's ratio and a negative Poisson's ratio were designed and simulated, respectively. An RLMAM system developed at the Research Center for Advanced Manufacturing of Southern Methodist University was used to print them. The results of the tensile tests indicated that the printed samples successfully achieved the corresponding mechanical properties.

Structural Acoustic Physics Based Modeling of Curved Composite Shells

DTIC Science & Technology

2017-09-19

Results show that the finite element computational models accurately match analytical calculations, and that the composite material studied in this...products. 15. SUBJECT TERMS Finite Element Analysis, Structural Acoustics, Fiber-Reinforced Composites, Physics-Based Modeling 16. SECURITY...2 4 FINITE ELEMENT MODEL DESCRIPTION

Bridging quantum mechanics and structure-based drug design.

PubMed

De Vivo, Marco

2011-01-01

The last decade has seen great advances in the use of quantum mechanics (QM) to solve biological problems of pharmaceutical relevance. For instance, enzymatic catalysis is often investigated by means of the so-called QM/MM approach, which uses QM and molecular mechanics (MM) methods to determine the (free) energy landscape of the enzymatic reaction mechanism. Here, I will discuss a few representative examples of QM and QM/MM studies of important metalloenzymes of pharmaceutical interest (i.e. metallophosphatases and metallo-beta-lactamases). This review article aims to show how QM-based methods can be used to elucidate ligand-receptor interactions. The challenge is then to exploit this knowledge for the structure-based design of new and potent inhibitors, such as transition state (TS) analogues that resemble the structure and physicochemical properties of the enzymatic TS. Given the results and potential expressed to date by QM-based methods in studying biological problems, the application of QM in structure-based drug design will likely increase, making of these once-prohibitive computations a routinely used tool for drug design.

Study of the structure of 3-D composites based on carbon nanotubes in bovine serum albumin matrix by X-ray microtomography

NASA Astrophysics Data System (ADS)

Ignatov, D.; Zhurbina, N.; Gerasimenko, A.

2017-01-01

3-D composites are widely used in tissue engineering. A comprehensive analysis by X-ray microtomography was conducted to study the structure of the 3-D composites. Comprehensive analysis of the structure of the 3-D composites consisted of scanning, image reconstruction of shadow projections, two-dimensional and three-dimensional visualization of the reconstructed images and quantitative analysis of the samples. Experimental samples of composites were formed by laser vaporization of the aqueous dispersion BSA and single-walled (SWCNTs) and multi-layer (MWCNTs) carbon nanotubes. The samples have a homogeneous structure over the entire volume, the percentage of porosity of 3-D composites based on SWCNTs and MWCNTs - 16.44%, 28.31%, respectively. An average pore diameter of 3-D composites based on SWCNTs and MWCNTs - 45 μm 93 μm. 3-D composites based on carbon nanotubes in bovine serum albumin matrix can be used in tissue engineering of bone and cartilage, providing cell proliferation and blood vessel sprouting.

The Value of Writing-to-Learn when Using Question Prompts to Support Web-Based Learning in Ill-Structured Domains

ERIC Educational Resources Information Center

Papadopoulos, Pantelis M.; Demetriadis, Stavros N.; Stamelos, Ioannis G.; Tsoukalas, Ioannis A.

2011-01-01

This study investigates the effectiveness of two variants of a prompting strategy that guides students to focus on important issues when learning in an ill-structured domain. Students in three groups studied individually Software Project Management (SPM) cases for a week, using a web-based learning environment designed especially for this purpose.…

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

PubMed

Nagata, Koji

2010-01-01

Peptides and proteins with similar amino acid sequences can have different biological functions. Knowledge of their three-dimensional molecular structures is critically important in identifying their functional determinants. In this review, I describe the results of our and other groups' structure-based functional characterization of insect insulin-like peptides, a crustacean hyperglycemic hormone-family peptide, a mammalian epidermal growth factor-family protein, and an intracellular signaling domain that recognizes proline-rich sequence.

The Packaging Technology Study on Smart Composite Structure Based on The Embedded FBG Sensor

NASA Astrophysics Data System (ADS)

Zhang, Youhong; Chang, Xinlong; Zhang, Xiaojun; He, Xiangyong

2018-03-01

It is convenient to carry out the health monitoring of the solid rocket engine composite shell based on the embedded FBG sensor. In this paper, the packaging technology using one-way fiber layer of prepreg fiberglass/epoxy resin was proposed. The proposed packaging process is simple, and the packaged sensor structure size is flexible and convenient to use, at the mean time, the packaged structure has little effect on the pristine composite material structure.

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

PubMed

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

Structural, morphological, and optical study of titania-based nanopowders suitable for photocatalytic applications

NASA Astrophysics Data System (ADS)

Šćepanović, M.; Grujić-Brojčin, M.; Abramović, B.; Golubović, A.

2017-01-01

Systematic investigation of the relationship between structural, morphological, optical and photocatalytic properties of the titania-based nanopowders is presented. A series of pure and doped titania catalysts with various (anatase and brookite) phase compositions have been prepared by sol-gel or hydrothermal route. The crystal structure and composition of the synthesized samples have been extensively characterised by XRD and Raman scattering measurements. The nanopowder morphology has been studied using microscopic methods (SEM, AFM, and STM), whereas the porous structure has been revealed by the analysis of nitrogen sorption data. The optical and electronic properties have been studied by spectroscopic ellipsometry. All investigated properties have been correlated to photocatalytic activity, tested in degradation of the pharmaceutically active substances (such as metoprolol and alprazolam) induced by UVA or visible radiation. Based on this correlation, the physical properties which contribute most to the increase in photocatalytic activity of synthesized nanopowders have been determined, in order to optimize the synthesis conditions which could lead to the maximal efficiency in degradation of particular pollutant.

Effect of a Near Fault on the Seismic Response of a Base-Isolated Structure with a Soft Storey

NASA Astrophysics Data System (ADS)

Athamnia, B.; Ounis, A.; Abdeddaim, M.

2017-12-01

This study focuses on the soft-storey behavior of RC structures with lead core rubber bearing (LRB) isolation systems under near and far-fault motions. Under near-fault ground motions, seismic isolation devices might perform poorly because of large isolator displacements caused by large velocity and displacement pulses associated with such strong motions. In this study, four different structural models have been designed to study the effect of soft-storey behavior under near-fault and far-fault motions. The seismic analysis for isolated reinforced concrete buildings is carried out using a nonlinear time history analysis method. Inter-story drifts, absolute acceleration, displacement, base shear forces, hysteretic loops and the distribution of plastic hinges are examined as a result of the analysis. These results show that the performance of a base isolated RC structure is more affected by increasing the height of a story under nearfault motion than under far-fault motion.

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

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.

Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition

PubMed Central

Clerc, Jérôme; Groll, Michael; Illich, Damir J.; Bachmann, André S.; Huber, Robert; Schellenberg, Barbara; Dudler, Robert; Kaiser, Markus

2009-01-01

Syrbactins, a family of natural products belonging either to the syringolin or glidobactin class, are highly potent proteasome inhibitors. Although sharing similar structural features, they differ in their macrocyclic lactam core structure and exocyclic side chain. These structural variations critically influence inhibitory potency and proteasome subsite selectivity. Here, we describe the total synthesis of syringolin A and B, which together with enzyme kinetic and structural studies, allowed us to elucidate the structural determinants underlying the proteasomal subsite selectivity and binding affinity of syrbactins. These findings were used successfully in the rational design and synthesis of a syringolin A-based lipophilic derivative, which proved to be the most potent syrbactin-based proteasome inhibitor described so far. With a Ki′ of 8.65 ± 1.13 nM for the chymotryptic activity, this syringolin A derivative displays a 100-fold higher potency than the parent compound syringolin A. In light of the medicinal relevance of proteasome inhibitors as anticancer compounds, the present findings may assist in the rational design and development of syrbactin-based chemotherapeutics. PMID:19359491

A review of recent developments in parametric based acoustic emission techniques applied to concrete structures

NASA Astrophysics Data System (ADS)

Vidya Sagar, R.; Raghu Prasad, B. K.

2012-03-01

This article presents a review of recent developments in parametric based acoustic emission (AE) techniques applied to concrete structures. It recapitulates the significant milestones achieved by previous researchers including various methods and models developed in AE testing of concrete structures. The aim is to provide an overview of the specific features of parametric based AE techniques of concrete structures carried out over the years. Emphasis is given to traditional parameter-based AE techniques applied to concrete structures. A significant amount of research on AE techniques applied to concrete structures has already been published and considerable attention has been given to those publications. Some recent studies such as AE energy analysis and b-value analysis used to assess damage of concrete bridge beams have also been discussed. The formation of fracture process zone and the AE energy released during the fracture process in concrete beam specimens have been summarised. A large body of experimental data on AE characteristics of concrete has accumulated over the last three decades. This review of parametric based AE techniques applied to concrete structures may be helpful to the concerned researchers and engineers to better understand the failure mechanism of concrete and evolve more useful methods and approaches for diagnostic inspection of structural elements and failure prediction/prevention of concrete structures.

The Interplay of Reader Goals, Working Memory, and Text Structure During Reading

PubMed Central

Bohn-Gettler, Catherine M.; Kendeou, Panayiota

2014-01-01

In the current study we examined the complex interactions of instructional context, text properties, and reader characteristics during comprehension. College students were tasked with the goal of reading for study versus entertainment (instructional context) while thinking-aloud about four different expository text structures (text properties). Working memory also was assessed (reader characteristics). Reading goals and working memory interacted to influence paraphrasing and non-coherence processes when thinking aloud. Reading goals, working memory, and text structure all interacted to influence text-based inferences. Text structure also influenced knowledge-based inferences. Post-reading recall was highest for those with the instructional goal of reading for study (compared to entertainment), as well as for problem-response and compare-contrast texts (compared to descriptive and chronological texts). Implications of the findings are discussed. PMID:25018581

Secure fingerprint identification based on structural and microangiographic optical coherence tomography.

PubMed

Liu, Xuan; Zaki, Farzana; Wang, Yahui; Huang, Qiongdan; Mei, Xin; Wang, Jiangjun

2017-03-10

Optical coherence tomography (OCT) allows noncontact acquisition of fingerprints and hence is a highly promising technology in the field of biometrics. OCT can be used to acquire both structural and microangiographic images of fingerprints. Microangiographic OCT derives its contrast from the blood flow in the vasculature of viable skin tissue, and microangiographic fingerprint imaging is inherently immune to fake fingerprint attack. Therefore, dual-modality (structural and microangiographic) OCT imaging of fingerprints will enable more secure acquisition of biometric data, which has not been investigated before. Our study on fingerprint identification based on structural and microangiographic OCT imaging is, we believe, highly innovative. In this study, we performed OCT imaging study for fingerprint acquisition, and demonstrated the capability of dual-modality OCT imaging for the identification of fake fingerprints.

Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints

PubMed Central

Day, Ryan; Qu, Xiaotao; Swanson, Rosemarie; Bohannan, Zach; Bliss, Robert

2011-01-01

Abstract Most current template-based structure prediction methods concentrate on finding the correct backbone conformation and then packing sidechains within that backbone. Our packing-based method derives distance constraints from conserved relative packing groups (RPGs). In our refinement approach, the RPGs provide a level of resolution that restrains global topology while allowing conformational sampling. In this study, we test our template-based structure prediction method using 51 prediction units from CASP7 experiments. RPG-based constraints are able to substantially improve approximately two-thirds of starting templates. Upon deeper investigation, we find that true positive spatial constraints, especially those non-local in sequence, derived from the RPGs were important to building nearer native models. Surprisingly, the fraction of incorrect or false positive constraints does not strongly influence the quality of the final candidate. This result indicates that our RPG-based true positive constraints sample the self-consistent, cooperative interactions of the native structure. The lack of such reinforcing cooperativity explains the weaker effect of false positive constraints. Generally, these findings are encouraging indications that RPGs will improve template-based structure prediction. PMID:21210729

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.

Chemical-Space-Based de Novo Design Method To Generate Drug-Like Molecules.

PubMed

Takeda, Shunichi; Kaneko, Hiromasa; Funatsu, Kimito

2016-10-24

To discover drug compounds in chemical space containing an enormous number of compounds, a structure generator is required to produce virtual drug-like chemical structures. The de novo design algorithm for exploring chemical space (DAECS) visualizes the activity distribution on a two-dimensional plane corresponding to chemical space and generates structures in a target area on a plane selected by the user. In this study, we modify the DAECS to enable the user to select a target area to consider properties other than activity and improve the diversity of the generated structures by visualizing the drug-likeness distribution and the activity distribution, generating structures by substructure-based structural changes, including addition, deletion, and substitution of substructures, as well as the slight structural changes used in the DAECS. Through case studies using ligand data for the human adrenergic alpha2A receptor and the human histamine H1 receptor, the modified DAECS can generate high diversity drug-like structures, and the usefulness of the modification of the DAECS is verified.

The Optimization of In-Memory Space Partitioning Trees for Cache Utilization

NASA Astrophysics Data System (ADS)

Yeo, Myung Ho; Min, Young Soo; Bok, Kyoung Soo; Yoo, Jae Soo

In this paper, a novel cache conscious indexing technique based on space partitioning trees is proposed. Many researchers investigated efficient cache conscious indexing techniques which improve retrieval performance of in-memory database management system recently. However, most studies considered data partitioning and targeted fast information retrieval. Existing data partitioning-based index structures significantly degrade performance due to the redundant accesses of overlapped spaces. Specially, R-tree-based index structures suffer from the propagation of MBR (Minimum Bounding Rectangle) information by updating data frequently. In this paper, we propose an in-memory space partitioning index structure for optimal cache utilization. The proposed index structure is compared with the existing index structures in terms of update performance, insertion performance and cache-utilization rate in a variety of environments. The results demonstrate that the proposed index structure offers better performance than existing index structures.

Crystalline modification of a rare earth nucleating agent for isotactic polypropylene based on its self-assembly.

PubMed

Zhang, Yuanming; Sun, Tingting; Jiang, Wei; Han, Guangting

2018-05-01

In this paper, the crystalline modification of a rare earth nucleating agent (WBG) for isotactic polypropylene (PP) based on its supramolecular self-assembly was investigated by differential scanning calorimetry, wide-angle X-ray diffraction and polarized optical microscopy. In addition, the relationship between the self-assembly structure of the nucleating agent and the crystalline structure, as well as the possible reason for the self-assembly behaviour, was further studied. The structure evolution of WBG showed that the self-assembly structure changed from a needle-like structure to a dendritic structure with increase in the content of WBG. When the content of WBG exceeded a critical value (0.4 wt%), it self-assembled into a strip structure. This revealed that the structure evolution of WBG contributed to the K β and the crystallization morphology of PP with different content of WBG. In addition, further studies implied that the behaviour of self-assembly was a liquid-solid transformation of WBG, followed by a liquid-liquid phase separation of molten isotactic PP and WBG. The formation of the self-assembly structure was based on the free molecules by hydrogen bond dissociation while being heated, followed by aggregation into another structure by hydrogen bond association while being cooled. Furthermore, self-assembly behaviour depends largely on the interaction between WBG themselves.

Feasibility study of archaeological structures scanning by muon tomography

NASA Astrophysics Data System (ADS)

Gómez, H.; Carloganu, C.; Gibert, D.; Marteau, J.; Niess, V.; Katsanevas, S.; Tonazzo, A.

2015-08-01

One of the main concerns in archaeology is to find of a method to study precisely archaeological structures in the least invasive way possible to avoid damage. The requirement of preserving the structures integrity prevents, in the case of pyramids or tumuli, the study of any internal structure (halls or tombs) which are not reachable by existing corridors. One non-invasive method is the muon tomography. By placing a detector which allows to register the muon direction after the structure, it is possible to have an idea of its composition based on the attenuation of the muon flux, which depends on the material length and density that muons have crossed. This technique, alone or together with other exploration techniques as seismic tomography or electrical resistivity tomography, can provide useful information about the internal structure of the archaeological form that can not be obtained by conventional archaeological methods. In this work, the time measurement necessary to obtain a significant result about the composition of an archaeological structure is estimated. To do that, a Monte Carlo simulation framework based on the MUSIC software, properly tuned for this study, has been developed. The particular case of the Kastas Amfipoli Macedonian tumulus has been considered to perform the simulations.

Identification of walking human model using agent-based modelling

NASA Astrophysics Data System (ADS)

Shahabpoor, Erfan; Pavic, Aleksandar; Racic, Vitomir

2018-03-01

The interaction of walking people with large vibrating structures, such as footbridges and floors, in the vertical direction is an important yet challenging phenomenon to describe mathematically. Several different models have been proposed in the literature to simulate interaction of stationary people with vibrating structures. However, the research on moving (walking) human models, explicitly identified for vibration serviceability assessment of civil structures, is still sparse. In this study, the results of a comprehensive set of FRF-based modal tests were used, in which, over a hundred test subjects walked in different group sizes and walking patterns on a test structure. An agent-based model was used to simulate discrete traffic-structure interactions. The occupied structure modal parameters found in tests were used to identify the parameters of the walking individual's single-degree-of-freedom (SDOF) mass-spring-damper model using 'reverse engineering' methodology. The analysis of the results suggested that the normal distribution with the average of μ = 2.85Hz and standard deviation of σ = 0.34Hz can describe human SDOF model natural frequency. Similarly, the normal distribution with μ = 0.295 and σ = 0.047 can describe the human model damping ratio. Compared to the previous studies, the agent-based modelling methodology proposed in this paper offers significant flexibility in simulating multi-pedestrian walking traffics, external forces and simulating different mechanisms of human-structure and human-environment interaction at the same time.

Monolithic-Structured Single-Layered Textile-Based Dye-Sensitized Solar Cells.

PubMed

Yun, Min Ju; Cha, Seung I; Kim, Han Seong; Seo, Seon Hee; Lee, Dong Y

2016-10-06

Textile-structured solar cells are frequently discussed in the literature due to their prospective applications in wearable devices and in building integrated solar cells that utilize their flexibility, mechanical robustness, and aesthetic appearance, but the current approaches for textile-based solar cells-including the preparation of fibre-type solar cells woven into textiles-face several difficulties from high friction and tension during the weaving process. This study proposes a new structural concept and fabrication process for monolithic-structured textile-based dye-sensitized solar cells that are fabricated by a process similar to the cloth-making process, including the preparation of wires and yarns that are woven for use in textiles, printed, dyed, and packaged. The fabricated single-layered textile-based dye-sensitized solar cells successfully act as solar cells in our study, even under bending conditions. By controlling the inter-weft spacing and the number of Ti wires for the photoelectrode conductor, we have found that the performance of this type of dye-sensitized solar cell was notably affected by the spacing between photoelectrodes and counter-electrodes, the exposed areas of Ti wires to photoelectrodes, and photoelectrodes' surface morphology. We believe that this study provides a process and concept for improved textile-based solar cells that can form the basis for further research.

Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.

PubMed

Houston, Simon; Lithgow, Karen Vivien; Osbak, Kara Krista; Kenyon, Chris Richard; Cameron, Caroline E

2018-05-16

Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale. Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens. Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T. pallidum proteome-wide structural modeling study and is one of few studies to apply this approach for the functional annotation of a whole proteome.

Time domain nonlinear SMA damper force identification approach and its numerical validation

NASA Astrophysics Data System (ADS)

Xin, Lulu; Xu, Bin; He, Jia

2012-04-01

Most of the currently available vibration-based identification approaches for structural damage detection are based on eigenvalues and/or eigenvectors extracted from vibration measurements and, strictly speaking, are only suitable for linear system. However, the initiation and development of damage in engineering structures under severe dynamic loadings are typical nonlinear procedure. Studies on the identification of restoring force which is a direct indicator of the extent of the nonlinearity have received increasing attention in recent years. In this study, a date-based time domain identification approach for general nonlinear system was developed. The applied excitation and the corresponding response time series of the structure were used for identification by means of standard least-square techniques and a power series polynomial model (PSPM) which was utilized to model the nonlinear restoring force (NRF). The feasibility and robustness of the proposed approach was verified by a 2 degree-of-freedoms (DOFs) lumped mass numerical model equipped with a shape memory ally (SMA) damper mimicking nonlinear behavior. The results show that the proposed data-based time domain method is capable of identifying the NRF in engineering structures without any assumptions on the mass distribution and the topology of the structure, and provides a promising way for damage detection in the presence of structural nonlinearities.

Computational predictive models for P-glycoprotein inhibition of in-house chalcone derivatives and drug-bank compounds.

PubMed

Ngo, Trieu-Du; Tran, Thanh-Dao; Le, Minh-Tri; Thai, Khac-Minh

2016-11-01

The human P-glycoprotein (P-gp) efflux pump is of great interest for medicinal chemists because of its important role in multidrug resistance (MDR). Because of the high polyspecificity as well as the unavailability of high-resolution X-ray crystal structures of this transmembrane protein, ligand-based, and structure-based approaches which were machine learning, homology modeling, and molecular docking were combined for this study. In ligand-based approach, individual two-dimensional quantitative structure-activity relationship models were developed using different machine learning algorithms and subsequently combined into the Ensemble model which showed good performance on both the diverse training set and the validation sets. The applicability domain and the prediction quality of the developed models were also judged using the state-of-the-art methods and tools. In our structure-based approach, the P-gp structure and its binding region were predicted for a docking study to determine possible interactions between the ligands and the receptor. Based on these in silico tools, hit compounds for reversing MDR were discovered from the in-house and DrugBank databases through virtual screening using prediction models and molecular docking in an attempt to restore cancer cell sensitivity to cytotoxic drugs.

Cortical Thinning and Altered Cortico-Cortical Structural Covariance of the Default Mode Network in Patients with Persistent Insomnia Symptoms

PubMed Central

Suh, Sooyeon; Kim, Hosung; Dang-Vu, Thien Thanh; Joo, Eunyeon; Shin, Chol

2016-01-01

Study Objectives: Recent studies have suggested that structural abnormalities in insomnia may be linked with alterations in the default-mode network (DMN). This study compared cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia (PI) and good sleepers (GS). Methods: The current study used a clinical subsample from the longitudinal community-based Korean Genome and Epidemiology Study (KoGES). Cortical thickness and structural connectivity linked to the DMN in patients with persistent insomnia symptoms (PIS; n = 57) were compared to good sleepers (GS; n = 40). All participants underwent MRI acquisition. Based on literature review, we selected cortical regions corresponding to the DMN. A seed-based structural covariance analysis measured cortical thickness correlation between each seed region of the DMN and other cortical areas. Association of cortical thickness and covariance with sleep quality and neuropsychological assessments were further assessed. Results: Compared to GS, cortical thinning was found in PIS in the anterior cingulate cortex, precentral cortex, and lateral prefrontal cortex. Decreased structural connectivity between anterior and posterior regions of the DMN was observed in the PIS group. Decreased structural covariance within the DMN was associated with higher PSQI scores. Cortical thinning in the lateral frontal lobe was related to poor performance in executive function in PIS. Conclusion: Disrupted structural covariance network in PIS might reflect malfunctioning of antero-posterior disconnection of the DMN during the wake to sleep transition that is commonly found during normal sleep. The observed structural network alteration may further implicate commonly observed sustained sleep difficulties and cognitive impairment in insomnia. Citation: Suh S, Kim H, Dang-Vu TT, Joo E, Shin C. Cortical thinning and altered cortico-cortical structural covariance of the default mode network in patients with persistent insomnia symptoms. SLEEP 2016;39(1):161–171. PMID:26414892

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Electrochemical Characterization of InP and GaAs Based Structures for Space Solar Cell Applications.

NASA Technical Reports Server (NTRS)

Faur, Maria; Faur, Mircea; Jenkins, Philip P.; Goradia, Manju; Wilt, David M.

1994-01-01

In this paper the emphasis is on accurate majority carrier concentration EC-V profiling of structures based on Indium Phosphide and Gallium Arsenide, using a newly developed electrolyte based on Hydrogen Flouride, Acetic Acid, Phosphoric Acid, 1-phenyl-2-propanamine and Ammonia Diflouride. Some preliminary data on the use of this electrolyte for determining the energy distribution of surface and deep states of these structures, applicable to fabrication process optimization and radiation induced defects studies of solar cells, are also provided.

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

PubMed

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

PubMed Central

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics. PMID:25250663

Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

PubMed

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

Betavoltaic Battery Conversion Efficiency Improvement Based on Interlayer Structures

NASA Astrophysics Data System (ADS)

Li, Da-Rang; Jiang, Lan; Yin, Jian-Hua; Tan, Yuan-Yuan; Lin, Nai

2012-07-01

Significant differences among the doping densities of PN junctions in semiconductors cause lattice mismatch and lattice defects that increase the recombination current of betavoltaic batteries. This extensively decreases the open circuit voltage and the short current, which results in low conversion efficiency. This study proposes P+PINN+-structure based betavoltaic batteries by adding an interlayer to typical PIN structures to improve conversion efficiency. Numerical simulations are conducted for the energy deposition of beta particles along the thickness direction in semiconductors. Based on this, 63Ni-radiation GaAs batteries with PIN and P+PINN+ structures are designed and fabricated to experimentally verify the proposed design. It turns out that the conversion efficiency of the betavoltaic battery with the proposed P+PINN+ structure is about 1.45 times higher than that with the traditional PIN structure.

Tuneable complementary metamaterial structures based on graphene for single and multiple transparency windows

PubMed Central

Ding, Jun; Arigong, Bayaner; Ren, Han; Zhou, Mi; Shao, Jin; Lu, Meng; Chai, Yang; Lin, Yuankun; Zhang, Hualiang

2014-01-01

Novel graphene-based tunable plasmonic metamaterials featuring single and multiple transparency windows are numerically studied in this paper. The designed structures consist of a graphene layer perforated with quadrupole slot structures and dolmen-like slot structures printed on a substrate. Specifically, the graphene-based quadrupole slot structure can realize a single transparency window, which is achieved without breaking the structure symmetry. Further investigations have shown that the single transparency window in the proposed quadrupole slot structure is more likely originated from the quantum effect of Autler-Townes splitting. Then, by introducing a dipole slot to the quadrupole slot structure to form the dolmen-like slot structure, an additional transmission dip could occur in the transmission spectrum, thus, a multiple-transparency-window system can be achieved (for the first time for graphene-based devices). More importantly, the transparency windows for both the quadrupole slot and the dolmen-like slot structures can be dynamically controlled over a broad frequency range by varying the Fermi energy levels of the graphene layer (through electrostatic gating). The proposed slot metamaterial structures with tunable single and multiple transparency windows could find potential applications in many areas such as multiple-wavelength slow-light devices, active plasmonic switching, and optical sensing. PMID:25146672

Tuneable complementary metamaterial structures based on graphene for single and multiple transparency windows.

PubMed

Ding, Jun; Arigong, Bayaner; Ren, Han; Zhou, Mi; Shao, Jin; Lu, Meng; Chai, Yang; Lin, Yuankun; Zhang, Hualiang

2014-08-22

Novel graphene-based tunable plasmonic metamaterials featuring single and multiple transparency windows are numerically studied in this paper. The designed structures consist of a graphene layer perforated with quadrupole slot structures and dolmen-like slot structures printed on a substrate. Specifically, the graphene-based quadrupole slot structure can realize a single transparency window, which is achieved without breaking the structure symmetry. Further investigations have shown that the single transparency window in the proposed quadrupole slot structure is more likely originated from the quantum effect of Autler-Townes splitting. Then, by introducing a dipole slot to the quadrupole slot structure to form the dolmen-like slot structure, an additional transmission dip could occur in the transmission spectrum, thus, a multiple-transparency-window system can be achieved (for the first time for graphene-based devices). More importantly, the transparency windows for both the quadrupole slot and the dolmen-like slot structures can be dynamically controlled over a broad frequency range by varying the Fermi energy levels of the graphene layer (through electrostatic gating). The proposed slot metamaterial structures with tunable single and multiple transparency windows could find potential applications in many areas such as multiple-wavelength slow-light devices, active plasmonic switching, and optical sensing.

Expanded Study on the accumulation effect of tourism under the constraint of structure

NASA Astrophysics Data System (ADS)

Wang, Qiang; Yang, Zhenzhi; Huang, Lu

2017-05-01

There is a mutual influence between departmental structure and accumulation and growth. Therefore, the accumulation and growth of the tourism industry will be subject to certain restrictions on the industrial structure, and, conversely, it will have an impact on the existing industrial structure. Li Jingyi reported special research in the paper called "Research on tourism growth based on structural constraints" about the relationship between the growth of tourism and the existing industrial structure. It pointed out the specific interdependence between tourism and other economic sectors in terms of accumulation and growth. However, the research of Li Jingyi is based on the trichotomy of social product value. It is too abstract, while the study is understandable in theory. In practice, it is difficult to use the model of the paper to deal with specific problems. Therefore, how to improve the industry association model in the paper of Li and make it more in line with the actual situation becomes our concern. In this paper, the author hopes to improve the model of Li's paper by simplifying the decomposition of social product value. At the same time, it makes a further study on accumulation elasticity and growth elasticity. On this basis, some suggestions are put forward to guide the development of other industries based on the tourism industry.

Fabrication and condensation characteristics of metallic superhydrophobic surface with hierarchical micro-nano structures

NASA Astrophysics Data System (ADS)

Chu, Fuqiang; Wu, Xiaomin

2016-05-01

Metallic superhydrophobic surfaces have various applications in aerospace, refrigeration and other engineering fields due to their excellent water repellent characteristics. This study considers a simple but widely applicable fabrication method using a two simultaneous chemical reactions method to prepare the acid-salt mixed solutions to process the metal surfaces with surface deposition and surface etching to construct hierarchical micro-nano structures on the surface and then modify the surface with low surface-energy materials. Al-based and Cu-based superhydrophobic surfaces were fabricated using this method. The Al-based superhydrophobic surface had a water contact angle of 164° with hierarchical micro-nano structures similar to the lotus leaves. The Cu-based surface had a water contact angle of 157° with moss-like hierarchical micro-nano structures. Droplet condensation experiments were also performed on these two superhydrophobic surfaces to investigate their condensation characteristics. The results show that the Al-based superhydrophobic surface has lower droplet density, higher droplet jumping probability, slower droplet growth rate and lower surface coverage due to the more structured hierarchical structures.

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.

Rotational stellar structures based on the Lagrangian variational principle

NASA Astrophysics Data System (ADS)

Yasutake, Nobutoshi; Fujisawa, Kotaro; Yamada, Shoichi

2017-06-01

A new method for multi-dimensional stellar structures is proposed in this study. As for stellar evolution calculations, the Heney method is the defacto standard now, but basically assumed to be spherical symmetric. It is one of the difficulties for deformed stellar-evolution calculations to trace the potentially complex movements of each fluid element. On the other hand, our new method is very suitable to follow such movements, since it is based on the Lagrange coordinate. This scheme is also based on the variational principle, which is adopted to the studies for the pasta structures inside of neutron stars. Our scheme could be a major break through for evolution calculations of any types of deformed stars: proto-planets, proto-stars, and proto-neutron stars, etc.

Governance Structures for Open Innovation: A Preliminary Framework

NASA Astrophysics Data System (ADS)

Feller, Joseph; Finnegan, Patrick; Hayes, Jeremy; O'Reilly, Philip

This research-in-progress paper presents a preliminary framework of four open innovation governance structures. The study seeks to describe four distinct ways in which firms utilize hierarchical relationships, organizational intermediaries, and the market system to supply and acquire intellectual property and/or innovation capabilities from sources external to the firm. This paper reports on phase one of the study, which involved an analysis of six open innovation exemplars based on public data. This phase of the study reveals that governance structures for open innovation can be categorized based on whether they (1) are mediated or direct or (2) seek to acquire intellectual property or innovation capability. We analyze the differences in four governance structures along seven dimensions, and reveal the importance of knowledge dispersion and uncertainty to the use of open innovation hierarchies, brokerages, and markets. The paper concludes by examining the implications of the findings and outlining the next phase of the study.

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Coach simplified structure modeling and optimization study based on the PBM method

NASA Astrophysics Data System (ADS)

Zhang, Miaoli; Ren, Jindong; Yin, Ying; Du, Jian

2016-09-01

For the coach industry, rapid modeling and efficient optimization methods are desirable for structure modeling and optimization based on simplified structures, especially for use early in the concept phase and with capabilities of accurately expressing the mechanical properties of structure and with flexible section forms. However, the present dimension-based methods cannot easily meet these requirements. To achieve these goals, the property-based modeling (PBM) beam modeling method is studied based on the PBM theory and in conjunction with the characteristics of coach structure of taking beam as the main component. For a beam component of concrete length, its mechanical characteristics are primarily affected by the section properties. Four section parameters are adopted to describe the mechanical properties of a beam, including the section area, the principal moments of inertia about the two principal axles, and the torsion constant of the section. Based on the equivalent stiffness strategy, expressions for the above section parameters are derived, and the PBM beam element is implemented in HyperMesh software. A case is realized using this method, in which the structure of a passenger coach is simplified. The model precision is validated by comparing the basic performance of the total structure with that of the original structure, including the bending and torsion stiffness and the first-order bending and torsional modal frequencies. Sensitivity analysis is conducted to choose design variables. The optimal Latin hypercube experiment design is adopted to sample the test points, and polynomial response surfaces are used to fit these points. To improve the bending and torsion stiffness and the first-order torsional frequency and taking the allowable maximum stresses of the braking and left turning conditions as constraints, the multi-objective optimization of the structure is conducted using the NSGA-II genetic algorithm on the ISIGHT platform. The result of the Pareto solution set is acquired, and the selection strategy of the final solution is discussed. The case study demonstrates that the mechanical performances of the structure can be well-modeled and simulated by PBM beam. Because of the merits of fewer parameters and convenience of use, this method is suitable to be applied in the concept stage. Another merit is that the optimization results are the requirements for the mechanical performance of the beam section instead of those of the shape and dimensions, bringing flexibility to the succeeding design.

Thermostabilisation of membrane proteins for structural studies

PubMed Central

Magnani, Francesca; Serrano-Vega, Maria J.; Shibata, Yoko; Abdul-Hussein, Saba; Lebon, Guillaume; Miller-Gallacher, Jennifer; Singhal, Ankita; Strege, Annette; Thomas, Jennifer A.; Tate, Christopher G.

2017-01-01

The thermostability of an integral membrane protein in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals suitable for structure determination. However, many mammalian membrane proteins are too unstable for crystallisation. We developed a thermostabilisation strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes approximately 6-12 months to thermostabilise a G protein-coupled receptor (GPCR) containing 300 amino acid residues. The resulting thermostabilised membrane proteins are more easily crystallised and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs, because it is possible to determine multiple structures of the thermostabilised receptors bound to low affinity ligands. Protocols and advice are given on how to develop thermostability assays for membrane proteins and how to combine mutations to make an optimally stable mutant suitable for structural studies. PMID:27466713

High pressure structural behavior of YGa2: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Sekar, M.; Shekar, N. V. Chandra; Babu, R.; Sahu, P. Ch.; Sinha, A. K.; Upadhyay, Anuj; Singh, M. N.; Babu, K. Ramesh; Appalakondaiah, S.; Vaitheeswaran, G.; Kanchana, V.

2015-03-01

High pressure structural stability studies were carried out on YGa2 (AlB2 type structure at NTP, space group P6/mmm) up to a pressure of 35 GPa using both laboratory based rotating anode and synchrotron X-ray sources. An isostructural transition with reduced c/a ratio, was observed at 6 GPa and above 17.5 GPa, the compound transformed to orthorhombic structure. Bulk modulus B0 for the parent and high pressure phases were estimated using Birch-Murnaghan and modified Birch-Murnaghan equation of state. Electronic structure calculations based on projector augmented wave method confirms the experimentally observed two high pressure structural transitions. The calculations also reveal that the 'Ga' networks remains as two dimensional in the high pressure isostructural phase, whereas the orthorhombic phase involves three dimensional networks of 'Ga' atoms interconnected by strong covalent bonds.

Efficient community-based control strategies in adaptive networks

NASA Astrophysics Data System (ADS)

Yang, Hui; Tang, Ming; Zhang, Hai-Feng

2012-12-01

Most studies on adaptive networks concentrate on the properties of steady state, but neglect transient dynamics. In this study, we pay attention to the emergence of community structure in the transient process and the effects of community-based control strategies on epidemic spreading. First, by normalizing the modularity, we investigate the evolution of community structure during the transient process, and find that a strong community structure is induced by the rewiring mechanism in the early stage of epidemic dynamics, which, remarkably, delays the outbreak of disease. We then study the effects of control strategies started at different stages on the prevalence. Both immunization and quarantine strategies indicate that it is not ‘the earlier, the better’ for the implementation of control measures. And the optimal control effect is obtained if control measures can be efficiently implemented in the period of a strong community structure. For the immunization strategy, immunizing the susceptible nodes on susceptible-infected links and immunizing susceptible nodes randomly have similar control effects. However, for the quarantine strategy, quarantining the infected nodes on susceptible-infected links can yield a far better result than quarantining infected nodes randomly. More significantly, the community-based quarantine strategy performs better than the community-based immunization strategy. This study may shed new light on the forecast and the prevention of epidemics among humans.

Single walled boron nitride nanotube-based biosensor: an atomistic finite element modelling approach.

PubMed

Panchal, Mitesh B; Upadhyay, Sanjay H

2014-09-01

The unprecedented dynamic characteristics of nanoelectromechanical systems make them suitable for nanoscale mass sensing applications. Owing to superior biocompatibility, boron nitride nanotubes (BNNTs) are being increasingly used for such applications. In this study, the feasibility of single walled BNNT (SWBNNT)-based bio-sensor has been explored. Molecular structural mechanics-based finite element (FE) modelling approach has been used to analyse the dynamic behaviour of SWBNNT-based biosensors. The application of an SWBNNT-based mass sensing for zeptogram level of mass has been reported. Also, the effect of size of the nanotube in terms of length as well as different chiral atomic structures of SWBNNT has been analysed for their sensitivity analysis. The vibrational behaviour of SWBNNT has been analysed for higher-order modes of vibrations to identify the intermediate landing position of biological object of zeptogram scale. The present molecular structural mechanics-based FE modelling approach is found to be very effectual to incorporate different chiralities of the atomic structures. Also, different boundary conditions can be effectively simulated using the present approach to analyse the dynamic behaviour of the SWBNNT-based mass sensor. The presented study has explored the potential of SWBNNT, as a nanobiosensor having the capability of zeptogram level mass sensing.

Assessing the structure of non-routine decision processes in Airline Operations Control.

PubMed

Richters, Floor; Schraagen, Jan Maarten; Heerkens, Hans

2016-03-01

Unfamiliar severe disruptions challenge Airline Operations Control professionals most, as their expertise is stretched to its limits. This study has elicited the structure of Airline Operations Control professionals' decision process during unfamiliar disruptions by mapping three macrocognitive activities on the decision ladder: sensemaking, option evaluation and action planning. The relationship between this structure and decision quality was measured. A simulated task was staged, based on which think-aloud protocols were obtained. Results show that the general decision process structure resembles the structure of experts working under routine conditions, in terms of the general structure of the macrocognitive activities, and the rule-based approach used to identify options and actions. Surprisingly, high quality of decision outcomes was found to relate to the use of rule-based strategies. This implies that successful professionals are capable of dealing with unfamiliar problems by reframing them into familiar ones, rather than to engage in knowledge-based processing. Practitioner Summary: We examined the macrocognitive structure of Airline Operations Control professionals' decision process during a simulated unfamiliar disruption in relation to decision quality. Results suggest that successful professionals are capable of dealing with unfamiliar problems by reframing them into familiar ones, rather than to engage in knowledge-based processing.

Atom and receptor based 3D QSAR models for generating new conformations from pyrazolopyrimidine as IL-2 inducible tyrosine kinase inhibitors.

PubMed

Ul-Haq, Zaheer; Effendi, Juweria Shahrukh; Ashraf, Sajda; Bkhaitan, Majdi M

2017-06-01

In the current study, quantitative three-dimensional structure-activity-relationship (3D-QSAR) method was performed to design a model for new chemical entities by utilizing pyrazolopyrimidines. Their inhibiting activity on receptor IL-2 Itk correlates descriptors based on topology and hydrophobicity. The best model developed by ligand-based (atom-based) approach has correlation-coefficient of r 2 : 0.987 and cross-validated squared correlation-coefficient of q 2 : 0.541 with an external prediction capability of r 2 : 0.944. Whereas the best selected model developed by structured-based (receptor-based) approach has correlation-coefficient of r 2 : 0.987, cross-validated squared correlation-coefficient of q 2 : 0.637 with an external predictive ability of r 2 : 0.941. The statistical parameters prove that structure-based gave a better model to design new chemical scaffolds. The results achieved indicated that hydrophobicity at R 1 location play a vital role in the inhibitory activity and introduction of appropriately bulky and strongly hydrophobic-groups at position 3 of the terminal phenyl-group which is highly significant to enhance the activity. Six new pyrazolopyrimidine derivatives were designed. Docking simulation study was carried out and their inhibitory activity was predicted by the best structure based model with predictive activity of ranging from 8.43 to 8.85 log unit. The interacting residues PHE435, ASP500, LYS391, GLU436, MET438, CYS442, ILE369, VAL377 of PDB 4HCT were studied with respect to type of bonding with the new compounds. This study was aimed to search out more potent inhibitors of IL-2 Itk. Copyright © 2017 Elsevier Inc. All rights reserved.

Is better beautiful or is beautiful better? Exploring the relationship between beauty and category structure.

PubMed

Sanders, Megan; Davis, Tyler; Love, Bradley C

2013-06-01

We evaluate two competing accounts of the relationship between beauty and category structure. According to the similarity-based view, beauty arises from category structure such that central items are favored due to their increased fluency. In contrast, the theory-based view holds that people's theories of beauty shape their perceptions of categories. In the present study, subjects learned to categorize abstract paintings into meaningfully labeled categories and rated the paintings' beauty, value, and typicality. Inconsistent with the similarity-based view, beauty ratings were highly correlated across conditions despite differences in fluency and assigned category structure. Consistent with the theory-based view, beautiful paintings were treated as central members for categories expected to contain beautiful paintings (e.g., art museum pieces), but not in others (e.g., student show pieces). These results suggest that the beauty of complex, real-world stimuli is not determined by fluency within category structure but, instead, interacts with people's prior knowledge to structure categories.

Passive vibration control: a structure-immittance approach.

PubMed

Zhang, Sara Ying; Jiang, Jason Zheng; Neild, Simon A

2017-05-01

Linear passive vibration absorbers, such as tuned mass dampers, often contain springs, dampers and masses, although recently there has been a growing trend to employ or supplement the mass elements with inerters. When considering possible configurations with these elements broadly, two approaches are normally used: one structure-based and one immittance-based. Both approaches have their advantages and disadvantages. In this paper, a new approach is proposed: the structure-immittance approach. Using this approach, a full set of possible series-parallel networks with predetermined numbers of each element type can be represented by structural immittances, obtained via a proposed general formulation process. Using the structural immittances, both the ability to investigate a class of absorber possibilities together (advantage of the immittance-based approach), and the ability to control the complexity, topology and element values in resulting absorber configurations (advantages of the structure-based approach) are provided at the same time. The advantages of the proposed approach are demonstrated through two case studies on building vibration suppression and automotive suspension design, respectively.

Passive vibration control: a structure-immittance approach

NASA Astrophysics Data System (ADS)

Zhang, Sara Ying; Jiang, Jason Zheng; Neild, Simon A.

2017-05-01

Linear passive vibration absorbers, such as tuned mass dampers, often contain springs, dampers and masses, although recently there has been a growing trend to employ or supplement the mass elements with inerters. When considering possible configurations with these elements broadly, two approaches are normally used: one structure-based and one immittance-based. Both approaches have their advantages and disadvantages. In this paper, a new approach is proposed: the structure-immittance approach. Using this approach, a full set of possible series-parallel networks with predetermined numbers of each element type can be represented by structural immittances, obtained via a proposed general formulation process. Using the structural immittances, both the ability to investigate a class of absorber possibilities together (advantage of the immittance-based approach), and the ability to control the complexity, topology and element values in resulting absorber configurations (advantages of the structure-based approach) are provided at the same time. The advantages of the proposed approach are demonstrated through two case studies on building vibration suppression and automotive suspension design, respectively.

Structure–activity relationships study of mTOR kinase inhibition using QSAR and structure-based drug design approaches

PubMed Central

Lakhlili, Wiame; Yasri, Abdelaziz; Ibrahimi, Azeddine

2016-01-01

The discovery of clinically relevant inhibitors of mammalian target of rapamycin (mTOR) for anticancer therapy has proved to be a challenging task. The quantitative structure–activity relationship (QSAR) approach is a very useful and widespread technique for ligand-based drug design, which can be used to identify novel and potent mTOR inhibitors. In this study, we performed two-dimensional QSAR tests, and molecular docking validation tests of a series of mTOR ATP-competitive inhibitors to elucidate their structural properties associated with their activity. The QSAR tests were performed using partial least square method with a correlation coefficient of r2=0.799 and a cross-validation of q2=0.714. The chemical library screening was done by associating ligand-based to structure-based approach using the three-dimensional structure of mTOR developed by homology modeling. We were able to select 22 compounds from two databases as inhibitors of the mTOR kinase active site. We believe that the method and applications highlighted in this study will help future efforts toward the design of selective ATP-competitive inhibitors. PMID:27980424

Followers Are Not Enough: A Multifaceted Approach to Community Detection in Online Social Networks

PubMed Central

2015-01-01

In online social media networks, individuals often have hundreds or even thousands of connections, which link these users not only to friends, associates, and colleagues, but also to news outlets, celebrities, and organizations. In these complex social networks, a ‘community’ as studied in the social network literature, can have very different meaning depending on the property of the network under study. Taking into account the multifaceted nature of these networks, we claim that community detection in online social networks should also be multifaceted in order to capture all of the different and valuable viewpoints of ‘community.’ In this paper we focus on three types of communities beyond follower-based structural communities: activity-based, topic-based, and interaction-based. We analyze a Twitter dataset using three different weightings of the structural network meant to highlight these three community types, and then infer the communities associated with these weightings. We show that interesting insights can be obtained about the complex community structure present in social networks by studying when and how these four community types give rise to similar as well as completely distinct community structure. PMID:26267868

Problem-Based Learning and Structural Redesign in a Choral Methods Course

ERIC Educational Resources Information Center

Freer, Patrick

2017-01-01

This article describes the process of structural redesign of an undergraduate music education choral methods course. A framework incorporating Problem-based Learning was developed to promote individualized student learning. Ten students participated in the accompanying research study, contributing an array of written and spoken comments as well as…

Designing Digital Problem Based Learning Tasks that Motivate Students

ERIC Educational Resources Information Center

van Loon, Anne-Marieke; Ros, Anje; Martens, Rob

2013-01-01

This study examines whether teachers are able to apply the principles of autonomy support and structure support in designing digital problem based learning (PBL) tasks. We examine whether these tasks are more autonomy- and structure-supportive and whether primary and secondary school students experience greater autonomy, competence, and motivation…

Feminine Faces of Leadership: Beyond Structural-Functionalism?

ERIC Educational Resources Information Center

Fennell, Hope-Arlene

2008-01-01

Leadership continues to be a central focus for research in educational administration. Until recently, many studies about leadership have been based largely on the experiences of white males and interpreted based on the structural-functionalist perspective. In this paper the writer explores the phenomenon of leadership through the eyes and…

Experimental Study on Welded Headed Studs Used In Steel Plate-Concrete Composite Structures Compared with Contactless Method of Measuring Displacement

NASA Astrophysics Data System (ADS)

Kisała, Dawid; Tekieli, Marcin

2017-10-01

Steel plate-concrete composite structures are a new innovative design concept in which a thin steel plate is attached to the reinforced concrete beam by means of welded headed studs. The comparison between experimental studies and theoretical analysis of this type of structures shows that their behaviour is dependent on the load-slip relationship of the shear connectors used to ensure sufficient bond between the concrete and steel parts of the structure. The aim of this paper is to describe an experimental study on headed studs used in steel plate-concrete composite structures. Push-out tests were carried out to investigate the behaviour of shear connectors. The test specimens were prepared according to standard push-out tests, however, instead of I-beam, a steel plate 16 mm thick was used to better reflect the conditions in the real structure. The test specimens were produced in two batches using concrete with significantly different compressive strength. The experimental study was carried out on twelve specimens. Besides the traditional measurements based on LVDT sensors, optical measurements based on the digital image correlation method (DIC) and pattern tracking methods were used. DIC is a full-field contactless optical method for measuring displacements in experimental testing, based on the correlation of the digital images taken during test execution. With respect to conventional methods, optical measurements offer a wider scope of results and can give more information about the material or construction behaviour during the test. The ultimate load capacity and load-slip curves obtained from the experiments were compared with the values calculated based on Eurocodes, American and Chinese design specifications. It was observed that the use of the relationships developed for the traditional steel-concrete composite structures is justified in the case of ultimate load capacity of shear connectors in steel plate-concrete composite structures.

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: A search tool for RNA 3D substructures

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

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes

NASA Astrophysics Data System (ADS)

Kaushik, Aman C.; Kumar, Sanjay; Wei, Dong Q.; Sahi, Shakti

2018-02-01

GPR142 (G protein receptor 142) is a novel orphan GPCR (G protein coupled receptor) belonging to ‘Class A’ of GPCR family and expressed in beta cells of pancreas. In this study, we reported the structure based virtual screening to identify the hit compounds which can be developed as leads for potential agonists. The results were validated through induced fit docking, pharmacophore modeling and system biology approaches. Since, there is no solved crystal structure of GPR142, we attempted to predict the 3D structure followed by validation and then identification of active site using threading and ab initio methods. Also, structure based virtual screening was performed against a total of 1171519 compounds from different libraries and only top 20 best hit compounds were screened and analyzed. Moreover, the biochemical pathway of GPR142 complex with screened compound2 was also designed and compared with experimental data. Interestingly, compound2 showed an increase in insulin production via Gq mediated signaling pathway suggesting the possible role of novel GPR142 agonists in therapy against type 2 diabetes.

Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

NASA Astrophysics Data System (ADS)

Pasturel, Alain; Jakse, Noel

2017-08-01

With sufficiently high cooling rates, liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before solidifying. Studies of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify, it remains a major challenge to capture the underlying structural link to these phenomena. Ab initio molecular dynamics (AIMD) simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in experiments. Through the AIMD-based study of Cr additions in Al-based liquids, we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling regime. In addition, we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order (CSRO) and local fivefold topology (ISRO) at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order (IMRO) upon undercooling. Finally, our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

Modularity in protein structures: study on all-alpha proteins.

PubMed

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

Ab Initio -Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures

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

Cherukara, Mathew J.; Narayanan, Badri; Kinaci, Alper

2016-08-28

We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m;more » graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.« less

Performance evaluation of structure based and ligand based virtual screening methods on ten selected anti-cancer targets.

PubMed

Ramasamy, Thilagavathi; Selvam, Chelliah

2015-10-15

Virtual screening has become an important tool in drug discovery process. Structure based and ligand based approaches are generally used in virtual screening process. To date, several benchmark sets for evaluating the performance of the virtual screening tool are available. In this study, our aim is to compare the performance of both structure based and ligand based virtual screening methods. Ten anti-cancer targets and their corresponding benchmark sets from 'Demanding Evaluation Kits for Objective In silico Screening' (DEKOIS) library were selected. X-ray crystal structures of protein-ligand complexes were selected based on their resolution. Openeye tools such as FRED, vROCS were used and the results were carefully analyzed. At EF1%, vROCS produced better results but at EF5% and EF10%, both FRED and ROCS produced almost similar results. It was noticed that the enrichment factor values were decreased while going from EF1% to EF5% and EF10% in many cases. Published by Elsevier Ltd.

Assessing an ensemble docking-based virtual screening strategy for kinase targets by considering protein flexibility.

PubMed

Tian, Sheng; Sun, Huiyong; Pan, Peichen; Li, Dan; Zhen, Xuechu; Li, Youyong; Hou, Tingjun

2014-10-27

In this study, to accommodate receptor flexibility, based on multiple receptor conformations, a novel ensemble docking protocol was developed by using the naïve Bayesian classification technique, and it was evaluated in terms of the prediction accuracy of docking-based virtual screening (VS) of three important targets in the kinase family: ALK, CDK2, and VEGFR2. First, for each target, the representative crystal structures were selected by structural clustering, and the capability of molecular docking based on each representative structure to discriminate inhibitors from non-inhibitors was examined. Then, for each target, 50 ns molecular dynamics (MD) simulations were carried out to generate an ensemble of the conformations, and multiple representative structures/snapshots were extracted from each MD trajectory by structural clustering. On average, the representative crystal structures outperform the representative structures extracted from MD simulations in terms of the capabilities to separate inhibitors from non-inhibitors. Finally, by using the naïve Bayesian classification technique, an integrated VS strategy was developed to combine the prediction results of molecular docking based on different representative conformations chosen from crystal structures and MD trajectories. It was encouraging to observe that the integrated VS strategy yields better performance than the docking-based VS based on any single rigid conformation. This novel protocol may provide an improvement over existing strategies to search for more diverse and promising active compounds for a target of interest.

DNA Based Molecular Scale Nanofabrication

DTIC Science & Technology

2015-12-04

structure. We developed a method to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer...to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer substrates. Developed a high... imprinting using DNA nanostructure templates. Soft lithography uses polymeric stamps with certain features to transfer the pattern for printing

Review on pressure sensors for structural health monitoring

NASA Astrophysics Data System (ADS)

Sikarwar, Samiksha; Satyendra; Singh, Shakti; Yadav, Bal Chandra

2017-12-01

This paper reports the state of art in a variety of pressure and the detailed study of various matrix based pressure sensors. The performances of the bridges, buildings, etc. are threatened by earthquakes, material degradations, and other environmental effects. Structural health monitoring (SHM) is crucial to protect the people and also for assets planning. This study is a contribution in developing the knowledge about self-sensing smart materials and structures for the construction industry. It deals with the study of self-sensing as well as mechanical and electrical properties of different matrices based on pressure sensors. The relationships among the compression, tensile strain, and crack length with electrical resistance change are also reviewed.

Structural and magnetic studies of half-metallic Heusler alloy Cr2CoSi nanoparticle synthesized by mechanical-alloying method

NASA Astrophysics Data System (ADS)

Saravanan, G.; Asvini, V.; Kalaiezhily, R. K.; Ravichandran, K.

2018-05-01

Heusler Alloy based Cr2CoSi nanoparticles were synthesized by using ball milling. X-ray diffractions studies were used to characterize the crystal structure of Cr2CoSi nanoparticles and magnetic properties were studied using VSM. XRD data analysis confirms the Heusler alloy phase showing the L21 structure. Magnetic properties are measured for synthesized samples having coercivity Hc = 389 Oe, with high saturation magnetization value Ms = 8.64 emu/g and remenance value Mr = 2.93 emu/g. Synthesized Heusler alloy Cr2CoSi nanoparticles can be potential materials for use in Spin polarized based spin sensors, spin devices, magnetic sensors and transducer applications.

8-week Mindfulness Based Stress Reduction induces brain changes similar to traditional long-term meditation practice - A systematic review.

PubMed

Gotink, Rinske A; Meijboom, Rozanna; Vernooij, Meike W; Smits, Marion; Hunink, M G Myriam

2016-10-01

The objective of the current study was to systematically review the evidence of the effect of secular mindfulness techniques on function and structure of the brain. Based on areas known from traditional meditation neuroimaging results, we aimed to explore a neuronal explanation of the stress-reducing effects of the 8-week Mindfulness Based Stress Reduction (MBSR) and Mindfulness Based Cognitive Therapy (MBCT) program. We assessed the effect of MBSR and MBCT (N=11, all MBSR), components of the programs (N=15), and dispositional mindfulness (N=4) on brain function and/or structure as assessed by (functional) magnetic resonance imaging. 21 fMRI studies and seven MRI studies were included (two studies performed both). The prefrontal cortex, the cingulate cortex, the insula and the hippocampus showed increased activity, connectivity and volume in stressed, anxious and healthy participants. Additionally, the amygdala showed decreased functional activity, improved functional connectivity with the prefrontal cortex, and earlier deactivation after exposure to emotional stimuli. Demonstrable functional and structural changes in the prefrontal cortex, cingulate cortex, insula and hippocampus are similar to changes described in studies on traditional meditation practice. In addition, MBSR led to changes in the amygdala consistent with improved emotion regulation. These findings indicate that MBSR-induced emotional and behavioral changes are related to functional and structural changes in the brain. Copyright © 2016 Elsevier Inc. All rights reserved.

Photonic structures in diamond based on femtosecond UV laser induced periodic surface structuring (LIPSS).

PubMed

Granados, Eduardo; Martinez-Calderon, Miguel; Gomez, Mikel; Rodriguez, Ainara; Olaizola, Santiago M

2017-06-26

We study the fabrication of photonic surface structures in single crystal diamond by means of highly controllable direct femtosecond UV laser induced periodic surface structuring. By appropriately selecting the excitation wavelength, intensity, number of impinging pulses and their polarization state, we demonstrate emerging high quality and fidelity diamond grating structures with surface roughness below 1.4 nm. We characterize their optical properties and study their potential for the fabrication of photonic structure anti-reflection coatings for diamond Raman lasers in the near-IR.

Investigation into adamantane-based M2 inhibitors with FB-QSAR.

PubMed

Wei, Hang; Wang, Cheng-Hua; Du, Qi-Shi; Meng, Jianzong; Chou, Kuo-Chen

2009-07-01

Because of their high resistance rate to the existing drugs, influenza A viruses have become a threat to human beings. It is known that the replication of influenza A viruses needs a pH-gated proton channel, the so-called M2 channel. Therefore, to develop effective drugs against influenza A, the most logic strategy is to inhibit the M2 channel. Recently, the atomic structure of the M2 channel was determined by NMR spectroscopy (Schnell, J.R. and Chou, J.J., Nature, 2008, 451, 591-595). The high-resolution NMR structure has provided a solid basis for structure-based drug design approaches. In this study, a benchmark dataset has been constructed that contains 34 newly-developed adamantane-based M2 inhibitors and covers considerable structural diversities and wide range of bioactivities. Based on these compounds, an in-depth analysis was performed with the newly developed fragment-based quantitative structure-activity relationship (FB-QSAR) algorithm. The results thus obtained provide useful insights for dealing with the drug-resistant problem and designing effective adamantane-based antiflu drugs.

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.

Hard and soft acids and bases: structure and process.

PubMed

Reed, James L

2012-07-05

Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

Structural damage identification using damping: a compendium of uses and features

NASA Astrophysics Data System (ADS)

Cao, M. S.; Sha, G. G.; Gao, Y. F.; Ostachowicz, W.

2017-04-01

The vibration responses of structures under controlled or ambient excitation can be used to detect structural damage by correlating changes in structural dynamic properties extracted from responses with damage. Typical dynamic properties refer to modal parameters: natural frequencies, mode shapes, and damping. Among these parameters, natural frequencies and mode shapes have been investigated extensively for their use in damage characterization by associating damage with reduction in local stiffness of structures. In contrast, the use of damping as a dynamic property to represent structural damage has not been comprehensively elucidated, primarily due to the complexities of damping measurement and analysis. With advances in measurement technologies and analysis tools, the use of damping to identify damage is becoming a focus of increasing attention in the damage detection community. Recently, a number of studies have demonstrated that damping has greater sensitivity for characterizing damage than natural frequencies and mode shapes in various applications, but damping-based damage identification is still a research direction ‘in progress’ and is not yet well resolved. This situation calls for an overall survey of the state-of-the-art and the state-of-the-practice of using damping to detect structural damage. To this end, this study aims to provide a comprehensive survey of uses and features of applying damping in structural damage detection. First, we present various methods for damping estimation in different domains including the time domain, the frequency domain, and the time-frequency domain. Second, we investigate the features and applications of damping-based damage detection methods on the basis of two predominant infrastructure elements, reinforced concrete structures and fiber-reinforced composites. Third, we clarify the influential factors that can impair the capability of damping to characterize damage. Finally, we recommend future research directions for advancing damping-based damage detection. This work holds the promise of (a) helping researchers identify crucial components in damping-based damage detection theories, methods, and technologies, and (b) leading practitioners to better implement damping-based structural damage identification.

Modeling of InGaAsSb-Based Avalanche Photodetectors for 2-Micron Wavelengths

NASA Technical Reports Server (NTRS)

Joshi, Ravindra P.; Abedin, M. Nurul (Technical Monitor)

2002-01-01

The main focus of this research is to study and evaluate the potential of InGaAsSb-AlGaAsSb based 2 micron avalanche photo-detectors. The photodetector contains a separate absorption and multiplication region (SAM) structure. The analysis has mainly been done to understand the electrical response characteristics of the devices existing at NASA, and to evaluate alternate structures proposed. Calculating the current flow for the existing detector structure, on the basis of its energy band diagram, is important. This analysis also helps to find shortcomings in the existing detector structure. It is shown that, unfortunately, the existing structure cannot lead to strong multiplication or voltage dependent gain. Two alternate structures are suggested, that could overcome the inherent flaws, and help achieve improved performance. These devices are obtained through modifications of the original structure, which include varying the doping levels, and changing the thicknesses of detector sub-regions. The results of our study are presented and discussed.

Multilayer photosensitive structures based on porous silicon and rare-earth-element compounds: Study of spectral characteristics

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

Kirsanov, N. Yu.; Latukhina, N. V., E-mail: natalat@yandex.ru; Lizunkova, D. A.

2017-03-15

The spectral characteristics of the specular reflectance, photosensitivity, and photoluminescence (PL) of multilayer structures based on porous silicon with rare-earth-element (REE) ions are investigated. It is shown that the photosensitivity of these structures in the wavelength range of 0.4–1.0 μm is higher than in structures free of REEs. The structures with Er{sup 3+} ions exhibit a luminescence response at room temperature in the spectral range from 1.1 to 1.7 μm. The PL spectrum of the erbium impurity is characterized by a fine line structure, which is determined by the splitting of the {sup 4}I{sub 15/2} multiplet of the Er{sup 3+}more » ion. It is shown that the structures with a porous layer on the working surface have a much lower reflectance in the entire spectral range under study (0.2–1.0 μm).« less

Research on Aeroheating of Hypersonic Reentry Vehicle Base Flow Fields

NASA Astrophysics Data System (ADS)

Xuguo, Qin; Yongtao, Shui; Yonghai, Wang; Gang, Chen; Qiang, Li

2017-09-01

The structure of the base flow of a hypersonic reentry vehicle and the resulting base pressure and heat transfer have been studied by numerical study. The compressible Navier-Stokes equations are solved by the finite-volume method. SST k-ω turbulence model is used, and comparisons are made with flight test. Attention was focused on assessing the effects of angle of attack and Mach number. It was found that angle of attack can significantly alter the wake flow structure and reentry vehicle base pressure and heating distributions. The results of the simulation may provide a theoretical basis for the design of the thermal protection system of hypersonic reentry vehicles.

Validation of clay modeling as a learning tool for the periventricular structures of the human brain.

PubMed

Akle, Veronica; Peña-Silva, Ricardo A; Valencia, Diego M; Rincón-Perez, Carlos W

2018-03-01

Visualizing anatomical structures and functional processes in three dimensions (3D) are important skills for medical students. However, contemplating 3D structures mentally and interpreting biomedical images can be challenging. This study examines the impact of a new pedagogical approach to teaching neuroanatomy, specifically how building a 3D-model from oil-based modeling clay affects learners' understanding of periventricular structures of the brain among undergraduate medical students in Colombia. Students were provided with an instructional video before building the models of the structures, and thereafter took a computer-based quiz. They then brought their clay models to class where they answered questions about the structures via interactive response cards. Their knowledge of periventricular structures was assessed with a paper-based quiz. Afterward, a focus group was conducted and a survey was distributed to understand students' perceptions of the activity, as well as the impact of the intervention on their understanding of anatomical structures in 3D. Quiz scores of students that constructed the models were significantly higher than those taught the material in a more traditional manner (P < 0.05). Moreover, the modeling activity reduced time spent studying the topic and increased understanding of spatial relationships between structures in the brain. The results demonstrated a significant difference between genders in their self-perception of their ability to contemplate and rotate structures mentally (P < 0.05). The study demonstrated that the construction of 3D clay models in combination with autonomous learning activities was a valuable and efficient learning tool in the anatomy course, and that additional models could be designed to promote deeper learning of other neuroanatomy topics. Anat Sci Educ 11: 137-145. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

The Utility of Magnetic Resonance Imaging in Assessing Patients With Pituitary Tumors Compressing the Anterior Visual Pathway.

PubMed

Ryu, Won Hyung A; Starreveld, Yves; Burton, Jodie M; Liu, Junjie; Costello, Fiona

2017-09-01

Pituitary tumors are one of the most common types of intracranial neoplasms, and can cause progressive visual loss. An ongoing challenge in the management of patients with pituitary tumors is the cost, availability, and reliability of current magnetic resonance imaging (MRI) techniques to capture clinically significant incremental tumor growth. The purpose of this study was to evaluate the various MRI-based structural analyses and to explore the relationship between measures of structure and function in the afferent visual pathway of patients with pituitary tumors. We performed a critical review of literature on MRI-based structural analyses of pituitary adenomas using PubMed, Embase, Cochrane Library, and Google Scholar. In addition, preoperative structural characteristics of the optic apparatus, optic nerve compression, and optic chiasm elevation identified as important in the literature review, were examined in 18 of our patients from October 2010 to January 2014. In our review of literature, a total of 443 citations were obtained from our search strategy and review of bibliographies. Eight of these studies met inclusion/exclusion criteria and were retrieved for critical review. Of the 8 included studies, only 2 studies examined the relationship between MRI-based structural measurements and postoperative visual recovery. In our small case-series, MRI analysis of chiasm elevation, severity of optic nerve compression, chiasm position, height of chiasm, tumor height, and tumor volume failed to differentiate patients with postoperative visual dysfunction vs those with visual recovery (P > 0.05). Although MRI-based structural analysis is an important and useful tool for managing patients with pituitary tumors, there are limited objective measures shown to be predictive of postoperative visual recovery.

Characterization of the Microchemical Structure of Seed Endosperm within a Cellular Dimension among Six Barley Varieties with Distinct Degradation Kinetics, Using Ultraspatially Resolved Synchrotron-Based Infrared Synchrotron-Based Infrared

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

Liu, N.; Yu, P

2010-01-01

Barley varieties have similar chemical composition but exhibit different rumen degradation kinetics and nutrient availability. These biological differences may be related to molecular, structural, and chemical makeup among the seed endosperm tissue. No detailed study was carried out. The objectives of this study were: (1) to use a molecular spectroscopy technique, synchrotron-based Fourier transform infrared microspectroscopy (SFTIRM), to determine the microchemical-structural features in seed endosperm tissue of six developed barley varieties; (2) to study the relationship among molecular-structural characteristics, degradation kinetics, and nutrient availability in six genotypes of barley. The results showed that inherent microchemical-structural differences in the endosperm amongmore » the six barley varieties were detected by the synchrotron-based analytical technique, SFTIRM, with the univariate molecular spectral analysis. The SFTIRM spectral profiles differed (P < 0.05) among the barley samples in terms of the peak ratio and peak area and height intensities of amides I (ca. 1650 cm{sup -1}) and II (ca. 1550 cm{sup -1}), cellulosic compounds (ca. 1240 cm{sup -1}), CHO component peaks (the first peak at the region ca. 1184-1132 cm{sup -1}, the second peak at ca. 1132-1066 cm{sup -1}, and the third peak at ca. 1066-950 cm{sup -1}). With the SFTIRM technique, the structural characteristics of the cereal seeds were illuminated among different cultivars at an ultraspatial resolution. The structural differences of barley seeds may be one reason for the various digestive behaviors and nutritive values in ruminants. The results show weak correlations between the functional groups spectral data (peak area, height intensities, and ratios) and rumen biodegradation kinetics (rate and extent of nutrient degradation). Weak correlations may indicate that limited variations of these six barley varieties might not be sufficient to interpret the relationship between spectroscopic information and the nutrient value of barley grain, although significant differences in biodegradation kinetics were observed. In conclusion, the studies demonstrated the potential of ultraspatially resolved synchrotron based technology (SFTIRM) to reveal the structural and chemical makeup within cellular and subcellular dimensions without destruction of the inherent structure of cereal grain tissue.« less

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions.

PubMed

Li, Yang; Yang, Jianyi

2017-04-24

The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBbind 2007 database, which is significantly higher than the performance of any conventional scoring function on the same benchmark. A few studies have been made to discuss the performance of machine-learning-based methods, but the reason for this improvement remains unclear. In this study, by systemically controlling the structural and sequence similarity between the training and test proteins of the PDBbind benchmark, we demonstrate that protein structural and sequence similarity makes a significant impact on machine-learning-based methods. After removal of training proteins that are highly similar to the test proteins identified by structure alignment and sequence alignment, machine-learning-based methods trained on the new training sets do not outperform the conventional scoring functions any more. On the contrary, the performance of conventional functions like X-Score is relatively stable no matter what training data are used to fit the weights of its energy terms.

Structure Modulates Similarity-Based Interference in Sluicing: An Eye Tracking study

PubMed Central

Harris, Jesse A.

2015-01-01

In cue-based content-addressable approaches to memory, a target and its competitors are retrieved in parallel from memory via a fast, associative cue-matching procedure under a severely limited focus of attention. Such a parallel matching procedure could in principle ignore the serial order or hierarchical structure characteristic of linguistic relations. I present an eye tracking while reading experiment that investigates whether the sentential position of a potential antecedent modulates the strength of similarity-based interference, a well-studied effect in which increased similarity in features between a target and its competitors results in slower and less accurate retrieval overall. The manipulation trades on an independently established Locality bias in sluiced structures to associate a wh-remnant (which ones) in clausal ellipsis with the most local correlate (some wines), as in The tourists enjoyed some wines, but I don't know which ones. The findings generally support cue-based parsing models of sentence processing that are subject to similarity-based interference in retrieval, and provide additional support to the growing body of evidence that retrieval is sensitive to both the structural position of a target antecedent and its competitors, and the specificity or diagnosticity of retrieval cues. PMID:26733893

A Confirmatory Factor Analysis of the Student Evidence-Based Practice Questionnaire (S-EBPQ) in an Australian sample.

PubMed

Beccaria, Lisa; Beccaria, Gavin; McCosker, Catherine

2018-03-01

It is crucial that nursing students develop skills and confidence in using Evidence-Based Practice principles early in their education. This should be assessed with valid tools however, to date, few measures have been developed and applied to the student population. To examine the structural validity of the Student Evidence-Based Practice Questionnaire (S-EBPQ), with an Australian online nursing student cohort. A cross-sectional study for constructing validity. Three hundred and forty-five undergraduate nursing students from an Australian regional university were recruited across two semesters. Confirmatory Factor Analysis was used to examine the structural validity. Confirmatory Factor Analysis was applied which resulted in a good fitting model, based on a revised 20-item tool. The S-EBPQ tool remains a psychometrically robust measure of evidence-based practice use, attitudes, and knowledge and skills and can be applied in an online Australian student context. The findings of this study provided further evidence of the reliability and four factor structure of the S-EBPQ. Opportunities for further refinement of the tool may result in improvements in structural validity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integration of ligand and structure based approaches for identification of novel MbtI inhibitors in Mycobacterium tuberculosis and molecular dynamics simulation studies.

PubMed

Maganti, Lakshmi; Grandhi, Pradeep; Ghoshal, Nanda

2016-11-01

Mycobacterium tuberculosis is an obligate pathogen of mammals and is responsible for more than two million deaths annually. The ability to acquire iron from the extracellular environment is a key determinant of pathogenicity in mycobacteria. M. tuberculosis acquires iron exclusively through the siderophores. Several lines of evidence suggest that siderophores have a critical role in bacterial growth and virulence. Hence, in the present study, we have used a combined ligand and structure-based drug design approach for identification of novel inhibitors against salicylate synthase MbtI, a unique and essential enzyme for the biosynthesis of siderophores in M. tuberculosis. We have generated the ligand based and structure based pharmacophores and validated exhaustively. From the validation results it was found that GH (Goodness of Hit) scores for the selected ligand based and structure based pharmacophore models were 0.89 and 0.97, respectively, which indicate that the quality of the pharmacophore models are acceptable as GH value is >0.7. The validated pharmacophores were used for screening the ZINC database. A total of 73 hits, obtained through various insilico screening techniques, were further enriched to 17 hits using docking studies. Molecular dynamics simulations were carried out to compare the binding mode and stability of complexes of MbtI bound with substrate, known inhibitors, and three top ranked hits. The results obtained in this study gave assurance about the identified hits as prospective inhibitors of MbtI. Copyright © 2016 Elsevier Inc. All rights reserved.

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Structural evolution of 2D microporous covalent triazine-based framework toward the study of high-performance supercapacitors.

PubMed

Hao, Long; Ning, Jing; Luo, Bin; Wang, Bin; Zhang, Yunbo; Tang, Zhihong; Yang, Junhe; Thomas, Arne; Zhi, Linjie

2015-01-14

A series of nitrogen-containing micropore-donimated materials, porous triazine-based frameworks (PTFs), are constructed through the structural evolution of a 2D microporous covalent triazine-based framework. The PTFs feature predictable and controllable nitrogen doping and pore structures, which serve as a model-like system to more deeply understand the heteroatom effect and micropore effect in ionic liquid-based supercapacitors. The experimental results reveal that the nitrogen doping can enhance the supercapacitor performance mainly through affecting the relative permittivity of the electrode materials. Although microspores' contribution is not as obvious as the doped nitrogen, the great performances of the micropore-dominated PTF suggest that micropore-dominated materials still have great potential in ionic liquid-based supercapacitors.

Using the [beta][subscript 2]-Adrenoceptor for Structure-Based Drug Design

ERIC Educational Resources Information Center

Manallack, David T.; Chalmers, David K.; Yuriev, Elizabeth

2010-01-01

The topics of molecular modeling and drug design are studied in a medicinal chemistry course. The recently reported structures of several G protein-coupled receptors (GPCR) with bound ligands have been used to develop a simple computer-based experiment employing molecular-modeling software. Knowledge of the specific interactions between a ligand…

Teaching Language Learners to Elaborate on Their Responses: A Structured, Genre-Based Approach

ERIC Educational Resources Information Center

Pryde, Michael

2015-01-01

Due to Japanese students' poor record of conversational ability in English in homestay contexts (Pryde, 2014), classroom English language curriculum decisions were reinvestigated in order to better prepare students to participate in study abroad experiences. A genre-based approach was used to teach and reinforce a conversational structure designed…

Incidental and Context-Responsive Activation of Structure- and Function-Based Action Features during Object Identification

ERIC Educational Resources Information Center

Lee, Chia-lin; Middleton, Erica; Mirman, Daniel; Kalenine, Solene; Buxbaum, Laurel J.

2013-01-01

Previous studies suggest that action representations are activated during object processing, even when task-irrelevant. In addition, there is evidence that lexical-semantic context may affect such activation during object processing. Finally, prior work from our laboratory and others indicates that function-based ("use") and structure-based…

Detangling the Interrelationships between Self- Regulation and Ill-Structured Problem Solving in Problem-Based Learning

ERIC Educational Resources Information Center

Ge, Xun; Law, Victor; Huang, Kun

2016-01-01

One of the goals for problem-based learning (PBL) is to promote self-regulation. Although self-regulation has been studied extensively, its interrelationships with ill-structured problem solving have been unclear. In order to clarify the interrelationships, this article proposes a conceptual framework illustrating the iterative processes among…

A Method to Examine Content Domain Structures

ERIC Educational Resources Information Center

D'Agostino, Jerome; Karpinski, Aryn; Welsh, Megan

2011-01-01

After a test is developed, most content validation analyses shift from ascertaining domain definition to studying domain representation and relevance because the domain is assumed to be set once a test exists. We present an approach that allows for the examination of alternative domain structures based on extant test items. In our example based on…

Electric field responsive origami structures using electrostriction-based active materials

NASA Astrophysics Data System (ADS)

Ahmed, Saad; Arrojado, Erika; Sigamani, Nirmal; Ounaies, Zoubeida

2015-04-01

The objective of origami engineering is to combine origami principles with advanced materials to yield active origami shapes, which fold and unfold in response to external stimuli. We are investigating the use of P(VDF-TrFE-CTFE), a relaxor ferroelectric terpolymer, to realize origami-inspired folding and unfolding of structures and to actuate so-called action origami structures. To accomplish these two objectives, we have explored different approaches to the P(VDF-TrFECTFE) polymer actuator construction, ranging from unimorph to multilayered stacks. Electromechanical characterization of the terpolymer-based actuators is conducted with a focus on free strain, force-displacement and blocked force. Moreover dynamic thickness strains of P(VDF-TrFE-CTFE) terpolymer at different frequencies ranging from 0.1Hz to 10Hz is also measured. Quantifying the performance of terpolymer-based actuators is important to the design of action origami structures. Following these studies, action origami prototypes based on catapult, flapping butterfly wings and barking fox are actuated and characterization of these prototypes are conducted by studying impact of various parameters such as electric field magnitude and frequency, number of active layers, and actuator dimensions.

Incidental and context-responsive activation of structure- and function-based action features during object identification

PubMed Central

Lee, Chia-lin; Middleton, Erica; Mirman, Daniel; Kalénine, Solène; Buxbaum, Laurel J.

2012-01-01

Previous studies suggest that action representations are activated during object processing, even when task-irrelevant. In addition, there is evidence that lexical-semantic context may affect such activation during object processing. Finally, prior work from our laboratory and others indicates that function-based (“use”) and structure-based (“move”) action subtypes may differ in their activation characteristics. Most studies assessing such effects, however, have required manual object-relevant motor responses, thereby plausibly influencing the activation of action representations. The present work utilizes eyetracking and a Visual World Paradigm task without object-relevant actions to assess the time course of activation of action representations, as well as their responsiveness to lexical-semantic context. In two experiments, participants heard a target word and selected its referent from an array of four objects. Gaze fixations on non-target objects signal activation of features shared between targets and non-targets. The experiments assessed activation of structure-based (Experiment 1) or function-based (Experiment 2) distractors, using neutral sentences (“S/he saw the …”) or sentences with a relevant action verb (Experiment 1: “S/he picked up the……”; Experiment 2: “S/he used the….”). We observed task-irrelevant activations of action information in both experiments. In neutral contexts, structure-based activation was relatively faster-rising but more transient than function-based activation. Additionally, action verb contexts reliably modified patterns of activation in both Experiments. These data provide fine-grained information about the dynamics of activation of function-based and structure-based actions in neutral and action-relevant contexts, in support of the “Two Action System” model of object and action processing (e.g., Buxbaum & Kalénine, 2010). PMID:22390294

Field Measurement-Based System Identification and Dynamic Response Prediction of a Unique MIT Building.

PubMed

Cha, Young-Jin; Trocha, Peter; Büyüköztürk, Oral

2016-07-01

Tall buildings are ubiquitous in major cities and house the homes and workplaces of many individuals. However, relatively few studies have been carried out to study the dynamic characteristics of tall buildings based on field measurements. In this paper, the dynamic behavior of the Green Building, a unique 21-story tall structure located on the campus of the Massachusetts Institute of Technology (MIT, Cambridge, MA, USA), was characterized and modeled as a simplified lumped-mass beam model (SLMM), using data from a network of accelerometers. The accelerometer network was used to record structural responses due to ambient vibrations, blast loading, and the October 16th 2012 earthquake near Hollis Center (ME, USA). Spectral and signal coherence analysis of the collected data was used to identify natural frequencies, modes, foundation rocking behavior, and structural asymmetries. A relation between foundation rocking and structural natural frequencies was also found. Natural frequencies and structural acceleration from the field measurements were compared with those predicted by the SLMM which was updated by inverse solving based on advanced multiobjective optimization methods using the measured structural responses and found to have good agreement.

Field Measurement-Based System Identification and Dynamic Response Prediction of a Unique MIT Building

PubMed Central

Cha, Young-Jin; Trocha, Peter; Büyüköztürk, Oral

2016-01-01

Tall buildings are ubiquitous in major cities and house the homes and workplaces of many individuals. However, relatively few studies have been carried out to study the dynamic characteristics of tall buildings based on field measurements. In this paper, the dynamic behavior of the Green Building, a unique 21-story tall structure located on the campus of the Massachusetts Institute of Technology (MIT, Cambridge, MA, USA), was characterized and modeled as a simplified lumped-mass beam model (SLMM), using data from a network of accelerometers. The accelerometer network was used to record structural responses due to ambient vibrations, blast loading, and the October 16th 2012 earthquake near Hollis Center (ME, USA). Spectral and signal coherence analysis of the collected data was used to identify natural frequencies, modes, foundation rocking behavior, and structural asymmetries. A relation between foundation rocking and structural natural frequencies was also found. Natural frequencies and structural acceleration from the field measurements were compared with those predicted by the SLMM which was updated by inverse solving based on advanced multiobjective optimization methods using the measured structural responses and found to have good agreement. PMID:27376303

X-ray and cryo-EM structures of inhibitor-bound cytochrome bc 1 complexes for structure-based drug discovery

PubMed Central

Amporndanai, Kangsa; O’Neill, Paul M.

2018-01-01

Cytochrome bc 1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc 1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes. PMID:29765610

Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

PubMed

Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

2015-02-25

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. Copyright © 2014 Elsevier B.V. All rights reserved.

Palladium and platinum based solid and hollow nanoparticles: An ab-initio study of structural and electronic properties

NASA Astrophysics Data System (ADS)

Yildizhan, Gulsum; Caliskan, Serkan; Ozturk, Ramazan

2018-04-01

Nanoparticles composed of palladium and platinum are particularly interesting for catalytic purposes, for instance, selective hydrogenation and alcohol oxidation. The reactivity and selectivity of nanostructures are mostly based on the size and shape of the nanocrystals in catalytic reactions. In this work, we studied the structural stabilities of Pd and Pt based nanocubes and nanocages and adsorption strength of chemisorbed species on these nanostructures to investigate their structure dependent catalytic activities. Solid cubic and hollow cage like nanostructures of different sizes were designed with Pd and Pt atoms. The volume of the crystal cavity in nanocage structures was tuned by removing of atoms from solid cubic structure. The effect of size and shape on the formation energies and HOMO-LUMO energy gap of nanostructures were elucidated and correlated to structural stabilities, hardness-softness, electronegativity and electrophilicity index. The relationship between size and chemical reactivity clearly showed that increasing the number of atoms participating in a catalyst enhances the activity. For further understanding of the catalytic activity we employed 4-nitro thiophenol, as an S-donor representative molecule, to evaluate the adsorption characteristics of the nanostructures.

An implemented method of asymmetric transmission for arbitrary polarization base in multi-layered chiral meta-surface

NASA Astrophysics Data System (ADS)

Xiao, Zhong-yin; Zou, Huan-ling; Xu, Kai-Kai; Tang, Jing-yao

2018-03-01

Asymmetric transmission of linearly or circularly polarized waves is a well-established property not only for three-layered chiral structures but for multi-layered ones. Here we show a method which can simultaneously implement asymmetric transmission for arbitrary base vector polarized wave in multi-layered chiral meta-surface. We systematically study the implemented method based on a multi-layered chiral structure consisting of a y-shape, a half gammadion and an S-shape in the terahertz gap. A numerical simulation was carried out, followed by an explanation of the asymmetric transmission mechanism in these structures proposed in this work. The simulated results indicate that the multi-layered chiral structure can realize a maximum asymmetric transmission of 0.89 and 0.28 for circularly and linearly polarized waves, respectively, which exhibit magnitude improvement over previous chiral metamaterials. Specifically, the maximum asymmetric transmitted coefficient of the multi-layered chiral structure is insensitivity to the incident angles from 0° to 45° for circularly polarized components. Additionally, we also study the influence of structural parameters on the asymmetric transmission effect for both linearly and circularly polarized waves in detail.

Structure- and ligand-based structure-activity relationships for a series of inhibitors of aldolase.

PubMed

Ferreira, Leonardo G; Andricopulo, Adriano D

2012-12-01

Aldolase has emerged as a promising molecular target for the treatment of human African trypanosomiasis. Over the last years, due to the increasing number of patients infected with Trypanosoma brucei, there is an urgent need for new drugs to treat this neglected disease. In the present study, two-dimensional fragment-based quantitative-structure activity relationship (QSAR) models were generated for a series of inhibitors of aldolase. Through the application of leave-one-out and leave-many-out cross-validation procedures, significant correlation coefficients were obtained (r²=0.98 and q²=0.77) as an indication of the statistical internal and external consistency of the models. The best model was employed to predict pKi values for a series of test set compounds, and the predicted values were in good agreement with the experimental results, showing the power of the model for untested compounds. Moreover, structure-based molecular modeling studies were performed to investigate the binding mode of the inhibitors in the active site of the parasitic target enzyme. The structural and QSAR results provided useful molecular information for the design of new aldolase inhibitors within this structural class.

Nonlinear finite element model updating for damage identification of civil structures using batch Bayesian estimation

NASA Astrophysics Data System (ADS)

Ebrahimian, Hamed; Astroza, Rodrigo; Conte, Joel P.; de Callafon, Raymond A.

2017-02-01

This paper presents a framework for structural health monitoring (SHM) and damage identification of civil structures. This framework integrates advanced mechanics-based nonlinear finite element (FE) modeling and analysis techniques with a batch Bayesian estimation approach to estimate time-invariant model parameters used in the FE model of the structure of interest. The framework uses input excitation and dynamic response of the structure and updates a nonlinear FE model of the structure to minimize the discrepancies between predicted and measured response time histories. The updated FE model can then be interrogated to detect, localize, classify, and quantify the state of damage and predict the remaining useful life of the structure. As opposed to recursive estimation methods, in the batch Bayesian estimation approach, the entire time history of the input excitation and output response of the structure are used as a batch of data to estimate the FE model parameters through a number of iterations. In the case of non-informative prior, the batch Bayesian method leads to an extended maximum likelihood (ML) estimation method to estimate jointly time-invariant model parameters and the measurement noise amplitude. The extended ML estimation problem is solved efficiently using a gradient-based interior-point optimization algorithm. Gradient-based optimization algorithms require the FE response sensitivities with respect to the model parameters to be identified. The FE response sensitivities are computed accurately and efficiently using the direct differentiation method (DDM). The estimation uncertainties are evaluated based on the Cramer-Rao lower bound (CRLB) theorem by computing the exact Fisher Information matrix using the FE response sensitivities with respect to the model parameters. The accuracy of the proposed uncertainty quantification approach is verified using a sampling approach based on the unscented transformation. Two validation studies, based on realistic structural FE models of a bridge pier and a moment resisting steel frame, are performed to validate the performance and accuracy of the presented nonlinear FE model updating approach and demonstrate its application to SHM. These validation studies show the excellent performance of the proposed framework for SHM and damage identification even in the presence of high measurement noise and/or way-out initial estimates of the model parameters. Furthermore, the detrimental effects of the input measurement noise on the performance of the proposed framework are illustrated and quantified through one of the validation studies.

A study of GaN-based LED structure etching using inductively coupled plasma

NASA Astrophysics Data System (ADS)

Wang, Pei; Cao, Bin; Gan, Zhiyin; Liu, Sheng

2011-02-01

GaN as a wide band gap semiconductor has been employed to fabricate optoelectronic devices such as light-emitting diodes (LEDs) and laser diodes (LDs). Recently several different dry etching techniques for GaN-based materials have been developed. ICP etching is attractive because of its superior plasma uniformity and strong controllability. Most previous reports emphasized on the ICP etching characteristics of single GaN film. In this study dry etching of GaN-based LED structure was performed by inductively coupled plasmas (ICP) etching with Cl2 as the base gas and BCl3 as the additive gas. The effects of the key process parameters such as etching gases flow rate, ICP power, RF power and chamber pressure on the etching properties of GaN-based LED structure including etching rate, selectivity, etched surface morphology and sidewall was investigated. Etch depths were measured using a depth profilometer and used to calculate the etch rates. The etch profiles were observed with a scanning electron microscope (SEM).

X-ray crystal structure and theoretical study of a new dinuclear Cu(II) complex with two different geometry centers bridged with an oxo group

NASA Astrophysics Data System (ADS)

Golbedaghi, Reza; Azimi, Saeid; Molaei, Atefeh; Hatami, Masoud; Notash, Behrouz

2017-10-01

A new Schiff base ligand HL, 1,3-bis(2-((Z)-(2-aminoethylimino)methyl)phenoxy)ethylene di amine, has been synthesized from the reaction of a new aldehyde and ethylenediamine. After preparation the Schiff base, a new dinuclear Cu(II) complex with two different geometry for each metal ion was synthesized. Single crystal X-ray structure analysis of the complex Cu(II) showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. The crystal structure studying shows, a perchlorate ion has been coordinated to the two Cu(II) metal centers as bridged and another perchlorate coordinated to the one of Cu(II) ion as terminal. However, two interesting structures square pyramidal and distorted octahedral Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, we had a theoretical study to have a comparison of experimental and theoretical results we determined the HOMO and LUMO orbitals.

On the structural context and identification of enzyme catalytic residues.

PubMed

Chien, Yu-Tung; Huang, Shao-Wei

2013-01-01

Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

A study of concept-based similarity approaches for recommending program examples

NASA Astrophysics Data System (ADS)

Hosseini, Roya; Brusilovsky, Peter

2017-07-01

This paper investigates a range of concept-based example recommendation approaches that we developed to provide example-based problem-solving support in the domain of programming. The goal of these approaches is to offer students a set of most relevant remedial examples when they have trouble solving a code comprehension problem where students examine a program code to determine its output or the final value of a variable. In this paper, we use the ideas of semantic-level similarity-based linking developed in the area of intelligent hypertext to generate examples for the given problem. To determine the best-performing approach, we explored two groups of similarity approaches for selecting examples: non-structural approaches focusing on examples that are similar to the problem in terms of concept coverage and structural approaches focusing on examples that are similar to the problem by the structure of the content. We also explored the value of personalized example recommendation based on student's knowledge levels and learning goal of the exercise. The paper presents concept-based similarity approaches that we developed, explains the data collection studies and reports the result of comparative analysis. The results of our analysis showed better ranking performance of the personalized structural variant of cosine similarity approach.

Visualization and manipulating the image of a formal data structure (FDS)-based database

NASA Astrophysics Data System (ADS)

Verdiesen, Franc; de Hoop, Sylvia; Molenaar, Martien

1994-08-01

A vector map is a terrain representation with a vector-structured geometry. Molenaar formulated an object-oriented formal data structure for 3D single valued vector maps. This FDS is implemented in a database (Oracle). In this study we describe a methodology for visualizing a FDS-based database and manipulating the image. A data set retrieved by querying the database is converted into an import file for a drawing application. An objective of this study is that an end-user can alter and add terrain objects in the image. The drawing application creates an export file, that is compared with the import file. Differences between these files result in updating the database which involves checks on consistency. In this study Autocad is used for visualizing and manipulating the image of the data set. A computer program has been written for the data exchange and conversion between Oracle and Autocad. The data structure of the FDS is compared to the data structure of Autocad and the data of the FDS is converted into the structure of Autocad equal to the FDS.

Development and application of induced-strain actuators for building structures

NASA Astrophysics Data System (ADS)

Morita, Koichi; Fujita, Takafumi; Ise, Shiro; Kawaguchi, Ken-ichi; Kamada, Takayoshi; Fujitani, Hideo

2001-07-01

Induced strain actuator (ISA) can change their own shapes according to external electric/magnetic fields, and vice versa. Recently these materials have been widely used for the small/precision. The objectives in this study are to develop smart members for building and to realize the smart, comfortable and safe structures. The research items are 1) Semi-active isolation of structures using piezoelectric actuator, 2) Using ISA as sensor materials and 3) Improvement of Acoustic Environment. Semi-active base isolation system with controllable friction damper using piezoelectric actuators is proposed. Simulation study was carried out, and by semi-active isolation, it could be realized to reduce response displacement of the structure to 50% of values of the passive isolation. ISA materials can act as sensors because they cause change of electric or magnetic fields under deformation. PVDF sensors are suitable for membrane structures. We evaluate performance of PVDF sensors for membrane structures by experiment. Polymer based ISA films or distributed ISA devices can control vibration mode of plane members. Applications to music halls or dwelling partition walls are expected. Results of experimental studies of noise control are discussed.

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.

PubMed

Li, Haiou; Lyu, Qiang; Cheng, Jianlin

2016-12-01

Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search. 3DRobot (a program that automatically generates diverse and well-packed protein structure decoys) was used to generate initial decoy models for the target from the templates. A stacked denoising autoencoder was trained on the decoys to obtain a deep learning model for the target protein. The trained deep model was then used to reconstruct the final structural model for the target sequence. With target proteins that have highly similar template proteins as benchmarks, the GDT-TS score of the predicted structures is greater than 0.7, suggesting that the deep autoencoder is a promising method for protein structure reconstruction.

Spinous TiO₂ and Au@TiO₂ octahedral nanocages: amorphisity-to-crystallinity transition-driven surface structural construction and photocatalytic study.

PubMed

Li, Jie; Zu, Lianhai; Li, Ying; Jin, Chao; Qin, Yao; Shi, Donglu; Yang, Jinhu

2014-07-15

Novel spinous TiO2 and Au@TiO2 octahedral nanocages have been prepared through a well-designed three-step strategy including templated TiO2 wet coating, subsequent structural ripening and final template removal or transformation. The strategy is built on an amorphisity-to-crystallinity transition-driven surface structural construction, which emphasizes the critical steps of crystallization-controlled TiO2 coating and consequent structural ripening. The influence of some key parameters, such as coating temperature, ripening temperature and ripening time, on the structure and morphology of the spinous TiO2 and Au@TiO2 nanocages have been investigated. In addition, in photocatalytic measurements, the prepared spinous TiO2-based nanocages exhibit enhanced photocatalytic efficiency relative to spinousless TiO2-based nanocages as well as P-25, owing to their structure advantages resulting from spinous surfaces. The photocatalytic activity of these TiO2 based photocatalysts has been systematically studied through the corresponding ·OH radical measurements. The synthetic strategy may work as a general method, through similarly designing, to realize surface structure engineering for various materials such as metals, hydroxide and other oxides besides TiO2. Copyright © 2014 Elsevier Inc. All rights reserved.

Thin-film chemical sensors based on electron tunneling

NASA Technical Reports Server (NTRS)

Khanna, S. K.; Lambe, J.; Leduc, H. G.; Thakoor, A. P.

1985-01-01

The physical mechanisms underlying a novel chemical sensor based on electron tunneling in metal-insulator-metal (MIM) tunnel junctions were studied. Chemical sensors based on electron tunneling were shown to be sensitive to a variety of substances that include iodine, mercury, bismuth, ethylenedibromide, and ethylenedichloride. A sensitivity of 13 parts per billion of iodine dissolved in hexane was demonstrated. The physical mechanisms involved in the chemical sensitivity of these devices were determined to be the chemical alteration of the surface electronic structure of the top metal electrode in the MIM structure. In addition, electroreflectance spectroscopy (ERS) was studied as a complementary surface-sensitive technique. ERS was shown to be sensitive to both iodine and mercury. Electrolyte electroreflectance and solid-state MIM electroreflectance revealed qualitatively the same chemical response. A modified thin-film structure was also studied in which a chemically active layer was introduced at the top Metal-Insulator interface of the MIM devices. Cobalt phthalocyanine was used for the chemically active layer in this study. Devices modified in this way were shown to be sensitive to iodine and nitrogen dioxide. The chemical sensitivity of the modified structure was due to conductance changes in the active layer.

DNS study on bursting and intermittency in late boundary layer transition

NASA Astrophysics Data System (ADS)

Wang, YiQian; Liu, ChaoQun

2017-11-01

Experimental and numerical investigations have suggested the existence of a strong correlation between the passage of coherent structures and events of bursting and intermittency. However, a detailed cause-and-effect study on the subject is rarely found in the literature due to the complexity and the nonlinear multiscale nature of turbulent flows. The primary goal of this research is to explore the motion and evolution of coherent structures during late transition, whose structure is much more ordered than that of fully developed turbulence, and their relationship with events of bursting and intermittency based on a verified high-order direct numerical simulation (DNS). The computation was carried out on a flat plate at Reynolds number 1000 (based on the inflow displacement thickness) with an inflow Mach number 0.5. It is concluded that bursting and intermittency detected by stationary sensors in a transitional boundary layer actually result from the passage and development of vortical structures, and it would be more rational to design transitional turbulence models based on modelling the moving vortical structures rather than the statistical features and experimental experiences.

A highly-sensitive label-free biosensor based on two dimensional photonic crystals with negative refraction

NASA Astrophysics Data System (ADS)

Malmir, Narges; Fasihi, Kiazand

2017-11-01

In this work, we present a novel high-sensitive optical label-free biosensor based on a two-dimensional photonic crystal (2D PC). The suggested structure is composed of a negative refraction structure in a hexagonal lattice PC, along with a positive refraction structure which is arranged in a square lattice PC. The frequency shift of the transmission peak is measured respect to the changes of refractive indices of the studied materials (the blood plasma, water, dry air and normal air). The studied materials are filled into a W1 line-defect waveguide which is located in the PC structure with positive refraction (the microfluidic nanochannel). Our numerical simulations, which are based on finite-difference time-domain (FDTD) method, show that in the proposed structure, a sensitivity about 1100 nm/RIU and a transmission efficiency more than 75% can be achieved. With this design, to the best of our knowledge, the obtained sensitivity and the transmission efficiency are one of the highest values in the reported PC label-free biosensors.

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.  

Aquatic toxicity of acrylates and methacrylates: quantitative structure-activity relationships based on Kow and LC50

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

Reinert, K.H.

1987-12-01

Recent EPA scrutiny of acrylate and methacrylate monomers has resulted in restrictive consent orders and Significant New Use Rules under the Toxic Substances Control Act, based on structure-activity relationships using mouse skin painting studies. The concern is centered on human health issues regarding worker and consumer exposure. Environmental issues, such as aquatic toxicity, are still of concern. Understanding the relationships and environmental risks to aquatic organisms may improve the understanding of the potential risks to human health. This study evaluates the quantitative structure-activity relationships from measured log Kow's and log LC50's for Pimephales promelas (fathead minnow) and Carassius auratus (goldfish).more » Scientific support of the current regulations is also addressed. Two monomer classes were designated: acrylates and methacrylates. Spearman rank correlation and linear regression were run. Based on this study, an ecotoxicological difference exists between acrylates and methacrylates. Regulatory activities and scientific study should reflect this difference.« less

Integrated thick-film nanostructures based on spinel ceramics

PubMed Central

2014-01-01

Integrated temperature-humidity-sensitive thick-film structures based on spinel-type semiconducting ceramics of different chemical compositions and magnesium aluminate ceramics were prepared and studied. It is shown that temperature-sensitive thick-film structures possess good electrophysical characteristics in the region from 298 to 358 K. The change of electrical resistance in integrated thick-film structures is 1 order, but these elements are stable in time and can be successfully used for sensor applications. PMID:24670141

Brain structural changes and their correlation with vascular disease in type 2 diabetes mellitus patients: a voxel-based morphometric study.

PubMed

Wang, Chunxia; Fu, Kailiang; Liu, Huaijun; Xing, Fei; Zhang, Songyun

2014-08-15

Voxel-based morphometry has been used in the study of alterations in brain structure in type 1 diabetes mellitus patients. These changes are associated with clinical indices. The age at onset, pathogenesis, and treatment of type 1 diabetes mellitus are different from those for type 2 diabetes mellitus. Thus, type 1 and type 2 diabetes mellitus may have different impacts on brain structure. Only a few studies of the alterations in brain structure in type 2 diabetes mellitus patients using voxel-based morphometry have been conducted, with inconsistent results. We detected subtle changes in the brain structure of 23 cases of type 2 diabetes mellitus, and demonstrated that there was no significant difference between the total volume of gray and white matter of the brain of type 2 diabetes mellitus patients and that in controls. Regional atrophy of gray matter mainly occurred in the right temporal and left occipital cortex, while regional atrophy of white matter involved the right temporal lobe and the right cerebellar hemisphere. The ankle-brachial index in patients with type 2 diabetes mellitus strongly correlated with the volume of brain regions in the default mode network. The ankle-brachial index, followed by the level of glycosylated hemoglobin, most strongly correlated with the volume of gray matter in the right temporal lobe. These data suggest that voxel-based morphometry could detect small structural changes in patients with type 2 diabetes mellitus. Early macrovascular atherosclerosis may play a crucial role in subtle brain atrophy in type 2 diabetes mellitus patients, with chronic hyperglycemia playing a lesser role.

Examining conifer canopy structural complexity across forest ages and elevations with LiDAR data

Treesearch

Van R. Kane; Jonathan D. Bakker; Robert J. McGaughey; James A. Lutz; Rolf F. Gersonde; Jerry F. Franklin

2010-01-01

LiDAR measurements of canopy structure can be used to classify forest stands into structural stages to study spatial patterns of canopy structure, identify habitat, or plan management actions. A key assumption in this process is that differences in canopy structure based on forest age and elevation are consistent with predictions from models of stand development. Three...

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

Structural covariance in the hallucinating brain: a voxel-based morphometry study

PubMed Central

Modinos, Gemma; Vercammen, Ans; Mechelli, Andrea; Knegtering, Henderikus; McGuire, Philip K.; Aleman, André

2009-01-01

Background Neuroimaging studies have indicated that a number of cortical regions express altered patterns of structural covariance in schizophrenia. The relation between these alterations and specific psychotic symptoms is yet to be investigated. We used voxel-based morphometry to examine regional grey matter volumes and structural covariance associated with severity of auditory verbal hallucinations. Methods We applied optimized voxel-based morphometry to volumetric magnetic resonance imaging data from 26 patients with medication-resistant auditory verbal hallucinations (AVHs); statistical inferences were made at p < 0.05 after correction for multiple comparisons. Results Grey matter volume in the left inferior frontal gyrus was positively correlated with severity of AVHs. Hallucination severity influenced the pattern of structural covariance between this region and the left superior/middle temporal gyri, the right inferior frontal gyrus and hippocampus, and the insula bilaterally. Limitations The results are based on self-reported severity of auditory hallucinations. Complementing with a clinician-based instrument could have made the findings more compelling. Future studies would benefit from including a measure to control for other symptoms that may covary with AVHs and for the effects of antipsychotic medication. Conclusion The results revealed that overall severity of AVHs modulated cortical intercorrelations between frontotemporal regions involved in language production and verbal monitoring, supporting the critical role of this network in the pathophysiology of hallucinations. PMID:19949723

Rare-earth metals in nickel aluminide-based alloys: III. Structure and properties of multicomponent Ni3Al-based alloys

NASA Astrophysics Data System (ADS)

Bazyleva, O. A.; Povarova, K. B.; Kazanskaya, N. K.; Drozdov, A. A.

2009-04-01

The possibility of increasing the life of heterophase cast light Ni3Al-based superalloys at temperatures higher than 0.8 T m of Ni3Al is studied when their directional structure is additionally stabilized by nanoprecipitates, which form upon additional alloying of these alloys by refractory and active metals, and using special methods for preparing and melting of an alloy charge. The effect of the method of introducing the main components and refractory reaction-active and surface-active alloying elements into Ni3Al-based cast superalloys, which are thermally stable natural composite materials of the eutectic type, on the structure-phase state and the life of these alloys is studied. When these alloys are melted, it is necessary to perform a set of measures to form particles of refractory oxide cores covered with the β-NiAl phase and, then, γ'prim-Ni3Al phase precipitates during solidification. The latter phase forms the outer shell of grain nuclei, which provides high thermal stability and hot strength of an intermetallic compound-based alloy. As a result, a modified structure that is stabilized by the nanoprecipitates of nickel and aluminum lanthanides and the nanoprecipitates of phases containing refractory metals is formed. This structure enhances the life of the alloy at 1000 °C by a factor of 1.8-2.5.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

Investing the effectiveness of retention performance in a non-volatile floating gate memory device with a core-shell structure of CdSe nanoparticles

NASA Astrophysics Data System (ADS)

Lee, Dong-Hoon; Kim, Jung-Min; Lim, Ki-Tae; Cho, Hyeong Jun; Bang, Jin Ho; Kim, Yong-Sang

2016-03-01

In this paper, we empirically investigate the retention performance of organic non-volatile floating gate memory devices with CdSe nanoparticles (NPs) as charge trapping elements. Core-structured CdSe NPs or core-shell-structured ZnS/CdSe NPs were mixed in PMMA and their performance in pentacene based device was compared. The NPs and self-organized thin tunneling PMMA inside the devices exhibited hysteresis by trapping hole during capacitance-voltage characterization. Despite of core-structured NPs showing a larger memory window, the retention time was too short to be adopted by an industry. By contrast core-shell structured NPs showed an improved retention time of >10000 seconds than core-structure NCs. Based on these results and the energy band structure, we propose the retention mechanism of each NPs. This investigation of retention performance provides a comparative and systematic study of the charging/discharging behaviors of NPs based memory devices. [Figure not available: see fulltext.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

PubMed Central

Christensen, Signe; Horowitz, Scott; Bardwell, James C.A.; Olsen, Johan G.; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R.

2017-01-01

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. PMID:27659562

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

PubMed

Johansson, Kristoffer E; Tidemand Johansen, Nicolai; Christensen, Signe; Horowitz, Scott; Bardwell, James C A; Olsen, Johan G; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R

2016-10-23

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification and calibration of the structural model of historical masonry building damaged during the 2016 Italian earthquakes: The case study of Palazzo del Podestà in Montelupone

NASA Astrophysics Data System (ADS)

Catinari, Federico; Pierdicca, Alessio; Clementi, Francesco; Lenci, Stefano

2017-11-01

The results of an ambient-vibration based investigation conducted on the "Palazzo del Podesta" in Montelupone (Italy) is presented. The case study was damaged during the 20I6 Italian earthquakes that stroke the central part of the Italy. The assessment procedure includes full-scale ambient vibration testing, modal identification from ambient vibration responses, finite element modeling and dynamic-based identification of the uncertain structural parameters of the model. A very good match between theoretical and experimental modal parameters was reached and the model updating has been performed identifying some structural parameters.

Features of the structure of a TiB2-based powder material obtained under self-propagating high-temperature synthesis and shear deformation

NASA Astrophysics Data System (ADS)

Bazhin, P. M.; Stolin, A. M.; Konstantinov, A. S.; Mukhina, N. I.; Pazniak, A.

2018-04-01

The results of an experimental study of TiB2-based powder material obtained under the combination of SHS processes with shear deformation are presented. The effects of the rotor velocity and the delay time before shear deformation application upon the structure of the synthesized powder are studied. The grain structure of titanium diboride is shown to become predominantly round with particles size of 1-5 μm with increasing the rotor velocity from 120 to 600 rpm. At the same time, particles of 200-400 nm size can be observed on the surface of the agglomerates.

Simulation of Thin-Film Damping and Thermal Mechanical Noise Spectra for Advanced Micromachined Microphone Structures.

PubMed

Hall, Neal A; Okandan, Murat; Littrell, Robert; Bicen, Baris; Degertekin, F Levent

2008-06-01

In many micromachined sensors the thin (2-10 μm thick) air film between a compliant diaphragm and backplate electrode plays a dominant role in shaping both the dynamic and thermal noise characteristics of the device. Silicon microphone structures used in grating-based optical-interference microphones have recently been introduced that employ backplates with minimal area to achieve low damping and low thermal noise levels. Finite-element based modeling procedures based on 2-D discretization of the governing Reynolds equation are ideally suited for studying thin-film dynamics in such structures which utilize relatively complex backplate geometries. In this paper, the dynamic properties of both the diaphragm and thin air film are studied using a modal projection procedure in a commonly used finite element software and the results are used to simulate the dynamic frequency response of the coupled structure to internally generated electrostatic actuation pressure. The model is also extended to simulate thermal mechanical noise spectra of these advanced sensing structures. In all cases simulations are compared with measured data and show excellent agreement-demonstrating 0.8 pN/√Hz and 1.8 μPa/√Hz thermal force and thermal pressure noise levels, respectively, for the 1.5 mm diameter structures under study which have a fundamental diaphragm resonance-limited bandwidth near 20 kHz.

Structured Sensory Trauma Interventions

ERIC Educational Resources Information Center

Steele, William; Kuban, Caelan

2010-01-01

This article features the National Institute of Trauma and Loss in Children (TLC), a program that has demonstrated via field testing, exploratory research, time series studies, and evidence-based research studies that its Structured Sensory Intervention for Traumatized Children, Adolescents, and Parents (SITCAP[R]) produces statistically…

Damage healing ability of a shape-memory-polymer-based particulate composite with small thermoplastic contents

NASA Astrophysics Data System (ADS)

Nji, Jones; Li, Guoqiang

2012-02-01

The purpose of this study is to investigate the potential of a shape-memory-polymer (SMP)-based particulate composite to heal structural-length scale damage with small thermoplastic additive contents through a close-then-heal (CTH) self-healing scheme that was introduced in a previous study (Li and Uppu 2010 Comput. Sci. Technol. 70 1419-27). The idea is to achieve reasonable healing efficiencies with minimal sacrifice in structural load capacity. By first closing cracks, the gap between two crack surfaces is narrowed and a lesser amount of thermoplastic particles is required to achieve healing. The particulate composite was fabricated by dispersing copolyester thermoplastic particles in a shape memory polymer matrix. It is found that, for small thermoplastic contents of less than 10%, the CTH scheme followed in this study heals structural-length scale damage in the SMP particulate composite to a meaningful extent and with less sacrifice of structural capacity.

Electronic structure and acid-base properties of Kojic acid and its dimers. A DFT and quantum topology study

NASA Astrophysics Data System (ADS)

Aziz, Saadullah G.; Alyoubi, Abdulrahman O.; Elroby, Shaaban A.; Hilal, Rifaat H.

2017-10-01

Kojic acid is a polyfunctional heterocyclic compound, with several important reaction centres; it has a wide range of applications in the cosmetic, medicine, food, agriculture and chemical industries. The present study aims at better insight into its electronic structure and bonding characteristics. Thus, density functional theory at the M06-2x /6-311++G** level of theory is used to investigate its ground state electronic and acid-base properties. Protonation and deprotonation enthalpies are computed and analysed. The ability of Kojic acid to form both water complexes and dimers is explored. Several different complexes and dimer structures were examined. Natural bond order and quantum topology features of the charge density were analysed. The origin of the stability of the studied complexes and dimer structures can be traced to hydrogen bonding, π-conjugative and non-covalent dispersive interactions.

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model

PubMed Central

Gordon, J.A.; Freedman, B.R.; Zuskov, A.; Iozzo, R.V.; Birk, D.E.; Soslowsky, L.J.

2015-01-01

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn−/−) and biglycan-null (Bgn−/−) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. PMID:25888014

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model.

PubMed

Gordon, J A; Freedman, B R; Zuskov, A; Iozzo, R V; Birk, D E; Soslowsky, L J

2015-07-16

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn(-/-)) and biglycan-null (Bgn(-/-)) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.

PubMed

Wang, Xiaoqiang

2011-03-01

Isoflavonoids are a large group of plant natural products and play important roles in plant defense. They also possess valuable health-promoting activities with significant health benefits for animals and humans. The isoflavonoids are identified primarily in leguminous plants and are synthesized through the central phenylpropanoid pathway and the specific isoflavonoid branch pathways in legumes. Structural studies of some key enzymes in the central phenylpropanoid pathway shed light on the early stages of the (iso)flavonoid biosynthetic process. Significant impact has also been made on structural studies of enzymes in the isoflavonoid branch pathways. Structures of isoflavonoid-specific NADPH-dependent reductases revealed how the (iso)flavonoid backbones are modified by reduction reactions and how enzymes specifically recognize isoflavonoids and catalyze stereo-specific reductions. Structural studies of isoflavonoid methyltransferases and glycosyltransferases revealed how isoflavonoids are further decorated with methyl group and sugars in different methylation and glycosylation patterns that determine their bioactivities and functions. In combination with mutagenesis and biochemical studies, the detailed structural information of these enzymes provides a basis for understanding the complex biosynthetic process, enzyme catalytic mechanisms, and substrate specificities. Structure-based homology modeling facilitates the functional characterization of these large groups of biosynthetic enzymes and their homologs. Structure-based enzyme engineering is becoming a new strategy for synthesis of bioactive isoflavonoids and also facilitates plant metabolic engineering towards improvement of quality and production of crop plants.

Effects of Piezoelectric (PZT) Sensor Bonding and the Characteristics of the Host Structure on Impedance Based Structural Health Monitoring

NASA Technical Reports Server (NTRS)

Jalloh, Abdul

2005-01-01

This study was conducted to investigate the effects of certain factors on the impedance signal in structural health monitoring. These factors were: the quality of the bond between the sensor and the host structure, and the characteristics of the host structure, such as geometry, mass, and material properties. This work was carried out to answer a set of questions, related to these factors, that were developed by the project team. The project team was comprised of Dr. Doug Ramers and Dr. Abdul Jalloh of the Summer Faculty Fellowship Program, Mr. Arnaldo Colon- Perez, a student intern from the University of Puerto Rico of Turabo, and Mr. John Lassiter and Mr. Bob Engberg of the Structural and Dynamics Test Group at NASA Marshall Space Flight Center (MSFC). This study was based on a review of the literature on structural health monitoring to investigate the factors referred to above because there was not enough time to plan and conduct the appropriate tests at MSFC during the tenure of the Summer Faculty Fellowship Program project members. The surveyed literature documents works on structural health monitoring that were based on laboratory tests that were conducted using bolted trusses and other civil engineering type structures for the most part. These are not the typical types of structures used in designing and building NASA s space vehicles and systems. It was therefore recommended that tests be conducted using NASA type structures, such as pressure vessels, to validate the observations made in this report.

Social capital calculations in economic systems: Experimental study

NASA Astrophysics Data System (ADS)

Chepurov, E. G.; Berg, D. B.; Zvereva, O. M.; Nazarova, Yu. Yu.; Chekmarev, I. V.

2017-11-01

The paper describes the social capital study for a system where actors are engaged in an economic activity. The focus is on the analysis of communications structural parameters (transactions) between the actors. Comparison between transaction network graph structure and the structure of a random Bernoulli graph of the same dimension and density allows revealing specific structural features of the economic system under study. Structural analysis is based on SNA-methodology (SNA - Social Network Analysis). It is shown that structural parameter values of the graph formed by agent relationship links may well characterize different aspects of the social capital structure. The research advocates that it is useful to distinguish the difference between each agent social capital and the whole system social capital.

Structural, electronic and magnetic properties of Pr-based filled skutterudites: A first principle study

NASA Astrophysics Data System (ADS)

Yadav, Priya; Nautiyal, Shashank; Verma, U. P.

2018-04-01

Ternary skutterudites materials exhibit good electronic properties due to the unpaired d- and f- electrons of the transition and rare-earth metals, respectively. In this communication, we have performed the structural optimization of Pr-based filled skutterudite (PrCo4P12) for the first time and obtained the electronic band structure, density of states and magnetic moments by using the full-potential linearized augmented plane wave (FP-LAPW) method based on density functional theory (DFT). Our obtained magnetic moment of PrCo4P12 is ˜ 1.8 µB in which main contribution is due to Pr atom. Behavior of this material is metallic and it is most stable in body centered cubic (BCC) structure.

Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning

PubMed Central

Prévost, Charlotte; McNamee, Daniel; Jessup, Ryan K.; Bossaerts, Peter; O'Doherty, John P.

2013-01-01

Contemporary computational accounts of instrumental conditioning have emphasized a role for a model-based system in which values are computed with reference to a rich model of the structure of the world, and a model-free system in which values are updated without encoding such structure. Much less studied is the possibility of a similar distinction operating at the level of Pavlovian conditioning. In the present study, we scanned human participants while they participated in a Pavlovian conditioning task with a simple structure while measuring activity in the human amygdala using a high-resolution fMRI protocol. After fitting a model-based algorithm and a variety of model-free algorithms to the fMRI data, we found evidence for the superiority of a model-based algorithm in accounting for activity in the amygdala compared to the model-free counterparts. These findings support an important role for model-based algorithms in describing the processes underpinning Pavlovian conditioning, as well as providing evidence of a role for the human amygdala in model-based inference. PMID:23436990

Theoretical study on the optical response behavior to hydrogen chloride gas of a series of Schiff-base-based star-shaped structures.

PubMed

Wang, Fei; Qi, Tianhong; Su, Zhongmin; Xie, Yuzhong

2018-02-17

Schiff-base compounds have many applications in the field of optoelectronic materials and chemical sensing because of their appealing coordination ability, and simple and easily accessible use in structural modification. Herein, five kinds of star-shaped Schiff-base compounds were designed and their optical response behavior to hydrogen chloride (HCl) gas was studied using dependent/time-dependent density functional theory (DFT/TDDFT). Moreover, the relationship between structures and properties was investigated upon changing the benzene group into N atom or triazine group at the core-position and introducing a methoxyl (-OCH 3 ) or nitro (-NO 2 ) group into the star-shaped Schiff-bases at the tail of the branches. The results show that all five Schiff-bases could be candidates for HCl gas sensing materials. Furthermore, introducing an electron-donating group at either the core or the tail forms a charge transfer channel with the electron deficient H-bonded imino group, which is convenient for charge transfer and subsequently promotes a red-shift in absorption spectra and fluorescence quenching.

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Revisiting the TALE repeat.

PubMed

Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

2014-04-01

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis

PubMed Central

Lu, Duo; Silhan, Jan; MacDonald, James T.; Carpenter, Elisabeth P.; Jensen, Kirsten; Tang, Christoph M.; Baldwin, Geoff S.; Freemont, Paul S.

2012-01-01

Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5′ to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures. PMID:23035246

Insights into the fold organization of TIM barrel from interaction energy based structure networks.

PubMed

Vijayabaskar, M S; Vishveshwara, Saraswathi

2012-01-01

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

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

PubMed

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

2017-02-01

Conventional diagnostic aids based upon imagery and patient symptoms do not indicate whether restorative treatments have eliminated structural pathology. The purpose of this clinical study was to evaluate quantitative percussion diagnostics (QPD), a mechanics-based methodology that tests the structural integrity of teeth noninvasively. The study hypothesis was that QPD would provide knowledge of the structural instability of teeth after restorative work. Eight participants with 60 sites needing restoration were enrolled in an IRB-approved clinical study. Each participant was examined comprehensively, including QPD testing. Each site was disassembled and microscopically video documented, and the results were recorded on a defect assessment sheet. A predictive model was developed for the pathology rating based on normalized fit error (NFE) values using data from the before treatment phase of the study published previously. Each restored site was then tested using QPD. The mean change in NFE values after restoration was evaluated by the pathology rating before treatment. The model was then used to predictively classify the rating after restoration based on the NFE values after treatment. The diagnostic potential of the rating was explored as a marker for risk of pathology after restoration. After restoration, 51 of the 60 sites fell below an NFE of 0.04, representing a greatly stabilized tooth site sample group. Several sites remained in the high-risk category and some increased in pathologic micromovement. Two models were used to determine severity with indicative cutoff points to group sites with similar values. The data support the hypothesis that QPD can indicate a revised level of structural instability of teeth after restoration. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Genetic programming based quantitative structure-retention relationships for the prediction of Kovats retention indices.

PubMed

Goel, Purva; Bapat, Sanket; Vyas, Renu; Tambe, Amruta; Tambe, Sanjeev S

2015-11-13

The development of quantitative structure-retention relationships (QSRR) aims at constructing an appropriate linear/nonlinear model for the prediction of the retention behavior (such as Kovats retention index) of a solute on a chromatographic column. Commonly, multi-linear regression and artificial neural networks are used in the QSRR development in the gas chromatography (GC). In this study, an artificial intelligence based data-driven modeling formalism, namely genetic programming (GP), has been introduced for the development of quantitative structure based models predicting Kovats retention indices (KRI). The novelty of the GP formalism is that given an example dataset, it searches and optimizes both the form (structure) and the parameters of an appropriate linear/nonlinear data-fitting model. Thus, it is not necessary to pre-specify the form of the data-fitting model in the GP-based modeling. These models are also less complex, simple to understand, and easy to deploy. The effectiveness of GP in constructing QSRRs has been demonstrated by developing models predicting KRIs of light hydrocarbons (case study-I) and adamantane derivatives (case study-II). In each case study, two-, three- and four-descriptor models have been developed using the KRI data available in the literature. The results of these studies clearly indicate that the GP-based models possess an excellent KRI prediction accuracy and generalization capability. Specifically, the best performing four-descriptor models in both the case studies have yielded high (>0.9) values of the coefficient of determination (R(2)) and low values of root mean squared error (RMSE) and mean absolute percent error (MAPE) for training, test and validation set data. The characteristic feature of this study is that it introduces a practical and an effective GP-based method for developing QSRRs in gas chromatography that can be gainfully utilized for developing other types of data-driven models in chromatography science. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

Detection of physical activities using a physical activity monitor system for wheelchair users.

PubMed

Hiremath, Shivayogi V; Intille, Stephen S; Kelleher, Annmarie; Cooper, Rory A; Ding, Dan

2015-01-01

Availability of physical activity monitors for wheelchair users can potentially assist these individuals to track regular physical activity (PA), which in turn could lead to a healthier and more active lifestyle. Therefore, the aim of this study was to develop and validate algorithms for a physical activity monitoring system (PAMS) to detect wheelchair based activities. The PAMS consists of a gyroscope based wheel rotation monitor (G-WRM) and an accelerometer device (wocket) worn on the upper arm or on the wrist. A total of 45 persons with spinal cord injury took part in the study, which was performed in a structured university-based laboratory environment, a semi-structured environment at the National Veterans Wheelchair Games, and in the participants' home environments. Participants performed at least ten PAs, other than resting, taken from a list of PAs. The classification performance for the best classifiers on the testing dataset for PAMS-Arm (G-WRM and wocket on upper arm) and PAMS-Wrist (G-WRM and wocket on wrist) was 89.26% and 88.47%, respectively. The outcomes of this study indicate that multi-modal information from the PAMS can help detect various types of wheelchair-based activities in structured laboratory, semi-structured organizational, and unstructured home environments. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Relaxation of the structure of simple metal ion complexes in aqueous solutions at up to supercritical conditions

USGS Publications Warehouse

Mayanovic, Robert A.; Jayanetti, Sumedha; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2003-01-01

Recently x-ray absorption fine structure (XAFS) studies of various ions in aqueous solutions showed a variation of cation-ligand bond lengths, often coupled with other structure changes, with increasing temperatures. Thus, the variations of the structure of several metal ion complexes with temperature based on observations from the X-ray absorption fine structure (XAFS) studies in the hope that it will stimulate the development of either first- principles theory or molecular dynamics simulations that might adequately describes these results are discussed.

Adverse Event extraction from Structured Product Labels using the Event-based Text-mining of Health Electronic Records (ETHER)system.

PubMed

Pandey, Abhishek; Kreimeyer, Kory; Foster, Matthew; Botsis, Taxiarchis; Dang, Oanh; Ly, Thomas; Wang, Wei; Forshee, Richard

2018-01-01

Structured Product Labels follow an XML-based document markup standard approved by the Health Level Seven organization and adopted by the US Food and Drug Administration as a mechanism for exchanging medical products information. Their current organization makes their secondary use rather challenging. We used the Side Effect Resource database and DailyMed to generate a comparison dataset of 1159 Structured Product Labels. We processed the Adverse Reaction section of these Structured Product Labels with the Event-based Text-mining of Health Electronic Records system and evaluated its ability to extract and encode Adverse Event terms to Medical Dictionary for Regulatory Activities Preferred Terms. A small sample of 100 labels was then selected for further analysis. Of the 100 labels, Event-based Text-mining of Health Electronic Records achieved a precision and recall of 81 percent and 92 percent, respectively. This study demonstrated Event-based Text-mining of Health Electronic Record's ability to extract and encode Adverse Event terms from Structured Product Labels which may potentially support multiple pharmacoepidemiological tasks.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

NASA Astrophysics Data System (ADS)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.

PubMed

Hristozov, Dimitar P; Oprea, Tudor I; Gasteiger, Johann

2007-01-01

Four different ligand-based virtual screening scenarios are studied: (1) prioritizing compounds for subsequent high-throughput screening (HTS); (2) selecting a predefined (small) number of potentially active compounds from a large chemical database; (3) assessing the probability that a given structure will exhibit a given activity; (4) selecting the most active structure(s) for a biological assay. Each of the four scenarios is exemplified by performing retrospective ligand-based virtual screening for eight different biological targets using two large databases--MDDR and WOMBAT. A comparison between the chemical spaces covered by these two databases is presented. The performance of two techniques for ligand--based virtual screening--similarity search with subsequent data fusion (SSDF) and novelty detection with Self-Organizing Maps (ndSOM) is investigated. Three different structure representations--2,048-dimensional Daylight fingerprints, topological autocorrelation weighted by atomic physicochemical properties (sigma electronegativity, polarizability, partial charge, and identity) and radial distribution functions weighted by the same atomic physicochemical properties--are compared. Both methods were found applicable in scenario one. The similarity search was found to perform slightly better in scenario two while the SOM novelty detection is preferred in scenario three. No method/descriptor combination achieved significant success in scenario four.

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

NASA Astrophysics Data System (ADS)

Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu D.; Petukhov, A. V.; Byelov, D.; Chernyshov, D.; Okorokov, A. I.; Bouwman, W. G.; Grigoriev, S. V.

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length Ltran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length Llong is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10°.

Locating damage using integrated global-local approach with wireless sensing system and single-chip impedance measurement device.

PubMed

Lin, Tzu-Hsuan; Lu, Yung-Chi; Hung, Shih-Lin

2014-01-01

This study developed an integrated global-local approach for locating damage on building structures. A damage detection approach with a novel embedded frequency response function damage index (NEFDI) was proposed and embedded in the Imote2.NET-based wireless structural health monitoring (SHM) system to locate global damage. Local damage is then identified using an electromechanical impedance- (EMI-) based damage detection method. The electromechanical impedance was measured using a single-chip impedance measurement device which has the advantages of small size, low cost, and portability. The feasibility of the proposed damage detection scheme was studied with reference to a numerical example of a six-storey shear plane frame structure and a small-scale experimental steel frame. Numerical and experimental analysis using the integrated global-local SHM approach reveals that, after NEFDI indicates the approximate location of a damaged area, the EMI-based damage detection approach can then identify the detailed damage location in the structure of the building.

Biomedical application of hierarchically built structures based on metal oxides

NASA Astrophysics Data System (ADS)

Korovin, M. S.; Fomenko, A. N.

2017-12-01

Nowadays, the use of hierarchically built structures in biology and medicine arouses much interest. The aim of this work is to review and summarize the available literature data about hierarchically organized structures in biomedical application. Nanoparticles can serve as an example of such structures. Medicine holds a special place among various application methods of similar systems. Special attention is paid to inorganic nanoparticles based on different metal oxides and hydroxides, such as iron, zinc, copper, and aluminum. Our investigations show that low-dimensional nanostructures based on aluminum oxides and hydroxides have an inhibitory effect on tumor cells and possess an antimicrobial activity. At the same time, it is obvious that the large-scale use of nanoparticles by humans needs to thoroughly study their properties. Special attention should be paid to the study of nanoparticle interaction with living biological objects. The numerous data show that there is no clear understanding of interaction mechanisms between nanoparticles and various cell types.

Ontology-based structured cosine similarity in document summarization: with applications to mobile audio-based knowledge management.

PubMed

Yuan, Soe-Tsyr; Sun, Jerry

2005-10-01

Development of algorithms for automated text categorization in massive text document sets is an important research area of data mining and knowledge discovery. Most of the text-clustering methods were grounded in the term-based measurement of distance or similarity, ignoring the structure of the documents. In this paper, we present a novel method named structured cosine similarity (SCS) that furnishes document clustering with a new way of modeling on document summarization, considering the structure of the documents so as to improve the performance of document clustering in terms of quality, stability, and efficiency. This study was motivated by the problem of clustering speech documents (of no rich document features) attained from the wireless experience oral sharing conducted by mobile workforce of enterprises, fulfilling audio-based knowledge management. In other words, this problem aims to facilitate knowledge acquisition and sharing by speech. The evaluations also show fairly promising results on our method of structured cosine similarity.

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

PubMed

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

Welded tie plate feasibility study for ITER central solenoid structure

NASA Astrophysics Data System (ADS)

Walsh, R.; McRae, D.; Dalder, E.; Litherland, S.; Goddard, R.; Han, K.; Trosen, M.; Kuhlmann, D. D.

2014-01-01

The result of a Nitronic 50 (N50) weld-screening program conducted in support of CS-Tie Plate Structure Design and Development is reported here. The goal of this program is to evaluate four different weld practices and to select the best weld practice for thick section welding of the N50 tie plate structure. The structure design specifies both the weld and base metals have the same minimum mechanical properties requirements. The criteria for selecting the best weld practice are based on the combination of the 295 K tensile properties and the 4 K-tensile, fatigue, and fracture-toughness properties.

The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine.

PubMed Central

Lynch, S R; Tinoco, I

1998-01-01

The structure of the L3 central hairpin loop isolated from the antigenomic sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems from the ribozyme stacked on top of the loop has been determined by NMR spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a 7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient catalysis in the intact ribozyme. The structure was determined using homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled RNA oligonucleotides. The overall root mean square deviation for the structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but without the lone purine in the loop, which is not well defined in the structure. The structure indicates a U.C base pair between the nucleotides on the 5'- and 3'-ends of the loop. This base pair is formed with a single hydrogen bond involving the cytosine exocyclic amino proton and the carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn cytidine. While not unprecedented, syn pyrimidines are highly unusual. This one can be confidently established by intranucleotide distances between the ribose and the base determined by NMR spectroscopy. A similar study of the structure of this loop showed a somewhat different three-dimensional structure. A discussion of differences in the two structures, as well as possible sites of interaction with the cleavage site, will be presented. PMID:9461457

A continuum-based structural modeling approach for cellulose nanocrystals (CNCs)

Treesearch

Mehdi Shishehbor; Fernando L. Dri; Robert J. Moon; Pablo D. Zavattieri

2018-01-01

We present a continuum-based structural model to study the mechanical behavior of cel- lulose nanocrystals (CNCs), and analyze the effect of bonded and non-bonded interactions on the mechanical properties under various loading conditions. In particular, this model assumes the uncoupling between the bonded and non-bonded interactions and their be- havior is obtained...

Grating-based X-ray tomography of 3D food structures

NASA Astrophysics Data System (ADS)

Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur; Lametsch, René

2016-10-01

A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiation light source using a grating interferometric set-up.

Studies on muon tomography for archaeological internal structures scanning

NASA Astrophysics Data System (ADS)

Gómez, H.; Carloganu, C.; Gibert, D.; Jacquemier, J.; Karyotakis, Y.; Marteau, J.; Niess, V.; Katsanevas, S.; Tonazzo, A.

2016-05-01

Muon tomography is a potential non-invasive technique for internal structure scanning. It has already interesting applications in geophysics and can be used for archaeological purposes. Muon tomography is based on the measurement of the muon flux after crossing the structure studied. Differences on the mean density of these structures imply differences on the detected muon rate for a given direction. Based on this principle, Monte Carlo simulations represent a useful tool to provide a model of the expected muon rate and angular distribution depending on the composition of the studied object, being useful to estimate the expected detected muons and to better understand the experimental results. These simulations are mainly dependent on the geometry and composition of the studied object and on the modelling of the initial muon flux at surface. In this work, the potential of muon tomography in archaeology is presented and evaluated with Monte Carlo simulations by estimating the differences on the muon rate due to the presence of internal structures and its composition. The influence of the chosen muon model at surface in terms of energy and angular distributions in the final result has been also studied.

Application of fiber Bragg grating sensor for rebar corrosion

NASA Astrophysics Data System (ADS)

Geng, Jiang; Wu, Jin; Zhao, Xinming

2009-07-01

Corrosion of rebar is one of the most important factors which can affect the durability of concrete structure, so in the service of these structures, measuring the degree of corrosion, and then evaluating the reliability of these structures are very important. The most significant characteristic of the rebar corrosion is its volume expansion. By the principle and characteristics of fiber bragg grating (FBG), a sensor for rebar corrosion is designed. In this paper, based upon laboratory studies, the fiber bragg grating sensor is applied in No.58 Berth of Lianyungang Port. According to the filed condition, a proper embedding scheme is proposed. Considering the optimal sensor placement, the monitoring points are determined and five sensor groups were applied in the structure. Based on the results of the calibration experiment, the relationship between corrosion ratio and the change of wavelength is established. So the corrosion status of the structure can be obtained by measuring wavelength. The study shows that the FBG sensor was feasible to monitor the status of rebar in concrete structures.

Accounting for Relatedness in Family Based Genetic Association Studies

PubMed Central

McArdle, P.F.; O’Connell, J.R.; Pollin, T.I.; Baumgarten, M.; Shuldiner, A.R.; Peyser, P.A.; Mitchell, B.D.

2007-01-01

Objective Assess the differences in point estimates, power and type 1 error rates when accounting for and ignoring family structure in genetic tests of association. Methods We compare by simulation the performance of analytic models using variance components to account for family structure and regression models that ignore relatedness for a range of possible family based study designs (i.e., sib pairs vs. large sibships vs. nuclear families vs. extended families). Results Our analyses indicate that effect size estimates and power are not significantly affected by ignoring family structure. Type 1 error rates increase when family structure is ignored, as density of family structures increases, and as trait heritability increases. For discrete traits with moderate levels of heritability and across many common sampling designs, type 1 error rates rise from a nominal 0.05 to 0.11. Conclusion Ignoring family structure may be useful in screening although it comes at a cost of a increased type 1 error rate, the magnitude of which depends on trait heritability and pedigree configuration. PMID:17570925

Nanotwinned and hierarchical nanotwinned metals: a review of experimental, computational and theoretical efforts

NASA Astrophysics Data System (ADS)

Sun, Ligang; He, Xiaoqiao; Lu, Jian

2018-02-01

The recent studies on nanotwinned (NT) and hierarchical nanotwinned (HNT) face-centered cubic (FCC) metals are presented in this review. The HNT structures have been supposed as a kind of novel structure to bring about higher strength/ductility than NT counterparts in crystalline materials. We primarily focus on the recent developments of the experimental, atomistic and theoretical studies on the NT and HNT structures in the metallic materials. Some advanced bottom-up and top-down techniques for the fabrication of NT and HNT structures are introduced. The deformation induced HNT structures are available by virtue of severe plastic deformation (SPD) based techniques while the synthesis of growth HNT structures is so far almost unavailable. In addition, some representative molecular dynamics (MD) studies on the NT and HNT FCC metals unveil that the nanoscale effects such as twin spacing, grain size and plastic anisotropy greatly alter the performance of NT and HNT metals. The HNT structures may initiate unique phenomena in comparison with the NT ones. Furthermore, based on the phenomena and mechanisms revealed by experimental and MD simulation observations, a series of theoretical models have been proposed. They are effective to describe the mechanical behaviors of NT and HNT metals within the applicable scope. So far the development of manufacturing technologies of HNT structures, as well as the studies on the effects of HNT structures on the properties of metals are still in its infancy. Further exploration is required to promote the design of advanced materials.

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…

Epistemological Beliefs across Cultures: Critique and Analysis of Beliefs Structure Studies

ERIC Educational Resources Information Center

Chan, Kwok-wai; Elliott, Robert G.

2004-01-01

The findings of epistemological beliefs studies in North America, Hong Kong and Taiwan were compared and interpreted in terms of the different cultural contexts and methodologies used in the research studies. Based on cross culture analysis a hypothesis for the structure of epistemological beliefs was proposed. Implications were also drawn for…

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.

Effect of structure in problem based learning on science teaching efficacy beliefs and science content knowledge of elementary preservice teachers

NASA Astrophysics Data System (ADS)

Sasser, Selena Kay

This study examined the effects of differing amounts of structure within the problem based learning instructional model on elementary preservice teachers' science teaching efficacy beliefs, including personal science teaching efficacy and science teaching outcome expectancy, and content knowledge acquisition. This study involved sixty (60) undergraduate elementary preservice teachers enrolled in three sections of elementary science methods classes at a large Midwestern research university. This study used a quasi-experimental nonequivalent design to collect and analyze both quantitative and qualitative data. Participants completed instruments designed to assess science teaching efficacy beliefs, science background, and demographic data. Quantitative data from pre and posttests was obtained using the science teaching efficacy belief instrument-preservice (STEBI-B) developed by Enochs and Riggs (1990) and modified by Bleicher (2004). Data collection instruments also included a demographic questionnaire, an analytic rubric, and a structured interview; both created by the researcher. Quantitative data was analyzed by conducting ANCOVA, paired samples t-test, and independent samples t-test. Qualitative data was analyzed using coding and themes. Each of the treatment groups received the same problem scenario, one group experienced a more structured PBL setting, and one group experienced a limited structure PBL setting. Research personnel administered pre and posttests to determine the elementary preservice teachers' science teaching efficacy beliefs. The results show elementary preservice teachers'science teaching efficacy beliefs can be influence by the problem based learning instructional model. This study did not find that the amount of structure in the form of core ideas to consider and resources for further research increased science teaching efficacy beliefs in this sample. Results from the science content knowledge rubric indicated that structure can increase science content knowledge in this sample. Qualitative data from the tutor, fidelity raters, and interviews indicated the participants were excited about the problem and were interested in the science content knowledge related to the problem. They also indicated they were motivated to continue informal study in the problem area. Participants indicated, during the interview, their initial frustration with the lack of knowledge gained from the tutor; however, indicated this led to more learning on their part. This study will contribute to the overall knowledge of problem based learning and its structures, science teaching efficacy beliefs of elementary preservice teachers, and to current teaching and learning practices.

Protein crystallography and infectious diseases.

PubMed Central

Verlinde, C. L.; Merritt, E. A.; Van den Akker, F.; Kim, H.; Feil, I.; Delboni, L. F.; Mande, S. C.; Sarfaty, S.; Petra, P. H.; Hol, W. G.

1994-01-01

The current rapid growth in the number of known 3-dimensional protein structures is producing a database of structures that is increasingly useful as a starting point for the development of new medically relevant molecules such as drugs, therapeutic proteins, and vaccines. This development is beautifully illustrated in the recent book, Protein structure: New approaches to disease and therapy (Perutz, 1992). There is a great and growing promise for the design of molecules for the treatment or prevention of a wide variety of diseases, an endeavor made possible by the insights derived from the structure and function of crucial proteins from pathogenic organisms and from man. We present here 2 illustrations of structure-based drug design. The first is the prospect of developing antitrypanosomal drugs based on crystallographic, ligand-binding, and molecular modeling studies of glycolytic glycosomal enzymes from Trypanosomatidae. These unicellular organisms are responsible for several tropical diseases, including African and American trypanosomiases, as well as various forms of leishmaniasis. Because the target enzymes are also present in the human host, this project is a pioneering study in selective design. The second illustrative case is the prospect of designing anti-cholera drugs based on detailed analysis of the structure of cholera toxin and the closely related Escherichia coli heat-labile enterotoxin. Such potential drugs can be targeted either at inhibiting the toxin's receptor binding site or at blocking the toxin's intracellular catalytic activity. Study of the Vibrio cholerae and E. coli toxins serves at the same time as an example of a general approach to structure-based vaccine design. These toxins exhibit a remarkable ability to stimulate the mucosal immune system, and early results have suggested that this property can be maintained by engineered fusion proteins based on the native toxin structure. The challenge is thus to incorporate selected epitopes from foreign pathogens into the native framework of the toxin such that crucial features of both the epitope and the toxin are maintained. That is, the modified toxin must continue to evoke a strong mucosal immune response, and this response must be directed against an epitope conformation characteristic of the original pathogen. PMID:7849584

Structural Violence in Health Care: Lived Experience of Street-Based Female Commercial Sex Workers in Kathmandu.

PubMed

Basnyat, Iccha

2017-01-01

Thirty-five in-depth, semi-structured interviews were conducted with female, street-based, commercial sex workers in Kathmandu, Nepal. The framework of structural violence guided this study in identifying the structural context that impacts the female sex workers' lives and may cause harm to their health. Structural violence in health care was revealed through thematic analysis as (a) discrimination, (b) forced choice, and (c) limitations to health information sources. Lived experiences highlight how the sex workers engaged with structural limitations in health care access, services, and utilization. Structural violence conveys a message about who is entitled to health care and what a society emphasizes and expects regarding acceptable health behavior. Examining the structural violence highlighted how the sex workers negotiated, understood, and engaged with structural limitations in health care access, services, and utilization. © The Author(s) 2015.

Content and structure of knowledge base used for virtual control of android arm motion in specified environment

NASA Astrophysics Data System (ADS)

Pritykin, F. N.; Nebritov, V. I.

2018-01-01

The paper presents the configuration of knowledge base necessary for intelligent control of android arm mechanism motion with different positions of certain forbidden regions taken into account. The present structure of the knowledge base characterizes the past experience of arm motion synthesis in the vector of velocities with due regard for the known obstacles. This structure also specifies its intrinsic properties. Knowledge base generation is based on the study of the arm mechanism instantaneous states implementations. Computational experiments connected with the virtual control of android arm motion with known forbidden regions using the developed knowledge base are introduced. Using the developed knowledge base to control virtually the arm motion reduces the time of test assignments calculation. The results of the research can be used in developing control systems of autonomous android robots in the known in advance environment.

Pressure-induced superconductivity in the iron-based ladder material BaFe2S3.

PubMed

Takahashi, Hiroki; Sugimoto, Akira; Nambu, Yusuke; Yamauchi, Touru; Hirata, Yasuyuki; Kawakami, Takateru; Avdeev, Maxim; Matsubayashi, Kazuyuki; Du, Fei; Kawashima, Chizuru; Soeda, Hideto; Nakano, Satoshi; Uwatoko, Yoshiya; Ueda, Yutaka; Sato, Taku J; Ohgushi, Kenya

2015-10-01

All the iron-based superconductors identified so far share a square lattice composed of Fe atoms as a common feature, despite having different crystal structures. In copper-based materials, the superconducting phase emerges not only in square-lattice structures but also in ladder structures. Yet iron-based superconductors without a square-lattice motif have not been found, despite being actively sought out. Here, we report the discovery of pressure-induced superconductivity in the iron-based spin-ladder material BaFe2S3, a Mott insulator with striped-type magnetic ordering below ∼120 K. On the application of pressure this compound exhibits a metal-insulator transition at about 11 GPa, followed by the appearance of superconductivity below Tc = 14 K, right after the onset of the metallic phase. Our findings indicate that iron-based ladder compounds represent promising material platforms, in particular for studying the fundamentals of iron-based superconductivity.

Morphing wing structure with controllable twist based on adaptive bending-twist coupling

NASA Astrophysics Data System (ADS)

Raither, Wolfram; Heymanns, Matthias; Bergamini, Andrea; Ermanni, Paolo

2013-06-01

A novel semi-passive morphing airfoil concept based on variable bending-twist coupling induced by adaptive shear center location and torsional stiffness is presented. Numerical parametric studies and upscaling show that the concept relying on smart materials permits effective twist control while offering the potential of being lightweight and energy efficient. By means of an experimental characterization of an adaptive beam and a scaled adaptive wing structure, effectiveness and producibility of the structural concept are demonstrated.

Properties of planar structures based on Policluster films of diamond and AlN

NASA Astrophysics Data System (ADS)

Belyanin, A. F.; Luchnikov, A. P.; Nalimov, S. A.; Bagdasarian, A. S.

2018-01-01

AlN films doped with zinc were grown on Si substrates by RF magnetron reactive sputtering of a compound target. Policluster films of diamond doped with boron were formed on layered Si/AlN substrates from the gas phase hydrogen and methane, activated arc discharge. By electron microscopy, X-ray diffraction and Raman spectroscopy the composition and structure of synthetic policluster films of diamond and AlN films were studied. Photovoltaic devices based on the AlN/PFD layered structure are presented.

Effects of alternative outcome scenarios and structured outcome evaluation on case-based ethics instruction.

PubMed

Peacock, Juandre; Harkrider, Lauren N; Bagdasarov, Zhanna; Connelly, Shane; Johnson, James F; Thiel, Chase E; Macdougall, Alexandra E; Mumford, Michael D; Devenport, Lynn D

2013-09-01

Case-based instruction has been regarded by many as a viable alternative to traditional lecture-based education and training. However, little is known about how case-based training techniques impact training effectiveness. This study examined the effects of two such techniques: (a) presentation of alternative outcome scenarios to a case, and (b) conducting a structured outcome evaluation. Consistent with the hypotheses, results indicate that presentation of alternative outcome scenarios reduced knowledge acquisition, reduced sensemaking and ethical decision-making strategy use, and reduced decision ethicality. Conducting a structured outcome evaluation had no impact on these outcomes. Results indicate that those who use case-based instruction should take care to use clear, less complex cases with only a singular outcome if they are seeking these types of outcomes.

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

The effects of Web site structure: the role of personal difference.

PubMed

Chung, Hwiman; Ahn, Euijin

2007-12-01

This study examined the effects of Web site structures in terms of advertising effectiveness- memory, attitude, and behavioral intentions. The primary research question for this study is, What type of Web site (Web ad) structure is most effective? In the pilot study, we tested the difference between two Web site structures, linear and interactive, in terms of traditional advertising effectiveness. Results from the pilot study did not support our research expectations. However, differences in terms of memory were noted between the two structures. After re-creating the Web site based on subjects' comments, in the final experiment, we examined the differences between the two structures and the moderating role of personality difference on the effects of Web site structure. The results confirm that participants' attitude, memory, and behavioral intentions were affected differently by the different Web site structures. However, some research hypotheses were not supported by the current data.

Study of structural design concepts for an arrow wing supersonic transport configuration, volume 1. Tasks 1 and 2

NASA Technical Reports Server (NTRS)

1976-01-01

A structural design study was made, based on a 1975 level of technology, to assess the relative merits of structural concepts and materials for an advanced supersonic transport cruising at Mach 2.7. Preliminary studies were made to insure compliance of the configuration with general design criteria, to integrate the propulsion system with the airframe, to select structural concepts and materials, and to define an efficient structural arrangement. An advanced computerized structural design system was used, in conjunction with a relatively large, complex finite element model, for detailed analysis and sizing of structural members to satisfy strength and flutter criteria. A baseline aircraft design was developed for assessment of current technology and for use in future studies of aerostructural trades, and application of advanced technology. Criteria, analysis methods, and results are presented.

Planning and Revising Written Arguments: The Effects of Two Text Structure-Based Interventions on Persuasiveness of 8th-Grade Students' Essays

ERIC Educational Resources Information Center

Midgette, Ekaterina; Haria, Priti

2016-01-01

The purpose of the study was to investigate the effects of two comprehensive argumentative writing interventions--Text Structure Instruction (TSI) and Text Structure Revision Instruction (TSRI)--on the eighth-grade students' ability to compose convincing essays that include structural elements of argumentative discourse. Both treatment groups…

A mathematical modeling method for determination of local vibroacoustic characteristics of structures

NASA Technical Reports Server (NTRS)

Tartakovskiy, B. D.; Dubner, A. B.

1973-01-01

A method is proposed for determining vibroacoustic characteristics from the results of measurements of the distribution of vibrational energy in a structure. The method is based on an energy model of a structure studied earlier. Equations are written to describe the distribution of vibrational energy in a hypothetical diffuse energy state in structural elements.

Damage of composite structures: Detection technique, dynamic response and residual strength

NASA Astrophysics Data System (ADS)

Lestari, Wahyu

2001-10-01

Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

4-d magnetism: Electronic structure and magnetism of some Mo-based alloys

NASA Astrophysics Data System (ADS)

Liu, Yong; Bose, S. K.; Kudrnovský, J.

2017-02-01

We report results of a first-principles density-functional study of alloys of the 4 d -element Mo with group IV elements Si, Ge and Sn in zinc blende (ZB) and rock salt (RS) structures. The study was motivated by a similar study of ours based on the 4 d -element Tc, which showed the presence of half-metallic states with integer magnetic moment (1μB) per formula unit in TcX (X=C, Si, Ge) alloys. The calculated Curie temperatures for the ferromagnetic (FM) phases were low, around or less than 300 K. Searching for the possibility of 4 d -based alloys with higher Curie temperatures we have carried out the study involving the elements Mo, Ru and Rh. Among these the most promising case appears to be that involving the element Mo. Among the MoX (X=Si, Ge, Sn) alloys in ZB and RS structures, both MoGe and MoSn in ZB structures are found to possess an integer magnetic moment of 2μB per formula unit. ZB MoSn can be classified as a marginal/weak half-metal or a spin gapless semiconductor, while ZB MoGe would be best described as a gapless magnetic semiconductor. The calculated Curie temperatures are in the range 300-700 K. Considering the theoretical uncertainty in the band gaps due not only to the treatment of exchange and correlation effects, but density functional theory itself, these classifications may change somewhat, but both merit investigation from the viewpoint of potential spintronic application. Based on their higher Curie temperatures, Mo-based alloys would serve such purpose better than the previously reported Tc-based ones.

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

NASA Technical Reports Server (NTRS)

Gutell, R. R.; Larsen, N.; Woese, C. R.

1994-01-01

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

Modification of the supramolecular structure of collagen with nanodisperse hydroxyapatite

NASA Astrophysics Data System (ADS)

Voloskova, E. V.; Berdnikova, L. K.; Poluboyarov, V. A.; Gur'yanova, T. I.

2015-02-01

The influence of nanodisperse particles of hydroxyapatite on the structure of films based on collagen with a molecular mass of 360 kDa was studied. When coatings formed, the collagen macromolecules aggregated into spherulites; modification led to structural changes related to the decomposition of the spherulite structure and the formation of a grain structure. The variation of the physicomechanical properties of film materials directly depends on the size of the structural units.

Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline

PubMed Central

Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

2014-01-01

Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual “atlases” that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures. PMID:24567717

Structure dependent selective efficacy of pyridine and pyrrole based Cu(II) Schiff base complexes towards in vitro cytotoxicity, apoptosis and DNA-bases binding in ground and excited state.

PubMed

Koley Seth, Banabithi; Saha, Arpita; Haldar, Srijan; Chakraborty, Partha Pratim; Saha, Partha; Basu, Samita

2016-09-01

This work highlights a systematic and comparative study of the structure-dependent influence of a series of biologically active Cu(II) Schiff base complexes (CSCs) on their in vitro cytotoxicity, apoptosis and binding with polymeric DNA-bases in ground and photo-excited states. The structure-activity relationship of the closely resembled CSCs towards in vitro cytotoxicity and apoptosis against cervical cancerous HeLa and normal human diploid WI-38 cell lines has been investigated by MTT assay and FACS techniques respectively. The steady-state and time-resolved spectroscopic studies have also been carried out to explore the selective binding affinities of the potential complexes towards different polymeric nucleic acid bases (poly d(A), poly d(T), poly d(G), poly d(C), Poly d(G)-Poly d(C)), which enlighten the knowledge regarding their ability in controlling the structure and medium dependent interactions in 'ground' and 'excited' states. The pyridine containing water soluble complexes (CuL(1) and CuL(3)) are much more cytotoxic than the corresponding pyrrole counterparts (CuL(2) and CuL(4)). Moreover the acidic hydrogens in CuL(1) increase its cytotoxicity much more than methyl substitution as in CuL(3). The results of MTT assay and double staining FACS experiments indicate selective inhibition of cell growth (cell viability 39% (HeLa) versus 85% (WI-38)) and occurrence of apoptosis rather than necrosis. The ground state binding of CuL(1) with polymeric DNA bases, especially with guanine rich DNA (Kb=6.41±0.122×10(5)), that enhances its cytotoxic activity, is further confirmed from its binding isotherms. On the other hand the pyrrole substituted CuL(4) complex exhibits the structure and medium dependent selective electron-transfer in triplet state as observed in laser flash photolysis studies followed by magnetic field (MF) effect. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

NASA Astrophysics Data System (ADS)

Qin, W.; Yang, L.

2004-05-01

Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study and the current multi-spectral and multi-angular satellite data (MODIS, MISR), a robust retrieval system to estimate woody vegetation structural/biophysical parameters is proposed.

Restructuring the High School: The Renaissance Program.

ERIC Educational Resources Information Center

Donavel, David F.

Based on the premise that deficiencies in student learning are inherent byproducts of the traditional school structure, this study compares the effects of an experimental curriculum program on student learning with its traditional structural counterpart. The traditional school structure is characterized by a heavy teacher workload, segmented…

A multi-frequency receiver function inversion approach for crustal velocity structure

NASA Astrophysics Data System (ADS)

Li, Xuelei; Li, Zhiwei; Hao, Tianyao; Wang, Sheng; Xing, Jian

2017-05-01

In order to constrain the crustal velocity structures better, we developed a new nonlinear inversion approach based on multi-frequency receiver function waveforms. With the global optimizing algorithm of Differential Evolution (DE), low-frequency receiver function waveforms can primarily constrain large-scale velocity structures, while high-frequency receiver function waveforms show the advantages in recovering small-scale velocity structures. Based on the synthetic tests with multi-frequency receiver function waveforms, the proposed approach can constrain both long- and short-wavelength characteristics of the crustal velocity structures simultaneously. Inversions with real data are also conducted for the seismic stations of KMNB in southeast China and HYB in Indian continent, where crustal structures have been well studied by former researchers. Comparisons of inverted velocity models from previous and our studies suggest good consistency, but better waveform fitness with fewer model parameters are achieved by our proposed approach. Comprehensive tests with synthetic and real data suggest that the proposed inversion approach with multi-frequency receiver function is effective and robust in inverting the crustal velocity structures.

ALI (Autonomous Lunar Investigator): Revolutionary Approach to Exploring the Moon with Addressable Reconfigurable Technology

NASA Technical Reports Server (NTRS)

Clark, P. E.; Curtis, S. A.; Rilee, M. L.; Floyd, S. R.

2005-01-01

Addressable Reconfigurable Technology (ART) based structures: Mission Concepts based on Addressable Reconfigurable Technology (ART), originally studied for future ANTS (Autonomous Nanotechnology Swarm) Space Architectures, are now being developed as rovers for nearer term use in lunar and planetary surface exploration. The architecture is based on the reconfigurable tetrahedron as a building block. Tetrahedra are combined to form space-filling networks, shaped for the required function. Basic structural components are highly modular, addressable arrays of robust nodes (tetrahedral apices) from which highly reconfigurable struts (tetrahedral edges), acting as supports or tethers, are efficiently reversibly deployed/stowed, transforming and reshaping the structures as required.

Relationship between unit cell type and porosity and the fatigue behavior of selective laser melted meta-biomaterials.

PubMed

Amin Yavari, S; Ahmadi, S M; Wauthle, R; Pouran, B; Schrooten, J; Weinans, H; Zadpoor, A A

2015-03-01

Meta-materials are structures when their small-scale properties are considered, but behave as materials when their homogenized macroscopic properties are studied. There is an intimate relationship between the design of the small-scale structure and the homogenized properties of such materials. In this article, we studied that relationship for meta-biomaterials that are aimed for biomedical applications, otherwise known as meta-biomaterials. Selective laser melted porous titanium (Ti6Al4V ELI) structures were manufactured based on three different types of repeating unit cells, namely cube, diamond, and truncated cuboctahedron, and with different porosities. The morphological features, static mechanical properties, and fatigue behavior of the porous biomaterials were studied with a focus on their fatigue behavior. It was observed that, in addition to static mechanical properties, the fatigue properties of the porous biomaterials are highly dependent on the type of unit cell as well as on porosity. None of the porous structures based on the cube unit cell failed after 10(6) loading cycles even when the applied stress reached 80% of their yield strengths. For both other unit cells, higher porosities resulted in shorter fatigue lives for the same level of applied stress. When normalized with respect to their yield stresses, the S-N data points of structures with different porosities very well (R(2)>0.8) conformed to one single power law specific to the type of the unit cell. For the same level of normalized applied stress, the truncated cuboctahedron unit cell resulted in a longer fatigue life as compared to the diamond unit cell. In a similar comparison, the fatigue lives of the porous structures based on both truncated cuboctahedron and diamond unit cells were longer than that of the porous structures based on the rhombic dodecahedron unit cell (determined in a previous study). The data presented in this study could serve as a basis for design of porous biomaterials as well as for corroboration of relevant analytical and computational models. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

NASA Astrophysics Data System (ADS)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.

A user exposure based approach for non-structural road network vulnerability analysis

PubMed Central

Jin, Lei; Wang, Haizhong; Yu, Le; Liu, Lin

2017-01-01

Aiming at the dense urban road network vulnerability without structural negative consequences, this paper proposes a novel non-structural road network vulnerability analysis framework. Three aspects of the framework are mainly described: (i) the rationality of non-structural road network vulnerability, (ii) the metrics for negative consequences accounting for variant road conditions, and (iii) the introduction of a new vulnerability index based on user exposure. Based on the proposed methodology, a case study in the Sioux Falls network which was usually threatened by regular heavy snow during wintertime is detailedly discussed. The vulnerability ranking of links of Sioux Falls network with respect to heavy snow scenario is identified. As a result of non-structural consequences accompanied by conceivable degeneration of network, there are significant increases in generalized travel time costs which are measurements for “emotionally hurt” of topological road network. PMID:29176832

NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes

PubMed Central

Dias, David M.; Ciulli, Alessio

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets. PMID:25175337

Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification.

PubMed

Jończyk, Jakub; Malawska, Barbara; Bajda, Marek

2017-01-01

The crucial role of G-protein coupled receptors and the significant achievements associated with a better understanding of the spatial structure of known receptors in this family encouraged us to undertake a study on the histamine H3 receptor, whose crystal structure is still unresolved. The latest literature data and availability of different software enabled us to build homology models of higher accuracy than previously published ones. The new models are expected to be closer to crystal structures; and therefore, they are much more helpful in the design of potential ligands. In this article, we describe the generation of homology models with the use of diverse tools and a hybrid assessment. Our study incorporates a hybrid assessment connecting knowledge-based scoring algorithms with a two-step ligand-based docking procedure. Knowledge-based scoring employs probability theory for global energy minimum determination based on information about native amino acid conformation from a dataset of experimentally determined protein structures. For a two-step docking procedure two programs were applied: GOLD was used in the first step and Glide in the second. Hybrid approaches offer advantages by combining various theoretical methods in one modeling algorithm. The biggest advantage of hybrid methods is their intrinsic ability to self-update and self-refine when additional structural data are acquired. Moreover, the diversity of computational methods and structural data used in hybrid approaches for structure prediction limit inaccuracies resulting from theoretical approximations or fuzziness of experimental data. The results of docking to the new H3 receptor model allowed us to analyze ligand-receptor interactions for reference compounds.

Experimental Research on the Dense CFB's Riser and the Simulation Based on the EMMS Model

NASA Astrophysics Data System (ADS)

Wang, X. Y.; Wang, S. D.; Fan, B. G.; Liao, L. L.; Jiang, F.; Xu, X.; Wu, X. Z.; Xiao, Y. H.

2010-03-01

The flow structure in the CFB (circulating fluidized bed) riser has been investigated. Experimental studies were performed in a cold square section unit with 270 mm×270 mm×10 m. Since the drag force model based on homogeneous two-phase flow such as the Gidaspow drag model could not depict the heterogeneous structures of the gas-solid flow, the structure-dependent energy-minimization multi-scale (EMMS) model based on the heterogenerity was applied in the paper and a revised drag force model based on the EMMS model was proposed. A 2D two-fluid model was used to simulate a bench-scale square cross-section riser of a cold CFB. The typical core-annulus structure and the back-mixing near the wall of the riser were observed and the assembly and fragmentation processes of clusters were captured. By comparing with the Gidaspow drag model, the results obtained by the revised drag model based on EMMS shows better consistency with the experimental data. The model can also depict the difference from the two exit configurations. This study once again proves the key role of drag force in CFD (Computational Fluid Dynamics) simulation and also shows the availability of the revised drag model to describe the gas-solid flow in CFB risers.

Characterizing the spatial structure of endangered species habitat using geostatistical analysis of IKONOS imagery

USGS Publications Warehouse

Wallace, C.S.A.; Marsh, S.E.

2005-01-01

Our study used geostatistics to extract measures that characterize the spatial structure of vegetated landscapes from satellite imagery for mapping endangered Sonoran pronghorn habitat. Fine spatial resolution IKONOS data provided information at the scale of individual trees or shrubs that permitted analysis of vegetation structure and pattern. We derived images of landscape structure by calculating local estimates of the nugget, sill, and range variogram parameters within 25 ?? 25-m image windows. These variogram parameters, which describe the spatial autocorrelation of the 1-m image pixels, are shown in previous studies to discriminate between different species-specific vegetation associations. We constructed two independent models of pronghorn landscape preference by coupling the derived measures with Sonoran pronghorn sighting data: a distribution-based model and a cluster-based model. The distribution-based model used the descriptive statistics for variogram measures at pronghorn sightings, whereas the cluster-based model used the distribution of pronghorn sightings within clusters of an unsupervised classification of derived images. Both models define similar landscapes, and validation results confirm they effectively predict the locations of an independent set of pronghorn sightings. Such information, although not a substitute for field-based knowledge of the landscape and associated ecological processes, can provide valuable reconnaissance information to guide natural resource management efforts. ?? 2005 Taylor & Francis Group Ltd.

Construction of an interim storage field using recovered municipal solid waste incineration bottom ash: Field performance study.

PubMed

Sormunen, Laura Annika; Kolisoja, Pauli

2017-06-01

The leaching of hazardous substances from municipal solid waste incineration (MSWI) bottom ash (BA) has been studied in many different scales for several years. Less attention has been given to the mechanical performance of MSWI BA in actual civil engineering structures. The durability of structures built with this waste derived material can have major influence on the functional properties of such structures and also the potential leaching of hazardous substances in the long term. Hence, it is necessary to properly evaluate in which type of structures MSWI BA can be safely used in a similar way as natural and crushed rock aggregates. In the current study, MSWI BA treated with ADR (Advance Dry Recovery) technology was used in the structural layers of an interim storage field built within a waste treatment centre. During and half a year after the construction, the development of technical and mechanical properties of BA materials and the built structures were investigated. The aim was to compare these results with the findings of laboratory studies in which the same material was previously investigated. The field results showed that the mechanical performance of recovered BA corresponds to the performance of natural aggregates in the lower structural layers of field structures. Conversely, the recovered MSWI BA cannot be recommended to be used in the base layers as such, even though its stiffness properties increased over time due to material aging and changes in moisture content. The main reason for this is that BA particles are prone for crushing and therefore inadequate to resist the higher stresses occurring in the upper parts of road and field structures. These results were in accordance with the previous laboratory findings. It can thus be concluded that the recovered MSWI BA is durable to be used as a replacement of natural aggregates especially in the lower structural layers of road and field structures, whereas if used in the base layers, an additional base layer of natural aggregate or a thicker asphalt pavement is recommended. Copyright © 2017 Elsevier Ltd. All rights reserved.

1983 Home Study Survey. A Report on Current Course Structure and Educational Practices in NHSC Member Institutions.

ERIC Educational Resources Information Center

National Home Study Council, Washington, DC.

A study examined the course structure and educational practices used by National Home Study Council (NHSC) member institutions. To gather data for the study, researchers mailed questionnaires to 60 members of the NHSC. Based on data from the 51 usable responses, the researchers determined that the average age of students enrolled in programs…

Novel nonlinear knowledge-based mean force potentials based on machine learning.

PubMed

Dong, Qiwen; Zhou, Shuigeng

2011-01-01

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge-based mean force potentials. The nonlinear potentials can be widely used for ab initio protein structure prediction, model quality assessment, protein docking, and other challenging problems in computational biology.

Rigidified pneumatic composites

NASA Astrophysics Data System (ADS)

van Dessel, Steven

2000-10-01

The overall objective of the research presented in this dissertation was to address global issues of adequate housing for all and the need for more sustainable human settlement. In order to address these, the emerging technology of rigidified pneumatic composites was investigated. Rigidified pneumatic composites (RPC) are defined as thin flexible membrane structures that are pneumatically deployed. After deployment, these structures harden due to chemical or physical change of the membrane. Because of this change, these structures do no longer require pneumatic pressure to maintain their shape. For the first time, a systematic listing of the various means available to develop polymeric materials useful in RPC technology is presented. With the aim to reduce the cost of RPC structures, a new material was proposed, developed, and evaluated. This material involved the formation of a semi-interpenetrating polymer network based on poly vinyl chloride and an acrylate based reactive plasticizer. The economical and environmental performances of RPC structures using this new material were assessed by means of a case study. In this study, the performance of RPC technology was compared with that of a typical wood light frame structure in the application of a small single-family house. The study indicated that the cost of ownership in present day value for the RPC structure was approximately 33% less than the cost of a comparable wood light frame structure. The study also indicated that significant environmental benefits exist with the use of RPC structures. It was found that the RPC structure used significantly less resources compared to the wood light frame structure. About 3.5 times less materials coming from non-renewable fossil resources, about 2.5 times less materials coming from trees, and about 19 times less materials coming from inorganic resources was used in the RPC structure relative to the wood light frame structure. The study concluded with pointing out various means available to further increase the economical and environmental performance of RPC technology. Directions were provided to guide future developments of RPC technology.

Identify Structural Flaw Location and Type with an Inverse Algorithm of Resonance Inspection

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

Xu, Wei; Lai, Canhai; Sun, Xin

To evaluate the fitness-for-service of a structural component and to quantify its remaining useful life, aging and service-induced structural flaws must be quantitatively determined in service or during scheduled maintenance shutdowns. Resonance inspection (RI), a non-destructive evaluation (NDE) technique, distinguishes the anomalous parts from the good parts based on changes in the natural frequency spectra. Known for its numerous advantages, i.e., low inspection cost, high testing speed, and broad applicability to complex structures, RI has been widely used in the automobile industry for quality inspection. However, compared to other contemporary direct visualization-based NDE methods, a more widespread application of RImore » faces a fundamental challenge because such technology is unable to quantify the flaw details, e.g. location, dimensions, and types. In this study, the applicability of a maximum correlation-based inverse RI algorithm developed by the authors is further studied for various flaw cases. It is demonstrated that a variety of common structural flaws, i.e. stiffness degradation, voids, and cracks, can be accurately retrieved by this algorithm even when multiple different types of flaws coexist. The quantitative relations between the damage identification results and the flaw characteristics are also developed to assist the evaluation of the actual state of health of the engineering structures.« less

Fat emulsions based on structured lipids (1,3-specific triglycerides): an investigation of the in vivo fate.

PubMed

Hedeman, H; Brøndsted, H; Müllertz, A; Frokjaer, S

1996-05-01

Structured lipids (1,3-specific triglycerides) are new chemical entities made by enzymatic transesterification of the fatty acids in the 1,3 positions of the triglyceride. The purpose of this study is to characterize structured lipids with either short chain fatty acids or medium chain fatty acids in the 1,3 positions with regard to their hydrophobicity, and investigate the in vivo fate in order to evaluate the potential of structured lipids as core material in fat emulsions used as parenteral drug delivery system. The lipids were characterized by employing reversed phase high performance liquid chromatography. The biodistribution of radioactively labeled emulsions was studied in rats. By employing high performance liquid chromatography a rank order of the hydrophobicities of the lipids could be given, with the triglycerides containing long chain fatty acids being the most hydrophobic and the structured lipid with short chain fatty acids in the 1,3 positions the least. When formulated as fat emulsions, the emulsion based on structured lipids with short fatty acids in the 1,3 positions was removed slower from the general blood circulation compared to emulsions based on lipids with long chain fatty acids in the 1,3 positions. The type of core material influences the in vivo circulation time of fat emulsions.

What We Know About the Brain Structure-Function Relationship.

PubMed

Batista-García-Ramó, Karla; Fernández-Verdecia, Caridad Ivette

2018-04-18

How the human brain works is still a question, as is its implication with brain architecture: the non-trivial structure–function relationship. The main hypothesis is that the anatomic architecture conditions, but does not determine, the neural network dynamic. The functional connectivity cannot be explained only considering the anatomical substrate. This involves complex and controversial aspects of the neuroscience field and that the methods and methodologies to obtain structural and functional connectivity are not always rigorously applied. The goal of the present article is to discuss about the progress made to elucidate the structure–function relationship of the Central Nervous System, particularly at the brain level, based on results from human and animal studies. The current novel systems and neuroimaging techniques with high resolutive physio-structural capacity have brought about the development of an integral framework of different structural and morphometric tools such as image processing, computational modeling and graph theory. Different laboratories have contributed with in vivo, in vitro and computational/mathematical models to study the intrinsic neural activity patterns based on anatomical connections. We conclude that multi-modal techniques of neuroimaging are required such as an improvement on methodologies for obtaining structural and functional connectivity. Even though simulations of the intrinsic neural activity based on anatomical connectivity can reproduce much of the observed patterns of empirical functional connectivity, future models should be multifactorial to elucidate multi-scale relationships and to infer disorder mechanisms.

Adjusting protein graphs based on graph entropy.

PubMed

Peng, Sheng-Lung; Tsay, Yu-Wei

2014-01-01

Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein-graph remodeling, instead of looking a minimum superimposition for pairwise proteins. When graphs are used to represent structured objects, the problem of measuring object similarity become one of computing the similarity between graphs. Graph theory provides an alternative perspective as well as efficiency. Once a protein graph has been created, its structural stability must be verified. Therefore, a criterion is needed to determine if a protein graph can be used for structural comparison. In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when applied, graph entropy helps a conformational on protein graph modeling. Furthermore, it indirectly contributes to protein structural comparison if a protein graph is solid.

System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions

NASA Astrophysics Data System (ADS)

Sakata, Katsumi; Ohyanagi, Hajime; Sato, Shinji; Nobori, Hiroya; Hayashi, Akiko; Ishii, Hideshi; Daub, Carsten O.; Kawai, Jun; Suzuki, Harukazu; Saito, Toshiyuki

2015-02-01

We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.

Adjusting protein graphs based on graph entropy

PubMed Central

2014-01-01

Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein-graph remodeling, instead of looking a minimum superimposition for pairwise proteins. When graphs are used to represent structured objects, the problem of measuring object similarity become one of computing the similarity between graphs. Graph theory provides an alternative perspective as well as efficiency. Once a protein graph has been created, its structural stability must be verified. Therefore, a criterion is needed to determine if a protein graph can be used for structural comparison. In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when applied, graph entropy helps a conformational on protein graph modeling. Furthermore, it indirectly contributes to protein structural comparison if a protein graph is solid. PMID:25474347

Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment.

PubMed

Li, Yaohang; Liu, Hui; Rata, Ionel; Jakobsson, Eric

2013-02-25

The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where high-order inter-residue interactions are taken into consideration. The CSSP potential is effective in identifying secondary structure predictions with good quality. In 56% of the targets in the CB513 benchmark, the optimal CSSP potential is able to recognize the native secondary structure or a prediction with Q3 accuracy higher than 90% as best scored in the predicted secondary structures generated by 10 popularly used secondary structure prediction servers. In more than 80% of the CB513 targets, the predicted secondary structures with the lowest CSSP potential values yield higher than 80% Q3 accuracy. Similar performance of CSSP is found on the CASP9 targets as well. Moreover, our computational results also show that the CSSP potential using triplets outperforms the CSSP potential using doublets and is currently better than the CSSP potential using quartets.

Fragment-Based Discovery of Pyrimido[1,2-b]indazole PDE10A Inhibitors.

PubMed

Chino, Ayaka; Seo, Ryushi; Amano, Yasushi; Namatame, Ichiji; Hamaguchi, Wataru; Honbou, Kazuya; Mihara, Takuma; Yamazaki, Mayako; Tomishima, Masaki; Masuda, Naoyuki

2018-01-01

In this study, we report the identification of potent pyrimidoindazoles as phosphodiesterase10A (PDE10A) inhibitors by using the method of fragment-based drug discovery (FBDD). The pyrazolopyridine derivative 2 was found to be a fragment hit compound which could occupy a part of the binding site of PDE10A enzyme by using the method of the X-ray co-crystal structure analysis. On the basis of the crystal structure of compound 2 and PDE10A protein, a number of compounds were synthesized and evaluated, by means of structure-activity relationship (SAR) studies, which culminated in the discovery of a novel pyrimidoindazole derivative 13 having good physicochemical properties.

Study on Wind-induced Vibration and Fatigue Life of Cable-stayed Flexible Antenna

NASA Astrophysics Data System (ADS)

He, Kongde; He, Xuehui; Fang, Zifan; Zheng, Xiaowei; Yu, Hongchang

2018-03-01

The cable-stayed flexible antenna is a large-span space structure composed of flexible multibody, with low frequency of vibration, vortex-induced resonance can occur under the action of Stochastic wind, and a larger amplitude is generated when resonance occurs. To solve this problem, based on the theory of vortex-induced vibration, this paper analyzes the vortex-induced vibration of a cable-stayed flexible antenna under the action of Wind. Based on the sinusoidal force model and Autoregressive Model (AR) method, the vortex-induced force is simulated, then the fatigue analysis of the structure is based on the linear fatigue cumulative damage principle and the rain-flow method. The minimum fatigue life of the structure is calculated to verify the vibration fatigue performance of the structure.

Around the macrolide - Impact of 3D structure of macrocycles on lipophilicity and cellular accumulation.

PubMed

Koštrun, Sanja; Munic Kos, Vesna; Matanović Škugor, Maja; Palej Jakopović, Ivana; Malnar, Ivica; Dragojević, Snježana; Ralić, Jovica; Alihodžić, Sulejman

2017-06-16

The aim of this study was to investigate lipophilicity and cellular accumulation of rationally designed azithromycin and clarithromycin derivatives at the molecular level. The effect of substitution site and substituent properties on a global physico-chemical profile and cellular accumulation of investigated compounds was studied using calculated structural parameters as well as experimentally determined lipophilicity. In silico models based on the 3D structure of molecules were generated to investigate conformational effect on studied properties and to enable prediction of lipophilicity and cellular accumulation for this class of molecules based on non-empirical parameters. The applicability of developed models was explored on a validation and test sets and compared with previously developed empirical models. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Theoretical Study on Structural Stability of Fully Filled p-Type Skutterudites RETM4Sb12 ( RE = Rare Earth; TM = Fe, Ru)

NASA Astrophysics Data System (ADS)

Chen, Zhuo; Yang, Jiong; Liu, Ruiheng; Xi, Lili; Zhang, Wenqing; Yang, Jihui

2013-08-01

The structural stability of filled p-type skutterudites RETM4Sb12 ( RE = rare earth; TM = Fe, Ru) was studied via ab initio calculations. Most of the RE metals (La-Ho and Yb) could be filled into the cages (voids) of Fe4Sb12 to form stable filled skutterudites. However, only a few RE metals (La-Nd and Eu) could be stably filled into the cage of Ru4Sb12-based skutterudites. Systematic analysis of bonding energy showed that the structural stability could be attributed to ionic radius and effective charge state differences of the RE fillers. Resonant rattling frequencies of the fillers in both Fe4Sb12- and Ru4Sb12-based skutterudites were also studied.

Haplotype Analysis of the Melanopsin Gene in Seasonal Affective Disorder and Controls

DTIC Science & Technology

2007-06-19

Cole, P. A. (2002). Serotonin n-acetyltransferase: Mechanism and inhibition. Current Medicinal Chemistry , 9(12), 1187-1199. 152 APPENDIX A STRUCTURED ...such that low light levels fall below this threshold during winter in individuals with SAD. The present study investigated the haplotype structure of...Association Studies 51 Advantages of Population-Based Case-Control Samples 52 Haplotype Structure 53 Linkage Disequilibrium: A Measure of Correlation Between

Learning New Grammatical Structures in Task-Based Language Learning: The Effects of Recasts and Prompts

ERIC Educational Resources Information Center

Van de Guchte, Marrit; Braaksma, Martine; Rijlaarsdam, Gert; Bimmel, Peter

2015-01-01

In the present study, we examine the effects of prompts and recasts on the acquisition of two new and different grammar structures in a task-based learning environment. Sixty-four 14-year-old 9th grade students (low intermediate) learning German as a foreign language were randomly assigned to three conditions: two experimental groups (one…

Web-Based Tutoring of the Structure Strategy with or without Elaborated Feedback or Choice for Fifth- and Seventh-Grade Readers

ERIC Educational Resources Information Center

Meyer, Bonnie J. F.; Wijekumar, Kay; Middlemiss, Wendy; Higley, Kelli; Lei, Pui-Wa; Meier, Catherine; Spielvogel, James

2010-01-01

This study investigated the effects of different versions of Web-based instruction focused on text structure on fifth- and seventh-grade students' reading comprehension. Stratified random assignment was employed in a two-factor experiment embedded within a pretest and multiple posttests design (immediate and four-month delayed posttests). The two…

An Evaluation of the Factor Structure of the Frost Multidimensional Perfectionism Scale

ERIC Educational Resources Information Center

Harvey, Bronwyn; Pallant, Julie; Harvey, David

2004-01-01

The purpose of the study was to investigate whether the six-factor structure of the Frost Multidimensional Perfectionism Scale could be replicated in a community-based sample. A sample of 255 adult participants (55.7% female, 44.3% male) ranging in age from 18 to 78 (mean = 37.0) completed the questionnaire. Based on the screen test and parallel…

Mechanical properties and the electronic structure of transition of metal alloys

NASA Technical Reports Server (NTRS)

Arsenault, R. J.; Drew, H. D.

1977-01-01

This interdiscipline research program was undertaken in an effort to investigate the relationship between the mechanical strength of Mo based alloys with their electronic structure. Electronic properties of these alloys were examined through optical studies, and the classical solid solution strengthening mechanisms were considered, based on size and molecular differences to determine if these mechanisms could explain the hardness data.

Simultaneous vibration control and energy harvesting using actor-critic based reinforcement learning

NASA Astrophysics Data System (ADS)

Loong, Cheng Ning; Chang, C. C.; Dimitrakopoulos, Elias G.

2018-03-01

Mitigating excessive vibration of civil engineering structures using various types of devices has been a conspicuous research topic in the past few decades. Some devices, such as electromagnetic transducers, which have a capability of exerting control forces while simultaneously harvesting energy, have been proposed recently. These devices make possible a self-regenerative system that can semi-actively mitigate structural vibration without the need of external energy. Integrating mechanical, electrical components, and control algorithms, these devices open up a new research domain that needs to be addressed. In this study, the feasibility of using an actor-critic based reinforcement learning control algorithm for simultaneous vibration control and energy harvesting for a civil engineering structure is investigated. The actor-critic based reinforcement learning control algorithm is a real-time, model-free adaptive technique that can adjust the controller parameters based on observations and reward signals without knowing the system characteristics. It is suitable for the control of a partially known nonlinear system with uncertain parameters. The feasibility of implementing this algorithm on a building structure equipped with an electromagnetic damper will be investigated in this study. Issues related to the modelling of learning algorithm, initialization and convergence will be presented and discussed.

PbSe-Based Colloidal Core/Shell Heterostructures for Optoelectronic Applications

PubMed Central

Zaiats, Gary; Yanover, Diana; Vaxenburg, Roman; Tilchin, Jenya; Sashchiuk, Aldona; Lifshitz, Efrat

2014-01-01

Lead-based (IV–VI) colloidal quantum dots (QDs) are of widespread scientific and technological interest owing to their size-tunable band-gap energy in the near-infrared optical region. This article reviews the synthesis of PbSe-based heterostructures and their structural and optical investigations at various temperatures. The review focuses on the structures consisting of a PbSe core coated with a PbSexS1–x (0 ≤ x ≤ 1) or CdSe shell. The former-type shells were epitaxially grown on the PbSe core, while the latter-type shells were synthesized using partial cation-exchange. The influence of the QD composition and the ambient conditions, i.e., exposure to oxygen, on the QD optical properties, such as radiative lifetime, Stokes shift, and other temperature-dependent characteristics, was investigated. The study revealed unique properties of core/shell heterostructures of various compositions, which offer the opportunity of fine-tuning the QD electronic structure by changing their architecture. A theoretical model of the QD electronic band structure was developed and correlated with the results of the optical studies. The review also outlines the challenges related to potential applications of colloidal PbSe-based heterostructures. PMID:28788244

Structuration of lipid bases with fully hydrogenated crambe oil and sorbitan monostearate for obtaining zero-trans/low sat fats.

PubMed

Stahl, Marcella Aparecida; Buscato, Monise Helen Masuchi; Grimaldi, Renato; Cardoso, Lisandro Pavie; Ribeiro, Ana Paula Badan

2018-05-01

Several studies have shown that excessive intake of trans and saturated fatty acids is associated with an increased risk of cardiovascular disease. In this context, the food industry has sought alternatives for the development of healthy lipid bases, with higher levels of unsaturated fatty acids, adapting to current legislation. The incorporation of structuring agents into liquid oils has proven to be a potential alternative for obtaining semi-plastic lipid bases with reduced levels of saturated fatty acids. Thus, the objective of this study was to produce zero trans fat bases with lower saturated fatty acids levels. Palm oil (PO) was used as a zero trans-lipid base reference because of its technological functionality. Blends containing different proportions of high oleic sunflower oil (HOSO) and PO were prepared as follows: control 100: 0; 80:20; 60:40; 40:60; 20:80; and 100: 0 PO: HOSO (w/w%), respectively. Then, 3% of fully hydrogenated crambe oil (FHCO) and 3% sorbitan monostearate (SMS) were added to the blends as structuring agents, forming the structured (S) blends. The addition of HOSO to the PO decreased the saturated fatty acids by up to 30.6%, with consequent increase of unsaturated fatty acids, especially oleic acid. The joint action of the SMS and the FCHO allowed for obtaining structured blends with plastic and spreadability characteristics, as well as modifications throughout the crystallization process of the original blends. Copyright © 2018 Elsevier Ltd. All rights reserved.

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

PubMed Central

Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

2014-01-01

Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic. Here we introduce MONGOOSE, a toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. We apply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass reaction is surprisingly blocked (unable to sustain non-zero flux) in nearly half of them. We propose a principled approach for unblocking these reactions and extend it to the problems of identifying essential and synthetic lethal reactions and minimal media. Our structural insights enable a systematic study of constraint-based metabolic models, yielding a deeper understanding of their possibilities and limitations. PMID:25291352

Low-Temperature Growth and Doping of Mercury-Based II-Vi Multiple Quantum Well Structures by Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Lansari, Yamina

The growth of Hg-based single layers and multiple quantum well structures by conventional molecular beam epitaxy (MBE) and photoassisted MBE was studied. The use of photoassisted MBE, an epitaxial growth technique developed at NCSU, has resulted in a substantial reduction of the film growth temperature. Indeed, substrate temperatures 50 to 100^circC lower than those customarily used by others for conventional MBE growth of Hg-based layers were successfully employed. Photoassisted MBE allowed the preparation of excellent structural quality HgTe layers (FWHM for the (400) diffraction peak ~ 40 arcsec), HgCdTe layers (FWHM for the (400) diffraction peak ~ 14 arcsec), and HgTeCdTe superlattices (FWHM for the (400) diffraction peak ~ 28 arcsec). In addition, n-type and p-type modulation-doping of Hg-based multilayers was accomplished by photoassisted MBE. This technique has been shown to have a significant effect on the growth process kinetics as well as on the desorption rates of the film species, thereby affecting dopant incorporation mechanisms and allowing for the successful substitutional doping of the multilayer structures. Finally, surface morphology studies were completed using scanning electron microscopy (SEM) and Nomarsky optical microscopy to study the effects of substrate surface preparation, growth initiation, and growth parameters on the density of pyramidal hillocks, a common growth defect plaguing the Hg-based layers grown in the (100) direction. Conditions which minimize the hillock density for (100) film growth have been determined.

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

Gómez, H.; Katsanevas, S.; Tonazzo, A.

One of the main concerns in archaeology is to find of a method to study precisely archaeological structures in the least invasive way possible to avoid damage. The requirement of preserving the structures integrity prevents, in the case of pyramids or tumuli, the study of any internal structure (halls or tombs) which are not reachable by existing corridors. One non-invasive method is the muon tomography. By placing a detector which allows to register the muon direction after the structure, it is possible to have an idea of its composition based on the attenuation of the muon flux, which depends onmore » the material length and density that muons have crossed. This technique, alone or together with other exploration techniques as seismic tomography or electrical resistivity tomography, can provide useful information about the internal structure of the archaeological form that can not be obtained by conventional archaeological methods. In this work, the time measurement necessary to obtain a significant result about the composition of an archaeological structure is estimated. To do that, a Monte Carlo simulation framework based on the MUSIC software, properly tuned for this study, has been developed. The particular case of the Kastas Amfipoli Macedonian tumulus has been considered to perform the simulations.« less

The Structure-Mapping Engine: Algorithm and Examples.

ERIC Educational Resources Information Center

Falkenhainer, Brian; And Others

This description of the Structure-Mapping Engine (SME), a flexible, cognitive simulation program for studying analogical processing which is based on Gentner's Structure-Mapping theory of analogy, points out that the SME provides a "tool kit" for constructing matching algorithms consistent with this theory. This report provides: (1) a…

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…

Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

NASA Astrophysics Data System (ADS)

El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

2016-12-01

Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

Characterization of microbial structures in Setul Limestone

NASA Astrophysics Data System (ADS)

Ezanie, A. S. Mohamad; Aziz, A. Che; Roslan, M. Kamal

2018-04-01

Setul Limestone in Langgun Island and Perlis are lack of sedimentary structures, which makes it difficult for paleoenvironmental study in the study area. The present study of limestone succession at Kaki Bukit and Teluk Mempelam area focuses on microbial related structure in order to constraint its depositional setting. The structures were identified as stromatolites and thrombolites, which resulted from the interaction of microbial with sediments by trapping, binding and/or precipitation of minerals. Both structures can be distinguished based on four main classifications, the megastructure, macrostructure, mesostructure and microstructure scales. These classifications assist in understanding its physical natures and lead to the recognition of paleoenvironment in the study area which is believed to be controlled by several factors such as environment, hydrodynamic, biological and chemical processes.

Hierarchical prediction of industrial water demand based on refined Laspeyres decomposition analysis.

PubMed

Shang, Yizi; Lu, Shibao; Gong, Jiaguo; Shang, Ling; Li, Xiaofei; Wei, Yongping; Shi, Hongwang

2017-12-01

A recent study decomposed the changes in industrial water use into three hierarchies (output, technology, and structure) using a refined Laspeyres decomposition model, and found monotonous and exclusive trends in the output and technology hierarchies. Based on that research, this study proposes a hierarchical prediction approach to forecast future industrial water demand. Three water demand scenarios (high, medium, and low) were then established based on potential future industrial structural adjustments, and used to predict water demand for the structural hierarchy. The predictive results of this approach were compared with results from a grey prediction model (GPM (1, 1)). The comparison shows that the results of the two approaches were basically identical, differing by less than 10%. Taking Tianjin, China, as a case, and using data from 2003-2012, this study predicts that industrial water demand will continuously increase, reaching 580 million m 3 , 776.4 million m 3 , and approximately 1.09 billion m 3 by the years 2015, 2020 and 2025 respectively. It is concluded that Tianjin will soon face another water crisis if no immediate measures are taken. This study recommends that Tianjin adjust its industrial structure with water savings as the main objective, and actively seek new sources of water to increase its supply.

Entropy-theory-based study on the relationship between land use structure and industry system: a case study of the eastern Hubei metropolitan area

NASA Astrophysics Data System (ADS)

Su, Lilan; Liu, Yanfang; Gao, Xiaoyong

2009-10-01

During the process of economic growth, the industry structure transforms at different developing sections and that industrial composition as well as each department interior demand for land resources would reflect on land-use structure reform. This paper takes Hubei as the research zone, through a consecutive time sequence of 10 years period (1996-2005) just before and after the 1 plus 8 Eastern Hubei Metropolitan Area project, a quantitative study of the correlation between the industry structure and land-use structure is made based on the entropy theory. According to the classification of industrial composition, the land-use structure here is also redefined into four types as Land Use for Primary Industry, Land Use for Secondary Industry, Land Use for Tertiary Industry, and Land Use for Potential Reserve, in the aim that it should model new methods for researching the relationship of industry structure and land-use structure, and the instinct driving force would be presented more evidently at the same time. The outcomes indicate that the change of land-use structure has close relationship with the structure of industry composition; the trend of information entropy in Hubei mostly keeps increasing during the past 10 years which predicating the symmetrical degree of land-use structure is gradually built; and Eastern Hubei Metropolitan Area is of favorable power far superiority other units within province in promoting regional development, yet land-use structure adjustments are still not stable and a optimal mode of land use needs further approach.

RECURSIVE PROTEIN MODELING: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9

PubMed Central

CHENG, JIANLIN; EICKHOLT, JESSE; WANG, ZHENG; DENG, XIN

2013-01-01

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of structural modeling, two types of modeling techniques — template-based modeling and template-free modeling — have been developed. Template-based modeling can often generate a moderate- to high-resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling, such as fragment-based assembly, may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e. certain) and template-free (i.e. uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can signicantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction. PMID:22809379

Isosteric And Non-Isosteric Base Pairs In RNA Motifs: Molecular Dynamics And Bioinformatics Study Of The Sarcin-Ricin Internal Loop

PubMed Central

Havrila, Marek; Réblová, Kamila; Zirbel, Craig L.; Leontis, Neocles B.; Šponer, Jiří

2013-01-01

The Sarcin-Ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, i.e., in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of SR motif. SHAPE probing experiment was also performed to confirm fidelity of MD simulations. We identified 57 instances of the SR motif in a non-redundant subset of the RNA X-ray structure database and analyzed their basepairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large ribosomal RNA alignments to determine frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Non isosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that inability to form stable cWW geometry is an important factor in case of the first base pair of the flexible region of the SR motif. Comparison of structural, bioinformatics, SHAPE probing and MD simulation data reveals that explicit solvent MD simulations neatly reflect viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions. PMID:24144333

A Study of Cognitive Linguistic Structure Based on the Four Conditions of the Mulamadhyamakakarika

ERIC Educational Resources Information Center

You, Hee Jong

2013-01-01

The main purpose of this study is to depict Nagarjuna's implication on how he redefined the Four Conditions ("atvarah pratyaya") as the cognitive linguistic structure by allocating 32 functional metadata throughout the texts of Mulamadhyamakakarika (MMK). Following subtle traces of "okasamvrtisatya" (the conventional truth) in…

How to get the most out of your orthopaedic fellowship: thinking about practice-based learning.

PubMed

Templeman, David

2012-09-01

Practice-based learning and improvement is an important skill set to develop during an orthopaedic trauma fellowship and is 1 of the 6 core competencies stated by the ACGME. The review of clinic cases is best done using a few simple models to develop a structured approach for studying cases. Three common sense and easy-to-use strategies to improve clinical practice are as follows: performing each case three times, studying the 4 quadrants of patient outcomes, and the application of the Pareto 80/20 rule. These principles help to develop a structured approach for analyzing and thinking about practice-based experiences.

Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

DOE PAGES

Yu, Peiqiang

2007-01-01

Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

A comparison of EBSD based strain indicators for the study of Fe-3Si steel subjected to cyclic loading

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

Schayes, Claire; Valeo Engine Electrical Systems, 2 Rue André Boulle, 94046 Créteil; Bouquerel, Jérémie, E-mail: jeremie.bouquerel@univ-lille1.fr

The current work aims at proposing an EBSD-based indicator for fatigue damage of a Fe-3Si steel. At the same time direct observation of dislocation structures is provided by electron channelling contrast imaging (ECCI). The investigation consisted in processing the EBSD data from patterns collected on specimen subjected to low cycle fatigue. It revealed two different regimes depending on the applied total strain variation which is explained by the identification of the dislocations structures and their evolution. At low strain variation, strain accommodation occurs by planar glide of dislocations uniformly distributed throughout the grains. No misorientation evolution is observed. At highermore » strain variation, the vein-channel structure is observed within the grain and the wall-channel structure in the vicinity of grain boundaries. The misorientation between these two dislocation structures is evaluated at about 0.7° which is detected by the EBSD analyses and explains the increase of the different misorientation based criteria. The EBSD study enables also the prediction of crack initiation mode. Finally, this study points out the limits of the EBSD technique as no misorientation evolution is detected at small strain variation. Indeed, the lattice distortion is too weak to be detected by conventional EBSD. - Highlights: • Microstructure investigation of the fatigue behaviour of an iron-silicon steel • Use of cECCI to investigate the fatigue dislocations structures • Characterisation of local plastic accommodation through EBSD misorientation criteria.« less

Health monitoring of reinforced concrete structures based on PZT admittance signal

NASA Astrophysics Data System (ADS)

Wang, Dansheng; Zhu, Hongping; Shen, Danyan; Ge, Dongdong

2009-07-01

Reinforced concrete (RC) structure is one of most familiar engineering structure styles in the civil engineering community, which often suffer crack damage during their service life because of some factors such as overloading, excessive use, and bad environmental conditions. Thus early detection of crack damage is of special concern for RC structures. Piezoelectric materials have direct and converse piezoelectric effects and can serve as actuators or sensors. A health monitoring method based on PZT admittance signals is addressed in this paper, which use the electromechanical coupling property of piezoelectric materials. An experimental study on health monitoring of a RC beam is implemented based on the PZT admittance signals. In this experiment, the electrical admittances of distributed PZT sheets are measured when the host beams are suffering from variable loads. From the obtained PZT admittance curves one can find that the presence of incipient crack can be captured and the cracking load of the RC beam can also generally determined. By the experimental study it is concluded that the health monitoring technique is quite effective and sensitive for RC structures, which indicates its favorable application foreground in civil engineering field.

Structure-activity relationship studies of chalcone leading to 3-hydroxy-4,3',4',5'-tetramethoxychalcone and its analogues as potent nuclear factor kappaB inhibitors and their anticancer activities.

PubMed

Srinivasan, Balasubramanian; Johnson, Thomas E; Lad, Rahul; Xing, Chengguo

2009-11-26

Chalcone is a privileged structure, demonstrating promising anti-inflammatory and anticancer activities. One potential mechanism is to suppress nuclear factor kappa B (NF-kappaB) activation. The structures of chalcone-based NF-kappaB inhibitors vary significantly that there is minimum information about their structure-activity relationships (SAR). This study aims to establish SAR of chalcone-based compounds to NF-kappaB inhibition, to explore the feasibility of developing simple chalcone-based potent NF-kappaB inhibitors, and to evaluate their anticancer activities. Three series of chalcones were synthesized in one to three steps with the key step being aldol condensation. These candidates demonstrated a wide range of NF-kappaB inhibitory activities, some of low micromolar potency, establishing that structural complexity is not required for NF-kappaB inhibition. Lead compounds also demonstrate potent cytotoxicity against lung cancer cells. Their cytotoxicities correlate moderately well with their NF-kappaB inhibitory activities, suggesting that suppressing NF-kappaB activation is likely responsible for at least some of the cytotoxicities. One lead compound effectively inhibits lung tumor growth with no signs of adverse side effects.

Hierarchical structural health monitoring system combining a fiber optic spinal cord network and distributed nerve cell devices

NASA Astrophysics Data System (ADS)

Minakuchi, Shu; Tsukamoto, Haruka; Takeda, Nobuo

2009-03-01

This study proposes novel hierarchical sensing concept for detecting damages in composite structures. In the hierarchical system, numerous three-dimensionally structured sensor devices are distributed throughout the whole structural area and connected with the optical fiber network through transducing mechanisms. The distributed "sensory nerve cell" devices detect the damage, and the fiber optic "spinal cord" network gathers damage signals and transmits the information to a measuring instrument. This study began by discussing the basic concept of the hierarchical sensing system thorough comparison with existing fiber optic based systems and nerve systems in the animal kingdom. Then, in order to validate the proposed sensing concept, impact damage detection system for the composite structure was proposed. The sensor devices were developed based on Comparative Vacuum Monitoring (CVM) system and the Brillouin based distributed strain sensing was utilized to gather the damage signals from the distributed devices. Finally a verification test was conducted using prototype devices. Occurrence of barely visible impact damage was successfully detected and it was clearly indicated that the hierarchical system has better repairability, higher robustness, and wider monitorable area compared to existing systems utilizing embedded optical fiber sensors.

Ab initio study of naphtho-homologated DNA bases.

PubMed

Vazquez-Mayagoita, Alvaro; Huertas, Oscar; Fuentes-Cabrera, Miguel; Sumpter, Bobby G; Orozco, Modesto; Luque, F Javier

2008-02-21

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening

NASA Astrophysics Data System (ADS)

Halim, Sobia A.; Khan, Shanza; Khan, Ajmal; Wadood, Abdul; Mabood, Fazal; Hussain, Javid; Al-Harrasi, Ahmed

2017-10-01

Dengue fever is an emerging public health concern, with several million viral infections occur annually, for which no effective therapy currently exist. Non-structural protein 3 (NS-3) Helicase encoded by the dengue virus (DENV) is considered as a potential drug target to design new and effective drugs against dengue. Helicase is involved in unwinding of dengue RNA. This study was conducted to design new NS-3 Helicase inhibitor by in silico ligand- and structure based approaches. Initially ligand-based pharmacophore model was generated that was used to screen a set of 1201474 compounds collected from ZINC Database. The compounds matched with the pharmacophore model were docked into the active site of NS-3 helicase. Based on docking scores and binding interactions, twenty five compounds are suggested to be potential inhibitors of NS3 Helicase. The pharmacokinetic properties of these hits were predicted. The selected hits revealed acceptable ADMET properties. This study identified potential inhibitors of NS-3 Helicase in silico, and can be helpful in the treatment of Dengue.

Optimum element density studies for finite-element thermal analysis of hypersonic aircraft structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Olona, Timothy; Muramoto, Kyle M.

1990-01-01

Different finite element models previously set up for thermal analysis of the space shuttle orbiter structure are discussed and their shortcomings identified. Element density criteria are established for the finite element thermal modelings of space shuttle orbiter-type large, hypersonic aircraft structures. These criteria are based on rigorous studies on solution accuracies using different finite element models having different element densities set up for one cell of the orbiter wing. Also, a method for optimization of the transient thermal analysis computer central processing unit (CPU) time is discussed. Based on the newly established element density criteria, the orbiter wing midspan segment was modeled for the examination of thermal analysis solution accuracies and the extent of computation CPU time requirements. The results showed that the distributions of the structural temperatures and the thermal stresses obtained from this wing segment model were satisfactory and the computation CPU time was at the acceptable level. The studies offered the hope that modeling the large, hypersonic aircraft structures using high-density elements for transient thermal analysis is possible if a CPU optimization technique was used.

Opinion dynamics in a group-based society

NASA Astrophysics Data System (ADS)

Gargiulo, F.; Huet, S.

2010-09-01

Many models have been proposed to analyze the evolution of opinion structure due to the interaction of individuals in their social environment. Such models analyze the spreading of ideas both in completely interacting backgrounds and on social networks, where each person has a finite set of interlocutors. In this paper we analyze the reciprocal feedback between the opinions of the individuals and the structure of the interpersonal relationships at the level of community structures. For this purpose we define a group-based random network and we study how this structure co-evolves with opinion dynamics processes. We observe that the adaptive network structure affects the opinion dynamics process helping the consensus formation. The results also show interesting behaviors in regards to the size distribution of the groups and their correlation with opinion structure.

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.

Model-based active control of a continuous structure subjected to moving loads

NASA Astrophysics Data System (ADS)

Stancioiu, D.; Ouyang, H.

2016-09-01

Modelling of a structure is an important preliminary step of structural control. The main objectives of the modelling, which are almost always antagonistic are accuracy and simplicity of the model. The first part of this study focuses on the experimental and theoretical modelling of a structure subjected to the action of one or two decelerating moving carriages modelled as masses. The aim of this part is to obtain a simple but accurate model which will include not only the structure-moving load interaction but also the actuators dynamics. A small scale rig is designed to represent a four-span continuous metallic bridge structure with miniature guiding rails. A series of tests are run subjecting the structure to the action of one or two minicarriages with different loads that were launched along the structure at different initial speeds. The second part is dedicated to model based control design where a feedback controller is designed and tested against the validated model. The study shows that a positive position feedback is able to improve system dynamics but also shows some of the limitations of state- space methods for this type of system.

Structure of Room Temperature Ionic Liquids on Charged Graphene: An integrated experimental and computational study

NASA Astrophysics Data System (ADS)

Uysal, Ahmet; Zhou, Hua; Lee, Sang Soo; Fenter, Paul; Feng, Guang; Li, Song; Cummings, Peter; Fulvio, Pasquale; Dai, Sheng; McDonough, Jake; Gogotsi, Yury

2014-03-01

Electrical double layer capacitors (EDLCs) with room temperature ionic liquid (RTIL) electrolytes and carbon electrodes are promising candidates for energy storage devices with high power density and long cycle life. We studied the potential and time dependent changes in the electric double layer (EDL) structure of an imidazolium-based room temperature ionic liquid (RTIL) electrolyte at an epitaxial graphene (EG) surface. We used in situ x-ray reflectivity (XR) to determine the EDL structure at static potentials, during cyclic voltammetry (CV) and potential step measurements. The static potential structures were also investigated with fully atomistic molecular dynamics (MD) simulations. Combined XR and MD results show that the EDL structure has alternating anion/cation layers within the first nanometer of the interface. The dynamical response of the EDL to potential steps has a slow component (>10 s) and the RTIL structure shows hysteresis during CV scans. We propose a conceptual model that connects nanoscale interfacial structure to the macroscopic measurements. This material is based upon work supported as part of the Fluid Interface Reactions, Structures and Transport (FIRST) Center, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science (SC), Office of Basic Energy

Controlling Tensegrity Robots through Evolution using Friction based Actuation

NASA Technical Reports Server (NTRS)

Kothapalli, Tejasvi; Agogino, Adrian K.

2017-01-01

Traditional robotic structures have limitations in planetary exploration as their rigid structural joints are prone to damage in new and rough terrains. In contrast, robots based on tensegrity structures, composed of rods and tensile cables, offer a highly robust, lightweight, and energy efficient solution over traditional robots. In addition tensegrity robots can be highly configurable by rearranging their topology of rods, cables and motors. However, these highly configurable tensegrity robots pose a significant challenge for locomotion due to their complexity. This study investigates a control pattern for successful locomotion in tensegrity robots through an evolutionary algorithm. A twelve-rod hardware model is rapidly prototyped to utilize a new actuation method based on friction. A web-based physics simulation is created to model the twelve-rod tensegrity ball structure. Square-waves are used as control policies for the actuators of the tensegrity structure. Monte Carlo trials are run to find the most successful number of amplitudes for the square-wave control policy. From the results, an evolutionary algorithm is implemented to find the most optimized solution for locomotion of the twelve-rod tensegrity structure. The software pattern coupled with the new friction based actuation method can serve as the basis for highly efficient tensegrity robots in space exploration.

Deoxycholate-Based Glycosides (DCGs) for Membrane Protein Stabilisation.

PubMed

Bae, Hyoung Eun; Gotfryd, Kamil; Thomas, Jennifer; Hussain, Hazrat; Ehsan, Muhammad; Go, Juyeon; Loland, Claus J; Byrne, Bernadette; Chae, Pil Seok

2015-07-06

Detergents are an absolute requirement for studying the structure of membrane proteins. However, many conventional detergents fail to stabilise denaturation-sensitive membrane proteins, such as eukaryotic proteins and membrane protein complexes. New amphipathic agents with enhanced efficacy in stabilising membrane proteins will be helpful in overcoming the barriers to studying membrane protein structures. We have prepared a number of deoxycholate-based amphiphiles with carbohydrate head groups, designated deoxycholate-based glycosides (DCGs). These DCGs are the hydrophilic variants of previously reported deoxycholate-based N-oxides (DCAOs). Membrane proteins in these agents, particularly the branched diglucoside-bearing amphiphiles DCG-1 and DCG-2, displayed favourable behaviour compared to previously reported parent compounds (DCAOs) and conventional detergents (LDAO and DDM). Given their excellent properties, these agents should have significant potential for membrane protein studies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

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

A new modal-based approach for modelling the bump foil structure in the simultaneous solution of foil-air bearing rotor dynamic problems

NASA Astrophysics Data System (ADS)

Bin Hassan, M. F.; Bonello, P.

2017-05-01

Recently-proposed techniques for the simultaneous solution of foil-air bearing (FAB) rotor dynamic problems have been limited to a simple bump foil model in which the individual bumps were modelled as independent spring-damper (ISD) subsystems. The present paper addresses this limitation by introducing a modal model of the bump foil structure into the simultaneous solution scheme. The dynamics of the corrugated bump foil structure are first studied using the finite element (FE) technique. This study is experimentally validated using a purpose-made corrugated foil structure. Based on the findings of this study, it is proposed that the dynamics of the full foil structure, including bump interaction and foil inertia, can be represented by a modal model comprising a limited number of modes. This full foil structure modal model (FFSMM) is then adapted into the rotordynamic FAB problem solution scheme, instead of the ISD model. Preliminary results using the FFSMM under static and unbalance excitation conditions are proven to be reliable by comparison against the corresponding ISD foil model results and by cross-correlating different methods for computing the deflection of the full foil structure. The rotor-bearing model is also validated against experimental and theoretical results in the literature.

Modeling Mediterranean forest structure using airborne laser scanning data

NASA Astrophysics Data System (ADS)

Bottalico, Francesca; Chirici, Gherardo; Giannini, Raffaello; Mele, Salvatore; Mura, Matteo; Puxeddu, Michele; McRoberts, Ronald E.; Valbuena, Ruben; Travaglini, Davide

2017-05-01

The conservation of biological diversity is recognized as a fundamental component of sustainable development, and forests contribute greatly to its preservation. Structural complexity increases the potential biological diversity of a forest by creating multiple niches that can host a wide variety of species. To facilitate greater understanding of the contributions of forest structure to forest biological diversity, we modeled relationships between 14 forest structure variables and airborne laser scanning (ALS) data for two Italian study areas representing two common Mediterranean forests, conifer plantations and coppice oaks subjected to irregular intervals of unplanned and non-standard silvicultural interventions. The objectives were twofold: (i) to compare model prediction accuracies when using two types of ALS metrics, echo-based metrics and canopy height model (CHM)-based metrics, and (ii) to construct inferences in the form of confidence intervals for large area structural complexity parameters. Our results showed that the effects of the two study areas on accuracies were greater than the effects of the two types of ALS metrics. In particular, accuracies were less for the more complex study area in terms of species composition and forest structure. However, accuracies achieved using the echo-based metrics were only slightly greater than when using the CHM-based metrics, thus demonstrating that both options yield reliable and comparable results. Accuracies were greatest for dominant height (Hd) (R2 = 0.91; RMSE% = 8.2%) and mean height weighted by basal area (R2 = 0.83; RMSE% = 10.5%) when using the echo-based metrics, 99th percentile of the echo height distribution and interquantile distance. For the forested area, the generalized regression (GREG) estimate of mean Hd was similar to the simple random sampling (SRS) estimate, 15.5 m for GREG and 16.2 m SRS. Further, the GREG estimator with standard error of 0.10 m was considerable more precise than the SRS estimator with standard error of 0.69 m.

Determination of anisotropy and multimorphology in fly ash based geopolymers

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

Khan, M. Irfan, E-mail: mirfanwazir@gmail.com; Azizli, Khairun, E-mail: khairun-azizli@petronas.com.my; Sufian, Suriati, E-mail: suriati@petronas.com.my

2015-07-22

In this study, Malaysian coal fly ash-based geopolymers were investigated for its morphology and chemical composition using scanning electron microscopy coupled with energy dispersive X-rays (SEM-EDX). Geopolymer was synthesized using sodium hydroxide as activator. SEM studies revealed multiphasous structure of the material, composed of geopolymeric gel, partially reacted fly ashparticles and selectively leached particles. EDX analysis confirmed the chemical composition of different regions. Infra red spectroscopic studies supported the SEM-EDX analysis by confirming presence of unreacted quartzite and mullite in geopolymers. It is concluded that geopolymers possese a non uniform chemistry through out the structure.

Determination of anisotropy and multimorphology in fly ash based geopolymers

NASA Astrophysics Data System (ADS)

Khan, M. Irfan; Azizli, Khairun; Sufian, Suriati; Man, Zakaria; Siyal, Ahmer Ali; Ullah, Hafeez

2015-07-01

In this study, Malaysian coal fly ash-based geopolymers were investigated for its morphology and chemical composition using scanning electron microscopy coupled with energy dispersive X-rays (SEM-EDX). Geopolymer was synthesized using sodium hydroxide as activator. SEM studies revealed multiphasous structure of the material, composed of geopolymeric gel, partially reacted fly ashparticles and selectively leached particles. EDX analysis confirmed the chemical composition of different regions. Infra red spectroscopic studies supported the SEM-EDX analysis by confirming presence of unreacted quartzite and mullite in geopolymers. It is concluded that geopolymers possese a non uniform chemistry through out the structure.

Invariom based electron density studies on the C/Si analogues haloperidol/sila-haloperidol and venlafaxine/sila-venlafaxine.

PubMed

Luger, Peter; Dittrich, Birger; Tacke, Reinhold

2015-09-14

The subjects of this study are the structures and electron densities of the carbon/silicon analogues haloperidol/sila-haloperidol (1a/1b) and venlafaxine/sila-venlafaxine (2a/2b). The parent carbon compounds 1a (an antipsychotic agent) and 2a (an antidepressant) are both in clinical use. For haloperidol/sila-haloperidol, three published structures were studied in more detail: the structures of haloperidol hydrochloride (1a·HCl), haloperidol hydropicrate (1a·HPic) and sila-haloperidol hydrochloride (1b·HCl). For venlafaxine/sila-venlafaxine, the published structures of venlafaxine (2a), venlafaxine hydrochloride (2a·HCl; as orthorhombic (2a·HCl-ortho) and monoclinic polymorph (2a·HCl-mono)) and sila-venlafaxine hydrochloride (2b·HCl) were investigated. Based on these structures, the molecular electron densities were reconstructed by using the invariom formalism. They were further analysed in terms of Bader's quantum theory of atoms in molecules, electrostatic potentials mapped onto electron density isosurfaces and Hirshfeld surfaces. These studies were performed with a special emphasis on the comparison of the corresponding carbon/silicon analogues.

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

Femtosecond laser-induced periodic structure adjustments based on electron dynamics control: from subwavelength ripples to double-grating structures.

PubMed

Shi, Xuesong; Jiang, Lan; Li, Xin; Wang, Sumei; Yuan, Yanping; Lu, Yongfeng

2013-10-01

This study proposes a method for adjusting subwavelength ripple periods and the corresponding double-grating structures formed on fused silica by designing femtosecond laser pulse trains based on localized transient electron density control. Four near-constant period ranges of 190-490 nm of ripples perpendicular to the polarization are obtained by designing pulse trains to excite and modulate the surface plasmon waves. In the period range of 350-490 nm, the double-grating structure is fabricated in one step, which is probably attributable to the grating-assisted enhanced energy deposition and subsequent thermal effects.

Load Diffusion in Composite Structures

NASA Technical Reports Server (NTRS)

Horgan, Cornelius O.; Simmonds, J. G.

2000-01-01

This research has been concerned with load diffusion in composite structures. 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. 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 results are also amendable to parameter study with a large parameter space and should be useful in structural tailoring studies.

Tertiary structural propensities reveal fundamental sequence/structure relationships.

PubMed

Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

2015-05-05

Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Towards development of enhanced fully-Lagrangian mesh-free computational methods for fluid-structure interaction

NASA Astrophysics Data System (ADS)

Khayyer, Abbas; Gotoh, Hitoshi; Falahaty, Hosein; Shimizu, Yuma

2018-02-01

Simulation of incompressible fluid flow-elastic structure interactions is targeted by using fully-Lagrangian mesh-free computational methods. A projection-based fluid model (moving particle semi-implicit (MPS)) is coupled with either a Newtonian or a Hamiltonian Lagrangian structure model (MPS or HMPS) in a mathematically-physically consistent manner. The fluid model is founded on the solution of Navier-Stokes and continuity equations. The structure models are configured either in the framework of Newtonian mechanics on the basis of conservation of linear and angular momenta, or Hamiltonian mechanics on the basis of variational principle for incompressible elastodynamics. A set of enhanced schemes are incorporated for projection-based fluid model (Enhanced MPS), thus, the developed coupled solvers for fluid structure interaction (FSI) are referred to as Enhanced MPS-MPS and Enhanced MPS-HMPS. Besides, two smoothed particle hydrodynamics (SPH)-based FSI solvers, being developed by the authors, are considered and their potential applicability and comparable performance are briefly discussed in comparison with MPS-based FSI solvers. The SPH-based FSI solvers are established through coupling of projection-based incompressible SPH (ISPH) fluid model and SPH-based Newtonian/Hamiltonian structure models, leading to Enhanced ISPH-SPH and Enhanced ISPH-HSPH. A comparative study is carried out on the performances of the FSI solvers through a set of benchmark tests, including hydrostatic water column on an elastic plate, high speed impact of an elastic aluminum beam, hydroelastic slamming of a marine panel and dam break with elastic gate.

Structural system identification based on variational mode decomposition

NASA Astrophysics Data System (ADS)

Bagheri, Abdollah; Ozbulut, Osman E.; Harris, Devin K.

2018-03-01

In this paper, a new structural identification method is proposed to identify the modal properties of engineering structures based on dynamic response decomposition using the variational mode decomposition (VMD). The VMD approach is a decomposition algorithm that has been developed as a means to overcome some of the drawbacks and limitations of the empirical mode decomposition method. The VMD-based modal identification algorithm decomposes the acceleration signal into a series of distinct modal responses and their respective center frequencies, such that when combined their cumulative modal responses reproduce the original acceleration response. The decaying amplitude of the extracted modal responses is then used to identify the modal damping ratios using a linear fitting function on modal response data. Finally, after extracting modal responses from available sensors, the mode shape vector for each of the decomposed modes in the system is identified from all obtained modal response data. To demonstrate the efficiency of the algorithm, a series of numerical, laboratory, and field case studies were evaluated. The laboratory case study utilized the vibration response of a three-story shear frame, whereas the field study leveraged the ambient vibration response of a pedestrian bridge to characterize the modal properties of the structure. The modal properties of the shear frame were computed using analytical approach for a comparison with the experimental modal frequencies. Results from these case studies demonstrated that the proposed method is efficient and accurate in identifying modal data of the structures.

Structural and functional differences in the cingulate cortex relate to disease severity in anorexia nervosa

PubMed Central

Bär, Karl-Jürgen; de la Cruz, Feliberto; Berger, Sandy; Schultz, Carl Christoph; Wagner, Gerd

2015-01-01

Background The dysfunction of specific brain areas might account for the distortion of body image in patients with anorexia nervosa. The present study was designed to reveal brain regions that are abnormal in structure and function in patients with this disorder. We hypothesized, based on brain areas of altered activity in patients with anorexia nervosa and regions involved in pain processing, an interrelation of structural aberrations in the frontoparietal–cingulate network and aberrant functional activation during thermal pain processing in patients with the disorder. Methods We determined pain thresholds outside the MRI scanner in patients with anorexia nervosa and matched healthy controls. Thereafter, thermal pain stimuli were applied during fMRI imaging. Structural analyses with high-resolution structural T1-weighted volumes were performed using voxel-based morphometry and a surface-based approach. Results Twenty-six patients and 26 controls participated in our study, and owing to technical difficulties, 15 participants in each group were included in our fMRI analysis. Structural analyses revealed significantly decreased grey matter volume and cortical thickness in the frontoparietal–cingulate network in patients with anorexia nervosa. We detected an increased blood oxygen level–dependent signal in patients during the painful 45°C condition in the midcingulate and posterior cingulate cortex, which positively correlated with increased pain thresholds. Decreased grey matter and cortical thickness correlated negatively with pain thresholds, symptom severity and illness duration, but not with body mass index. Limitations The lack of a specific quantification of body image distortion is a limitation of our study. Conclusion This study provides further evidence for confined structural and functional brain abnormalities in patients with anorexia nervosa in brain regions that are involved in perception and integration of bodily stimuli. The association of structural and functional deviations with thermal thresholds as well as with clinical characteristics might indicate a common neuronal origin. PMID:25825813

Complexes of oligo(poly)nucleotides with structural anomalies

NASA Astrophysics Data System (ADS)

Dolinnaya, N. G.; Gryaznova, O. I.

1989-08-01

The results of studies on the structure and properties of DNA-RNA hybrids and complexes of oligo(poly)nucleotides containing non-canonical base pairs or unpaired bases both within and at the ends of the double helix are surveyed. The methods used in the study of such systems are briefly characterised: X-ray diffraction analysis, NMR and UV spectroscopy, circular dichroism, scanning microcalorimetry, etc. A comparative analysis of the influence of the non-canonical pairs on the structure and the energetic and kinetic parameters of the formation and dissociation of the oligonucleotide complexes has been carried out. The question of the stability of the non-canonical pairs as a function of their nature and position in the double helix is considered. The mechanisms of the formation of the hydrogen bonds between the bases of non-complementary pairs are discussed. The bibliography includes 171 references.

System reliability of randomly vibrating structures: Computational modeling and laboratory testing

NASA Astrophysics Data System (ADS)

Sundar, V. S.; Ammanagi, S.; Manohar, C. S.

2015-09-01

The problem of determination of system reliability of randomly vibrating structures arises in many application areas of engineering. We discuss in this paper approaches based on Monte Carlo simulations and laboratory testing to tackle problems of time variant system reliability estimation. The strategy we adopt is based on the application of Girsanov's transformation to the governing stochastic differential equations which enables estimation of probability of failure with significantly reduced number of samples than what is needed in a direct simulation study. Notably, we show that the ideas from Girsanov's transformation based Monte Carlo simulations can be extended to conduct laboratory testing to assess system reliability of engineering structures with reduced number of samples and hence with reduced testing times. Illustrative examples include computational studies on a 10-degree of freedom nonlinear system model and laboratory/computational investigations on road load response of an automotive system tested on a four-post test rig.

Homosexuality as a Discrete Class.

PubMed

Norris, Alyssa L; Marcus, David K; Green, Bradley A

2015-12-01

Previous research on the latent structure of sexual orientation has returned conflicting results, with some studies finding a dimensional structure (i.e., ranging quantitatively along a spectrum) and others a taxonic structure (i.e., categories of individuals with distinct orientations). The current study used a sample (N = 33,525) from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC). A series of taxometric analyses were conducted using three indicators of sexual orientation: identity, behavior, and attraction. These analyses, performed separately for women and men, revealed low-base-rate same-sex-oriented taxa for men (base rate = 3.0%) and women (base rate = 2.7%). Generally, taxon membership conferred an increased risk for psychiatric and substance-use disorders. Although taxa were present for men and women, women demonstrated greater sexual fluidity, such that any level of same-sex sexuality conferred taxon membership for men but not for women. © The Author(s) 2015.

DFT-BASED AB INITIO STUDY OF THE ELECTRONIC AND OPTICAL PROPERTIES OF CESIUM BASED FLUORO-PEROVSKITE CsMF3 (M = Ca AND Sr)

NASA Astrophysics Data System (ADS)

Harmel, M.; Khachai, H.; Ameri, M.; Khenata, R.; Baki, N.; Haddou, A.; Abbar, B.; UǦUR, Ş.; Omran, S. Bin; Soyalp, F.

2012-12-01

Density functional theory (DFT) is performed to study the structural, electronic and optical properties of cubic fluoroperovskite AMF3 (A = Cs; M = Ca and Sr) compounds. The calculations are based on the total-energy calculations within the full-potential linearized augmented plane wave (FP-LAPW) method. The exchange-correlation potential is treated by local density approximation (LDA) and generalized gradient approximation (GGA). The structural properties, including lattice constants, bulk modulus and their pressure derivatives are in very good agreement with the available experimental and theoretical data. The calculations of the electronic band structure, density of states and charge density reveal that compounds are both ionic insulators. The optical properties (namely: the real and the imaginary parts of the dielectric function ɛ(ω), the refractive index n(ω) and the extinction coefficient k(ω)) were calculated for radiation up to 40.0 eV.

Vibration-based structural health monitoring of the aircraft large component

NASA Astrophysics Data System (ADS)

Pavelko, V.; Kuznetsov, S.; Nevsky, A.; Marinbah, M.

2017-10-01

In the presented paper there are investigated the basic problems of the local system of SHM of large scale aircraft component. Vibration-based damage detection is accepted as a basic condition, and main attention focused to a low-cost solution that would be attractive for practice. The conditions of small damage detection in the full scale structural component at low-frequency excitation were defined in analytical study and modal FEA. In experimental study the dynamic test of the helicopter Mi-8 tail beam was performed at harmonic excitation with frequency close to first natural frequency of the beam. The index of correlation coefficient deviation (CCD) was used for extraction of the features due to embedded pseudo-damage. It is shown that the problem of vibration-based detection of a small damage in the large scale structure at low-frequency excitation can be solved successfully.

Progress in the Modeling of NiAl-Based Alloys Using the BFS Method

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Ronald D.; Ferrante, John; Garg, Anita

1997-01-01

The BFS method has been applied to the study of NiAl-based materials to assess the effect of alloying additions on structure. Ternary, quaternary and even pent-alloys based on Ni-rich NiAl with additions of Ti, Cr and Cu were studied. Two approaches were used, Monte Carlo simulations to determine ground state structures and analytical calculations of high symmetry configurations which give physical insight into preferred bonding. Site occupancy energetics for ternary and the more complicated case of quaternary additions were determined, and solubility limits and precipitate formation with corresponding information concerning structure and lattice parameter were also 'observed' computationally. The method was also applied to determine the composition of alloy surfaces and interfaces. Overall, the results demonstrate that the BFS method for alloys is a powerful tool for alloy design and with its simplicity and obvious advantages can be used to complement any experimental alloy design program.

Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids

PubMed Central

Ge, Wei; Schneider, Bohdan; Olson, Wilma K.

2005-01-01

Elastic ellipsoidal functions defined by the observed hydration patterns around the DNA bases provide a new basis for measuring the recognition of ligands in the grooves of double-helical structures. Here a set of knowledge-based potentials suitable for quantitative description of such behavior is extracted from the observed positions of water molecules and amino acid atoms that form hydrogen bonds with the nitrogenous bases in high resolution crystal structures. Energies based on the displacement of hydrogen-bonding sites on drugs in DNA-crystal complexes relative to the preferred locations of water binding around the heterocyclic bases are low, pointing to the reliability of the potentials and the apparent displacement of water molecules by drug atoms in these structures. The validity of the energy functions has been further examined in a series of sequence substitution studies based on the structures of DNA bound to polyamides that have been designed to recognize the minor-groove edges of Watson-Crick basepairs. The higher energies of binding to incorrect sequences superimposed (without conformational adjustment or displacement of polyamide ligands) on observed high resolution structures confirm the hypothesis that the drug subunits associate with specific DNA bases. The knowledge-based functions also account satisfactorily for the measured free energies of DNA-polyamide association in solution and the observed sites of polyamide binding on nucleosomal DNA. The computations are generally consistent with mechanisms by which minor-groove binding ligands are thought to recognize DNA basepairs. The calculations suggest that the asymmetric distributions of hydrogen-bond-forming atoms on the minor-groove edge of the basepairs may underlie ligand discrimination of G·C from C·G pairs, in addition to the commonly believed role of steric hindrance. The analysis of polyamide-bound nucleosomal structures reveals other discrepancies in the expected chemical design, including unexpected contacts to DNA and modified basepair targets of some ligands. The ellipsoidal potentials thus appear promising as a mathematical tool for the study of drug- and protein-DNA interactions and for gaining new insights into DNA-binding mechanisms. PMID:15501936

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

An overview of structurally complex network-based modeling of public opinion in the “We the Media” era

NASA Astrophysics Data System (ADS)

Wang, Guanghui; Wang, Yufei; Liu, Yijun; Chi, Yuxue

2018-05-01

As the transmission of public opinion on the Internet in the “We the Media” era tends to be supraterritorial, concealed and complex, the traditional “point-to-surface” transmission of information has been transformed into “point-to-point” reciprocal transmission. A foundation for studies of the evolution of public opinion and its transmission on the Internet in the “We the Media” era can be laid by converting the massive amounts of fragmented information on public opinion that exists on “We the Media” platforms into structurally complex networks of information. This paper describes studies of structurally complex network-based modeling of public opinion on the Internet in the “We the Media” era from the perspective of the development and evolution of complex networks. The progress that has been made in research projects relevant to the structural modeling of public opinion on the Internet is comprehensively summarized. The review considers aspects such as regular grid-based modeling of the rules that describe the propagation of public opinion on the Internet in the “We the Media” era, social network modeling, dynamic network modeling, and supernetwork modeling. Moreover, an outlook for future studies that address complex network-based modeling of public opinion on the Internet is put forward as a summary from the perspective of modeling conducted using the techniques mentioned above.

Carbon nanotube based hybrid nanostructures: Synthesis and applications

NASA Astrophysics Data System (ADS)

Ou, Fung Suong

Hybrid nanostructures are fascinating materials for their promising applications in future nanoelectronics, electrical interconnects and energy storage devices. Practical ways of connecting individual carbon nanotubes to metal contacts for their use as interconnects and in electronic devices have been challenging. In this thesis, carbon nanotube based hybrids that combine the best properties of carbon nanotubes and metal nanowires have been fabricated. The electrical properties and Raman spectra of the hybrid nanowires are also studied. This thesis will focus on our recent results in the development of carbon nanotube hybrids for various applications. Various hybrid structures of multiwalled carbon nanotubes and metal nanowires can be fabricated using a combination of electrodeposition and chemical vapor deposition techniques. Controlled fabrication of multi-segmented structures will be studied. Several novel applications of these structures, for example, as electrodes in ultra-high power supercapacitors, multi-functional smart materials are also studied. The thesis will also highlight the development of carbon nanotube hybrids based smart materials. Hybrid nanowires with hydrophobic carbon nanotube tails and hydrophilic metal nanowire heads, allows for the assembly of spheres in solution. The design and manipulation of these carbon nanotube hybrids based smart structures for various novel applications will be discussed. Such new class of carbon nanotube hybrids surfactants are likely to lead as new tools in various fields such as microfluidics or water purification. In addition, we will also look at other variations of hybrid nanostructures fabricated from our method.

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

PubMed

Akmatov, Manas K; Koch, Nadine; Vital, Marius; Ahrens, Wolfgang; Flesch-Janys, Dieter; Fricke, Julia; Gatzemeier, Anja; Greiser, Halina; Günther, Kathrin; Illig, Thomas; Kaaks, Rudolf; Krone, Bastian; Kühn, Andrea; Linseisen, Jakob; Meisinger, Christine; Michels, Karin; Moebus, Susanne; Nieters, Alexandra; Obi, Nadia; Schultze, Anja; Six-Merker, Julia; Pieper, Dietmar H; Pessler, Frank

2017-05-12

We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.

Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure.

PubMed

Mondal, Sudipa; Mandal, Santi M; Mondal, Tapan Kumar; Sinha, Chittaranjan

2015-01-01

New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 μg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 μg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters. Copyright © 2015 Elsevier B.V. All rights reserved.

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

PubMed Central

Park, Danny S.; Brown, Brielin; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Torgerson, Dara G.; Burchard, Esteban G.; Zaitlen, Noah

2015-01-01

Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix. Contact: noah.zaitlen@ucsf.edu PMID:26072481

Using a non-invasive technique in nutrition: synchrotron radiation infrared microspectroscopy spectroscopic characterization of oil seeds treated with different processing conditions on molecular spectral factors influencing nutrient delivery.

PubMed

Zhang, Xuewei; Yu, Peiqiang

2014-07-02

Non-invasive techniques are a key to study nutrition and structure interaction. Fourier transform infrared microspectroscopy coupled with a synchrotron radiation source (SR-IMS) is a rapid, non-invasive, and non-destructive bioanalytical technique. To understand internal structure changes in relation to nutrient availability in oil seed processing is vital to find optimal processing conditions. The objective of this study was to use a synchrotron-based bioanalytical technique SR-IMS as a non-invasive and non-destructive tool to study the effects of heat-processing methods and oil seed canola type on modeled protein structure based on spectral data within intact tissue that were randomly selected and quantify the relationship between the modeled protein structure and protein nutrient supply to ruminants. The results showed that the moisture heat-related processing significantly changed (p<0.05) modeled protein structures compared to the raw canola (control) and those processing by dry heating. The moisture heating increased (p<0.05) spectral intensities of amide I, amide II, α-helices, and β-sheets but decreased (p<0.05) the ratio of modeled α-helices to β-sheet spectral intensity. There was no difference (p>0.05) in the protein spectral profile between the raw and dry-heated canola tissue and between yellow- and brown-type canola tissue. The results indicated that different heat processing methods have different impacts on the protein inherent structure. The protein intrinsic structure in canola seed tissue was more sensitive and more response to the moisture heating in comparison to the dry heating. These changes are expected to be related to the nutritive value. However, the current study is based on limited samples, and more large-scale studies are needed to confirm our findings.

NMR spectroscopy and molecular modelling studies of nitrosylcobalamin: further evidence that the deprotonated, base-off form is important for nitrosylcobalamin in solution†

PubMed Central

Hassanin, Hanaa A.; Hannibal, Luciana; Jacobsen, Donald W.; Brown, Kenneth L.

2009-01-01

The structure of nitrosylcobalamin (NOCbl) in solution has been studied by NMR spectroscopy and the 1H and 13C NMR spectra have been assigned. 13C and 31P NMR chemical shifts, the UV-vis spectrum of NOCbl and the observed pK base-off value of ~5.1 for NOCbl provide evidence that a significant fraction of NOCbl is present in the base-off, 5,6-dimethylbenzimidazole (DMB) deprotonated, form in solution. NOE-restrained molecular mechanics modelling of base-on NOCbl gave annealed structures with minor conformational differences in the flexible side chains and the nucleotide loop position compared with the X-ray structure. A molecular dynamics simulation at 300 K showed that DMB remains in close proximity to the α face of the corrin in the base-off form of NOCbl. Simulated annealing calculations produced two major conformations of base-off NOCbl. In the first, the DMB is perpendicular to the corrin and its B3 nitrogen is about 3.1 Å away from and pointing directly at the metal ion; in the second the DMB is parallel to and tucked beneath the D ring of the corrin. PMID:19122899

Selected approaches for rational drug design and high throughput screening to identify anti-cancer molecules.

PubMed

Hedvat, Michael; Emdad, Luni; Das, Swadesh K; Kim, Keetae; Dasgupta, Santanu; Thomas, Shibu; Hu, Bin; Zhu, Shan; Dash, Rupesh; Quinn, Bridget A; Oyesanya, Regina A; Kegelman, Timothy P; Sokhi, Upneet K; Sarkar, Siddik; Erdogan, Eda; Menezes, Mitchell E; Bhoopathi, Praveen; Wang, Xiang-Yang; Pomper, Martin G; Wei, Jun; Wu, Bainan; Stebbins, John L; Diaz, Paul W; Reed, John C; Pellecchia, Maurizio; Sarkar, Devanand; Fisher, Paul B

2012-11-01

Structure-based modeling combined with rational drug design, and high throughput screening approaches offer significant potential for identifying and developing lead compounds with therapeutic potential. The present review focuses on these two approaches using explicit examples based on specific derivatives of Gossypol generated through rational design and applications of a cancer-specificpromoter derived from Progression Elevated Gene-3. The Gossypol derivative Sabutoclax (BI-97C1) displays potent anti-tumor activity against a diverse spectrum of human tumors. The model of the docked structure of Gossypol bound to Bcl-XL provided a virtual structure-activity-relationship where appropriate modifications were predicted on a rational basis. These structure-based studies led to the isolation of Sabutoclax, an optically pure isomer of Apogossypol displaying superior efficacy and reduced toxicity. These studies illustrate the power of combining structure-based modeling with rational design to predict appropriate derivatives of lead compounds to be empirically tested and evaluated for bioactivity. Another approach to cancer drug discovery utilizes a cancer-specific promoter as readouts of the transformed state. The promoter region of Progression Elevated Gene-3 is such a promoter with cancer-specific activity. The specificity of this promoter has been exploited as a means of constructing cancer terminator viruses that selectively kill cancer cells and as a systemic imaging modality that specifically visualizes in vivo cancer growth with no background from normal tissues. Screening of small molecule inhibitors that suppress the Progression Elevated Gene-3-promoter may provide relevant lead compounds for cancer therapy that can be combined with further structure-based approaches leading to the development of novel compounds for cancer therapy.

Assessment of Teachers' Reactions to a Knowledge- and Skills-Based Pay Structure at an International School

ERIC Educational Resources Information Center

Lowe, Joel Courtney

2013-01-01

This study explores teachers' reactions to a knowledge- and skills-based pay (KSBP) system implemented in a large international school. Such systems are designed to set teacher compensation based on demonstrated professional knowledge and skills as opposed to the traditional scale based on years of experience and degrees attained. This study fills…

Space construction base control system

NASA Technical Reports Server (NTRS)

1978-01-01

Aspects of an attitude control system were studied and developed for a large space base that is structurally flexible and whose mass properties change rather dramatically during its orbital lifetime. Topics of discussion include the following: (1) space base orbital pointing and maneuvering; (2) angular momentum sizing of actuators; (3) momentum desaturation selection and sizing; (4) multilevel control technique applied to configuration one; (5) one-dimensional model simulation; (6) N-body discrete coordinate simulation; (7) structural analysis math model formulation; and (8) discussion of control problems and control methods.

Magnetic-mechanical-electrical-optical coupling effects in GaN-based LED/rare-earth terfenol-D structures.

PubMed

Peng, Mingzeng; Zhang, Yan; Liu, Yudong; Song, Ming; Zhai, Junyi; Wang, Zhong Lin

2014-10-22

A multi-field coupling structure is designed and investigated, which combines GaN-based optoelectronic devices and Terfenol-D. The abundant coupling effects and multifunctionalities among magnetics, mechanics, electrics, and optics are investigated by a combination of non-magnetic GaN-based piezoelectronic optoelectronic characteristics and the giant magnetomechanical properties of Terfenol-D. A few potential new areas of studies are proposed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sorptive Activity and Hydrophobic Behavior of Aerogels Based on Reduced Graphene Oxide and Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Sultanov, F.; Bakbolat, B.; Daulbaev, Ch.; Urazgalieva, A.; Azizov, Z.; Mansurov, Z.; Tulepov, M.; Pei, S. S.

2017-07-01

A study has been made of the possibility of obtaining three-dimensional porous aerogel structures based on reduced graphene oxide and carbon nanotubes. Carbon nanotubes in the structure of the finished aerogel based on reduced graphene oxide were grown by thermal decomposition of ferrocene into cyclopentadienyl and iron ions which served as the source of carbon and a catalyst respectively. The obtained composite aerogels exhibit high sorptive activity for organic liquids of different densities.

Performance-based plastic design of earthquake resistant reinforced concrete moment frames

NASA Astrophysics Data System (ADS)

Liao, Wen-Cheng

Performance-Based Plastic Design (PBPD) method has been recently developed to achieve enhanced performance of earthquake resistant structures. The design concept uses pre-selected target drift and yield mechanism as performance criteria. The design base shear for selected hazard level is determined by equating the work needed to push the structure monotonically up to the target drift to the corresponding energy demand of an equivalent SDOF oscillator. This study presents development of the PBPD approach as applied to reinforced concrete special moment frame (RC SMF) structures. RC structures present special challenge because of their complex and degrading ("pinched") hysteretic behavior. In order to account for the degrading hysteretic behavior the 1-EMA 440 C2 factor approach was used in the process of determining the design base shear. Four baseline RC SMF (4, 8, 12 and 20-story) as used in the FEMA P695 were selected for this study. Those frames were redesigned by the PBPD approach. The baseline frames and the PBPD frames were subjected to extensive inelastic pushover and time-history analyses. The PBPD frames showed much improved response meeting all desired performance objectives, including the intended yield mechanisms and the target drifts. On the contrary, the baseline frames experienced large story drifts due to flexural yielding of the columns. The work-energy equation to determine design base shear can also be used to estimate seismic demands, called the energy spectrum method. In this approach the skeleton force-displacement (capacity) curve of the structure is converted into energy-displacement plot (Ec) which is superimposed over the corresponding energy demand plot ( Ed) for the specified hazard level to determine the expected peak displacement demands. In summary, this study shows that the PBPD approach can be successfully applied to RC moment frame structures as well, and that the responses of the example moment frames were much improved over those of the corresponding baseline frames. In addition, the drift demands of all study frames as computed by the energy spectrum method were in excellent agreement with those obtained from detailed inelastic dynamic analyses.

Synthesis, characterization, spectroscopic and theoretical studies of new zinc(II), copper(II) and nickel(II) complexes based on imine ligand containing 2-aminothiophenol moiety

NASA Astrophysics Data System (ADS)

Shafaatian, Bita; Mousavi, S. Sedighe; Afshari, Sadegh

2016-11-01

New dimer complexes of zinc(II), copper(II) and nickel(II) were synthesized using the Schiff base ligand which was formed by the condensation of 2-aminothiophenol and 2-hydroxy-5-methyl benzaldehyde. This tridentate Schiff base ligand was coordinated to the metal ions through the NSO donor atoms. In order to prevent the oxidation of the thiole group during the formation of Schiff base and its complexes, all of the reactions were carried out under an inert atmosphere of argon. The X-ray structure of the Schiff base ligand showed that in the crystalline form the SH groups were oxidized to produce a disulfide Schiff base as a new double Schiff base ligand. The molar conductivity values of the complexes in dichloromethane implied the presence of non-electrolyte species. The fluorescence properties of the Schiff base ligand and its complexes were also studied in dichloromethane. The products were characterized by FT-IR, 1H NMR, UV/Vis spectroscopies, elemental analysis, and conductometry. The crystal structure of the double Schiff base was determined by single crystal X-ray diffraction. Furthermore, the density functional theory (DFT) calculations were performed at the B3LYP/6-31G(d,p) level of theory for the determination of the optimized structures of Schiff base complexes.

Student-to-Student Confirmation in the College Classroom: The Development and Validation of the Student-to-Student Confirmation Scale

ERIC Educational Resources Information Center

LaBelle, Sara; Johnson, Zac D.

2018-01-01

Three studies were conducted to generate a valid and reliable instrument to measure student-to-student confirmation. Study One (N = 396) sought to establish a factor structure based on previous research. Study Two (N = 396) sought to confirm this factor structure and assess criterion-related validity. Study Three (N = 283) sought to assess…

A corrosion monitoring system for existing reinforced concrete structures.

DOT National Transportation Integrated Search

2015-05-01

This study evaluated a multi-parameter corrosion monitoring system for existing reinforced concrete structures in chloride-laden service environments. The system was fabricated based on a prototype concrete corrosion measurement system that : had bee...

A computer-assisted study of pulse dynamics in anisotropic media

NASA Astrophysics Data System (ADS)

Krishnan, J.; Engelborghs, K.; Bär, M.; Lust, K.; Roose, D.; Kevrekidis, I. G.

2001-06-01

This study focuses on the computer-assisted stability analysis of travelling pulse-like structures in spatially periodic heterogeneous reaction-diffusion media. The physical motivation comes from pulse propagation in thin annular domains on a diffusionally anisotropic catalytic surface. The study was performed by computing the travelling pulse-like structures as limit cycles of the spatially discretized PDE, which in turn is performed in two ways: a Newton method based on a pseudospectral discretization of the PDE, and a Newton-Picard method based on a finite difference discretization. Details about the spectra of these modulated pulse-like structures are discussed, including how they may be compared with the spectra of pulses in homogeneous media. The effects of anisotropy on the dynamics of pulses and pulse pairs are studied. Beyond shifting the location of bifurcations present in homogeneous media, anisotropy can also introduce certain new instabilities.

Structure-Based Approach To Identify 5-[4-Hydroxyphenyl]pyrrole-2-carbonitrile Derivatives as Potent and Tissue Selective Androgen Receptor Modulators.

PubMed

Unwalla, Ray; Mousseau, James J; Fadeyi, Olugbeminiyi O; Choi, Chulho; Parris, Kevin; Hu, Baihua; Kenney, Thomas; Chippari, Susan; McNally, Christopher; Vishwanathan, Karthick; Kilbourne, Edward; Thompson, Catherine; Nagpal, Sunil; Wrobel, Jay; Yudt, Matthew; Morris, Carl A; Powell, Dennis; Gilbert, Adam M; Chekler, Eugene L Piatnitski

2017-07-27

In an effort to find new and safer treatments for osteoporosis and frailty, we describe a novel series of selective androgen receptor modulators (SARMs). Using a structure-based approach, we identified compound 7, a potent AR (ARE EC 50 = 0.34 nM) and selective (N/C interaction EC 50 = 1206 nM) modulator. In vivo data, an AR LBD X-ray structure of 7, and further insights from modeling studies of ligand receptor interactions are also presented.

Planets of the solar system. [Jupiter and Venus

NASA Technical Reports Server (NTRS)

Kondratyev, K. Y.; Moskalenko, N. I.

1978-01-01

Venera and Mariner spacecraft and ground based radio astronomy and spectroscopic observations of the atmosphere and surface of venus are examined. The composition and structural parameters of the atmosphere are discussed as the basis for development of models and theories of the vertical structure of the atmosphere, the greenhouse effect, atmospheric circulation and cloud cover. Recommendations for further meteorological studies are given. Ground based and Pioneer satellite observation data on Jupiter are explored as well as calculations and models of the cloud structure, atmospheric circulation and thermal emission field of Jupiter.

Q factor of megahertz LC circuits based on thin films of YBaCuO high-temperature superconductor

NASA Astrophysics Data System (ADS)

Masterov, D. V.; Pavlov, S. A.; Parafin, A. E.

2008-05-01

High-frequency properties of resonant structures based on thin films of YBa2Cu3O7 δ high-temperature superconductor are studied experimentally in the frequency range 30 100 MHz. The structures planar induction coils with a self-capacitance fabricated on neodymium gallate and lanthanum aluminate substrates. The unloaded Q factor of the circuits exceeds 2 × 105 at 77 K and 40 MHz. Possible loss mechanisms that determine the Q factor of the superconducting resonant structures in the megahertz range are considered.

A composite structure based on reduced graphene oxide and metal oxide nanomaterials for chemical sensors.

PubMed

Galstyan, Vardan; Comini, Elisabetta; Kholmanov, Iskandar; Ponzoni, Andrea; Sberveglieri, Veronica; Poli, Nicola; Faglia, Guido; Sberveglieri, Giorgio

2016-01-01

A hybrid nanostructure based on reduced graphene oxide and ZnO has been obtained for the detection of volatile organic compounds. The sensing properties of the hybrid structure have been studied for different concentrations of ethanol and acetone. The response of the hybrid material is significantly higher compared to pristine ZnO nanostructures. The obtained results have shown that the nanohybrid is a promising structure for the monitoring of environmental pollutants and for the application of breath tests in assessment of exposure to volatile organic compounds.

Social Network Influences on Adolescent Substance Use: Disentangling Structural Equivalence from Cohesion

PubMed Central

Fujimoto, Kayo; Valente, Thomas W.

2012-01-01

This study investigates two contagion mechanisms of peer influence based on direct communication (cohesion) versus comparison through peers who occupy similar network positions (structural equivalence) in the context of adolescents' drinking alcohol and smoking. To date, the two contagion mechanisms have been considered observationally inseparable, but this study attempts to disentangle structural equivalence from cohesion as a contagion mechanism by examining the extent to which the transmission of drinking and smoking behaviors attenuates as a function of social distance (i.e., from immediate friends to indirectly connected peers). Using the U.S. Add Health data consisting of a nationally representative sample of American adolescents (Grades 7-12), this study measured peer risk-taking up to four steps away from the adolescent (friends of friends of friends of friends) using a network exposure model. Peer influence was tested using a logistic regression model of alcohol drinking and cigarette smoking. Results indicate that influence based on structural equivalence tended to be stronger than influence based on cohesion in general, and that the magnitude of the effect decreased up to three steps away from the adolescent (friends of friends of friends). Further analysis indicated that structural equivalence acted as a mechanism of contagion for drinking and cohesion acted as one for smoking. These results indicate that the two transmission mechanisms with differing network proximities can differentially affect drinking and smoking behaviors in American adolescents. PMID:22475405

Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library.

PubMed

Shah, Falgun; Mukherjee, Prasenjit; Gut, Jiri; Legac, Jennifer; Rosenthal, Philip J; Tekwani, Babu L; Avery, Mitchell A

2011-04-25

Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.

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

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results, we estimate that the construction of the conservation structures in our study area in Eritrea required over 300,000 person-days of work, which underlines the huge efforts involved in soil and water conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mechanics based model for predicting structure-induced rolling resistance (SRR) of the tire-pavement system

NASA Astrophysics Data System (ADS)

Shakiba, Maryam; Ozer, Hasan; Ziyadi, Mojtaba; Al-Qadi, Imad L.

2016-11-01

The structure-induced rolling resistance of pavements, and its impact on vehicle fuel consumption, is investigated in this study. The structural response of pavement causes additional rolling resistance and fuel consumption of vehicles through deformation of pavement and various dissipation mechanisms associated with inelastic material properties and damping. Accurate and computationally efficient models are required to capture these mechanisms and obtain realistic estimates of changes in vehicle fuel consumption. Two mechanistic-based approaches are currently used to calculate vehicle fuel consumption as related to structural rolling resistance: dissipation-induced and deflection-induced methods. The deflection-induced approach is adopted in this study, and realistic representation of pavement-vehicle interactions (PVIs) is incorporated. In addition to considering viscoelastic behavior of asphalt concrete layers, the realistic representation of PVIs in this study includes non-uniform three-dimensional tire contact stresses and dynamic analysis in pavement simulations. The effects of analysis type, tire contact stresses, pavement viscoelastic properties, pavement damping coefficients, vehicle speed, and pavement temperature are then investigated.

Effective communication network structures for hospital infection prevention: a study protocol.

PubMed

Rangachari, Pavani

2013-01-01

Many hospitals are unable to successfully implement "evidence-based practices" at the unit level. For example, consistent implementation of the central line bundle (CLB), proven to prevent catheter-related bloodstream infections (CRBSIs) is often difficult. This problem has been broadly characterized as "change implementation failure" in health care organizations. Several studies have used retrospective designs to examine the problem; however, there are few prospective studies examining communication dynamics underlying successful implementation of change (eg, evidence-based practices). This prospective study will be set in 2 intensive care units at an academic medical center. At baseline, both units have low compliance with CLB and higher-than-expected CRBSIs. Periodic quality improvement (QI) interventions will be conducted over a 52-week period to promote implementation of CLB in both units. Simultaneously, the following parameters will be examined: (1) Structure and content of communication related to CLB in both units through "communication logs" completed weekly by nurses, physicians, and managers; and (2) outcomes, that is, CLB adherence in both units through weekly chart review. Catheter utilization and CRBSI (infection) rates will serve as additional unit-level outcome measures. The aim is 2-fold: (1) to examine associations between QI interventions and structure and content of communication at the unit level; and (2) to examine associations between structure and content of communication and outcomes at the unit level. The periodic QI interventions are expected to increase CLB adherence and reduce CRBSIs through their influence on structure and content of communication. The prospective design would help examine dynamics in unit-level communication structure and content related to CLB, as well as unit-level outcomes. The study has potential to make significant contributions to theory and practice, particularly if interventions are found to be effective in enabling successful practice change at the unit level. To this effect, the study has potential to provide insights into communication structure and content associated with collective learning and culture change at the unit level. Results and insights are expected to lay a foundation for generating context-sensitive "evidence-based management" strategies for successful practice change at the unit level. An ultimate expected deliverable is the development of an "action-learning framework" for successful implementation of evidence-based practices in health care organizations.

Computed Energetics of Nucleotides in Spatial Ribozyme Structures: An Accurate Identification of Functional Regions from Structure

PubMed Central

Torshin, Ivan Y.

2004-01-01

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensive in silico mutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of “relative stability” and “mutational stability” is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence. PMID:15105962

Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images.

PubMed

Nguyen, Luong; Tosun, Akif Burak; Fine, Jeffrey L; Lee, Adrian V; Taylor, D Lansing; Chennubhotla, S Chakra

2017-07-01

Segmenting a broad class of histological structures in transmitted light and/or fluorescence-based images is a prerequisite for determining the pathological basis of cancer, elucidating spatial interactions between histological structures in tumor microenvironments (e.g., tumor infiltrating lymphocytes), facilitating precision medicine studies with deep molecular profiling, and providing an exploratory tool for pathologists. This paper focuses on segmenting histological structures in hematoxylin- and eosin-stained images of breast tissues, e.g., invasive carcinoma, carcinoma in situ, atypical and normal ducts, adipose tissue, and lymphocytes. We propose two graph-theoretic segmentation methods based on local spatial color and nuclei neighborhood statistics. For benchmarking, we curated a data set of 232 high-power field breast tissue images together with expertly annotated ground truth. To accurately model the preference for histological structures (ducts, vessels, tumor nets, adipose, etc.) over the remaining connective tissue and non-tissue areas in ground truth annotations, we propose a new region-based score for evaluating segmentation algorithms. We demonstrate the improvement of our proposed methods over the state-of-the-art algorithms in both region- and boundary-based performance measures.

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Di Felice, Rosa

2011-05-01

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.

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.

Modulation of electronic structures of bases through DNA recognition of protein.

PubMed

Hagiwara, Yohsuke; Kino, Hiori; Tateno, Masaru

2010-04-21

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.

An expert system for integrated structural analysis and design optimization for aerospace structures

NASA Technical Reports Server (NTRS)

1992-01-01

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and design optimization tasks in the integrated aerospace structural design process. These expert systems were developed to work in conjunction with procedural finite element structural analysis and design optimization modules (developed in-house at SAT, Inc.). The complete software, AutoDesign, so developed, can be used for integrated 'intelligent' structural analysis and design optimization. The software was beta-tested at a variety of companies, used by a range of engineers with different levels of background and expertise. Based on the feedback obtained by such users, conclusions were developed and are provided.

An expert system for integrated structural analysis and design optimization for aerospace structures

NASA Astrophysics Data System (ADS)

1992-04-01

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and design optimization tasks in the integrated aerospace structural design process. These expert systems were developed to work in conjunction with procedural finite element structural analysis and design optimization modules (developed in-house at SAT, Inc.). The complete software, AutoDesign, so developed, can be used for integrated 'intelligent' structural analysis and design optimization. The software was beta-tested at a variety of companies, used by a range of engineers with different levels of background and expertise. Based on the feedback obtained by such users, conclusions were developed and are provided.

Structural and viscoelastic characterization of ternary mixtures of sunflower oil, saturated monoglycerides and aqueous phases containing different bases.

PubMed

Valoppi, Fabio; Calligaris, Sonia; Barba, Luisa; Nicoli, Maria Cristina

2015-08-01

The structure at different length scales and the viscoelastic properties of ternary mixtures composed of saturated monoglycerides, sunflower oil and aqueous solutions of weak bases (KHCO 3 , NaHCO 3 , and NH 4 HCO 3 ) or strong bases (NaOH and KOH) were investigated. The characteristics of ternary mixtures were studied systematically by using polarized light microscopy, differential scanning calorimetry (DSC), synchrotron X-ray diffraction (XRD) and rheological analysis. Results showed that the base type and concentration greatly affected the structure of the mixtures. The use of strong bases allowed gelled systems to be obtained only at low concentrations (<10mM). On the contrary, the presence of weak bases induced gelling at all concentrations considered (from 1 to 1000mM). The increase of base concentration led to a reduction of the mean droplet diameter and melting temperature. At the same time, the viscoelastic characteristics as a function of base concentration followed a more complex behavior: G' and G″ progressively decreased as the salt concentration increased in a concentration range from 1 to 100mM, while the rheological parameters increased when salt concentration increased from 100 to 1000mM. The structural and viscoelastic behavior of systems prepared with different salts were commonly independent of the cation present in the medium. Results highlight that it is possible to tailor the structure of these gels by using specific bases. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Effects of Computer-Assisted Instruction Based on Top-Level Structure Method in English Reading and Writing Abilities of Thai EFL Students

ERIC Educational Resources Information Center

Jinajai, Nattapong; Rattanavich, Saowalak

2015-01-01

This research aims to study the development of ninth grade students' reading and writing abilities and interests in learning English taught through computer-assisted instruction (CAI) based on the top-level structure (TLS) method. An experimental group time series design was used, and the data was analyzed by multivariate analysis of variance…

3-cyanoindole-based inhibitors of inosine monophosphate dehydrogenase: synthesis and initial structure-activity relationships.

PubMed

Dhar, T G Murali; Shen, Zhongqi; Gu, Henry H; Chen, Ping; Norris, Derek; Watterson, Scott H; Ballentine, Shelley K; Fleener, Catherine A; Rouleau, Katherine A; Barrish, Joel C; Townsend, Robert; Hollenbaugh, Diane L; Iwanowicz, Edwin J

2003-10-20

A series of novel small molecule inhibitors of inosine monophosphate dehydrogenase (IMPDH), based upon a 3-cyanoindole core, were explored. IMPDH catalyzes the rate determining step in guanine nucleotide biosynthesis and is a target for anticancer, immunosuppressive and antiviral therapy. The synthesis and the structure-activity relationships (SAR), derived from in vitro studies, for this new series of inhibitors is given.

Photoluminescence Characteristics of Yag:Ce, Gd Based Phosphors with Different Prehistories

NASA Astrophysics Data System (ADS)

Lisitsyn, V. M.; Soshchin, N. P.; Yang yang, Yu; Stepanov, S. A.; Lisitsyna, L. A.; Tulegenova, A. T.; Abdullin, Kh. A.

2017-09-01

Luminescence characteristics of yttrium-aluminum garnet based phosphor samples differed by their elemental composition and prehistory of synthesis are studied. The morphology, structure, and elemental composition of phosphor samples, their excitation and emission spectra, efficiency of phosphor conversion of chip emission, and kinetics of luminescence decay are measured. The emission characteristics of phosphors are compared with their structural properties and elemental composition.

Knowledge based identification of MAO-B selective inhibitors using pharmacophore and structure based virtual screening models.

PubMed

Boppana, Kiran; Dubey, P K; Jagarlapudi, Sarma A R P; Vadivelan, S; Rambabu, G

2009-09-01

Monoamine Oxidase B interaction with known ligands was investigated using combined pharmacophore and structure based modeling approach. The docking results suggested that the pharmacophore and docking models are in good agreement and are used to identify the selective MAO-B inhibitors. The best model, Hypo2 consists of three pharmacophore features, i.e., one hydrogen bond acceptor, one hydrogen bond donor and one ring aromatic. The Hypo2 model was used to screen an in-house database of 80,000 molecules and have resulted in 5500 compounds. Docking studies were performed, subsequently, on the cluster representatives of 530 hits from 5500 compounds. Based on the structural novelty and selectivity index, we have suggested 15 selective MAO-B inhibitors for further synthesis and pharmacological screening.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Discovery of novel human acrosin inhibitors by virtual screening

NASA Astrophysics Data System (ADS)

Liu, Xuefei; Dong, Guoqiang; Zhang, Jue; Qi, Jingjing; Zheng, Canhui; Zhou, Youjun; Zhu, Ju; Sheng, Chunquan; Lü, Jiaguo

2011-10-01

Human acrosin is an attractive target for the discovery of male contraceptive drugs. For the first time, structure-based drug design was applied to discover structurally diverse human acrosin inhibitors. A parallel virtual screening strategy in combination with pharmacophore-based and docking-based techniques was used to screen the SPECS database. From 16 compounds selected by virtual screening, a total of 10 compounds were found to be human acrosin inhibitors. Compound 2 was found to be the most potent hit (IC50 = 14 μM) and its binding mode was investigated by molecular dynamics simulations. The hit interacted with human acrosin mainly through hydrophobic and hydrogen-bonding interactions, which provided a good starting structure for further optimization studies.

The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation

PubMed Central

Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

2016-01-01

Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (x¯), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir. PMID:26992168

The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation.

PubMed

Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

2016-01-01

Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (mean), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir.

Numerical analysis of light extraction enhancement of GaN-based thin-film flip-chip light-emitting diodes with high-refractive-index buckling nanostructures

NASA Astrophysics Data System (ADS)

Yue, Qing-Yang; Yang, Yang; Cheng, Zhen-Jia; Guo, Cheng-Shan

2018-06-01

In this work, the light extraction efficiency enhancement of GaN-based thin-film flip-chip (TFFC) light-emitting diodes (LEDs) with high-refractive-index (TiO2) buckling nanostructures was studied using the three-dimensional finite difference time domain method. Compared with 2-D photonic crystals, the buckling structures have the advantages of a random directionality and a broad distribution in periodicity, which can effectively extract the guided light propagating in all azimuthal directions over a wide spectrum. Numerical studies revealed that the light extraction efficiency of buckling-structured LEDs reaches 1.1 times that of triangular lattice photonic crystals. The effects of the buckling structure feature sizes and the thickness of the N-GaN layer on the light extraction efficiency for TFFC LEDs were also investigated systematically. With optimized structural parameters, a significant light extraction enhancement of about 2.6 times was achieved for TiO2 buckling-structured TFFC LEDs compared with planar LEDs.

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.

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.

PubMed

Kumar, Avishek; Campitelli, Paul; Thorpe, M F; Ozkan, S Banu

2015-12-01

The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled. © 2015 Wiley Periodicals, Inc.

Organizations in America: Analyzing Their Structures and Human Resource Practices Based on the National Organizations Study.

ERIC Educational Resources Information Center

Kalleberg, Arne L.; Knoke, David; Marsden, Peter V.; Spaeth, Joe L.

In 1991 the National Organizations Study (NOS) surveyed a number of U.S. businesses about their structure, context, and personnel practices to produce a database for answering questions about social behavior in work organizations. This book presents the results of that survey. The study aimed to create a national database on organizations--based…

A Project-Based Biochemistry Laboratory Promoting the Understanding and Uses of Fluorescence Spectroscopy in the Study of Biomolecular Structures and Interactions

ERIC Educational Resources Information Center

Briese, Nicholas; Jakubowsk, Henry V.

2007-01-01

A laboratory project for a first semester biochemistry course is described, which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study of these molecules using fluorescence spectroscopy. Students are assigned a specific question addressing the stability/function of lipids, proteins, or…

G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

PubMed

Musumeci, Domenica; Riccardi, Claudia; Montesarchio, Daniela

2015-09-22

Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.

Contemporary State of the Elbrus Volcanic Center (The Northern Caucasus)

NASA Astrophysics Data System (ADS)

Milyukov, Vadim; Rogozhin, Eugeny; Gorbatikov, Andrey; Mironov, Alexey; Myasnikov, Andrey; Stepanova, Marina

2018-05-01

The Elbrus volcanic center is located in southern Russia on the northern slope of the main ridge of the Greater Caucasus. Current classifications define Elbrus as a dormant volcano that could become active even after millennia of quiescence. In this study, we use two new geophysical methods to assess the contemporary state of the Elbrus volcano. The first method is based on an evaluation of parameters of resonant modes "reemitted" by the resonant structure (i.e., volcanic chamber) in response to the excitation of a seismic impact and recorded by a precise laser interferometer-strainmeter. The second method is based on low-frequency microseismic sounding and allows determination of the deep structure of complicated geological objects. Our study locates the magma chamber at depths of 1-8 km and extended magma source at depths of 15-40 km beneath the Elbrus eastern summit. An unknown magmatic structure, comparable to the Elbrus magmatic structure but currently much colder, was also identified 50 km from Mt. Elbrus. Based on our analysis, we assess the Elbrus volcano to be currently in a quasi-stable state of thermodynamic equilibrium.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Manual of Structural Kinesiology. Eighth Edition.

ERIC Educational Resources Information Center

Thompson, Clem W.

This manual is intended for use in college-level courses in structural kinesiology; mechanical kinesiology is introduced only briefly. The first chapter introduces the bases for structural kinesiology. Subsequent chapters are organized according to the areas of the body to be studied (e.g., the shoulder girdle, the shoulder joint, the elbow joint,…

Introducing Students to Structural Dynamics and Earthquake Engineering

ERIC Educational Resources Information Center

Anthoine, Armelle; Marazzi, Francesco; Tirelli, Daniel

2010-01-01

The European Laboratory for Structural Assessment (ELSA) is one of the world's main laboratories for seismic studies. Besides its research activities, it also aims to bring applied science closer to the public. This article describes teaching activities based on a demonstration shaking table which is used to introduce the structural dynamics of…

Communication of Geometrical Structure and Its Relationship to Student Mathematical Achievement.

ERIC Educational Resources Information Center

Norrie, Alexander L.

The purpose of this study was to examine whether the mathematical structures inherent in grade 7 geometry curriculum objectives can be used to improve the communication of the objectives to students. Teacher inservice based upon geometrical properties and structures was combined with student teaching materials to try to improve student achievement…

Deeper than Shallow: Evidence for Structure-Based Parsing Biases in Second-Language Sentence Processing

ERIC Educational Resources Information Center

Witzel, Jeffrey; Witzel, Naoko; Nicol, Janet

2012-01-01

This study examines the reading patterns of native speakers (NSs) and high-level (Chinese) nonnative speakers (NNSs) on three English sentence types involving temporarily ambiguous structural configurations. The reading patterns on each sentence type indicate that both NSs and NNSs were biased toward specific structural interpretations. These…

Altai Empathy Culture: Ontological Design of Altai Cognitive Environment

ERIC Educational Resources Information Center

Voronin, Maksim; Belousova, Valeria; Khalina, Natalya

2016-01-01

This study considers the features of Altai cultural semantics through the cognitive materialism of culture basing on the assumption that the linguistic structures are part of culture, and the metaphorical linguistic use is the basis for cultural cognitive structures forming. Altai text is considered as a structural unit of Altai cognitive…

Teacher Observation of Classroom Adaptation--Checklist: Development and Factor Structure

ERIC Educational Resources Information Center

Koth, Christine W.; Bradshaw, Catherine P.; Leaf, Philip J.

2009-01-01

Two studies examined the validity and factor structure of the Teacher Observation of Classroom Adaptation-Checklist, an instrument used to evaluate school-based programs. The checklist is a cost-effective alternative to the original interview format, and the factor structure is consistent across gender, race, age, and time of administration.…

Breadth and Intensity: Salient, Separable, and Developmentally Significant Dimensions of Structured Youth Activity Involvement

ERIC Educational Resources Information Center

Busseri, Michael A.; Rose-Krasnor, Linda

2009-01-01

In recent years, an impressive volume of evidence has accumulated demonstrating that youth involvement in structured, organized activities (e.g. school sports, community clubs) may facilitate positive youth development. We present a theory-based framework for studying structured activity involvement (SAI) as a context for positive youth…

Dominant and Emerging Approaches in the Study of Higher Education Policy Change

ERIC Educational Resources Information Center

Saarinen, Taina; Ursin, Jani

2012-01-01

The purpose of the article is to analyse recent literature on higher education policy change. Based on the review, three different approaches are distinguished: structural, actor and agency. In the structural approach the dynamic of policy change originates in well-established structures. The actor approach focuses on either individual or…

Conductivity and local structure in LaNiO3

NASA Astrophysics Data System (ADS)

Fowlie, Jennifer; Gibert, Marta; Tieri, Giulio; Gloter, Alexandre; à+/-Iguez, Jorge; Filippetti, Alessio; Catalano, Sara; Gariglio, Stefano; StéPhan, Odile; Triscone, Jean-Marc

In this study we approach the thickness-dependence of the properties of LaNiO3 films along multiple, complementary avenues: sophisticated ab initio calculations, scanning transmission electron microscopy and electronic transport. Specifically, we find an unexpected maximum in conductivity in films of thickness 6 - 10 unit cells (3 nm) for several series of LaNiO3 films. Ab initio transport based on the detailed crystal structure also reveals a maximum in conductivity at the same thickness. In agreement with the structure obtained from scanning transmission electron microscopy (STEM), our simulated structures reveal that the substrate- and surface-induced distortions lead to three types of local structure (heterointerface, interior-layer, surface). Based on this observation, a 3-element parallel conductor model neatly reproduces the trend of conductivity with thickness. This study addresses the question of how structural distortions at the atomic scale evolve in a thin film under the influence of the substrate and the surface. This topic is key to the understanding of the physics of heterostructures and the design of functional oxides.

Using an SU-8 photoresist structure and cytochrome C thin film sensing material for a microbolometer.

PubMed

Lai, Jian-Lun; Liao, Chien-Jen; Su, Guo-Dung John

2012-11-27

There are two critical parameters for microbolometers: the temperature coefficient of resistance (TCR) of the sensing material, and the thermal conductance of the insulation structure. Cytochrome c protein, having a high TCR, is a good candidate for infrared detection. We can use SU-8 photoresist for the thermal insulation structure, given its low thermal conductance. In this study, we designed a platform structure based on a SU-8 photoresist. We fabricated an infrared sensing pixel and recorded a high TCR for this new structure. The SU-8 photoresist insulation structure was fabricated using the exposure dose method. We experimentally demonstrated high values of TCR from 22%/K to 25.7%/K, and the measured noise was 1.2 × 10(-8) V2/Hz at 60 Hz. When the bias current was 2 μA, the calculated voltage responsivity was 1.16 × 10(5) V/W. This study presents a new kind of microbolometer based on cytochrome c protein on top of an SU-8 photoresist platform that does not require expensive vacuum deposition equipment.

Using an SU-8 Photoresist Structure and Cytochrome C Thin Film Sensing Material for a Microbolometer

PubMed Central

Lai, Jian-Lun; Liao, Chien-Jen; Su, Guo-Dung John

2012-01-01

There are two critical parameters for microbolometers: the temperature coefficient of resistance (TCR) of the sensing material, and the thermal conductance of the insulation structure. Cytochrome c protein, having a high TCR, is a good candidate for infrared detection. We can use SU-8 photoresist for the thermal insulation structure, given its low thermal conductance. In this study, we designed a platform structure based on a SU-8 photoresist. We fabricated an infrared sensing pixel and recorded a high TCR for this new structure. The SU-8 photoresist insulation structure was fabricated using the exposure dose method. We experimentally demonstrated high values of TCR from 22%/K to 25.7%/K, and the measured noise was 1.2 × 10−8 V2/Hz at 60 Hz. When the bias current was 2 μA, the calculated voltage responsivity was 1.16 × 105 V/W. This study presents a new kind of microbolometer based on cytochrome c protein on top of an SU-8 photoresist platform that does not require expensive vacuum deposition equipment. PMID:23443384

Reliability Analysis of Sealing Structure of Electromechanical System Based on Kriging Model

NASA Astrophysics Data System (ADS)

Zhang, F.; Wang, Y. M.; Chen, R. W.; Deng, W. W.; Gao, Y.

2018-05-01

The sealing performance of aircraft electromechanical system has a great influence on flight safety, and the reliability of its typical seal structure is analyzed by researcher. In this paper, we regard reciprocating seal structure as a research object to study structural reliability. Having been based on the finite element numerical simulation method, the contact stress between the rubber sealing ring and the cylinder wall is calculated, and the relationship between the contact stress and the pressure of the hydraulic medium is built, and the friction force on different working conditions are compared. Through the co-simulation, the adaptive Kriging model obtained by EFF learning mechanism is used to describe the failure probability of the seal ring, so as to evaluate the reliability of the sealing structure. This article proposes a new idea of numerical evaluation for the reliability analysis of sealing structure, and also provides a theoretical basis for the optimal design of sealing structure.

General theoretical description of angle-resolved photoemission spectroscopy of van der Waals structures

NASA Astrophysics Data System (ADS)

Amorim, B.

2018-04-01

We develop a general theory to model the angle-resolved photoemission spectroscopy (ARPES) of commensurate and incommensurate van der Waals (vdW) structures, formed by lattice mismatched and/or misaligned stacked layers of two-dimensional materials. The present theory is based on a tight-binding description of the structure and the concept of generalized umklapp processes, going beyond previous descriptions of ARPES in incommensurate vdW structures, which are based on continuous, low-energy models, being limited to structures with small lattice mismatch/misalignment. As applications of the general formalism, we study the ARPES bands and constant energy maps for two structures: twisted bilayer graphene and twisted bilayer MoS2. The present theory should be useful in correctly interpreting experimental results of ARPES of vdW structures and other systems displaying competition between different periodicities, such as two-dimensional materials weakly coupled to a substrate and materials with density wave phases.

Validating the Proposed Structure of the Relationships among Test Anxiety and Its Predictors Based on Control-Value Theory: Evidence for Gender-Specific Patterns

ERIC Educational Resources Information Center

Ringeisen, Tobias; Raufelder, Diana; Schnell, Kerstin; Rohrmann, Sonja

2016-01-01

Control-value theory (CVT) proposes a framework for the structure of the relationships between the various predictors of achievement-related emotions, particularly anxiety. Despite existing evidence for the role of anxiety predictors, research has not yet justified their proposed structure. Hence, the current study validated the structure of test…

A novel sensitivity-based method for damage detection of structures under unknown periodic excitations

NASA Astrophysics Data System (ADS)

Naseralavi, S. S.; Salajegheh, E.; Fadaee, M. J.; Salajegheh, J.

2014-06-01

This paper presents a technique for damage detection in structures under unknown periodic excitations using the transient displacement response. The method is capable of identifying the damage parameters without finding the input excitations. We first define the concept of displacement space as a linear space in which each point represents displacements of structure under an excitation and initial condition. Roughly speaking, the method is based on the fact that structural displacements under free and forced vibrations are associated with two parallel subspaces in the displacement space. Considering this novel geometrical viewpoint, an equation called kernel parallelization equation (KPE) is derived for damage detection under unknown periodic excitations and a sensitivity-based algorithm for solving KPE is proposed accordingly. The method is evaluated via three case studies under periodic excitations, which confirm the efficiency of the proposed method.

Structural attributes of individual trees for identifying homogeneous patches in a tropical rainforest

NASA Astrophysics Data System (ADS)

Alexander, Cici; Korstjens, Amanda H.; Hill, Ross A.

2017-03-01

Mapping and monitoring tropical rainforests and quantifying their carbon stocks are important, both for devising strategies for their conservation and mitigating the effects of climate change. Airborne Laser Scanning (ALS) has advantages over other remote sensing techniques for describing the three-dimensional structure of forests. This study identifies forest patches using ALS-based structural attributes in a tropical rainforest in Sumatra, Indonesia. A method to group trees with similar attributes into forest patches based on Thiessen polygons and k-medoids clustering is developed, combining the advantages of both raster and individual tree-based methods. The structural composition of the patches could be an indicator of habitat type and quality. The patches could also be a basis for developing allometric models for more accurate estimation of carbon stock than is currently possible with generalised models.

Ground-based testing of the dynamics of flexible space structures using band mechanisms

NASA Technical Reports Server (NTRS)

Yang, L. F.; Chew, Meng-Sang

1991-01-01

A suspension system based on a band mechanism is studied to provide the free-free conditions for ground based validation testing of flexible space structures. The band mechanism consists of a noncircular disk with a convex profile, preloaded by torsional springs at its center of rotation so that static equilibrium of the test structure is maintained at any vertical location; the gravitational force will be directly counteracted during dynamic testing of the space structure. This noncircular disk within the suspension system can be configured to remain unchanged for test articles with the different weights as long as the torsional spring is replaced to maintain the originally designed frequency ratio of W/k sub s. Simulations of test articles which are modeled as lumped parameter as well as continuous parameter systems, are also presented.

Ring system-based chemical graph generation for de novo molecular design

NASA Astrophysics Data System (ADS)

Miyao, Tomoyuki; Kaneko, Hiromasa; Funatsu, Kimito

2016-05-01

Generating chemical graphs in silico by combining building blocks is important and fundamental in virtual combinatorial chemistry. A premise in this area is that generated structures should be irredundant as well as exhaustive. In this study, we develop structure generation algorithms regarding combining ring systems as well as atom fragments. The proposed algorithms consist of three parts. First, chemical structures are generated through a canonical construction path. During structure generation, ring systems can be treated as reduced graphs having fewer vertices than those in the original ones. Second, diversified structures are generated by a simple rule-based generation algorithm. Third, the number of structures to be generated can be estimated with adequate accuracy without actual exhaustive generation. The proposed algorithms were implemented in structure generator Molgilla. As a practical application, Molgilla generated chemical structures mimicking rosiglitazone in terms of a two dimensional pharmacophore pattern. The strength of the algorithms lies in simplicity and flexibility. Therefore, they may be applied to various computer programs regarding structure generation by combining building blocks.

High temperature thermoelectric properties of rock-salt structure PbS

DOE PAGES

Parker, David S.; Singh, David J.

2013-12-18

We present an analysis of the high temperature transport properties of rock-salt structure PbS, a sister compound to the better studied lead chalcogenides PbSe and PbTe. In this study, we find thermopower magnitudes exceeding 200 V/K in a wide doping range for temperatures of 800 K and above. Based on these calculations, and an analysis of recent experimental work we find that this material has a potential for high thermoelectric performance. Also, we find favorable mechanical properties, based on an analysis of published data.

Example-Based Learning: Exploring the Use of Matrices and Problem Variability

ERIC Educational Resources Information Center

Hancock-Niemic, Mary A.; Lin, Lijia; Atkinson, Robert K.; Renkl, Alexander; Wittwer, Joerg

2016-01-01

The purpose of the study was to investigate the efficacy of using faded worked examples presented in matrices with problem structure variability to enhance learners' ability to recognize the underlying structure of the problems. Specifically, this study compared the effects of matrix-format versus linear-format faded worked examples combined with…

Post-Traumatic Stress Disorder in Maltreated Youth: A Study of Diagnostic Comorbidity and Child Factors

ERIC Educational Resources Information Center

Linning, Lisa M.; Kearney, Christopher A.

2004-01-01

The study of post-traumatic stress disorder (PTSD) in maltreated youth has received increased attention, though extensive comparisons to maltreated youth without PTSD and administrations of anxiety-based structured diagnostic interviews remain needed. We examined maltreated youth with or without PTSD using structured diagnostic interviews and…

Teacher Need-Structure and Instructional Preference in Reading: A Pilot Study.

ERIC Educational Resources Information Center

Duncan, Patricia H.

Thirty-one experienced teachers enrolled in graduate reading courses served as subjects in a study conducted to determine whether simple instruments could be developed to assess teacher need structure, frequency of teacher behaviors related to reading, and the relationship between the two. A 25-item instrument was developed based on Abraham…

Organizational Commitment of Teachers in Urban Schools: Examining the Effects of Team Structures

ERIC Educational Resources Information Center

Dee, Jay R.; Henkin, Alan B.; Singleton, Carole A.

2006-01-01

This study examines the effects of four team-based structures on the organizational commitment of elementary teachers in an urban school district. The study model focuses on organizational commitment and includes three intervening, endogenous variables: teacher empowerment, school communication, and work autonomy. Team teaching had both direct and…

Analyzing the Structure of the International Business Curriculum in India

ERIC Educational Resources Information Center

Srivastava, Deepak K.

2012-01-01

This article analyzes the structure of the international business curriculum through a questionnaire-based survey among current students and young managers who are studying or have studied international business courses in one of the top B-Schools of India. Respondents have the opinion that international business is more than internationalization…

Students using visual thinking to learn science in a Web-based environment

NASA Astrophysics Data System (ADS)

Plough, Jean Margaret

United States students' science test scores are low, especially in problem solving, and traditional science instruction could be improved. Consequently, visual thinking, constructing science structures, and problem solving in a web-based environment may be valuable strategies for improving science learning. This ethnographic study examined the science learning of fifteen fourth grade students in an after school computer club involving diverse students at an inner city school. The investigation was done from the perspective of the students, and it described the processes of visual thinking, web page construction, and problem solving in a web-based environment. The study utilized informal group interviews, field notes, Visual Learning Logs, and student web pages, and incorporated a Standards-Based Rubric which evaluated students' performance on eight science and technology standards. The Visual Learning Logs were drawings done on the computer to represent science concepts related to the Food Chain. Students used the internet to search for information on a plant or animal of their choice. Next, students used this internet information, with the information from their Visual Learning Logs, to make web pages on their plant or animal. Later, students linked their web pages to form Science Structures. Finally, students linked their Science Structures with the structures of other students, and used these linked structures as models for solving problems. Further, during informal group interviews, students answered questions about visual thinking, problem solving, and science concepts. The results of this study showed clearly that (1) making visual representations helped students understand science knowledge, (2) making links between web pages helped students construct Science Knowledge Structures, and (3) students themselves said that visual thinking helped them learn science. In addition, this study found that when using Visual Learning Logs, the main overall ideas of the science concepts were usually represented accurately. Further, looking for information on the internet may cause new problems in learning. Likewise, being absent, starting late, and/or dropping out all may negatively influence students' proficiency on the standards. Finally, the way Science Structures are constructed and linked may provide insights into the way individual students think and process information.

Comparative Analysis of Virtual Screening Approaches in the Search for Novel EphA2 Receptor Antagonists.

PubMed

Callegari, Donatella; Pala, Daniele; Scalvini, Laura; Tognolini, Massimiliano; Incerti, Matteo; Rivara, Silvia; Mor, Marco; Lodola, Alessio

2015-09-17

The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aimed at finding novel EphA2 antagonists, we investigated the ability of both ligand-based and structure-based approaches to retrieve known EphA2 antagonists from libraries of decoys with similar molecular properties. While ligand-based VSs were conducted using UniPR129 and ephrin-A1 ligand as reference structures, structure-based VSs were performed with Glide, using the X-ray structure of the EphA2 receptor/ephrin-A1 complex. A comparison of enrichment factors showed that ligand-based approaches outperformed the structure-based ones, suggesting ligand-based methods using the G-H loop of ephrin-A1 ligand as template as the most promising protocols to search for novel EphA2 antagonists.

CSM research: Methods and application studies

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

1989-01-01

Computational mechanics is that discipline of applied science and engineering devoted to the study of physical phenomena by means of computational methods based on mathematical modeling and simulation, utilizing digital computers. The discipline combines theoretical and applied mechanics, approximation theory, numerical analysis, and computer science. Computational mechanics has had a major impact on engineering analysis and design. When applied to structural mechanics, the discipline is referred to herein as computational structural mechanics. Complex structures being considered by NASA for the 1990's include composite primary aircraft structures and the space station. These structures will be much more difficult to analyze than today's structures and necessitate a major upgrade in computerized structural analysis technology. NASA has initiated a research activity in structural analysis called Computational Structural Mechanics (CSM). The broad objective of the CSM activity is to develop advanced structural analysis technology that will exploit modern and emerging computers, such as those with vector and/or parallel processing capabilities. Here, the current research directions for the Methods and Application Studies Team of the Langley CSM activity are described.

First principles prediction of amorphous phases using evolutionary algorithms

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

Nahas, Suhas, E-mail: shsnhs@iitk.ac.in; Gaur, Anshu, E-mail: agaur@iitk.ac.in; Bhowmick, Somnath, E-mail: bsomnath@iitk.ac.in

2016-07-07

We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bondmore » angle are within ∼2% of those reported by ab initio MD calculations and experimental studies.« less

Construction and identification of a D-Vine model applied to the probability distribution of modal parameters in structural dynamics

NASA Astrophysics Data System (ADS)

Dubreuil, S.; Salaün, M.; Rodriguez, E.; Petitjean, F.

2018-01-01

This study investigates the construction and identification of the probability distribution of random modal parameters (natural frequencies and effective parameters) in structural dynamics. As these parameters present various types of dependence structures, the retained approach is based on pair copula construction (PCC). A literature review leads us to choose a D-Vine model for the construction of modal parameters probability distributions. Identification of this model is based on likelihood maximization which makes it sensitive to the dimension of the distribution, namely the number of considered modes in our context. To this respect, a mode selection preprocessing step is proposed. It allows the selection of the relevant random modes for a given transfer function. The second point, addressed in this study, concerns the choice of the D-Vine model. Indeed, D-Vine model is not uniquely defined. Two strategies are proposed and compared. The first one is based on the context of the study whereas the second one is purely based on statistical considerations. Finally, the proposed approaches are numerically studied and compared with respect to their capabilities, first in the identification of the probability distribution of random modal parameters and second in the estimation of the 99 % quantiles of some transfer functions.

Comprehensive risk analysis for structure type selection.

DOT National Transportation Integrated Search

2010-04-01

Optimization of bridge selection and design traditionally has been sought in terms of the finished structure. This study presents a : more comprehensive risk-based analysis that includes user costs and accidents during the construction phase. Costs f...

Structural damage continuous monitoring by using a data driven approach based on principal component analysis and cross-correlation analysis

NASA Astrophysics Data System (ADS)

Camacho-Navarro, Jhonatan; Ruiz, Magda; Villamizar, Rodolfo; Mujica, Luis; Moreno-Beltrán, Gustavo; Quiroga, Jabid

2017-05-01

Continuous monitoring for damage detection in structural assessment comprises implementation of low cost equipment and efficient algorithms. This work describes the stages involved in the design of a methodology with high feasibility to be used in continuous damage assessment. Specifically, an algorithm based on a data-driven approach by using principal component analysis and pre-processing acquired signals by means of cross-correlation functions, is discussed. A carbon steel pipe section and a laboratory tower were used as test structures in order to demonstrate the feasibility of the methodology to detect abrupt changes in the structural response when damages occur. Two types of damage cases are studied: crack and leak for each structure, respectively. Experimental results show that the methodology is promising in the continuous monitoring of real structures.

The role of self-defined race/ethnicity in population structure control.

PubMed

Liu, X-Q; Paterson, A D; John, E M; Knight, J A

2006-07-01

Population-based association studies are powerful tools for the genetic mapping of complex diseases. However, this method is sensitive to potential confounding by population structure. While statistical methods that use genetic markers to detect and control for population structure have been the focus of current literature, the utility of self-defined race/ethnicity in controlling for population structure has been controversial. In this study of 1334 individuals, who self-identified as either African American, European American or Hispanic, we demonstrated that when the true underlying genetic structure and the self-defined racial/ethnic groups were roughly in agreement with each other, the self-defined race/ethnicity information was useful in the control of population structure.

The Prediction of Botulinum Toxin Structure Based on in Silico and in Vitro Analysis

NASA Astrophysics Data System (ADS)

Suzuki, Tomonori; Miyazaki, Satoru

2011-01-01

Many of biological system mediated through protein-protein interactions. Knowledge of protein-protein complex structure is required for understanding the function. The determination of huge size and flexible protein-protein complex structure by experimental studies remains difficult, costly and five-consuming, therefore computational prediction of protein structures by homolog modeling and docking studies is valuable method. In addition, MD simulation is also one of the most powerful methods allowing to see the real dynamics of proteins. Here, we predict protein-protein complex structure of botulinum toxin to analyze its property. These bioinformatics methods are useful to report the relation between the flexibility of backbone structure and the activity.

Role of zero-point effects in stabilizing the ground state structure of bulk Fe2P

NASA Astrophysics Data System (ADS)

Bhat, Soumya S.; Gupta, Kapil; Bhattacharjee, Satadeep; Lee, Seung-Cheol

2018-05-01

Structural stability of Fe2P is investigated in detail using first-principles calculations based on density functional theory. While the orthorhombic C23 phase is found to be energetically more stable, the experiments suggest it to be hexagonal C22 phase. In the present study, we show that in order to obtain the correct ground state structure of Fe2P from the first-principles based methods it is utmost necessary to consider the zero-point effects such as zero-point vibrations and spin fluctuations. This study demonstrates an exceptional case where a bulk material is stabilized by quantum effects, which are usually important in low-dimensional materials. Our results also indicate the possibility of magnetic field induced structural quantum phase transition in Fe2P, which should form the basis for further theoretical and experimental efforts.

Spectroscopy of Isolated Prebiotic Nucleobases

NASA Technical Reports Server (NTRS)

Svadlenak, Nathan; Callahan, Michael P.; Ligare, Marshall; Gulian, Lisa; Gengeliczki, Zsolt; Nachtigallova, Dana; Hobza, Pavel; deVries, Mattanjah

2011-01-01

We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions.

Research and application of borehole structure optimization based on pre-drill risk assessment

NASA Astrophysics Data System (ADS)

Zhang, Guohui; Liu, Xinyun; Chenrong; Hugui; Yu, Wenhua; Sheng, Yanan; Guan, Zhichuan

2017-11-01

Borehole structure design based on pre-drill risk assessment and considering risks related to drilling operation is the pre-condition for safe and smooth drilling operation. Major risks of drilling operation include lost circulation, blowout, sidewall collapsing, sticking and failure of drilling tools etc. In the study, studying data from neighboring wells was used to calculate the profile of formation pressure with credibility in the target well, then the borehole structure design for the target well assessment by using the drilling risk assessment to predict engineering risks before drilling. Finally, the prediction results were used to optimize borehole structure design to prevent such drilling risks. The newly-developed technique provides a scientific basis for lowering probability and frequency of drilling engineering risks, and shortening time required to drill a well, which is of great significance for safe and high-efficient drilling.

Emission Testing Results of Thermally Stable, Metamaterial, Selective-Emitters for Thermophotovoltaics

NASA Astrophysics Data System (ADS)

Levinson, Katherine; Naka, Norihito; Pfiester, Nicole; Licht, Abigail; Vandervelde, Tom

2015-03-01

In thermophotovoltaics, the energy from a heated emitter is converted to electricity by a photovoltaic diode. A selective emitter can be used to emit a narrow band of wavelengths tailored to the bandgap of the photovoltaic diode. This spectral shaping improves the conversion efficiency of the diode and reduces undesirable diode heating. In our research, we study selective emitters based on metamaterials composed of repeating nanoscale structures. The emission characteristics of these materials vary based on the compositional structure, allowing the emitted spectrum to be tunable. Simulations were performed with CST Microwave Studio to design emitters with peak wavelengths ranging from 1-10 microns. The structures were then fabricated using physical vapor deposition and electron beam lithography on a sapphire substrate. Emitter materials studied include gold, platinum, and iridium. Here we report on the emission spectra of the selective emitters and the post-heating structural integrity.

Structure of the alexithymic brain: A parametric coordinate-based meta-analysis.

PubMed

Xu, Pengfei; Opmeer, Esther M; van Tol, Marie-José; Goerlich, Katharina S; Aleman, André

2018-04-01

Alexithymia refers to deficiencies in identifying and expressing emotions. This might be related to changes in structural brain volumes, but its neuroanatomical basis remains uncertain as studies have shown heterogeneous findings. Therefore, we conducted a parametric coordinate-based meta-analysis. We identified seventeen structural neuroimaging studies (including a total of 2586 individuals with different levels of alexithymia) investigating the association between gray matter volume and alexithymia. Volumes of the left insula, left amygdala, orbital frontal cortex and striatum were consistently smaller in people with high levels of alexithymia. These areas are important for emotion perception and emotional experience. Smaller volumes in these areas might lead to deficiencies in appropriately identifying and expressing emotions. These findings provide the first quantitative integration of results pertaining to the structural neuroanatomical basis of alexithymia. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes.

PubMed

Kulén, Martina; Lindgren, Marie; Hansen, Sabine; Cairns, Andrew G; Grundström, Christin; Begum, Afshan; van der Lingen, Ingeborg; Brännström, Kristoffer; Hall, Michael; Sauer, Uwe H; Johansson, Jörgen; Sauer-Eriksson, A Elisabeth; Almqvist, Fredrik

2018-05-10

Listeria monocytogenes is a bacterial pathogen that controls much of its virulence through the transcriptional regulator PrfA. In this study, we describe structure-guided design and synthesis of a set of PrfA inhibitors based on ring-fused 2-pyridone heterocycles. Our most effective compound decreased virulence factor expression, reduced bacterial uptake into eukaryotic cells, and improved survival of chicken embryos infected with L. monocytogenes compared to previously identified compounds. Crystal structures identified an intraprotein "tunnel" as the main inhibitor binding site (A I ), where the compounds participate in an extensive hydrophobic network that restricts the protein's ability to form functional DNA-binding helix-turn-helix (HTH) motifs. Our studies also revealed a hitherto unsuspected structural plasticity of the HTH motif. In conclusion, we have designed 2-pyridone analogues that function as site-A I selective PrfA inhibitors with potent antivirulence properties.

Effect of deep centers on the radiative characteristics of epitaxial structures in the Ga-As-P system

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

Ermakov, O.P.

1986-08-01

This paper studies the radiative characteristics of structures not doped with nitrogen based on AgP and GaAs /SUB 1-y/ P /SUB y/ in a wide range of compositions, containing stoichiometry and radiation defects. The structures studied were obtained by the methods of liquid-phase and gas-phase epitaxy. Zn was used as the acceptor impurity in obtaining the p-n structures. The radiation defects were introduced by irradiation with a beam of fast 2.5-MeV electrons and the radiative characteristics were studied with the help of the method of electroluminescence (EL).

Experimental and theoretical determination of σ bands on ("2 √{3 }×2 √{3 } ") silicene grown on Ag(111)

NASA Astrophysics Data System (ADS)

Wang, W.; Olovsson, W.; Uhrberg, R. I. G.

2015-11-01

Silicene, the two-dimensional (2D) allotrope of silicon, has very recently attracted a lot of attention. It has a structure that is similar to graphene and it is theoretically predicted to show the same kind of electronic properties which have put graphene into the focus of large research and development projects worldwide. In particular, a 2D structure made from Si is of high interest because of the application potential in Si-based electronic devices. However, so far there is not much known about the silicene band structure from experimental studies. A comprehensive study is here presented of the atomic and electronic structure of the silicene phase on Ag(111) denoted as (2 √ 3 ×2 √ 3 )R30° in the literature. Low energy electron diffraction (LEED) shows an unconventional rotated ("2 √ 3 ×2 √ 3 ") pattern with a complicated set of split diffraction spots. Scanning tunneling microscopy (STM) results reveal a Ag(111) surface that is homogeneously covered by the ("2 √ 3 ×2 √ 3 ") silicene which exhibits an additional quasiperiodic long-range ordered superstructure. The complex structure, revealed by STM, has been investigated in detail and we present a consistent picture of the silicene structure based on both STM and LEED. The homogeneous coverage by the ("2 √ 3 ×2 √ 3 ") silicene facilitated an angle-resolved photoelectron spectroscopy study which reveals a silicene band structure of unprecedented detail. Here we report four silicene bands which are compared to calculated dispersions based on a relaxed (2 √ 3 ×2 √ 3 ) model. We find good qualitative agreement between the experimentally observed bands and calculated silicene bands of σ character.

Study on Microstructure and Electrochemical Corrosion Behavior of PEO Coatings Formed on Aluminum Alloy

NASA Astrophysics Data System (ADS)

Xiang, N.; Song, R. G.; Li, H.; Wang, C.; Mao, Q. Z.; Xiong, Y.

2015-12-01

Plasma electrolytic oxidation (PEO) treated 6063 aluminum alloy was applied in a silicate- and borate-based alkaline solution. The microstructure and electrochemical corrosion behavior were studied by scanning electron microscopy, electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization techniques. The results showed that the silicate-based PEO coating was of a denser structure compared with that of borate-based PEO coating. In addition, the silicate-based PEO coating was composed of more phased (Al9Si) than borate-based PEO coating. The results of corrosion test indicated that the silicate-based PEO coating provided a superior protection to 6063 aluminum alloy substrate, while borate-based PEO coating with a porous structure showed an inferior conservancy against corrosive electrolyte. Furthermore, the EIS tests proved that both coatings were capable to resist the aggressive erosion in 0.5 M NaCl solution after 72 h of immersion. However, the borate-based PEO coating could not provide sufficient protection to the substrate after 72-h immersion in 1 M NaCl solution.

Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.

PubMed

Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

2013-12-01

AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.