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Sample records for integrated 4-dimensional patterning

  1. Vertebrate limb development: moving from classical morphogen gradients to an integrated 4-dimensional patterning system.

    PubMed

    Bénazet, Jean-Denis; Zeller, Rolf

    2009-10-01

    A wealth of classical embryological manipulation experiments taking mainly advantage of the chicken limb buds identified the apical ectodermal ridge (AER) and the zone of polarizing activity (ZPA) as the respective ectodermal and mesenchymal key signaling centers coordinating proximodistal (PD) and anteroposterior (AP) limb axis development. These experiments inspired Wolpert's French flag model, which is a classic among morphogen gradient models. Subsequent molecular and genetic analysis in the mouse identified retinoic acid as proximal signal, and fibroblast growth factors (FGFs) and sonic hedgehog (SHH) as the essential instructive signals produced by AER and ZPA, respectively. Recent studies provide good evidence that progenitors are specified early with respect to their PD and AP fates and that morpho-regulatory signaling is also required for subsequent proliferative expansion of the specified progenitor pools. The determination of particular fates seems to occur rather late and depends on additional signals such as bone morphogenetic proteins (BMPs), which indicates that cells integrate signaling inputs over time and space. The coordinate regulation of PD and AP axis patterning is controlled by an epithelial-mesenchymal feedback signaling system, in which transcriptional regulation of the BMP antagonist Gremlin1 integrates inputs from the BMP, SHH, and FGF pathways. Vertebrate limb-bud development is controlled by a 4-dimensional (4D) patterning system integrating positive and negative regulatory feedback loops, rather than thresholds set by morphogen gradients.

  2. A 4-Dimensional Representation of Antennal Lobe Output Based on an Ensemble of Characterized Projection Neurons

    PubMed Central

    Staudacher, Erich M.; Huetteroth, Wolf; Schachtner, Joachim; Daly, Kevin C.

    2009-01-01

    A central problem facing studies of neural encoding in sensory systems is how to accurately quantify the extent of spatial and temporal responses. In this study, we take advantage of the relatively simple and stereotypic neural architecture found in invertebrates. We combine standard electrophysiological techniques, recently developed population analysis techniques, and novel anatomical methods to form an innovative 4-dimensional view of odor output representations in the antennal lobe of the moth Manduca sexta. This novel approach allows quantification of olfactory responses of characterized neurons with spike time resolution. Additionally, arbitrary integration windows can be used for comparisons with other methods such as imaging. By assigning statistical significance to changes in neuronal firing, this method can visualize activity across the entire antennal lobe. The resulting 4-dimensional representation of antennal lobe output complements imaging and multi-unit experiments yet provides a more comprehensive and accurate view of glomerular activation patterns in spike time resolution. PMID:19464513

  3. Pattern uniformity control in integrated structures

    NASA Astrophysics Data System (ADS)

    Kobayashi, Shinji; Okada, Soichiro; Shimura, Satoru; Nafus, Kathleen; Fonseca, Carlos; Biesemans, Serge; Enomoto, Masashi

    2017-03-01

    In our previous paper dealing with multi-patterning, we proposed a new indicator to quantify the quality of final wafer pattern transfer, called interactive pattern fidelity error (IPFE). It detects patterning failures resulting from any source of variation in creating integrated patterns. IPFE is a function of overlay and edge placement error (EPE) of all layers comprising the final pattern (i.e. lower and upper layers). In this paper, we extend the use cases with Via in additional to the bridge case (Block on Spacer). We propose an IPFE budget and CD budget using simple geometric and statistical models with analysis of a variance (ANOVA). In addition, we validate the model with experimental data. From the experimental results, improvements in overlay, local-CDU (LCDU) of contact hole (CH) or pillar patterns (especially, stochastic pattern noise (SPN)) and pitch walking are all critical to meet budget requirements. We also provide a special note about the importance of the line length used in analyzing LWR. We find that IPFE and CD budget requirements are consistent to the table of the ITRS's technical requirement. Therefore the IPFE concept can be adopted for a variety of integrated structures comprising digital logic circuits. Finally, we suggest how to use IPFE for yield management and optimization requirements for each process.

  4. Time dependent electromagnetic fields and 4-dimensional Stokes' theorem

    NASA Astrophysics Data System (ADS)

    Andosca, Ryan; Singleton, Douglas

    2016-11-01

    Stokes' theorem is central to many aspects of physics—electromagnetism, the Aharonov-Bohm effect, and Wilson loops to name a few. However, the pedagogical examples and research work almost exclusively focus on situations where the fields are time-independent so that one need only deal with purely spatial line integrals (e.g., ∮ A . d x ) and purely spatial area integrals (e.g., ∫ ( ∇ × A ) . d a = ∫ B . d a ). Here, we address this gap by giving some explicit examples of how Stokes' theorem plays out with time-dependent fields in a full 4-dimensional spacetime context. We also discuss some unusual features of Stokes' theorem with time-dependent fields related to gauge transformations and non-simply connected topology.

  5. Understanding Patterns for System-of-Systems Integration

    DTIC Science & Technology

    2013-12-01

    5.5.4 Publish-Subscribe 25 5.6 Pattern-Oriented Software Architecture 26 5.6.1 Blackboard 26 5.7 Messaging 27 5.7.1 Pipes and Filters 27 5.7.2...for Publish-Subscribe Pattern 26 Table 13: Matrix for Blackboard Pattern 27 Table 14: Matrix for Pipes and Filters Pattern 28 Table 15: Matrix for...integration patterns are all found in the book Pattern-Oriented Software Architec- ture, Volume 4 [Buschmann 2007]. 5.6.1 Blackboard By its very

  6. Patterns of craniofacial integration in extant Homo, Pan, and Gorilla.

    PubMed

    Polanski, Joshua M; Franciscus, Robert G

    2006-09-01

    Brain size increased greatly during Pleistocene human evolution, while overall facial and dentognathic size decreased markedly. This mosaic pattern is due to either selective forces that acted uniquely on each functional unit in a modularized, developmentally uncoupled craniofacial complex, or alternatively, selection that acted primarily on one unit, with the other responding passively as part of a coevolved set of ontogenetically and evolutionarily integrated structures. Using conditional independence modeling on homologous linear measurements of the height, breadth, and depth of the cranium in Pan (n = 95), Gorilla (n = 102), and recent Homo (n = 120), we reject the null hypothesis of equal levels of overall cranial integration. While all three groups share the pattern of greater neurocranial integration with distinct separation between the face and neurocranium (modularization), family differences do exist. The apes are more integrated in their entire crania, but display a particularly strong pattern of integration within the facial complex related to prognathism. Modern humans display virtually no facial integration, a pattern which is likely related to their markedly decreased facial projection. Modern humans also differ from their great ape counterparts in being more integrated within the breadth dimension of the cranial vault, likely tied to the increase in brain size and eventual globularity seen in human evolution. That the modern human integration pattern differs from the ancestral African great ape pattern along the inverse neurocranial-facial trend seen in human evolution indicates that this shift in the pattern of integration is evolutionarily significant, and may help to clarify aspects of the current debate over defining modern humans. 2006 Wiley-Liss, Inc.

  7. Verification and clarification of patterns of sensory integrative dysfunction.

    PubMed

    Mailloux, Zoe; Mulligan, Shelley; Roley, Susanne Smith; Blanche, Erna; Cermak, Sharon; Coleman, Gina Geppert; Bodison, Stefanie; Lane, Christianne Joy

    2011-01-01

    Building on established relationships between the constructs of sensory integration in typical and special needs populations, in this retrospective study we examined patterns of sensory integrative dysfunction in 273 children ages 4-9 who had received occupational therapy evaluations in two private practice settings. Test results on the Sensory Integration and Praxis Tests, portions of the Sensory Processing Measure representing tactile overresponsiveness, and parent report of attention and activity level were included in the analyses. Exploratory factor analysis identified patterns similar to those found in early studies by Ayres (1965, 1966a, 1966b, 1969, 1972b, 1977, & 1989), namely Visuodyspraxia and Somatodyspraxia, Vestibular and Proprioceptive Bilateral Integration and Sequencing, Tactile and Visual Discrimination, and Tactile Defensiveness and Attention. Findings reinforce associations between constructs of sensory integration and assist with understanding sensory integration disorders that may affect childhood occupation. Limitations include the potential for subjective interpretation in factor analysis and inability to adjust measures available in charts in a retrospective research.

  8. Sensory integration and praxis patterns in children with autism.

    PubMed

    Roley, Susanne Smith; Mailloux, Zoe; Parham, L Diane; Schaaf, Roseann C; Lane, Christianne Joy; Cermak, Sharon

    2015-01-01

    We sought to characterize sensory integration (SI) and praxis patterns of children with autism spectrum disorder (ASD) and discern whether these patterns relate to social participation. We extracted Sensory Integration and Praxis Tests (SIPT) and Sensory Processing Measure (SPM) scores from clinical records of children with ASD ages 4-11 yr (N=89) and used SIPT and SPM standard scores to describe SI and praxis patterns. Correlation coefficients were generated to discern relationships among SI and praxis scores and these scores' associations with SPM Social Participation scores. Children with ASD showed relative strengths in visual praxis. Marked difficulties were evident in imitation praxis, vestibular bilateral integration, somatosensory perception, and sensory reactivity. SPM Social Participation scores were inversely associated with areas of deficit on SIPT measures. Children with ASD characteristically display strengths in visuopraxis and difficulties with somatopraxis and vestibular functions, which appear to greatly affect participation. Copyright © 2015 by the American Occupational Therapy Association, Inc.

  9. Regional Logistics Information Resources Integration Patterns and Countermeasures

    NASA Astrophysics Data System (ADS)

    Wu, Hui; Shangguan, Xu-ming

    Effective integration of regional logistics information resources can provide collaborative services in information flow, business flow and logistics for regional logistics enterprises, which also can reduce operating costs and improve market responsiveness. First, this paper analyzes the realistic significance on the integration of regional logistics information. Second, this paper brings forward three feasible patterns on the integration of regional logistics information resources, These three models have their own strengths and the scope of application and implementation, which model is selected will depend on the specific business and the regional distribution of enterprises. Last, this paper discusses the related countermeasures on the integration of regional logistics information resources, because the integration of regional logistics information is a systems engineering, when the integration is advancing, the countermeasures should pay close attention to the current needs and long-term development of regional enterprises.

  10. System integration of pattern recognition, adaptive aided, upper limb prostheses

    NASA Technical Reports Server (NTRS)

    Lyman, J.; Freedy, A.; Solomonow, M.

    1975-01-01

    The requirements for successful integration of a computer aided control system for multi degree of freedom artificial arms are discussed. Specifications are established for a system which shares control between a human amputee and an automatic control subsystem. The approach integrates the following subsystems: (1) myoelectric pattern recognition, (2) adaptive computer aiding; (3) local reflex control; (4) prosthetic sensory feedback; and (5) externally energized arm with the functions of prehension, wrist rotation, elbow extension and flexion and humeral rotation.

  11. Energy dependent 4-dimensional multiple scattering distributions

    NASA Astrophysics Data System (ADS)

    Tschalär, C.

    1984-12-01

    A complete analytic solution in Fourier space is presented of the four dimensional small angle, multiple scattering distribution MSD in angle and space, produced by an energy dependent single scattering cross section from an initial pencil beam of heavy particles. Independently, simple integrals are derived for the central moments of the energy dependent MSD in the continuous-slowing-down approximation. The distributions of the projections t and x of the scattering angle and displacement into a plane through the axis of propagation are evaluated numerically for a truncated Rutherford scattering cross section using a fast Fourier transform. The resulting MSDs for a wide range of particles, initial and final momenta, and scattering materials are found to be approximately represented by one-dimensional set of standard distributions symmetrized by a linear transformation in t- x-space.

  12. Dynamic phase imaging utilizing a 4-dimensional microscope system

    NASA Astrophysics Data System (ADS)

    Creath, Katherine

    2011-03-01

    This paper describes a new, novel interference Linnik microscope system and presents images and data of live biological samples. The specially designed optical system enables instantaneous 4-dimensional video measurements of dynamic motions within and among live cells without the need for contrast agents. This "label-free", vibration insensitive imaging system enables measurement of biological objects in reflection using harmless light levels with a variety of magnifications and wavelengths with fields of view from several hundred microns up to a millimeter. At the core of the instrument is a phase measurement camera (PMC) enabling simultaneous measurement of multiple interference patterns utilizing a pixelated phase mask taking advantage of the polarization properties of light. Utilizing this technology enables the creation of phase image movies in real time at video rates so that dynamic motions and volumetric changes can be tracked. Objects are placed on a reflective surface in liquid under a coverslip. Phase values are converted to optical thickness data enabling volumetric, motion and morphological studies. Data from a number of different organisms such as flagellates and rotifers will be presented, as will measurements of human breast cancer cells with the addition of various agents that break down the cells. These data highlight examples of monitoring different biological processes and motions.

  13. Dynamic phase imaging utilizing a 4-dimensional microscope system

    PubMed Central

    Creath, Katherine

    2011-01-01

    This paper describes a new, novel interference Linnik microscope system and presents images and data of live biological samples. The specially designed optical system enables instantaneous 4-dimensional video measurements of dynamic motions within and among live cells without the need for contrast agents. This "label-free", vibration insensitive imaging system enables measurement of biological objects in reflection using harmless light levels with a variety of magnifications and wavelengths with fields of view from several hundred microns up to a millimeter. At the core of the instrument is a phase measurement camera (PMC) enabling simultaneous measurement of multiple interference patterns utilizing a pixelated phase mask taking advantage of the polarization properties of light. Utilizing this technology enables the creation of phase image movies in real time at video rates so that dynamic motions and volumetric changes can be tracked. Objects are placed on a reflective surface in liquid under a coverslip. Phase values are converted to optical thickness data enabling volumetric, motion and morphological studies. Data from a number of different organisms such as flagellates and rotifers will be presented, as will measurements of human breast cancer cells with the addition of various agents that break down the cells. These data highlight examples of monitoring different biological processes and motions. PMID:24357901

  14. Peer Interaction Patterns in an Integrated Middle School

    ERIC Educational Resources Information Center

    Schofield, Janet W.; Sagar, H. Andrew

    1977-01-01

    Analysis of seating patterns in a newly integrated middle school suggests that while race is an important grouping criterion, sex is a more important criterion; and girls show more racial aggregation than boys. Racial aggregation decreased over time in seventh grade, but increased in eighth grade, perhaps due to academic grouping. (Author/MV)

  15. Pattern-integrated interference lithography: prospects for nano- and microelectronics.

    PubMed

    Leibovici, Matthieu C R; Burrow, Guy M; Gaylord, Thomas K

    2012-10-08

    In recent years, limitations in optical lithography have challenged the cost-effective manufacture of nano- and microelectronic chips. Spatially regular designs have been introduced to improve manufacturability. However, regular designed layouts typically require an interference step followed by a trim step. These multiple steps increase cost and reduce yield. In the present work, Pattern-Integrated Interference Lithography (PIIL) is introduced to address this problem. PIIL is the integration of interference lithography and superposed pattern mask imaging, combining the interference and the trim into a single-exposure step. Example PIIL implementations and experimental demonstrations are presented. The degrees of freedom associated with the source, pattern mask, and Fourier filter designs are described.

  16. Integrative visualization of temporally varying medical image patterns.

    PubMed

    Soh, Jung; Xiao, Mei; Do, Thao; Meruvia-Pastor, Oscar; Sensen, Christoph W

    2011-07-21

    We have developed a tool for the visualization of temporal changes of disease patterns, using stacks of medical images collected in time-series experiments. With this tool, users can generate 3D surface models representing disease patterns and observe changes over time in size, shape, and location of clinically significant image patterns. Statistical measurements of the volume of the observed disease patterns can be performed simultaneously. Spatial data integration occurs through the combination of 2D slices of an image stack into a 3D surface model. Temporal integration occurs through the sequential visualization of the 3D models from different time points. Visual integration enables the tool to show 2D images, 3D models and statistical data simultaneously. As an example, the tool has been used to visualize brain MRI scans of several multiple sclerosis patients. It has been developed in Java™, to ensure portability and platform independence, with a user-friendly interface and can be downloaded free of charge for academic users.

  17. Respiratory Amplitude Guided 4-Dimensional Magnetic Resonance Imaging

    SciTech Connect

    Hu, Yanle; Caruthers, Shelton D.; Low, Daniel A.; Parikh, Parag J.; Mutic, Sasa

    2013-05-01

    Purpose: To evaluate the feasibility of prospectively guiding 4-dimensional (4D) magnetic resonance imaging (MRI) image acquisition using triggers at preselected respiratory amplitudes to achieve T{sub 2} weighting for abdominal motion tracking. Methods and Materials: A respiratory amplitude-based triggering system was developed and integrated into a commercial turbo spin echo MRI sequence. Initial feasibility tests were performed on healthy human study participants. Four respiratory states, the middle and the end of inhalation and exhalation, were used to trigger 4D MRI image acquisition of the liver. To achieve T{sub 2} weighting, the echo time and repetition time were set to 75 milliseconds and 4108 milliseconds, respectively. Single-shot acquisition, together with parallel imaging and partial k-space imaging techniques, was used to improve image acquisition efficiency. 4D MRI image sets composed of axial or sagittal slices were acquired. Results: Respiratory data measured and logged by the MRI scanner showed that the triggers occurred at the appropriate respiratory levels. Liver motion could be easily observed on both 4D MRI image datasets by sensing either the change of liver in size and shape (axial) or diaphragm motion (sagittal). Both 4D MRI image datasets were T{sub 2}-weighted as expected. Conclusions: This study demonstrated the feasibility of achieving T{sub 2}-weighted 4D MRI images using amplitude-based respiratory triggers. With the aid of the respiratory amplitude-based triggering system, the proposed method is compatible with most MRI sequences and therefore has the potential to improve tumor-tissue contrast in abdominal tumor motion imaging.

  18. A new concept of vertically integrated pattern recognition associative memory

    SciTech Connect

    Liu, Ted; Hoff, Jim; Deptuch, Grzegorz; Yarema, Ray; /Fermilab

    2011-11-01

    Hardware-based pattern recognition for fast triggering on particle tracks has been successfully used in high-energy physics experiments for some time. The CDF Silicon Vertex Trigger (SVT) at the Fermilab Tevatron is an excellent example. The method used there, developed in the 1990's, is based on algorithms that use a massively parallel associative memory architecture to identify patterns efficiently at high speed. However, due to much higher occupancy and event rates at the LHC, and the fact that the LHC detectors have a much larger number of channels in their tracking detectors, there is an enormous challenge in implementing fast pattern recognition for a track trigger, requiring about three orders of magnitude more associative memory patterns than what was used in the original CDF SVT. Scaling of current technologies is unlikely to satisfy the scientific needs of the future, and investments in transformational new technologies need to be made. In this paper, we will discuss a new concept of using the emerging 3D vertical integration technology to significantly advance the state-of-the-art for fast pattern recognition within and outside HEP. A generic R and D proposal based on this new concept, with a few institutions involved, has recently been submitted to DOE with the goal to design and perform the ASIC engineering necessary to realize a prototype device. The progress of this R and D project will be reported in the future. Here we will only focus on the concept of this new approach.

  19. Integration and macroevolutionary patterns in the pollination biology of conifers.

    PubMed

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

    2015-06-01

    Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology.

  20. Human midsagittal brain shape variation: patterns, allometry and integration

    PubMed Central

    Bruner, Emiliano; Martin-Loeches, Manuel; Colom, Roberto

    2010-01-01

    Midsagittal cerebral morphology provides a homologous geometrical reference for brain shape and cortical vs. subcortical spatial relationships. In this study, midsagittal brain shape variation is investigated in a sample of 102 humans, in order to describe and quantify the major patterns of correlation between morphological features, the effect of size and sex on general anatomy, and the degree of integration between different cortical and subcortical areas. The only evident pattern of covariation was associated with fronto-parietal cortical bulging. The allometric component was weak for the cortical profile, but more robust for the posterior subcortical areas. Apparent sex differences were evidenced in size but not in brain shape. Cortical and subcortical elements displayed scarcely integrated changes, suggesting a modular separation between these two areas. However, a certain correlation was found between posterior subcortical and parietal cortical variations. These results should be directly integrated with information ranging from functional craniology to wiring organization, and with hypotheses linking brain shape and the mechanical properties of neurons during morphogenesis. PMID:20345859

  1. Integrating patterns of knowing in an undergraduate nursing course.

    PubMed

    Carr, J M

    1999-01-01

    A complex and changing contemporary healthcare system and holistic consideration of patients create a need for nurses who have a sophisticated, broad knowledge base. Empirical, ethical, personal, and aesthetic patterns of knowing provide a meaningful background for course development and offer students the opportunity to understand themselves and their patients through multiple modes of awareness. In this article, the author describes the integration of patterns of knowing into an undergraduate nursing course. Course objectives, content, assignments, and evaluation are discussed. A course such as this one that incorporates scientific knowledge of humans in health and illness, aesthetic perception of human experiences, personal understanding of self and others, and the capacity to make ethical choices enriches student learning about the art and science of nursing.

  2. Spatiotemporal integration of tactile patterns along and across fingers.

    PubMed

    Trojan, Jörg; Heil, Maruschka; Maihöfner, Christian; Hölzl, Rupert; Kleinböhl, Dieter; Flor, Herta; Benrath, Justus

    2014-01-01

    The volar sides of the fingers can be seen as the haptic counterpart to the fovea for visual perception. This study assessed the localisation of individual tactile stimuli and spatiotemporal patterns presented to the volar side of the fingers. Participants performed the localisation task by pointing at the perceived positions with a 3D tracker. Based on the pointing data, perceptual maps were devised in which perceived positions, their relationship to each other and to veridical stimulus positions could be analysed. Participants were able to accurately and consistently report the locations of the stimuli. Localisation of stimuli presented within a spatiotemporal pattern generally differed from localization of individual stimuli presented to the same positions. In most cases, stimuli were perceived as being spatially closer when they were presented within a spatiotemporal pattern compared to when being presented individually. Spatiotemporal integration along the fingers followed the predictions of the sensory saltation paradigm: The shorter the temporal delay between the two stimuli, the closer together they were perceived. For spatiotemporal patterns across fingers, the results were inconclusive: No general relationship between temporal delay and the difference between the perceived positions could be demonstrated, presumably because the effect could only be elicited in some finger combinations. Temporal delay did have, however, an effect on overall lateral shifts in localisation.

  3. The ISDF Framework: Integrating Security Patterns and Best Practices

    NASA Astrophysics Data System (ADS)

    Alkussayer, Abdulaziz; Allen, William H.

    The rapid growth of communication and globalization has changed the software engineering process. Security has become a crucial component of any software system. However, software developers often lack the knowledge and skills needed to develop secure software. Clearly, the creation of secure software requires more than simply mandating the use of a secure software development lifecycle, the components produced by each stage of the lifecycle must be correctly implemented for the resulting system to achieve its intended goals. In this paper, we demonstrate that a more effective approach to the development of secure software can result from the integration of carefully selected security patterns into appropriate stages of the software development lifecycle to ensure that security designs are correctly implemented. The goal of this work is to provide developers with an Integrated Security Development Framework (ISDF) that can assist them in building more secure software intuitively.

  4. Optical and SAR data integration for automatic change pattern detection

    NASA Astrophysics Data System (ADS)

    Mishra, B.; Susaki, J.

    2014-09-01

    Automatic change pattern mapping in urban and sub-urban area is important but challenging due to the diversity of urban land use pattern. With multi-sensor imagery, it is possible to generate multidimensional unique information of Earth surface features that allow developing a relationship between a response of each feature to synthetic aperture radar (SAR) and optical sensors to track the change automatically. Thus, a SAR and optical data integration framework for change detection and a relationship for automatic change pattern detection were developed. It was carried out in three steps: (i) Computation of indicators from SAR and optical images, namely: normalized difference ratio (NDR) from multi-temporal SAR images and the normalized difference vegetation index difference (NDVI) from multi-temporal optical images, (ii) computing the change magnitude image from NDR and ΔNDVI and delineating the change area and (iii) the development of an empirical relationship, for automatic change pattern detection. The experiment was carried out in an outskirts part of Ho Chi Minh City, one of the fastest growing cities in the world. The empirical relationship between the response of surface feature to optical and SAR imagery has successfully delineated six changed classes in a very complex urban sprawl area that was otherwise impossible with multi-spectral imagery. The improvement of the change detection results by making use of the unique information on both sensors, optical and SAR, is also noticeable with a visual inspection and the kappa index was increased by 0.13 (0.75 to 0.88) in comparison to only optical images.

  5. Covariant 4-dimensional fuzzy spheres, matrix models and higher spin

    NASA Astrophysics Data System (ADS)

    Sperling, Marcus; Steinacker, Harold C.

    2017-09-01

    We study in detail generalized 4-dimensional fuzzy spheres with twisted extra dimensions. These spheres can be viewed as SO(5) -equivariant projections of quantized coadjoint orbits of SO(6) . We show that they arise as solutions in Yang-Mills matrix models, which naturally leads to higher-spin gauge theories on S 4. Several types of embeddings in matrix models are found, including one with self-intersecting fuzzy extra dimensions \

  6. Multiscale patterning of a biomimetic scaffold integrated with composite microspheres.

    PubMed

    Minardi, Silvia; Sandri, Monica; Martinez, Jonathan O; Yazdi, Iman K; Liu, Xeuwu; Ferrari, Mauro; Weiner, Bradley K; Tampieri, Anna; Tasciotti, Ennio

    2014-10-15

    The ideal scaffold for regenerative medicine should concurrently mimic the structure of the original tissue from the nano- up to the macroscale and recapitulate the biochemical composition of the extracellular matrix (ECM) in space and time. In this study, a multiscale approach is followed to selectively integrate different types of nanostructured composite microspheres loaded with reporter proteins, in a multi-compartment collagen scaffold. Through the preservation of the structural cues of the functionalized collagen scaffold at the nano- and microscale, its macroscopic features (pore size, porosity, and swelling) are not altered. Additionally, the spatial confinement of the microspheres allows the release of the reporter proteins in each of the layers of the scaffold. Finally, the staged and zero-order release kinetics enables the temporal biochemical patterning of the scaffold. The versatile manufacturing of each component of the scaffold results in the ability to customize it to better mimic the architecture and composition of the tissues and biological systems.

  7. Integrative modelling for One Health: pattern, process and participation

    PubMed Central

    Redding, D. W.; Wood, J. L. N.

    2017-01-01

    This paper argues for an integrative modelling approach for understanding zoonoses disease dynamics, combining process, pattern and participatory models. Each type of modelling provides important insights, but all are limited. Combining these in a ‘3P’ approach offers the opportunity for a productive conversation between modelling efforts, contributing to a ‘One Health’ agenda. The aim is not to come up with a composite model, but seek synergies between perspectives, encouraging cross-disciplinary interactions. We illustrate our argument with cases from Africa, and in particular from our work on Ebola virus and Lassa fever virus. Combining process-based compartmental models with macroecological data offers a spatial perspective on potential disease impacts. However, without insights from the ground, the ‘black box’ of transmission dynamics, so crucial to model assumptions, may not be fully understood. We show how participatory modelling and ethnographic research of Ebola and Lassa fever can reveal social roles, unsafe practices, mobility and movement and temporal changes in livelihoods. Together with longer-term dynamics of change in societies and ecologies, all can be important in explaining disease transmission, and provide important complementary insights to other modelling efforts. An integrative modelling approach therefore can offer help to improve disease control efforts and public health responses. This article is part of the themed issue ‘One Health for a changing world: zoonoses, ecosystems and human well-being’. PMID:28584172

  8. Integrative modelling for One Health: pattern, process and participation.

    PubMed

    Scoones, I; Jones, K; Lo Iacono, G; Redding, D W; Wilkinson, A; Wood, J L N

    2017-07-19

    This paper argues for an integrative modelling approach for understanding zoonoses disease dynamics, combining process, pattern and participatory models. Each type of modelling provides important insights, but all are limited. Combining these in a '3P' approach offers the opportunity for a productive conversation between modelling efforts, contributing to a 'One Health' agenda. The aim is not to come up with a composite model, but seek synergies between perspectives, encouraging cross-disciplinary interactions. We illustrate our argument with cases from Africa, and in particular from our work on Ebola virus and Lassa fever virus. Combining process-based compartmental models with macroecological data offers a spatial perspective on potential disease impacts. However, without insights from the ground, the 'black box' of transmission dynamics, so crucial to model assumptions, may not be fully understood. We show how participatory modelling and ethnographic research of Ebola and Lassa fever can reveal social roles, unsafe practices, mobility and movement and temporal changes in livelihoods. Together with longer-term dynamics of change in societies and ecologies, all can be important in explaining disease transmission, and provide important complementary insights to other modelling efforts. An integrative modelling approach therefore can offer help to improve disease control efforts and public health responses.This article is part of the themed issue 'One Health for a changing world: zoonoses, ecosystems and human well-being'. © 2017 The Authors.

  9. Ablation of atrial fibrillation using novel 4-dimensional catheter tracking within autoregistered left atrial angiograms.

    PubMed

    Rolf, Sascha; Sommer, Philipp; Gaspar, Thomas; John, Silke; Arya, Arash; Hindricks, Gerhard; Piorkowski, Christopher

    2012-08-01

    We describe a novel fluoroscopy coregistered, 4-dimensional catheter tracking technology (MediGuide Technology [MGT]) used for treatment of patients with atrial fibrillation. The aim of the study was to investigate (1) the feasibility of nonfluoroscopic catheter manipulation within dynamic left atrial chamber models; (2) the integration of the technology into an established electroanatomical mapping system; and (3) potential clinical impact. Forty-nine patients received atrial fibrillation ablation using MGT-enabled NavX-EnSite. Matched patients ablated with a conventional NavX-EnSite system served as a control group. MGT was used for the deployment of diagnostic catheters within preacquired cine loops, for nonfluoroscopic chamber mapping within dynamic angiograms, and for 4-dimensional tagging of anatomical landmarks. Integration with the electroanatomical mapping system allowed correction of field distortions and a reference tool to detect and correct map shifts. Catheter ablation was done without MGT because the ablation catheter was not MGT enabled. MGT worked safely and stably in all 49 patients. Catheter deployment within the preacquired cine loops was successfully performed in 45 of 49 (92%) patients. Catheter tracking within dynamic left atrial angiograms allowed nearly nonfluoroscopic creation of NavX-EnSite geometries with subsequent computed tomography model registration in all 49 patients. Overall, MGT significantly reduced total procedural fluoroscopy time (median [quartiles]) from 31 minutes (25, 43 minutes) to 16 minutes (10, 23 minutes) and irradiation dose from 14 453±7403 to 7363±5827 cGy*cm(2) (mean±SD), respectively (P<0.001). MGT is a tracking technology that allows 4-dimensional visualization of dedicated catheters within moving chamber models. Integration of the MGT with an established electroanatomical mapping system provided algorithms to facilitate mapping in the electroanatomical mapping system environment. As a first measurable

  10. Quantum error correcting codes and 4-dimensional arithmetic hyperbolic manifolds

    SciTech Connect

    Guth, Larry; Lubotzky, Alexander

    2014-08-15

    Using 4-dimensional arithmetic hyperbolic manifolds, we construct some new homological quantum error correcting codes. They are low density parity check codes with linear rate and distance n{sup ε}. Their rate is evaluated via Euler characteristic arguments and their distance using Z{sub 2}-systolic geometry. This construction answers a question of Zémor [“On Cayley graphs, surface codes, and the limits of homological coding for quantum error correction,” in Proceedings of Second International Workshop on Coding and Cryptology (IWCC), Lecture Notes in Computer Science Vol. 5557 (2009), pp. 259–273], who asked whether homological codes with such parameters could exist at all.

  11. Quantum error correcting codes and 4-dimensional arithmetic hyperbolic manifolds

    NASA Astrophysics Data System (ADS)

    Guth, Larry; Lubotzky, Alexander

    2014-08-01

    Using 4-dimensional arithmetic hyperbolic manifolds, we construct some new homological quantum error correcting codes. They are low density parity check codes with linear rate and distance nɛ. Their rate is evaluated via Euler characteristic arguments and their distance using {Z}_2-systolic geometry. This construction answers a question of Zémor ["On Cayley graphs, surface codes, and the limits of homological coding for quantum error correction," in Proceedings of Second International Workshop on Coding and Cryptology (IWCC), Lecture Notes in Computer Science Vol. 5557 (2009), pp. 259-273], who asked whether homological codes with such parameters could exist at all.

  12. Lyapunov exponent diagrams of a 4-dimensional Chua system.

    PubMed

    Stegemann, Cristiane; Albuquerque, Holokx A; Rubinger, Rero M; Rech, Paulo C

    2011-09-01

    We report numerical results on the existence of periodic structures embedded in chaotic and hyperchaotic regions on the Lyapunov exponent diagrams of a 4-dimensional Chua system. The model was obtained from the 3-dimensional Chua system by the introduction of a feedback controller. Both the largest and the second largest Lyapunov exponents were considered in our colorful Lyapunov exponent diagrams, and allowed us to characterize periodic structures and regions of chaos and hyperchaos. The shrimp-shaped periodic structures appear to be malformed on some of Lyapunov exponent diagrams, and they present two different bifurcation scenarios to chaos when passing the boundaries of itself, namely via period-doubling and crisis. Hyperchaos-chaos transition can also be observed on the Lyapunov exponent diagrams for the second largest exponent.

  13. A Lie based 4-dimensional higher Chern-Simons theory

    NASA Astrophysics Data System (ADS)

    Zucchini, Roberto

    2016-05-01

    We present and study a model of 4-dimensional higher Chern-Simons theory, special Chern-Simons (SCS) theory, instances of which have appeared in the string literature, whose symmetry is encoded in a skeletal semistrict Lie 2-algebra constructed from a compact Lie group with non discrete center. The field content of SCS theory consists of a Lie valued 2-connection coupled to a background closed 3-form. SCS theory enjoys a large gauge and gauge for gauge symmetry organized in an infinite dimensional strict Lie 2-group. The partition function of SCS theory is simply related to that of a topological gauge theory localizing on flat connections with degree 3 second characteristic class determined by the background 3-form. Finally, SCS theory is related to a 3-dimensional special gauge theory whose 2-connection space has a natural symplectic structure with respect to which the 1-gauge transformation action is Hamiltonian, the 2-curvature map acting as moment map.

  14. BOOK REVIEW: Nonlinear Dynamics: Integrability, Chaos and Patterns

    NASA Astrophysics Data System (ADS)

    Grammaticos, B.

    2004-02-01

    When the editorial office of Journal of Physics A: Mathematical and General of the Institute of Physics Publishing asked me to review a book on nonlinear dynamics I experienced an undeniable apprehension. Indeed, the domain is a rapidly expanding one and writing a book aiming at a certain degree of completeness looks like an almost impossible task. My uneasiness abated somewhat when I saw the names of the authors, two well-known specialists of the nonlinear domain, but it was only when I held the book in my hands that I felt really reassured. The book is not just a review of the recent (and less so) findings on nonlinear systems. It is also a textbook. The authors set out to provide a detailed, step by step, introduction to the domain of nonlinearity and its various subdomains: chaos, integrability and pattern formation (although this last topic is treated with far less detail than the other two). The public they have in mind is obviously that of university students, graduate or undergraduate, who are interested in nonlinear phenomena. I suspect that a non-negligible portion of readers will be people who have to teach topics which figure among those included in the book: they will find this monograph an excellent companion to their course. The book is written in a pedagogical way, with a profusion of examples, detailed explanations and clear diagrams. The point of view is that of a physicist, which to my eyes is a major advantage. The mathematical formulation remains simple and perfectly intelligible. Thus the reader is not bogged down by fancy mathematical formalism, which would have discouraged the less experienced ones. A host of exercises accompanies every chapter. This will give the novice the occasion to develop his/her problem-solving skills and acquire competence in the use of nonlinear techniques. Some exercises are quite straightforward, like `verify the relation 14.81'. Others are less so, such as `prepare a write-up on a) frequency-locking and b) devil

  15. Integrated Insect Control May Alter Pesticide Use Pattern

    ERIC Educational Resources Information Center

    Worthy, Ward

    1973-01-01

    Discusses the use of predators, parasites, bacteria, viruses, hormones, pheromones, and sterile-male release and insect-resistance imparting techniques in pest control. Concludes with comments from chemical pesticide companies as popular attitudes toward the integrated pest management. (CC)

  16. Integrated Insect Control May Alter Pesticide Use Pattern

    ERIC Educational Resources Information Center

    Worthy, Ward

    1973-01-01

    Discusses the use of predators, parasites, bacteria, viruses, hormones, pheromones, and sterile-male release and insect-resistance imparting techniques in pest control. Concludes with comments from chemical pesticide companies as popular attitudes toward the integrated pest management. (CC)

  17. Broadly expressed repressors integrate patterning across orthogonal axes in embryos.

    PubMed

    Koromila, Theodora; Stathopoulos, Angelike

    2017-07-18

    The role of spatially localized repressors in supporting embryonic patterning is well appreciated, but, alternatively, the role ubiquitously expressed repressors play in this process is not well understood. We investigated the function of two broadly expressed repressors, Runt (Run) and Suppressor of Hairless [Su(H)], in patterning the Drosophila embryo. Previous studies have shown that Run and Su(H) regulate gene expression along anterior-posterior (AP) or dorsal-ventral (DV) axes, respectively, by spatially limiting activator action, but here we characterize a different role. Our data show that broadly expressed repressors silence particular enhancers within cis-regulatory systems, blocking their expression throughout the embryo fully but transiently, and, in this manner, regulate spatiotemporal outputs along both axes. Our results suggest that Run and Su(H) regulate the temporal action of enhancers and are not dedicated regulators of one axis but, instead, act coordinately to pattern both axes, AP and DV.

  18. Individualized 4-dimensional computed tomography proton treatment for pancreatic tumors

    PubMed Central

    Wang, Ning; Vassantachart, April; Mifflin, Rachel; Slater, Jerry D; Yang, Gary Y

    2017-01-01

    Background The goal of this study is to determine whether a phase or reconstruction of a 10-phase 4 dimensional computed tomography (4D CT) scan can be used as the primary planning scan for proton treatment of the pancreas, thus eliminating the need for second a slow CT or free breathing CT. Methods Ten patients with pancreatic adenocarcinoma were simulated with 4D CT and a proton treatment plan generated based upon one of three primary planning scans, the T0 phase, T50 phase or average reconstruction. These plans were then exported to each of the remaining phases of the 4D CT and the dose to 95% of the target (D95) calculated. Plans were deemed adequate if the D95 remained at 99% of the prescribed dose or greater. Results For the ten patients in this study anterior abdominal motion was found to range from 2–27 mm (mean 7.50±6.79 mm). For 9 of 10 patients the anterior abdominal motion was ≤8 mm and all three primary planning scans provided adequate target coverage, resulting in minimum D95 coverage per plan of T0_plan 99.7%, T50_plan 99.3% and AVE_plan 99%. However no plan provided adequate target coverage on the single patient with the largest anterior abdominal motion, 27 mm, and cranio-caudal motion, 20 mm, with minimum D95 values of T0_plan 96.3%, T50_plan 68%, and AVE_plan 68%. Conclusions The primary plans tested based up on the T0, T50 and average reconstructions provided adequate D95 coverage throughout the respiratory cycle as long as the anterior abdominal motion was ≤8 mm and can be considered for use as the primary proton planning scan. PMID:28890818

  19. Exploring Student Integration Patterns in Two-Way Immersion Schools

    ERIC Educational Resources Information Center

    Martinez, Martha I.

    2011-01-01

    Two-way immersion (TWI) programs teach English Learners (ELs) and native English speakers in the same classroom using both languages in an immersion approach. Studies suggest that TWI programs result in greater student integration, thus providing a promising alternative for Spanish speaking ELs, who are frequently concentrated in high poverty,…

  20. Internet Integration in High Schools: Patterns, Opportunities, and Barriers.

    ERIC Educational Resources Information Center

    Thomas, Ruth; Adams, Marilyn; Meghani, Naheed; Smith, Maria

    Internet integration in high schools on a schoolwide scale was examined through case studies of five high schools in inner city, urban, suburban, and rural communities across the United States. A total of 322 teachers, 19 administrators, 19 counselors, 7 technology coordinators, and 3,822 students were surveyed, and 219 staff and students were…

  1. Integrating Temporal Pattern Mining in Ischemic Stroke Prediction and Treatment Pathway Discovery for Atrial Fibrillation.

    PubMed

    Guo, Shijing; Li, Xiang; Liu, Haifeng; Zhang, Ping; Du, Xin; Xie, Guotong; Wang, Fei

    2017-01-01

    Atrial fibrillation (AF) is associated with an increased risk of acute ischemic stroke (AIS). Accurately predicting AIS and planning effective treatment pathways for AIS prevention are crucial for AF patients. Because of the temporality of patients' disease progressions, sequential disease and treatment patterns have the potential to improve risk prediction performance and contribute to effective treatment pathways. This paper integrates temporal pattern mining into the AF study of AIS prediction and treatment pathway discovery. We combine temporal pattern mining with feature selection to identify temporal risk factors that have predictive ability, and integrate temporal pattern mining with treatment efficacy analysis to discover temporal treatment patterns that are statistically effective. Results show that our approach has identified new potential temporal risk factors for AIS that can improve the prediction performance, and has discovered treatment pathway patterns that are statistically effective to prevent AIS for AF patients.

  2. An integral equation formulation for predicting radiation patterns of a space shuttle annular slot antenna

    NASA Technical Reports Server (NTRS)

    Jones, J. E.; Richmond, J. H.

    1974-01-01

    An integral equation formulation is applied to predict pitch- and roll-plane radiation patterns of a thin VHF/UHF (very high frequency/ultra high frequency) annular slot communications antenna operating at several locations in the nose region of the space shuttle orbiter. Digital computer programs used to compute radiation patterns are given and the use of the programs is illustrated. Experimental verification of computed patterns is given from measurements made on 1/35-scale models of the orbiter.

  3. Proposal for the development of 3D Vertically Integrated Pattern Recognition Associative Memory (VIPRAM)

    SciTech Connect

    Deptuch, Gregory; Hoff, Jim; Kwan, Simon; Lipton, Ron; Liu, Ted; Ramberg, Erik; Todri, Aida; Yarema, Ray; Demarteua, Marcel,; Drake, Gary; Weerts, Harry; /Argonne /Chicago U. /Padua U. /INFN, Padua

    2010-10-01

    Future particle physics experiments looking for rare processes will have no choice but to address the demanding challenges of fast pattern recognition in triggering as detector hit density becomes significantly higher due to the high luminosity required to produce the rare process. The authors propose to develop a 3D Vertically Integrated Pattern Recognition Associative Memory (VIPRAM) chip for HEP applications, to advance the state-of-the-art for pattern recognition and track reconstruction for fast triggering.

  4. An integrated pattern recognition approach for intrusion detection.

    PubMed

    Pandit, Amod; Stanley, R Joe; McMillin, Bruce

    2002-01-01

    Intrusion detection systems (IDS) attempt to address the vulnerability of computer-based systems for abuse by insiders and to penetration by outsiders. An IDS is required to examine an enormous amount of data generated by computer networks to assist in the abuse detection process. Thus, there is a need to develop automated tools that address these requirements to assist system operators in the detection of violations of existing security policies. In this research, an automated IDS is proposed for insider threats in a distributed system. The proposed IDS functions as an anomaly detector for insider system operations based on the analysis of the system's log files. The approach integrates dynamic programming and adaptive resonance theory (ART1) clustering. The integrated approach aligns sequences of log events with prototypical sequences of events for performing tasks and classifies the aligned sequences for intrusion detection. The system examined for this research is a Boots System for controlling the movement of boots from one place to another under specific security restrictions related to the boot orders. We present the proposed model, the results achieved and the analysis of an implemented prototype.

  5. Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

    PubMed Central

    Li, Yan; Li, Weiguo; Chen, Xin; Sun, Jiatong; Chen, Huan; Lv, Sali

    2014-01-01

    Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. PMID:25114931

  6. Automatic Authorship Detection Using Textual Patterns Extracted from Integrated Syntactic Graphs

    PubMed Central

    Gómez-Adorno, Helena; Sidorov, Grigori; Pinto, David; Vilariño, Darnes; Gelbukh, Alexander

    2016-01-01

    We apply the integrated syntactic graph feature extraction methodology to the task of automatic authorship detection. This graph-based representation allows integrating different levels of language description into a single structure. We extract textual patterns based on features obtained from shortest path walks over integrated syntactic graphs and apply them to determine the authors of documents. On average, our method outperforms the state of the art approaches and gives consistently high results across different corpora, unlike existing methods. Our results show that our textual patterns are useful for the task of authorship attribution. PMID:27589740

  7. Automatic Authorship Detection Using Textual Patterns Extracted from Integrated Syntactic Graphs.

    PubMed

    Gómez-Adorno, Helena; Sidorov, Grigori; Pinto, David; Vilariño, Darnes; Gelbukh, Alexander

    2016-08-29

    We apply the integrated syntactic graph feature extraction methodology to the task of automatic authorship detection. This graph-based representation allows integrating different levels of language description into a single structure. We extract textual patterns based on features obtained from shortest path walks over integrated syntactic graphs and apply them to determine the authors of documents. On average, our method outperforms the state of the art approaches and gives consistently high results across different corpora, unlike existing methods. Our results show that our textual patterns are useful for the task of authorship attribution.

  8. Limbic Tract Integrity Contributes to Pattern Separation Performance Across the Lifespan.

    PubMed

    Bennett, Ilana J; Huffman, Derek J; Stark, Craig E L

    2015-09-01

    Accurate memory for discrete events is thought to rely on pattern separation to orthogonalize the representations of similar events. Previously, we reported that a behavioral index of pattern separation was correlated with activity in the hippocampus (dentate gyrus, CA3) and with integrity of the perforant path, which provides input to the hippocampus. If the hippocampus operates as part of a broader neural network, however, pattern separation would likely also relate to integrity of limbic tracts (fornix, cingulum bundle, and uncinate fasciculus) that connect the hippocampus to distributed brain regions. In this study, healthy adults (20-89 years) underwent diffusion tensor imaging and completed the Behavioral Pattern Separation Task-Object Version (BPS-O) and Rey Auditory Verbal Learning Test (RAVLT). After controlling for global effects of brain aging, exploratory skeleton-wise and targeted tractography analyses revealed that fornix integrity (fractional anisotropy, mean diffusivity, and radial diffusivity; but not mode) was significantly related to pattern separation (measured using BPS-O and RAVLT tasks), but not to recognition memory. These data suggest that hippocampal disconnection, via individual- and age-related differences in limbic tract integrity, contributes to pattern separation performance. Extending our earlier work, these results also support the notion that pattern separation relies on broad neural networks interconnecting the hippocampus.

  9. Limbic Tract Integrity Contributes to Pattern Separation Performance Across the Lifespan

    PubMed Central

    Bennett, Ilana J.; Huffman, Derek J.; Stark, Craig E.L.

    2015-01-01

    Accurate memory for discrete events is thought to rely on pattern separation to orthogonalize the representations of similar events. Previously, we reported that a behavioral index of pattern separation was correlated with activity in the hippocampus (dentate gyrus, CA3) and with integrity of the perforant path, which provides input to the hippocampus. If the hippocampus operates as part of a broader neural network, however, pattern separation would likely also relate to integrity of limbic tracts (fornix, cingulum bundle, and uncinate fasciculus) that connect the hippocampus to distributed brain regions. In this study, healthy adults (20–89 years) underwent diffusion tensor imaging and completed the Behavioral Pattern Separation Task-Object Version (BPS-O) and Rey Auditory Verbal Learning Test (RAVLT). After controlling for global effects of brain aging, exploratory skeleton-wise and targeted tractography analyses revealed that fornix integrity (fractional anisotropy, mean diffusivity, and radial diffusivity; but not mode) was significantly related to pattern separation (measured using BPS-O and RAVLT tasks), but not to recognition memory. These data suggest that hippocampal disconnection, via individual- and age-related differences in limbic tract integrity, contributes to pattern separation performance. Extending our earlier work, these results also support the notion that pattern separation relies on broad neural networks interconnecting the hippocampus. PMID:24825784

  10. Integrated approach to improving local CD uniformity in EUV patterning

    NASA Astrophysics Data System (ADS)

    Liang, Andrew; Hermans, Jan; Tran, Timothy; Viatkina, Katja; Liang, Chen-Wei; Ward, Brandon; Chuang, Steven; Yu, Jengyi; Harm, Greg; Vandereyken, Jelle; Rio, David; Kubis, Michael; Tan, Samantha; Dusa, Mircea; Singhal, Akhil; van Schravendijk, Bart; Dixit, Girish; Shamma, Nader

    2017-03-01

    Extreme ultraviolet (EUV) lithography is crucial to enabling technology scaling in pitch and critical dimension (CD). Currently, one of the key challenges of introducing EUV lithography to high volume manufacturing (HVM) is throughput, which requires high source power and high sensitivity chemically amplified photoresists. Important limiters of high sensitivity chemically amplified resists (CAR) are the effects of photon shot noise and resist blur on the number of photons received and of photoacids generated per feature, especially at the pitches required for 7 nm and 5 nm advanced technology nodes. These stochastic effects are reflected in via structures as hole-to-hole CD variation or local CD uniformity (LCDU). Here, we demonstrate a synergy of film stack deposition, EUV lithography, and plasma etch techniques to improve LCDU, which allows the use of high sensitivity resists required for the introduction of EUV HVM. Thus, to improve LCDU to a level required by 5 nm node and beyond, film stack deposition, EUV lithography, and plasma etch processes were combined and co-optimized to enhance LCDU reduction from synergies. Test wafers were created by depositing a pattern transfer stack on a substrate representative of a 5 nm node target layer. The pattern transfer stack consisted of an atomically smooth adhesion layer and two hardmasks and was deposited using the Lam VECTOR PECVD product family. These layers were designed to mitigate hole roughness, absorb out-of-band radiation, and provide additional outlets for etch to improve LCDU and control hole CD. These wafers were then exposed through an ASML NXE3350B EUV scanner using a variety of advanced positive tone EUV CAR. They were finally etched to the target substrate using Lam Flex dielectric etch and Kiyo conductor etch systems. Metrology methodologies to assess dimensional metrics as well as chip performance and defectivity were investigated to enable repeatable patterning process development. Illumination

  11. Quantification of neonatal amplitude-integrated EEG patterns.

    PubMed

    Thorngate, Lauren; Foreman, Shuyuann Wang; Thomas, Karen A

    2013-12-01

    Amplitude-integrated EEG (aEEG) is increasingly used in research with premature infants; however, comprehensive interpretation is limited by the lack of simple approaches for reliably quantifying and summarizing the data. Explore operational measures for quantifying continuity and discontinuity, measured by aEEG as components of infant brain function. An exploratory naturalistic study of neonates while in the Neonatal Intensive Care Unit (NICU). One single channel aEEG recording per infant was obtained without disruption of nursing care practices. 24 infants with mean postmenstrual age (PMA) of 33.11 weeks (SD 3.49), average age of 2.62 weeks (SD 1.35) and mean birth weights of 1.39 kg (SD 0.73). Quantification of continuity and discontinuity included bandwidth and lower border of aEEG, calculated proportion of time with signal amplitude below 10 μV, and peak counts. Variance of bandwidth and lower border denoted cycling. Group mean bandwidth was 52.98 μV (SD 27.62). Median peak count in 60 second epochs averaged 3.63 (SD 1.74), while median proportion < 10 μV was 22% (SD 0.20). The group mean of lower border within-subject aggregated medians was 6.20 μV (SD 2.13). Group mean lower border standard deviation was 3.96 μV. Proportion < 10 μV showed a strong negative correlation with the natural log of the lower border median (r = -0.906, p < .0001) after controlling for PMA. This study introduces a novel quantification process by counting peaks and proportion of time < 10 μV. Expanded definitions and analytic techniques will serve to strengthen the application of existing scoring systems for use in naturalistic research settings and clinical practice. © 2013 Elsevier Ireland Ltd. All rights reserved.

  12. Pattern-integrated interference lithography: single-exposure fabrication of photonic-crystal structures.

    PubMed

    Burrow, Guy M; Leibovici, Matthieu C R; Gaylord, Thomas K

    2012-06-20

    Multibeam interference represents an approach for producing one-, two-, and three-dimensional periodic optical-intensity distributions with submicrometer features and periodicities. Accordingly, interference lithography (IL) has been used in a wide variety of applications, typically requiring additional lithographic steps to modify the periodic interference pattern and create integrated functional elements. In the present work, pattern-integrated interference lithography (PIIL) is introduced. PIIL is the integration of superposed pattern imaging with IL. Then a pattern-integrated interference exposure system (PIIES) is presented that implements PIIL by incorporating a projection imaging capability in a novel three-beam interference configuration. The purpose of this system is to fabricate, in a single-exposure step, a two-dimensional periodic photonic-crystal lattice with nonperiodic functional elements integrated into the periodic pattern. The design of the basic system is presented along with a model that simulates the resulting optical-intensity distribution at the system sample plane where the three beams simultaneously interfere and integrate a superposed image of the projected mask pattern. Appropriate performance metrics are defined in order to quantify the characteristics of the resulting photonic-crystal structure. These intensity and lattice-vector metrics differ markedly from the metrics used to evaluate traditional photolithographic imaging systems. Simulation and experimental results are presented that demonstrate the fabrication of example photonic-crystal structures in a single-exposure step. Example well-defined photonic-crystal structures exhibiting favorable intensity and lattice-vector metrics demonstrate the potential of PIIL for fabricating dense integrated optical circuits.

  13. Direct light pattern integration of low-temperature solution-processed all-oxide flexible electronics.

    PubMed

    Rim, You Seung; Chen, Huajun; Liu, Yongsheng; Bae, Sang-Hoon; Kim, Hyun Jae; Yang, Yang

    2014-09-23

    The rise of solution-processed electronics, together with their processing methods and materials, provides unique opportunities to achieve low-cost and low-temperature roll-to-roll printing of non-Si-based devices. Here, we demonstrate a wafer-scale direct light-patterned, fully transparent, all-solution-processed, and layer-by-layer-integrated electronic device. The deep ultraviolet irradiation of specially designed metal oxide gel films can generate fine-patterned shapes of ∼3 μm, which easily manifest their intrinsic properties at low-temperature annealing. This direct light patterning can be easily applied to the 4 in. wafer scale and diverse pattern shapes and provides feasibility for integrated circuit applications through the penetration of the deep ultraviolet range on the quartz mask. With this approach, we successfully fabricate all-oxide-based high-performance transparent thin-film transistors on flexible polymer substrates.

  14. Self-aligned blocking integration demonstration for critical sub-40nm pitch Mx level patterning

    NASA Astrophysics Data System (ADS)

    Raley, Angélique; Mohanty, Nihar; Sun, Xinghua; Farrell, Richard A.; Smith, Jeffrey T.; Ko, Akiteru; Metz, Andrew W.; Biolsi, Peter; Devilliers, Anton

    2017-04-01

    Multipatterning has enabled continued scaling of chip technology at the 28nm node and beyond. Selfaligned double patterning (SADP) and self-aligned quadruple patterning (SAQP) as well as Litho- Etch/Litho-Etch (LELE) iterations are widely used in the semiconductor industry to enable patterning at sub 193 immersion lithography resolutions for layers such as FIN, Gate and critical Metal lines. Multipatterning requires the use of multiple masks which is costly and increases process complexity as well as edge placement error variation driven mostly by overlay. To mitigate the strict overlay requirements for advanced technology nodes (7nm and below), a self-aligned blocking integration is desirable. This integration trades off the overlay requirement for an etch selectivity requirement and enables the cut mask overlay tolerance to be relaxed from half pitch to three times half pitch. Selfalignement has become the latest trend to enable scaling and self-aligned integrations are being pursued and investigated for various critical layers such as contact, via, metal patterning. In this paper we propose and demonstrate a low cost flexible self-aligned blocking strategy for critical metal layer patterning for 7nm and beyond from mask assembly to low -K dielectric etch. The integration is based on a 40nm pitch SADP flow with 2 cut masks compatible with either cut or block integration and employs dielectric films widely used in the back end of the line. As a consequence this approach is compatible with traditional etch, deposition and cleans tools that are optimized for dielectric etches. We will review the critical steps and selectivities required to enable this integration along with bench-marking of each integration option (cut vs. block).

  15. Photolithography-Based Patterning of Liquid Metal Interconnects for Monolithically Integrated Stretchable Circuits.

    PubMed

    Park, Chan Woo; Moon, Yu Gyeong; Seong, Hyejeong; Jung, Soon Won; Oh, Ji-Young; Na, Bock Soon; Park, Nae-Man; Lee, Sang Seok; Im, Sung Gap; Koo, Jae Bon

    2016-06-22

    We demonstrate a new patterning technique for gallium-based liquid metals on flat substrates, which can provide both high pattern resolution (∼20 μm) and alignment precision as required for highly integrated circuits. In a very similar manner as in the patterning of solid metal films by photolithography and lift-off processes, the liquid metal layer painted over the whole substrate area can be selectively removed by dissolving the underlying photoresist layer, leaving behind robust liquid patterns as defined by the photolithography. This quick and simple method makes it possible to integrate fine-scale interconnects with preformed devices precisely, which is indispensable for realizing monolithically integrated stretchable circuits. As a way for constructing stretchable integrated circuits, we propose a hybrid configuration composed of rigid device regions and liquid interconnects, which is constructed on a rigid substrate first but highly stretchable after being transferred onto an elastomeric substrate. This new method can be useful in various applications requiring both high-resolution and precisely aligned patterning of gallium-based liquid metals.

  16. A new 4-dimensional imaging system for jaw tracking.

    PubMed

    Lauren, Mark

    2014-01-01

    A non-invasive 4D imaging system that produces high resolution time-based 3D surface data has been developed to capture jaw motion. Fluorescent microspheres are brushed onto both tooth and soft-tissue areas of the upper and lower arches to be imaged. An extraoral hand-held imaging device, operated about 12 cm from the mouth, captures a time-based set of perspective image triplets of the patch areas. Each triplet, containing both upper and lower arch data, is converted to a high-resolution 3D point mesh using photogrammetry, providing the instantaneous relative jaw position. Eight 3D positions per second are captured. Using one of the 3D frames as a reference, a 4D model can be constructed to describe the incremental free body motion of the mandible. The surface data produced by this system can be registered to conventional 3D models of the dentition, allowing them to be animated. Applications include integration into prosthetic CAD and CBCT data.

  17. System integration and radiation pattern measurements of a phased array antenna employing an integrated photonic beamformer for radio astronomy applications.

    PubMed

    Burla, Maurizio; Roeloffzen, Chris G H; Zhuang, Leimeng; Marpaung, David; Khan, Muhammad Rezaul; Maat, Peter; Dijkstra, Klaas; Leinse, Arne; Hoekman, Marcel; Heideman, René

    2012-03-01

    In this paper we describe the system integration and the experimental demonstration of a photonically beamformed four-element receiving array antenna for radio astronomy applications. To our knowledge, the work described here is the first demonstration of the squint-free, continuously tunable beamsteering capability offered by an integrated photonic beamformer based on optical ring resonator true-time-delay units, with measured radiation patterns. The integrated beamformer is realized in a low loss, complementary metal-oxide-semiconductor (CMOS) compatible optical waveguide technology. The measurements show a wideband, continuous beamsteering operation over a steering angle of 23.5 degrees and an instantaneous bandwidth of 500 MHz limited only by the measurement setup. © 2012 Optical Society of America

  18. Support vector machines for spike pattern classification with a leaky integrate-and-fire neuron

    PubMed Central

    Ambard, Maxime; Rotter, Stefan

    2012-01-01

    Spike pattern classification is a key topic in machine learning, computational neuroscience, and electronic device design. Here, we offer a new supervised learning rule based on Support Vector Machines (SVM) to determine the synaptic weights of a leaky integrate-and-fire (LIF) neuron model for spike pattern classification. We compare classification performance between this algorithm and other methods sharing the same conceptual framework. We consider the effect of postsynaptic potential (PSP) kernel dynamics on patterns separability, and we propose an extension of the method to decrease computational load. The algorithm performs well in generalization tasks. We show that the peak value of spike patterns separability depends on a relation between PSP dynamics and spike pattern duration, and we propose a particular kernel that is well-suited for fast computations and electronic implementations. PMID:23181017

  19. Variable Temporal Integration of Stimulus Patterns in the Mouse Barrel Cortex.

    PubMed

    Pitas, Anna; Albarracín, Ana Lía; Molano-Mazón, Manuel; Maravall, Miguel

    2016-02-01

    Making sense of the world requires distinguishing temporal patterns and sequences lasting hundreds of milliseconds or more. How cortical circuits integrate over time to represent specific sensory sequences remains elusive. Here we assessed whether neurons in the barrel cortex (BC) integrate information about temporal patterns of whisker movements. We performed cell-attached recordings in anesthetized mice while delivering whisker deflections at variable intervals and compared the information carried by neurons about the latest interstimulus interval (reflecting sensitivity to instantaneous frequency) and earlier intervals (reflecting integration over timescales up to several hundred milliseconds). Neurons carried more information about the latest interval than earlier ones. The amount of temporal integration varied with neuronal responsiveness and with the cortical depth of the recording site, that is, with laminar location. A subset of neurons in the upper layers displayed the strongest integration. Highly responsive neurons in the deeper layers encoded the latest interval but integrated particularly weakly. Under these conditions, BC neurons act primarily as encoders of current stimulation parameters; however, our results suggest that temporal integration over hundreds of milliseconds can emerge in some neurons within BC.

  20. Patterns in Teachers' Instructional Design When Integrating Apps in Middle School Content-Area Teaching

    ERIC Educational Resources Information Center

    Karchmer-Klein, Rachel; Mouza, Chrystalla; Harlow Shinas, Valerie; Park, Sohee

    2017-01-01

    The purpose of this study was to examine patterns evident in the ways middle school teachers, who value technology integration, design instruction that leverages educational applications (app) affordances. Using the pedagogy of multiliteracies (Cope & Kalantzis, 2015) and app affordances of multimodality, collaboration, and interactivity as…

  1. Pedagogies across Subjects: What Are Preservice Teachers' TPACK Patterns of Integrating Technology in Practice?

    ERIC Educational Resources Information Center

    Szeto, Elson; Cheng, Annie Yan Ni

    2017-01-01

    This case study examines preservice teachers' integration of technology in teaching various subject domains. It aims to gain in-depth understandings of preservice teachers' pedagogical patterns for teaching through the theoretical lens of technological pedagogical and content knowledge. Multiple data sources were collected in a teacher education…

  2. An Integrated Modeling Analysis of Unsaturated Flow Patterns inFractured Rock

    SciTech Connect

    Wu, Yu-Shu; Lu, Guoping; Zhang, Keni; Pan, Lehua; Bodvarsson,Gudmundur S.

    2005-03-21

    Characterizing percolation patterns in unsaturated zones hasposed a greater challenge to numerical modeling investigations thancomparable saturated zone studies, because of the heterogeneous nature ofunsaturated media as well as the great number of variables impactingunsaturated zone flow. This paper presents an integrated modelingmethodology for quantitatively characterizing percolation patterns in theunsaturated zone of Yucca Mountain, Nevada, a proposed undergroundrepository site for storing high-level radioactive waste. It takes intoaccount the multiple coupled processes of air, water, heat flow andchemical isotopic transport in Yucca Mountain s highly heterogeneous,unsaturated fractured tuffs. The modeling approach integrates a widevariety of moisture, pneumatic, thermal, and isotopic geochemical fielddata into a comprehensive three-dimensional numerical model for modelinganalyses. Modeling results are examined against different types offield-measured data and then used to evaluate different hydrogeologicalconceptual models and their results of flow patterns in the unsaturatedzone. In particular, this integration model provides a much clearerunderstanding of percolation patterns and flow behavior through theunsaturated zone, both crucial issues in assessing repositoryperformance. The integrated approach for quantifying Yucca Mountain sflow system is also demonstrated to provide a comprehensive modeling toolfor characterizing flow and transport processes in complex subsurfacesystems.

  3. Analyzing flow patterns in unsaturated fractured rock of YuccaMountain using an integrated modeling approach

    SciTech Connect

    Wu, Yu-Shu; Lu, Guoping; Zhang, Keni; Pan, Lehua; Bodvarsson,Gudmundur S.

    2003-11-03

    This paper presents a series of modeling investigations to characterize percolation patterns in the unsaturated zone of Yucca Mountain, Nevada, a proposed underground repository site for storing high-level radioactive waste. The investigations are conducted using a modeling approach that integrates a wide variety of moisture, pneumatic, thermal, and isotopic geochemical field data into a comprehensive three-dimensional numerical model through model calibration. This integrated modeling approach, based on a dual-continuum formulation, takes into account the coupled processes of fluid and heat flow and chemical isotopic transport in Yucca Mountain's highly heterogeneous, unsaturated fractured tuffs. In particular, the model results are examined against different types of field-measured data and used to evaluate different hydrogeological conceptual models and their effects on flow patterns in the unsaturated zone. The objective of this work to provide understanding of percolation patterns and flow behavior through the unsaturated zone, which is a crucial issue in assessing repository performance.

  4. Patterns of morphological integration in the appendicular skeleton of mammalian carnivores.

    PubMed

    Martín-Serra, Alberto; Figueirido, Borja; Pérez-Claros, Juan Antonio; Palmqvist, Paul

    2015-02-01

    We investigated patterns of evolutionary integration in the appendicular skeleton of mammalian carnivores. The findings are discussed in relation to performance selection in terms of organismal function as a potential mechanism underlying integration. Interspecific shape covariation was quantified by two-block partial least-squares (2B-PLS) analysis of 3D landmark data within a phylogenetic context. Specifically, we compared pairs of anatomically connected bones (within-limbs) and pairs of both serially homologous and functional equivalent bones (between-limbs). The statistical results of all the comparisons suggest that the carnivoran appendicular skeleton is highly integrated. Strikingly, the main shape covariation relates to bone robustness in all cases. A bootstrap test was used to compare the degree of integration between specialized cursorial taxa (i.e., those whose forelimbs are primarily involved in locomotion) and noncursorial species (i.e., those whose forelimbs are involved in more functions than their hindlimb) showed that cursors have a more integrated appendicular skeleton than noncursors. The findings demonstrate that natural selection can influence the pattern and degree of morphological integration by increasing the degree of bone shape covariation in parallel to ecological specialization.

  5. Analyzing Unsatirated Flow Patterns in Fractured Rock Using an Integrated Modeling Approach

    SciTech Connect

    Y.S. Wu; G. Lu; K. Zhang; L. Pan; G.S. Bodvarsson

    2006-08-03

    Characterizing percolation patterns in unsaturated fractured rock has posed a greater challenge to modeling investigations than comparable saturated zone studies, because of the heterogeneous nature of unsaturated media and the great number of variables impacting unsaturated flow. This paper presents an integrated modeling methodology for quantitatively characterizing percolation patterns in the unsaturated zone of Yucca Mountain, Nevada, a proposed underground repository site for storing high-level radioactive waste. The modeling approach integrates a wide variety of moisture, pneumatic, thermal, and isotopic geochemical field data into a comprehensive three-dimensional numerical model for modeling analyses. It takes into account the coupled processes of fluid and heat flow and chemical isotopic transport in Yucca Mountain's highly heterogeneous, unsaturated fractured tuffs. Modeling results are examined against different types of field-measured data and then used to evaluate different hydrogeological conceptualizations and their results of flow patterns in the unsaturated zone. In particular, this model provides a much clearer understanding of percolation patterns and flow behavior through the unsaturated zone, both crucial issues in assessing repository performance. The integrated approach for quantifying Yucca Mountain's flow system is demonstrated to provide a practical modeling tool for characterizing flow and transport processes in complex subsurface systems.

  6. Fully integrated patterned carbon nanotube strain sensors on flexible sensing skin substrates for structural health monitoring

    NASA Astrophysics Data System (ADS)

    Burton, Andrew R.; Kurata, Masahiro; Nishino, Hiromichi; Lynch, Jerome P.

    2016-04-01

    New advances in nanotechnology and material processing is creating opportunities for the design and fabrication of a new generation of thin film sensors that can used to assess structural health. In particular, thin film sensors attached to large areas of the structure surface has the potential to provide spatially rich data on the performance and health of a structure. This study focuses on the development of a fully integrated strain sensor that is fabricated on a flexible substrate for potentially use in sensing skins. This is completed using a carbon nanotube-polymer composite material that is patterned on a flexible polyimide substrate using optical lithography. The piezoresistive carbon nanotube elements are integrated into a complete sensing system by patterning copper electrodes and integrating off-the-shelf electrical components on the flexible film for expanded functionality. This diverse material utilization is realized in a versatile process flow to illustrate a powerful toolbox for sensing severity, location, and failure mode of damage on structural components. The fully integrated patterned carbon nanotube strain sensor is tested on a quarter-scale, composite beam column connection. The results and implications for future structural damage detection are discussed.

  7. Pattern scaling with directed self assembly through lithography and etch process integration

    NASA Astrophysics Data System (ADS)

    Rathsack, Benjamen; Somervell, Mark; Hooge, Josh; Muramatsu, Makoto; Tanouchi, Keiji; Kitano, Takahiro; Nishimura, Eiichi; Yatsuda, Koichi; Nagahara, Seiji; Hiroyuki, Iwaki; Akai, Keiji; Hayakawa, Takashi

    2012-03-01

    Directed self-assembly (DSA) has the potential to extend scaling for both line/space and hole patterns. DSA has shown the capability for pitch reduction (multiplication), hole shrinks, CD self-healing as well as a pathway towards line edge roughness (LER) and pattern collapse improvement [1-4]. The current challenges for industry adoption are materials maturity, practical process integration, hardware capability, defect reduction and design integration. Tokyo Electron (TEL) has created close collaborations with customers, consortia and material suppliers to address these challenges with the long term goal of robust manufacturability. This paper provides a wide range of DSA demonstrations to accommodate different device applications. In collaboration with IMEC, directed line/space patterns at 12.5 and 14 nm HP are demonstrated with PS-b-PMMA (poly(styrene-b-methylmethacrylate)) using both chemo and grapho-epitaxy process flows. Pre-pattern exposure latitudes of >25% (max) have been demonstrated with 4X directed self-assembly on 300 mm wafers for both the lift off and etch guide chemo-epitaxy process flows. Within TEL's Technology Development Center (TDC), directed selfassembly processes have been applied to holes for both CD shrink and variation reduction. Using a PS-b-PMMA hole shrink process, negative tone developed pre-pattern holes are reduced to below 30 nm with critical dimension uniformity (CDU) of 0.9 nm (3s) and contact edge roughness (CER) of 0.8 nm. To generate higher resolution beyond a PS-b-PMMA system, a high chi material is used to demonstrate 9 nm HP line/ space post-etch patterns. In this paper, TEL presents process solutions for both line/space and hole DSA process integrations.

  8. Self-aligned quadruple patterning using spacer on spacer integration optimization for N5

    NASA Astrophysics Data System (ADS)

    Thibaut, Sophie; Raley, Angélique; Mohanty, Nihar; Kal, Subhadeep; Liu, Eric; Ko, Akiteru; O'Meara, David; Tapily, Kandabara; Biolsi, Peter

    2017-04-01

    To meet scaling requirements, the semiconductor industry has extended 193nm immersion lithography beyond its minimum pitch limitation using multiple patterning schemes such as self-aligned double patterning, self-aligned quadruple patterning and litho-etch / litho etch iterations. Those techniques have been declined in numerous options in the last few years. Spacer on spacer pitch splitting integration has been proven to show multiple advantages compared to conventional pitch splitting approach. Reducing the number of pattern transfer steps associated with sacrificial layers resulted in significant decrease of cost and an overall simplification of the double pitch split technique. While demonstrating attractive aspects, SAQP spacer on spacer flow brings challenges of its own. Namely, material set selections and etch chemistry development for adequate selectivities, mandrel shape and spacer shape engineering to improve edge placement error (EPE). In this paper we follow up and extend upon our previous learning and proceed into more details on the robustness of the integration in regards to final pattern transfer and full wafer critical dimension uniformity. Furthermore, since the number of intermediate steps is reduced, one will expect improved uniformity and pitch walking control. This assertion will be verified through a thorough pitch walking analysis.

  9. Quantification of Pediatric Abdominal Organ Motion With a 4-Dimensional Magnetic Resonance Imaging Method.

    PubMed

    Uh, Jinsoo; Krasin, Matthew J; Li, Yimei; Li, Xingyu; Tinkle, Christopher; Lucas, John T; Merchant, Thomas E; Hua, Chiaho

    2017-09-01

    To characterize respiration-induced abdominal organ motion in children receiving radiation treatment with a 4-dimensional (4D) magnetic resonance imaging (MRI) method. We analyzed free-breathing coronal 4D MRI datasets acquired from 35 patients (aged 1-20 years) with abdominal tumors. A deformable image registration of the 4D MRI datasets was performed to derive motion trajectories of selected anatomic landmarks, from which organ motions were quantified. The association between organ motion and patient characteristics was investigated and compared with previous studies. The relation between patient height and organ motion was further investigated to predict organ motion in prospective patients. Organ motion and its individual variation were reduced in younger patients (eg, kidney peak-to-peak motion <5 mm for all but 1 patient aged ≤8 years), although special motion management may be warranted in some adolescents. The liver and spleen exhibited greater motion than did the kidneys, while intraorgan variation was present. The motions in the liver and kidneys agreed with those reported by the previous 4D computed tomography studies. Individual variations of organ motion in younger patients were due, in part, to changes in respiration rate, which ostensibly reflected the effect of anesthesia. The prediction of organ motion was limited by large individual variations, particularly for older patients. The 4D MRI acquisition method and motion analysis described in this study provide a nonionizing approach to understand age-associated organ motion, which aids in the planning of abdominal radiation therapy for pediatric patients. Use of 4D MRI facilitates monitoring of changes in target motion patterns during treatment courses and in various studies of the effect of organ motion on radiation treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis.

    PubMed

    Burgess, Alexandra J; Retkute, Renata; Preston, Simon P; Jensen, Oliver E; Pound, Michael P; Pridmore, Tony P; Murchie, Erik H

    2016-01-01

    accurate modeling of mechanical canopy excitation (here coined the 4-dimensional plant) and some associated biological and applied implications of such techniques. We hypothesize that biomechanical plant properties are a specific adaptation to achieve wind-induced photosynthetic enhancement and we outline how traits facilitating canopy excitation could be used as a route for improving crop yield.

  11. The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis

    PubMed Central

    Burgess, Alexandra J.; Retkute, Renata; Preston, Simon P.; Jensen, Oliver E.; Pound, Michael P.; Pridmore, Tony P.; Murchie, Erik H.

    2016-01-01

    accurate modeling of mechanical canopy excitation (here coined the 4-dimensional plant) and some associated biological and applied implications of such techniques. We hypothesize that biomechanical plant properties are a specific adaptation to achieve wind-induced photosynthetic enhancement and we outline how traits facilitating canopy excitation could be used as a route for improving crop yield. PMID:27708654

  12. Satellite derived integrated water vapor and rain intensity patterns: Indicators of rapid cyclogenesis

    NASA Technical Reports Server (NTRS)

    Mcmurdie, Lynn; Katsaros, Kristina

    1992-01-01

    We examine integrated water vapor fields and rain intensity patterns derived from the Scanning Multichannel Microwave Radiometer (SMMR) and Special Sensor Microwave/Imager (SSM/I) for several rapidly deepening and non-rapidly deepening midlatitude cyclones in the North Atlantic. Our goal is to identify features in the satellite data unique to the rapidly deepening cases, and to explore how these data can potentially be used in the analysis and forecasting of these events.

  13. Modeling of multiple-optical-axis pattern-integrated interference lithography systems.

    PubMed

    Sedivy, Donald E; Gaylord, Thomas K

    2014-06-01

    The image quality and collimation in a multiple-optical-axis pattern-integrated interference lithography system are evaluated for an elementary optical system composed of single-element lenses. Image quality and collimation are individually and jointly optimized for these lenses. Example images for a jointly optimized system are simulated using a combination of ray tracing and Fourier analysis. Even with these nonoptimized components, reasonable fidelity is shown to be possible.

  14. [Establishment of diagnosis and treatment patterns of holistic integrated medicine for neuro-ophthalmology].

    PubMed

    Wang, Yanling

    2014-12-01

    Neuro-ophthalmology, as an interdisciplinary, covers at least three disciplines- ophthalmology, neurology and neurosurgery. With limited knowledge in each discipline, doctors often make misdiagnoses for neuro-ophthalmology diseases. Therefore, it is imperative to abandon the distinction between disciplines and combine all the knowledge to diagnose and treat patients in patterns of holistic integrated medicine in order to effectively improve the diagnosis and treatment of neuro-ophthalmology.

  15. Parallel streams versus integrated timing in multilimb pattern generation: A test of Korte's Third Law.

    PubMed

    Jagacinski, Richard J; Rizzi, Emanuele; Kim, Tae Hoon; Lavender, Steven A; Speller, Lassiter F; Klapp, Stuart T

    2016-11-01

    Skilled drummers performed a 4:3:2 polyrhythm with 2 hands and 1 foot. For each pair of limbs patterns of temporal covariation were used to infer relatively independent parallel streams versus integrated timing relationships. Parallel timing was more prevalent between hand and foot than between the 2 hands, and parallel timing generally increased with tapping rate. Different combinations of integrated and parallel timing were found among the 3 limbs. A second experiment used a wider range of tapping rates and explored 3:2 tapping with 2 hands, 2 feet, or hand and foot. The latter 2 limb pairs resulted in greater prevalence of parallel timing. These results can be interpreted in terms of a Gestalt principle of grouping known as Korte's Third Law, which can be extended from the perceptual domain to the perceptual-motor domain. This principle indicates that perceived velocity is a key factor in determining whether a sequence of events is represented as a single integrated pattern or as multiple parallel patterns. The present results put disparate previous findings on bimanual polyrhythmic tapping and rhythmic aspects of the golf swing under a common theoretical perspective. (PsycINFO Database Record

  16. Integration of local pattern elements into a global shape in human vision

    PubMed Central

    Saarinen, Jukka; Levi, Dennis M.; Shen, Bridgitte

    1997-01-01

    The spatial extent of the cortical filters selective for different spatial frequencies and orientations is limited. We studied psychophysically how information from the local filters is integrated into global pattern shapes, i.e., whether performance in the identification of a global pattern consisting of small, locally oriented Gabor elements depends on the orientations of those elements. The observer was presented with an E-like stimulus pattern shape comprised of oriented Gabor patches on a blank background, and the performance measure was the threshold contrast for identifying the orientation of the E pattern (four possible rotated orientations). The results showed that contrast thresholds were significantly lower when the local elements all shared the same orientation (e.g., all horizontal) compared with the condition in which the elements had mixed orientations (both horizontal and vertical). The enhancement effect due to uniform local orientations can be explained by two factors: One is local facilitatory interactions between the orientation selective filters, and the other is second-order information integration across the filters. PMID:9223350

  17. Integration of Spectral Reflectance across the Plumage: Implications for Mating Patterns

    PubMed Central

    Laczi, Miklós; Török, János; Rosivall, Balázs; Hegyi, Gergely

    2011-01-01

    Background In complex sexual signaling systems such as plumage color, developmental or genetic links may occur among seemingly distinct traits. However, the interrelations of such traits and the functional significance of their integration rarely have been examined. Methodology/Principal Findings We investigated the parallel variation of two reflectance descriptors (brightness and UV chroma) across depigmented and melanized plumage areas of collared flycatchers (Ficedula albicollis), and the possible role of integrated color signals in mate acquisition. We found moderate integration in brightness and UV chroma across the plumage, with similar correlation structures in the two sexes despite the strong sexual dichromatism. Patterns of parallel color change across the plumage were largely unrelated to ornamental white patch sizes, but they all showed strong assortative mating between the sexes. Comparing different types of assortative mating patterns for individual spectral variables suggested a distinct role for plumage-level color axes in mate acquisition. Conclusions/Significance Our results indicate that the plumage-level, parallel variation of coloration might play a role in mate acquisition. This study underlines the importance of considering potential developmental and functional integration among apparently different ornaments in studies of sexual selection. PMID:21853088

  18. Custom-modified three-dimensional periodic microstructures by pattern-integrated interference lithography.

    PubMed

    Leibovici, Matthieu C R; Gaylord, Thomas K

    2014-07-01

    By combining interference lithography and projection photolithography concurrently, pattern-integrated interference lithography (PIIL) enables the wafer-scale, rapid, and single-exposure fabrication of multidimensional periodic microstructures that integrate arbitrary functional elements. To date, two-dimensional PIIL has been simulated and experimentally demonstrated. In this paper, we report new simulated results of PIIL exposures for various custom-modified three-dimensional (3D) periodic structures. These results were generated using custom PIIL comprehensive vector modeling. Simulations include mask-integrated and mask-shaped 3D periodic arrangements as well as microcavities on top of or fully embedded within 3D periodic structures. These results indicate PIIL is a viable method for making versatile 3D periodic microstructures.

  19. Integrative Inferences on Pattern Geometries of Grapes Grown under Water Stress and Their Resulting Wines

    PubMed Central

    Hsieh, Fushing; Hsueh, Chih-Hsin; Heitkamp, Constantin; Matthews, Mark

    2016-01-01

    Multiple datasets of two consecutive vintages of replicated grape and wines from six different deficit irrigation regimes are characterized and compared. The process consists of four temporal-ordered signature phases: harvest field data, juice composition, wine composition before bottling and bottled wine. A new computing paradigm and an integrative inferential platform are developed for discovering phase-to-phase pattern geometries for such characterization and comparison purposes. Each phase is manifested by a distinct set of features, which are measurable upon phase-specific entities subject to the common set of irrigation regimes. Throughout the four phases, this compilation of data from irrigation regimes with subsamples is termed a space of media-nodes, on which measurements of phase-specific features were recoded. All of these collectively constitute a bipartite network of data, which is then normalized and binary coded. For these serial bipartite networks, we first quantify patterns that characterize individual phases by means of a new computing paradigm called “Data Mechanics”. This computational technique extracts a coupling geometry which captures and reveals interacting dependence among and between media-nodes and feature-nodes in forms of hierarchical block sub-matrices. As one of the principal discoveries, the holistic year-factor persistently surfaces as the most inferential factor in classifying all media-nodes throughout all phases. This could be deemed either surprising in its over-arching dominance or obvious based on popular belief. We formulate and test pattern-based hypotheses that confirm such fundamental patterns. We also attempt to elucidate the driving force underlying the phase-evolution in winemaking via a newly developed partial coupling geometry, which is designed to integrate two coupling geometries. Such partial coupling geometries are confirmed to bear causal and predictive implications. All pattern inferences are performed with

  20. Integrative Inferences on Pattern Geometries of Grapes Grown under Water Stress and Their Resulting Wines.

    PubMed

    Hsieh, Fushing; Hsueh, Chih-Hsin; Heitkamp, Constantin; Matthews, Mark

    2016-01-01

    Multiple datasets of two consecutive vintages of replicated grape and wines from six different deficit irrigation regimes are characterized and compared. The process consists of four temporal-ordered signature phases: harvest field data, juice composition, wine composition before bottling and bottled wine. A new computing paradigm and an integrative inferential platform are developed for discovering phase-to-phase pattern geometries for such characterization and comparison purposes. Each phase is manifested by a distinct set of features, which are measurable upon phase-specific entities subject to the common set of irrigation regimes. Throughout the four phases, this compilation of data from irrigation regimes with subsamples is termed a space of media-nodes, on which measurements of phase-specific features were recoded. All of these collectively constitute a bipartite network of data, which is then normalized and binary coded. For these serial bipartite networks, we first quantify patterns that characterize individual phases by means of a new computing paradigm called "Data Mechanics". This computational technique extracts a coupling geometry which captures and reveals interacting dependence among and between media-nodes and feature-nodes in forms of hierarchical block sub-matrices. As one of the principal discoveries, the holistic year-factor persistently surfaces as the most inferential factor in classifying all media-nodes throughout all phases. This could be deemed either surprising in its over-arching dominance or obvious based on popular belief. We formulate and test pattern-based hypotheses that confirm such fundamental patterns. We also attempt to elucidate the driving force underlying the phase-evolution in winemaking via a newly developed partial coupling geometry, which is designed to integrate two coupling geometries. Such partial coupling geometries are confirmed to bear causal and predictive implications. All pattern inferences are performed with

  1. Patterns of morphological integration in marine modular organisms: supra-module organization in branching octocoral colonies.

    PubMed Central

    Sánchez, Juan Armando; Lasker, Howard R

    2003-01-01

    Despite the relative simplicity of their modular growth, marine invertebrates such as arborescent gorgonian octocorals (Octocorallia: Cnidaria) generate complex colonial forms. Colony form in these taxa is a consequence of modular (polyp) replication, and if there is a tight integration among modular and supramodular traits (e.g. polyp aperture, inter-polyp spacing, branch thickness, internode and branch length), then changes at the module level may lead to changes in colony architecture. Alternatively, different groups of traits may evolve semi-independently (or conditionally independent). To examine the patterns of integration among morphological traits in Caribbean octocorals, we compared five morphological traits across 21 species, correcting for the effects of phylogenetic relationships among the taxa. Graphical modelling and phylogenetic independence contrasts among the five morphological characters indicate two groups of integrated traits based on whether they were polyp- or colony-level traits. Although all characters exhibited bivariate associations, multivariate analyses (partial correlation coefficients) showed the strongest integration among the colony-level characters (internode distance and branch length). It is a quantitative demonstration that branching characters within the octocorals studied are independent of characters of the polyps. Despite the universally recognized modularity of octocorals at the level of polyps, branching during colony development may represent an emergent level of integration and modularity. PMID:14561292

  2. Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species.

    PubMed

    Yoshida, Takanori; Furihata, Hazuka Y; Kawabe, Akira

    2017-09-12

    Sequences homologous to organellar DNA that have been integrated into nuclear genomes are referred to as nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). NUMTs in nine plant species were analyzed to reveal the integration patterns and possible factors involved. The cumulative lengths of NUMTs in two-thirds of species analyzed were greater than those of NUPTs observed in a previous study. The age distribution of NUMTs was similar to that of NUPTs, suggesting similar mechanisms for integration and degradation of both NUPTs and NUMTs. Nuclear genome size and the cumulative length of NUMTs showed a significant positive correlation for older but not younger NUMTs. The same correlation was also found between nuclear genome size and older NUPTs in 17 species. These results suggested that genome size is a key factor to determine the cumulative length of relatively older NUPTs/NUMTs. Although the factor(s) determining the cumulative length of younger NUPTs/NUMTs is unclear, these sequences may be more deleterious, which could explain the different manner of determining the cumulative length of younger NUPTs/NUMTs in nuclear genomes. In addition, a relationship between the cumulative length of integrated NUMTs and complexity of mitochondrial genomes (i.e., the number of repeats) was found. The results indicate that the structural complexity of both NUMTs and their original mitochondrial sequences affects integration and degradation processes.

  3. Integrated routing and fill for self-aligned double patterning (SADP) using grid-based design

    NASA Astrophysics Data System (ADS)

    Song, Youngsoo; Lee, Jeemyung; Lee, Seongmin; Shin, Youngsoo

    2016-03-01

    Self-aligned double patterning (SADP) has been proposed as an alternative patterning solution for sub-10nm technology because of delay of advanced lithography beyond 193nm ArF. In conventional SADP, line and space style of dummy metal fills are inserted once main design is complete. A large buffer distance is required around the main design because no further verification of main design (in presence of fills) is performed. This causes irregular pattern density, which becomes a source of process variations. We propose integrated-fill, in which main design and dummy fill insertion are performed together. This requires a change in overall design flow, which we discuss. Integrated-fill is demonstrated in M2 layer of SADP process; M2 density increases by 15.7% with 2.3% reduction in standard deviation of density distribution; metal thickness variation is also reduced by 24%. More dummy fills cause increased coupling capacitance, which however is shown to be insignificant.

  4. An integrative framework of the skin receptors activation: mechanoreceptors activity patterns versus "labeled lines".

    PubMed

    Zeveke, Alexander V; Efes, Ekaterina D; Polevaya, Sofia A

    2013-03-01

    The paper presents a review of electrophysiological data which indicate the integrative mechanisms of information coded in the human and animal peripheral skin receptors. The activity of the skin sensory receptors was examined by applying various natural stimuli. It was revealed that numerous identical receptors respond to various stimuli (mechanical, temperature, and pain ones), but the spike patterns of these receptors were found to be specific for each stimulus. The description of characteristic structures of spike patterns in the cutaneous nerve fibers in response to five major modalities, namely: "touch", "pain", "vibration/breath", "cold", and "heat", is being presented. The recordings of the cutaneous physical state revealed a correlation between the patterns of spatiotemporal skin deformation and the receptors activity. A rheological state of the skin can be changed either in response to external temperature variation or by the sympathetic pilomotor activation. These results indicate that the skin sensory receptors activity may be considered as an integrative process. It depends not only on the receptors themselves, but also on the changes in the surrounding tissue and on the adaptive influence of the central nervous system. A new framework for the sensory channel system related to the skin is proposed on the basis of experimental results.

  5. The recalibration patterns of perceptual synchrony and multisensory integration after exposure to asynchronous speech.

    PubMed

    Yuan, Xiangyong; Bi, Cuihua; Yin, Huazhan; Li, Baolin; Huang, Xiting

    2014-05-21

    Perceptual synchrony and multisensory integration both vary as a function of stimulus onset asynchrony, but evidences from behavioral, patient, and lesion studies all support some dissociation between these two processes. Although it has been found that both perceptual synchrony and multisensory integration are recalibrated after exposure to asynchronous multisensory stimuli, no studies have directly compared these two recalibration patterns. We addressed this by using McGurk speech and requiring participants to perform simultaneity judgments and a syllable identification task in separate sessions. The results revealed that after exposure to asynchrony, both perceptual synchrony and McGurk fusion shifted toward the temporal lag. The recalibration aftereffects (i.e., the magnitude of shifts) of these two processes have no significant difference and correlation. In addition, McGurk fusion increased strongly at the direction of the temporal lag, which could not be fully explained by fusion shifts. Thus, the present research implies that recalibration patterns of explicit and implicit timing represented by perceptual synchrony and multisensory integration have both similarity and difference.

  6. Some blackhole and compactification solutions of noncanonical global monopole in 4-dimensional spacetime

    NASA Astrophysics Data System (ADS)

    Prasetyo, I.; Ramadhan, H. S.

    2017-07-01

    Here we present some solutions with noncanonical global monopole in nonlinear sigma model in 4-dimensional spacetime. We discuss some blackhole solutions and its horizons. We also obtain some compactification solutions. We list some possible compactification channels from 4-space to 2 × 2-spaces of constant curvatures.

  7. Integrating Entropy and Closed Frequent Pattern Mining for Social Network Modelling and Analysis

    NASA Astrophysics Data System (ADS)

    Adnan, Muhaimenul; Alhajj, Reda; Rokne, Jon

    The recent increase in the explicitly available social networks has attracted the attention of the research community to investigate how it would be possible to benefit from such a powerful model in producing effective solutions for problems in other domains where the social network is implicit; we argue that social networks do exist around us but the key issue is how to realize and analyze them. This chapter presents a novel approach for constructing a social network model by an integrated framework that first preparing the data to be analyzed and then applies entropy and frequent closed patterns mining for network construction. For a given problem, we first prepare the data by identifying items and transactions, which arc the basic ingredients for frequent closed patterns mining. Items arc main objects in the problem and a transaction is a set of items that could exist together at one time (e.g., items purchased in one visit to the supermarket). Transactions could be analyzed to discover frequent closed patterns using any of the well-known techniques. Frequent closed patterns have the advantage that they successfully grab the inherent information content of the dataset and is applicable to a broader set of domains. Entropies of the frequent closed patterns arc used to keep the dimensionality of the feature vectors to a reasonable size; it is a kind of feature reduction process. Finally, we analyze the dynamic behavior of the constructed social network. Experiments were conducted on a synthetic dataset and on the Enron corpus email dataset. The results presented in the chapter show that social networks extracted from a feature set as frequent closed patterns successfully carry the community structure information. Moreover, for the Enron email dataset, we present an analysis to dynamically indicate the deviations from each user's individual and community profile. These indications of deviations can be very useful to identify unusual events.

  8. High-Quality T2-Weighted 4-Dimensional Magnetic Resonance Imaging for Radiation Therapy Applications

    SciTech Connect

    Du, Dongsu; Caruthers, Shelton D.; Glide-Hurst, Carri; Low, Daniel A.; Li, H. Harold; Mutic, Sasa; Hu, Yanle

    2015-06-01

    Purpose: The purpose of this study was to improve triggering efficiency of the prospective respiratory amplitude-triggered 4-dimensional magnetic resonance imaging (4DMRI) method and to develop a 4DMRI imaging protocol that could offer T2 weighting for better tumor visualization, good spatial coverage and spatial resolution, and respiratory motion sampling within a reasonable amount of time for radiation therapy applications. Methods and Materials: The respiratory state splitting (RSS) and multi-shot acquisition (MSA) methods were analytically compared and validated in a simulation study by using the respiratory signals from 10 healthy human subjects. The RSS method was more effective in improving triggering efficiency. It was implemented in prospective respiratory amplitude-triggered 4DMRI. 4DMRI image datasets were acquired from 5 healthy human subjects. Liver motion was estimated using the acquired 4DMRI image datasets. Results: The simulation study showed the RSS method was more effective for improving triggering efficiency than the MSA method. The average reductions in 4DMRI acquisition times were 36% and 10% for the RSS and MSA methods, respectively. The human subject study showed that T2-weighted 4DMRI with 10 respiratory states, 60 slices at a spatial resolution of 1.5 × 1.5 × 3.0 mm{sup 3} could be acquired in 9 to 18 minutes, depending on the individual's breath pattern. Based on the acquired 4DMRI image datasets, the ranges of peak-to-peak liver displacements among 5 human subjects were 9.0 to 12.9 mm, 2.5 to 3.9 mm, and 0.5 to 2.3 mm in superior-inferior, anterior-posterior, and left-right directions, respectively. Conclusions: We demonstrated that with the RSS method, it was feasible to acquire high-quality T2-weighted 4DMRI within a reasonable amount of time for radiation therapy applications.

  9. Planning 4-Dimensional Computed Tomography (4DCT) Cannot Adequately Represent Daily Intrafractional Motion of Abdominal Tumors

    SciTech Connect

    Ge, Jiajia; Santanam, Lakshmi; Noel, Camille; Parikh, Parag J.

    2013-03-15

    Purpose: To evaluate whether planning 4-dimensional computed tomography (4DCT) can adequately represent daily motion of abdominal tumors in regularly fractionated and stereotactic body radiation therapy (SBRT) patients. Methods and Materials: Intrafractional tumor motion of 10 patients with abdominal tumors (4 pancreas-fractionated and 6 liver-stereotactic patients) with implanted fiducials was measured based on daily orthogonal fluoroscopic movies over 38 treatment fractions. The needed internal margin for at least 90% of tumor coverage was calculated based on a 95th and fifth percentile of daily 3-dimensional tumor motion. The planning internal margin was generated by fusing 4DCT motion from all phase bins. The disagreement between needed and planning internal margin was analyzed fraction by fraction in 3 motion axes (superior-inferior [SI], anterior-posterior [AP], and left-right [LR]). The 4DCT margin was considered as an overestimation/underestimation of daily motion when disagreement exceeded at least 3 mm in the SI axis and/or 1.2 mm in the AP and LR axes (4DCT image resolution). The underlying reasons for this disagreement were evaluated based on interfractional and intrafractional breathing variation. Results: The 4DCT overestimated daily 3-dimensional motion in 39% of the fractions in 7 of 10 patients and underestimated it in 53% of the fractions in 8 of 10 patients. Median underestimation was 3.9 mm, 3.0 mm, and 1.7 mm in the SI axis, AP axis, and LR axis, respectively. The 4DCT was found to capture irregular deep breaths in 3 of 10 patients, with 4DCT motion larger than mean daily amplitude by 18 to 21 mm. The breathing pattern varied from breath to breath and day to day. The intrafractional variation of amplitude was significantly larger than intrafractional variation (2.7 mm vs 1.3 mm) in the primary motion axis (ie, SI axis). The SBRT patients showed significantly larger intrafractional amplitude variation than fractionated patients (3.0 mm vs 2

  10. Nanoimprint, DSA, and multi-beam lithography: patterning technologies with new integration challenges

    NASA Astrophysics Data System (ADS)

    Landis, S.; Teyssedre, H.; Claveau, G.; Servin, I.; Delachat, F.; Pourteau, M. L.; Gharbi, A.; Pimenta Barros, P.; Tiron, R.; Nouri, L.; Possemé, N.; May, M.; Brianceau, P.; Barnola, S.; Blancquaert, Y.; Pradelles, J.; Essomba, P.; Bernadac, A.; Dal'zotto, B.; Bos, S.; Argoud, M.; Chamiot-Maitral, G.; Sarrazin, A.; Tallaron, C.; Lapeyre, C.; Pain, L.

    2017-04-01

    In the lithography landscape, EUV technology recovered some credibility recently. However, its large adoption remains uncertain. Meanwhile, 193nm immersion lithography, with multiple-patterning strategies, supports the industry preference for advanced-node developments. In this landscape, lithography alternatives maintain promise for continued R&D. Massively parallel electron-beam and nano-imprint lithography techniques remain highly attractive, as they can provide noteworthy cost-of-ownership benefits. Directed self-assembly lithography shows promising resolution capabilities and appears to be an option to reduce multi-patterning strategies. Even if large amount of efforts are dedicated to overcome the lithography side issues, these solutions introduce also new challenges and opportunities for the integration schemes.

  11. Integral scale histogram local binary patterns for classification of narrow-band gastroenterology images.

    PubMed

    Riaz, Farhan; Ribeiro, Mario-Dinis; Pimentel-Nunes, Pedro; Coimbra, Miguel Tavares

    2013-01-01

    The introduction of various novel imaging technologies such as narrow-band imaging have posed novel image processing challenges to the design of computer assisted decision systems. In this paper, we propose an image descriptor referred to as integrated scale histogram local binary patterns. We propagate an aggregated histogram of local binary patterns of an image at various resolutions. This results in low dimensional feature vectors for the images while incorporating their multiresolution analysis. The descriptor was used to classify gastroenterology images into four distinct groups. Results produced by the proposed descriptor exhibit around 92% accuracy for classification of gastroenteroloy images outperforming other state-of-the-art methods, endorsing the effectiveness of the proposed descriptor.

  12. Mining maximal cohesive induced subnetworks and patterns by integrating biological networks with gene profile data.

    PubMed

    Alroobi, Rami; Ahmed, Syed; Salem, Saeed

    2013-09-01

    With the availability of vast amounts of protein-protein, protein-DNA interactions, and genome-wide mRNA expression data for several organisms, identifying biological complexes has emerged as a major task in systems biology. Most of the existing approaches for complex identification have focused on utilizing one source of data. Recent research has shown that systematic integration of gene profile data with interaction data yields significant patterns. In this paper, we introduce the problem of mining maximal cohesive subnetworks that satisfy user-defined constraints defined over the gene profiles of the reported subnetworks. Moreover, we introduce the problem of finding maximal cohesive patterns which are sets of cohesive genes. Experiments on Yeast and Human datasets show the effectiveness of the proposed approach by assessing the overlap of the discovered subnetworks with known biological complexes. Moreover, GO enrichment analysis shows that the discovered subnetworks are biologically significant.

  13. Patterns of classroom discourse in an integrated, interpreted elementary school setting.

    PubMed

    Shaw, J; Jamieson, J

    1997-03-01

    The purpose of this study was to describe the patterns of classroom discourse experienced by an integrated deaf child with full-time interpreting services in an elementary setting. The child was videotaped for 3 hours during classroom instructional time. The videotapes were analyzed to determine patterns of discourse between the child and the teacher and the child and the interpreter, as well as to gauge the deaf student's accessibility to teacher-class discourse. It was found that the deaf student interacted predominantly with the interpreter; in fact, this student received more direct instruction from the interpreter than from the teacher. The discourse to which the student was exposed was largely academic, rather than cultural or social. Findings are discussed in terms of the extent to which implicit classroom discourse and cultural knowledge were inaccessible to the deaf student.

  14. Mining and analysing spatio-temporal patterns of gene expression in an integrative database framework.

    PubMed

    Belmamoune, M; Potikanond, D; Verbeek, F J

    2010-03-25

    Mining patterns of gene expression provides a crucial approach in discovering knowledge such as finding genetic networks that underpin the embryonic development. Analysis of mining results and evaluation of their relevance in the domain remains a major concern. In this paper we describe our explorative studies in support of solutions to facilitate the analysis and interpretation of mining results. In our particular case we describe a solution that is found in the extension of the Gene Expression Management System (GEMS), i.e. an integrative framework for spatio-temporal organization of gene expression patterns of zebrafish to a framework supporting data mining, data analysis and patterns interpretation As a proof of principle, the GEMS has been equipped with data mining functionality suitable for spatio-temporal tracking, thereby generating added value to the submission of data for data mining and analysis. The analysis of the genetic networks is based on the availability of domain ontologies which dynamically provides meaning to the discovered patterns of gene expression data. Combination of data mining with the already presently available capabilities of GEMS will significantly augment current data processing and functional analysis strategies.

  15. Firing patterns in the adaptive exponential integrate-and-fire model.

    PubMed

    Naud, Richard; Marcille, Nicolas; Clopath, Claudia; Gerstner, Wulfram

    2008-11-01

    For simulations of large spiking neuron networks, an accurate, simple and versatile single-neuron modeling framework is required. Here we explore the versatility of a simple two-equation model: the adaptive exponential integrate-and-fire neuron. We show that this model generates multiple firing patterns depending on the choice of parameter values, and present a phase diagram describing the transition from one firing type to another. We give an analytical criterion to distinguish between continuous adaption, initial bursting, regular bursting and two types of tonic spiking. Also, we report that the deterministic model is capable of producing irregular spiking when stimulated with constant current, indicating low-dimensional chaos. Lastly, the simple model is fitted to real experiments of cortical neurons under step current stimulation. The results provide support for the suitability of simple models such as the adaptive exponential integrate-and-fire neuron for large network simulations.

  16. Health spending in the 1980's: Integration of clinical practice patterns with management

    PubMed Central

    Freeland, Mark S.; Schendler, Carol E.

    1984-01-01

    Health care spending in the United States more than tripled between 1972 and 1982, increasing from $94 billion to $322 billion. This growth substantially outpaced overall growth in the economy. National health expenditures are projected to reach approximately $690 billion in 1990 and consume roughly 12 percent of the gross national product. Government spending for health care is projected to reach $294 billion by 1990, with the Federal Government paying 72 percent. The Medicare prospective payment system and increasing competition in the health services sector are providing incentives to integrate clinical practice patterns with improved management practices. PMID:10310595

  17. Clinical Validation of 4-Dimensional Computed Tomography Ventilation With Pulmonary Function Test Data

    SciTech Connect

    Brennan, Douglas; Schubert, Leah; Diot, Quentin; Castillo, Richard; Castillo, Edward; Guerrero, Thomas; Martel, Mary K.; Linderman, Derek; Gaspar, Laurie E.; Miften, Moyed; Kavanagh, Brian D.; Vinogradskiy, Yevgeniy

    2015-06-01

    Purpose: A new form of functional imaging has been proposed in the form of 4-dimensional computed tomography (4DCT) ventilation. Because 4DCTs are acquired as part of routine care for lung cancer patients, calculating ventilation maps from 4DCTs provides spatial lung function information without added dosimetric or monetary cost to the patient. Before 4DCT-ventilation is implemented it needs to be clinically validated. Pulmonary function tests (PFTs) provide a clinically established way of evaluating lung function. The purpose of our work was to perform a clinical validation by comparing 4DCT-ventilation metrics with PFT data. Methods and Materials: Ninety-eight lung cancer patients with pretreatment 4DCT and PFT data were included in the study. Pulmonary function test metrics used to diagnose obstructive lung disease were recorded: forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity. Four-dimensional CT data sets and spatial registration were used to compute 4DCT-ventilation images using a density change–based and a Jacobian-based model. The ventilation maps were reduced to single metrics intended to reflect the degree of ventilation obstruction. Specifically, we computed the coefficient of variation (SD/mean), ventilation V20 (volume of lung ≤20% ventilation), and correlated the ventilation metrics with PFT data. Regression analysis was used to determine whether 4DCT ventilation data could predict for normal versus abnormal lung function using PFT thresholds. Results: Correlation coefficients comparing 4DCT-ventilation with PFT data ranged from 0.63 to 0.72, with the best agreement between FEV1 and coefficient of variation. Four-dimensional CT ventilation metrics were able to significantly delineate between clinically normal versus abnormal PFT results. Conclusions: Validation of 4DCT ventilation with clinically relevant metrics is essential. We demonstrate good global agreement between PFTs and 4DCT-ventilation, indicating that 4DCT

  18. Clinical validation of 4-dimensional computed tomography ventilation with pulmonary function test data.

    PubMed

    Brennan, Douglas; Schubert, Leah; Diot, Quentin; Castillo, Richard; Castillo, Edward; Guerrero, Thomas; Martel, Mary K; Linderman, Derek; Gaspar, Laurie E; Miften, Moyed; Kavanagh, Brian D; Vinogradskiy, Yevgeniy

    2015-06-01

    A new form of functional imaging has been proposed in the form of 4-dimensional computed tomography (4DCT) ventilation. Because 4DCTs are acquired as part of routine care for lung cancer patients, calculating ventilation maps from 4DCTs provides spatial lung function information without added dosimetric or monetary cost to the patient. Before 4DCT-ventilation is implemented it needs to be clinically validated. Pulmonary function tests (PFTs) provide a clinically established way of evaluating lung function. The purpose of our work was to perform a clinical validation by comparing 4DCT-ventilation metrics with PFT data. Ninety-eight lung cancer patients with pretreatment 4DCT and PFT data were included in the study. Pulmonary function test metrics used to diagnose obstructive lung disease were recorded: forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity. Four-dimensional CT data sets and spatial registration were used to compute 4DCT-ventilation images using a density change-based and a Jacobian-based model. The ventilation maps were reduced to single metrics intended to reflect the degree of ventilation obstruction. Specifically, we computed the coefficient of variation (SD/mean), ventilation V20 (volume of lung ≤20% ventilation), and correlated the ventilation metrics with PFT data. Regression analysis was used to determine whether 4DCT ventilation data could predict for normal versus abnormal lung function using PFT thresholds. Correlation coefficients comparing 4DCT-ventilation with PFT data ranged from 0.63 to 0.72, with the best agreement between FEV1 and coefficient of variation. Four-dimensional CT ventilation metrics were able to significantly delineate between clinically normal versus abnormal PFT results. Validation of 4DCT ventilation with clinically relevant metrics is essential. We demonstrate good global agreement between PFTs and 4DCT-ventilation, indicating that 4DCT-ventilation provides a reliable assessment of lung

  19. Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for BMD Variation.

    PubMed

    Zhang, Ji-Gang; Tan, Li-Jun; Xu, Chao; He, Hao; Tian, Qing; Zhou, Yu; Qiu, Chuan; Chen, Xiang-Ding; Deng, Hong-Wen

    2015-01-01

    Integration of multiple profiling data and construction of functional gene networks may provide additional insights into the molecular mechanisms of complex diseases. Osteoporosis is a worldwide public health problem, but the complex gene-gene interactions, post-transcriptional modifications and regulation of functional networks are still unclear. To gain a comprehensive understanding of osteoporosis etiology, transcriptome gene expression microarray, epigenomic miRNA microarray and methylome sequencing were performed simultaneously in 5 high hip BMD (Bone Mineral Density) subjects and 5 low hip BMD subjects. SPIA (Signaling Pathway Impact Analysis) and PCST (Prize Collecting Steiner Tree) algorithm were used to perform pathway-enrichment analysis and construct the interaction networks. Through integrating the transcriptomic and epigenomic data, firstly we identified 3 genes (FAM50A, ZNF473 and TMEM55B) and one miRNA (hsa-mir-4291) which showed the consistent association evidence from both gene expression and methylation data; secondly in network analysis we identified an interaction network module with 12 genes and 11 miRNAs including AKT1, STAT3, STAT5A, FLT3, hsa-mir-141 and hsa-mir-34a which have been associated with BMD in previous studies. This module revealed the crosstalk among miRNAs, mRNAs and DNA methylation and showed four potential regulatory patterns of gene expression to influence the BMD status. In conclusion, the integration of multiple layers of omics can yield in-depth results than analysis of individual omics data respectively. Integrative analysis from transcriptomics and epigenomic data improves our ability to identify causal genetic factors, and more importantly uncover functional regulation pattern of multi-omics for osteoporosis etiology.

  20. Patterned photostimulation with digital micromirror devices to investigate dendritic integration across branch points.

    PubMed

    Liang, Conrad W; Mohammadi, Michael; Santos, M Daniel; Santos, M Danial; Tang, Cha-Min

    2011-03-02

    Light is a versatile and precise means to control neuronal excitability. The recent introduction of light sensitive effectors such as channel-rhodopsin and caged neurotransmitters have led to interests in developing better means to control patterns of light in space and time that are useful for experimental neuroscience. One conventional strategy, employed in confocal and 2-photon microscopy, is to focus light to a diffraction limited spot and then scan that single spot sequentially over the region of interest. This approach becomes problematic if large areas have to be stimulated within a brief time window, a problem more applicable to photostimulation than for imaging. An alternate strategy is to project the complete spatial pattern on the target with the aid of a digital micromirror device (DMD). The DMD approach is appealing because the hardware components are relatively inexpensive and is supported by commercial interests. Because such a system is not available for upright microscopes, we will discuss the critical issues in the construction and operations of such a DMD system. Even though we will be primarily describing the construction of the system for UV photolysis, the modifications for building the much simpler visible light system for optogenetic experiments will also be provided. The UV photolysis system was used to carryout experiments to study a fundamental question in neuroscience, how are spatially distributed inputs integrated across distal dendritic branch points. The results suggest that integration can be non-linear across branch points and the supralinearity is largely mediated by NMDA receptors.

  1. Design and testing of the first 2D Prototype Vertically Integrated Pattern Recognition Associative Memory

    SciTech Connect

    Liu, T.; Deptuch, G.; Hoff, J.; Jindariani, S.; Joshi, S.; Olsen, J.; Tran, N.; Trimpl, M.

    2015-02-01

    An associative memory-based track finding approach has been proposed for a Level 1 tracking trigger to cope with increasing luminosities at the LHC. The associative memory uses a massively parallel architecture to tackle the intrinsically complex combinatorics of track finding algorithms, thus avoiding the typical power law dependence of execution time on occupancy and solving the pattern recognition in times roughly proportional to the number of hits. This is of crucial importance given the large occupancies typical of hadronic collisions. The design of an associative memory system capable of dealing with the complexity of HL-LHC collisions and with the short latency required by Level 1 triggering poses significant, as yet unsolved, technical challenges. For this reason, an aggressive R&D program has been launched at Fermilab to advance state of-the-art associative memory technology, the so called VIPRAM (Vertically Integrated Pattern Recognition Associative Memory) project. The VIPRAM leverages emerging 3D vertical integration technology to build faster and denser Associative Memory devices. The first step is to implement in conventional VLSI the associative memory building blocks that can be used in 3D stacking, in other words, the building blocks are laid out as if it is a 3D design. In this paper, we report on the first successful implementation of a 2D VIPRAM demonstrator chip (protoVIPRAM00). The results show that these building blocks are ready for 3D stacking.

  2. Design and testing of the first 2D Prototype Vertically Integrated Pattern Recognition Associative Memory

    NASA Astrophysics Data System (ADS)

    Liu, T.; Deptuch, G.; Hoff, J.; Jindariani, S.; Joshi, S.; Olsen, J.; Tran, N.; Trimpl, M.

    2015-02-01

    An associative memory-based track finding approach has been proposed for a Level 1 tracking trigger to cope with increasing luminosities at the LHC. The associative memory uses a massively parallel architecture to tackle the intrinsically complex combinatorics of track finding algorithms, thus avoiding the typical power law dependence of execution time on occupancy and solving the pattern recognition in times roughly proportional to the number of hits. This is of crucial importance given the large occupancies typical of hadronic collisions. The design of an associative memory system capable of dealing with the complexity of HL-LHC collisions and with the short latency required by Level 1 triggering poses significant, as yet unsolved, technical challenges. For this reason, an aggressive R&D program has been launched at Fermilab to advance state of-the-art associative memory technology, the so called VIPRAM (Vertically Integrated Pattern Recognition Associative Memory) project. The VIPRAM leverages emerging 3D vertical integration technology to build faster and denser Associative Memory devices. The first step is to implement in conventional VLSI the associative memory building blocks that can be used in 3D stacking; in other words, the building blocks are laid out as if it is a 3D design. In this paper, we report on the first successful implementation of a 2D VIPRAM demonstrator chip (protoVIPRAM00). The results show that these building blocks are ready for 3D stacking.

  3. Phylogenetic tests of distribution patterns in South Asia: towards an integrative approach.

    PubMed

    Biswas, Sayantan; Pawar, Samraat S

    2006-03-01

    The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.

  4. Patterned Photostimulation with Digital Micromirror Devices to Investigate Dendritic Integration Across Branch Points

    PubMed Central

    Santos, M. Daniel; Tang, Cha-Min

    2011-01-01

    Light is a versatile and precise means to control neuronal excitability. The recent introduction of light sensitive effectors such as channel-rhodopsin and caged neurotransmitters have led to interests in developing better means to control patterns of light in space and time that are useful for experimental neuroscience. One conventional strategy, employed in confocal and 2-photon microscopy, is to focus light to a diffraction limited spot and then scan that single spot sequentially over the region of interest. This approach becomes problematic if large areas have to be stimulated within a brief time window, a problem more applicable to photostimulation than for imaging. An alternate strategy is to project the complete spatial pattern on the target with the aid of a digital micromirror device (DMD). The DMD approach is appealing because the hardware components are relatively inexpensive and is supported by commercial interests. Because such a system is not available for upright microscopes, we will discuss the critical issues in the construction and operations of such a DMD system. Even though we will be primarily describing the construction of the system for UV photolysis, the modifications for building the much simpler visible light system for optogenetic experiments will also be provided. The UV photolysis system was used to carryout experiments to study a fundamental question in neuroscience, how are spatially distributed inputs integrated across distal dendritic branch points. The results suggest that integration can be non-linear across branch points and the supralinearity is largely mediated by NMDA receptors. PMID:21403635

  5. Acquisition and Generalization of Word Decoding in Students with Reading Disabilities by Integrating Vowel Pattern Analysis and Children's Literature

    ERIC Educational Resources Information Center

    Cohen, E. Judith; Brady, Michael P.

    2011-01-01

    This study investigated the effects of a reading intervention that integrated vowel pattern analysis and children's literature on the word decoding performance of second graders with reading disabilities. The intervention evaluated students' abilities to decode a set of training words using 3 common vowel patterns (syllable types), in isolation…

  6. Acquisition and Generalization of Word Decoding in Students with Reading Disabilities by Integrating Vowel Pattern Analysis and Children's Literature

    ERIC Educational Resources Information Center

    Cohen, E. Judith; Brady, Michael P.

    2011-01-01

    This study investigated the effects of a reading intervention that integrated vowel pattern analysis and children's literature on the word decoding performance of second graders with reading disabilities. The intervention evaluated students' abilities to decode a set of training words using 3 common vowel patterns (syllable types), in isolation…

  7. Developement of 3D Vertically Integrated Pattern Recognition Associative Memory (VIPRAM)

    SciTech Connect

    Deputch, G.; Hoff, J.; Lipton, R.; Liu, T.; Olsen, J.; Ramberg, E.; Wu, Jin-Yuan; Yarema, R.; Shochet, M.; Tang, F.; Demarteau, M.; /Argonne /INFN, Padova

    2011-04-13

    Many next-generation physics experiments will be characterized by the collection of large quantities of data, taken in rapid succession, from which scientists will have to unravel the underlying physical processes. In most cases, large backgrounds will overwhelm the physics signal. Since the quantity of data that can be stored for later analysis is limited, real-time event selection is imperative to retain the interesting events while rejecting the background. Scaling of current technologies is unlikely to satisfy the scientific needs of future projects, so investments in transformational new technologies need to be made. For example, future particle physics experiments looking for rare processes will have to address the demanding challenges of fast pattern recognition in triggering as detector hit density becomes significantly higher due to the high luminosity required to produce the rare processes. In this proposal, we intend to develop hardware-based technology that significantly advances the state-of-the-art for fast pattern recognition within and outside HEP using the 3D vertical integration technology that has emerged recently in industry. The ultimate physics reach of the LHC experiments will crucially depend on the tracking trigger's ability to help discriminate between interesting rare events and the background. Hardware-based pattern recognition for fast triggering on particle tracks has been successfully used in high-energy physics experiments for some time. The CDF Silicon Vertex Trigger (SVT) at the Fermilab Tevatron is an excellent example. The method used there, developed in the 1990's, is based on algorithms that use a massively parallel associative memory architecture to identify patterns efficiently at high speed. However, due to much higher occupancy and event rates at the LHC, and the fact that the LHC detectors have a much larger number of channels in their tracking detectors, there is an enormous challenge in implementing pattern recognition

  8. Integrated β-catenin, BMP, PTEN, and Notch signalling patterns the nephron

    PubMed Central

    Lindström, Nils O; Lawrence, Melanie L; Burn, Sally F; Johansson, Jeanette A; Bakker, Elvira RM; Ridgway, Rachel A; Chang, C-Hong; Karolak, Michele J; Oxburgh, Leif; Headon, Denis J; Sansom, Owen J; Smits, Ron; Davies, Jamie A; Hohenstein, Peter

    2015-01-01

    The different segments of the nephron and glomerulus in the kidney balance the processes of water homeostasis, solute recovery, blood filtration, and metabolite excretion. When segment function is disrupted, a range of pathological features are presented. Little is known about nephron patterning during embryogenesis. In this study, we demonstrate that the early nephron is patterned by a gradient in β-catenin activity along the axis of the nephron tubule. By modifying β-catenin activity, we force cells within nephrons to differentiate according to the imposed β-catenin activity level, thereby causing spatial shifts in nephron segments. The β-catenin signalling gradient interacts with the BMP pathway which, through PTEN/PI3K/AKT signalling, antagonises β-catenin activity and promotes segment identities associated with low β-catenin activity. β-catenin activity and PI3K signalling also integrate with Notch signalling to control segmentation: modulating β-catenin activity or PI3K rescues segment identities normally lost by inhibition of Notch. Our data therefore identifies a molecular network for nephron patterning. DOI: http://dx.doi.org/10.7554/eLife.04000.001 PMID:25647637

  9. Integrated β-catenin, BMP, PTEN, and Notch signalling patterns the nephron.

    PubMed

    Lindström, Nils O; Lawrence, Melanie L; Burn, Sally F; Johansson, Jeanette A; Bakker, Elvira R M; Ridgway, Rachel A; Chang, C-Hong; Karolak, Michele J; Oxburgh, Leif; Headon, Denis J; Sansom, Owen J; Smits, Ron; Davies, Jamie A; Hohenstein, Peter

    2015-02-03

    The different segments of the nephron and glomerulus in the kidney balance the processes of water homeostasis, solute recovery, blood filtration, and metabolite excretion. When segment function is disrupted, a range of pathological features are presented. Little is known about nephron patterning during embryogenesis. In this study, we demonstrate that the early nephron is patterned by a gradient in β-catenin activity along the axis of the nephron tubule. By modifying β-catenin activity, we force cells within nephrons to differentiate according to the imposed β-catenin activity level, thereby causing spatial shifts in nephron segments. The β-catenin signalling gradient interacts with the BMP pathway which, through PTEN/PI3K/AKT signalling, antagonises β-catenin activity and promotes segment identities associated with low β-catenin activity. β-catenin activity and PI3K signalling also integrate with Notch signalling to control segmentation: modulating β-catenin activity or PI3K rescues segment identities normally lost by inhibition of Notch. Our data therefore identifies a molecular network for nephron patterning.

  10. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

    PubMed

    Wilkinson, Mark D; Vandervalk, Benjamin; McCarthy, Luke

    2011-10-24

    The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in

  11. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

    PubMed Central

    2011-01-01

    Background The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner

  12. Directed self-assembly process integration: Fin patterning approaches and challenges

    NASA Astrophysics Data System (ADS)

    Sayan, Safak; Chan, B. T.; Gronheid, Roel; Van Roey, Frieda; Kim, Min-Soo; Williamson, Lance; Nealey, Paul

    2014-03-01

    Resolution requirements for photolithography have reached beyond the wavelength of light. Consequently, it is becoming increasingly complicated and expensive to further minimize feature dimensions as required to push the limits of Moore's law. EUV lithography has been the much anticipated solution; however, its insertion timing for High Volume Manufacturing is still an uncertainty due to source power and EUV mask infrastructure limitations. Extending the limits of 193nm immersion lithography requires pitch division using either Double Patterning Pitch Division (DPPD), and/or Spacer Based Pitch Division (SBPD) schemes (e.g. Hard mask image transfer methods (Double, Triple, Quadruple)). While these approaches reduce pitch, there is an associated risk/compromise of process complexity, and overlay accuracy budget issues. Directed Self Assembly (DSA) processes offer the promise of providing alternative ways to extend optical lithography cost-effectively for sub-10nm nodes and present itself as an alternative pitch division approach. As a result, DSA has gained increased momentum in recent years, as a means for extending optical lithography past its current limits. The availability of a DSA processing line can enable to further push the limits of 193nm immersion lithography and overcome some of the critical concerns for EUV lithography. Robust etch transfer of DSA patterns into commonly used device integration materials such as silicon, silicon nitride, and silicon dioxide had been previously demonstrated [1,2]. However DSA integration to CMOS process flows, including cut/keep structures to form fin arrays, is yet to be demonstrated on relevant film stacks (front-end-of-line device integration such as hard mask stacks, and STI stacks). Such a demonstration will confirm and reinforce its viability as a candidate for sub-10nm technology nodes.

  13. Conserved patterns of integrated developmental plasticity in a group of polyphenic tropical butterflies.

    PubMed

    van Bergen, Erik; Osbaldeston, Dave; Kodandaramaiah, Ullasa; Brattström, Oskar; Aduse-Poku, Kwaku; Brakefield, Paul M

    2017-02-27

    Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics. Our data indicate that an integrated response of a suite of key traits is shared amongst these species. Interestingly, the traits that make up the functional suite are all known to be regulated by ecdysteroid signalling in Bicyclus anynana, one of the species included in this study, suggesting the same underlying hormonal regulator may be conserved within this group of polyphenic butterflies. We also detect developmental thresholds for the expression of alternative morphs. The phenotypic plasticity of a broad suite of morphological and life history traits is integrated and shared among species from three geographically independent lineages of mycalesine butterflies, despite considerable periods of independent evolution and exposure to disparate environments. At the same time, we have detected examples of evolutionary change where independent traits show different patterns of reaction norms. We argue that the expression of more robust phenotypes may occur by shifting developmental thresholds beyond the boundaries of the typical environmental variation.

  14. Incorporating pattern identification of Chinese medicine into precision medicine: An integrative model for individualized medicine.

    PubMed

    Li, Jin-gen; Xu, Hao

    2015-11-01

    On 20 January, 2015, U.S. President Obama announced an ambitious plan called "Precision Medicine (PM) Initiative", aiming to deliver genetics-based medical treatments. PM has shown a promising prospect by tailoring disease treatments and preventions to individuals. However, a predominantly genetics-based method restricts its benefit and applicability in most chronic and complex diseases. Pattern identification (PI) is one of the representative characteristics of Chinese medicine implying the concept of holism and individualized treatment. It is another classification method taking environmental, psychosocial and other individual factors into account. Integrating PI with disease diagnosis of Western medicine will provide a strong complement to genetics-based PM, thus establish an integrative model for individualized medicine. PI provides new perspectives for PM, not only in clinical practice, but also in new drug development and clinical trial design. It is for sure that the integrative approach will ultimately lead to a safer, more convenient and effective patient-centered healthcare and most patients will benefit in the era of PM.

  15. Pattern of social interactions after group integration: a possibility to keep stallions in group.

    PubMed

    Briefer Freymond, Sabrina; Briefer, Elodie F; Von Niederhäusern, Rudolf; Bachmann, Iris

    2013-01-01

    Horses are often kept in individual stables, rather than in outdoor groups, despite such housing system fulfilling many of their welfare needs, such as the access to social partners. Keeping domestic stallions in outdoor groups would mimic bachelor bands that are found in the wild. Unfortunately, the high level of aggression that unfamiliar stallions display when they first encounter each other discourages owners from keeping them in groups. However, this level of aggression is likely to be particularly important only during group integration, when the dominance hierarchy is being established, whereas relatively low aggression rates have been observed among stable feral bachelor bands. We investigated the possibility of housing breeding stallions owned by the Swiss National Stud in groups on a large pasture (5 stallions in 2009 and 8 stallions in 2010). We studied the pattern of agonistic, ritual and affiliative interactions after group integration (17-23 days), and the factors influencing these interactions (time after group integration, dominance rank, age or experience of group housing). We found that stallions displayed generally more ritual than agonistic and than affiliative interactions. The frequency of agonistic and ritual interactions decreased quickly within the first three to four days. The frequency of affiliative interactions increased slowly with time before decreasing after 9-14 days. A stable hierarchy could be measured after 2-3 months. The highest-ranking males had less ritual interactions than the lowest-ranking. Males had also less agonistic, ritual and affiliative interactions if they had already been housed in a group the previous year. Therefore, we found that breeding stallions could be housed together on a large pasture, because the frequency of agonistic interactions decreased quickly and remained at a minimal level from the fourth day following group integration. This housing system could potentially increase horse welfare and reduce

  16. The integrated ultradian organization of behavior and physiology in mice and the contribution of orexin to the ultradian patterning.

    PubMed

    Miyata, Kohei; Kuwaki, Tomoyuki; Ootsuka, Youichirou

    2016-10-15

    Our series of rat experiments have shown that locomotor activity, arousal level, body and brown adipose tissue temperatures, heart rate and arterial pressure increase episodically in an integrated manner approximately every 100min (ultradian manner). Although it has been proposed that the integrated ultradian pattern is a fundamental biological rhythm across species, there are no reports of the integrated ultradian pattern in species other than rats. The aim of the present study was to establish a mouse model using simultaneous recording of locomotor activity, eating behavior, body temperature, heart rate and arousal in order to determine whether their behavior and physiology are organized in an ultradian manner in normal (wild-type) mice. We also incorporated the same recording in prepro-orexin knockout (ORX-KO) mice to reveal the role of orexin in the brain mechanisms underlying ultradian patterning. The orexin system is one of the key conductors required for coordinating autonomic functions and behaviors, and thus may contribute to ultradian patterning. In wild-type mice, locomotor activity, arousal level, body temperature and heart rate increased episodically every 93±18min (n=8) during 24h. Eating was integrated into the ultradian pattern, commencing 23±4min (n=8) after the onset of an electroencephalogram (EEG) ultradian episode. The integrated ultradian pattern in wild-type mice is very similar to that observed in rats. In ORX-KO mice, the ultradian episodic changes in locomotor activity, EEG arousal indices and body temperature were significantly attenuated, but the ultradian patterning was preserved. Our findings support the view that the ultradian pattern is common across species. The present results also suggest that orexin contributes to driving ultradian episodic changes, however, this neuropeptide is not essential for the generation of the ultradian pattern. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  17. Integration considerations for 130-nm device patterning using ArF lithography

    NASA Astrophysics Data System (ADS)

    Okoroanyanwu, Uzodinma; Levinson, Harry J.; Yang, Chih-Yuh; Pangrle, Suzette K.; Schefske, Jeff A.; Kent, Eric

    2000-07-01

    With the delivery of ful field ArF steppers and scanners to the leading edge IC manufacturers in 1999 for process development work, the industry is poised to implement ArF lithography in volume production in a few years from now. The introduction of ArF lithography in large volume deice manufacturing will be at the 130-nm technology node, with a k1-factor of roughly 0.4. This will represent the first time in the history of the semiconductor industry when the critical feature size of first generation devices for a given technology node is significantly smaller than the lithographic wavelength used in the patterning. Accordingly, there are a number of integration issues that must be resolved to ensure the successful implement of this technology. Such issues include antireflection coatings issues like reflectivity control and thickness, and the tradeoffs between using organic and inorganic ARCs; resist material issues like optical absorption, feature profile, CD uniformity and line edge roughness; and etch issues like resist loss, line edge roughening, endcap pullback, etc. For instance, one of the major problems with most currently available 193-nm resists is their high optical absorption at the exposure wavelength. This necessitates the use of significantly thinner 193-nm resist films than have been the case in earlier lithographic regimes, but etch considerations preclude this option as these materials do not have bey good etch stability. A balance between absorption and etch requirements must therefore be struck to ensure the successful implementation of this lithography. The above outlined integration issues involved in striking this balance are the subject of this paper, and they will be presented from a patterning perspective. Our exposures are made with ASML/900 full field scanner.

  18. Integrating Nano-patterned Ferromagnetic and Ferroelectric Thin Films for Electrically Tunable RF Applications

    SciTech Connect

    Wang, Tengxing; Peng, Yujia; Jiang, Wei; Huang, Yong Mao; Rahman, B.M. Farid; Divan, Ralu; Rosenmann, Daniel; Wang, Guoan

    2016-10-31

    Tunable radio frequency (RF) components are pivotal elements in frequency-agile and multifunctional systems. However, there is a technical barrier to achieve miniaturized fully electrically tunable RF components. This paper provides and demonstrates the efficacy of a first unique design methodology in developing fully electrically tunable RF components by integrating ferromagnetic (e.g., Permalloy) and ferroelectric (e.g., Lead Zirconate Titanate: PZT) thin films patterns. Permalloy thin film has been patterned in nanometer scale to improve its ferromagnetic resonance frequency (FMR) for RF applications. Tunable inductors are developed with the utilization of different thickness of Permalloy thin film, which show over 50% increment in inductance and over 4% in tunability with DC current. More tunability can be achieved with multiple layers of Permalloy thin film and optimized thickness. A fully electrically tunable slow wave RF transmission line with simultaneously variable inductance and capacitance density has been implemented and thoroughly investigated for the first time. Measured results show that a fixed phase shift of 90° can be achieved from 1.5 GHz to 1.85 GHz continuously by applying external DC current from 0 to 200 mA and external DC voltage from 0 to 15 Volts, respectively.

  19. Integrating Nano-patterned Ferromagnetic and Ferroelectric Thin Films for Electrically Tunable RF Applications

    DOE PAGES

    Wang, Tengxing; Peng, Yujia; Jiang, Wei; ...

    2016-10-31

    Tunable radio frequency (RF) components are pivotal elements in frequency-agile and multifunctional systems. However, there is a technical barrier to achieve miniaturized fully electrically tunable RF components. This paper provides and demonstrates the efficacy of a first unique design methodology in developing fully electrically tunable RF components by integrating ferromagnetic (e.g., Permalloy) and ferroelectric (e.g., Lead Zirconate Titanate: PZT) thin films patterns. Permalloy thin film has been patterned in nanometer scale to improve its ferromagnetic resonance frequency (FMR) for RF applications. Tunable inductors are developed with the utilization of different thickness of Permalloy thin film, which show over 50% incrementmore » in inductance and over 4% in tunability with DC current. More tunability can be achieved with multiple layers of Permalloy thin film and optimized thickness. A fully electrically tunable slow wave RF transmission line with simultaneously variable inductance and capacitance density has been implemented and thoroughly investigated for the first time. Measured results show that a fixed phase shift of 90° can be achieved from 1.5 GHz to 1.85 GHz continuously by applying external DC current from 0 to 200 mA and external DC voltage from 0 to 15 Volts, respectively.« less

  20. Texture classification using rotation invariant models on integrated local binary pattern and Zernike moments

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Zhao, Yongsheng; Chen, Yi

    2014-12-01

    More and more attention has been paid to the invariant texture analysis, because the training and testing samples generally have not identical or similar orientations, or are not acquired from the same viewpoint in many practical applications, which often has negative influences on texture analysis. Local binary pattern (LBP) has been widely applied to texture classification due to its simplicity, efficiency, and rotation invariant property. In this paper, an integrated local binary pattern (ILBP) scheme including original rotation invariant LBP, improved contrast rotation invariant LBP, and direction rotation invariant LBP is proposed which can effectively overcome the deficiency of original LBP that is ignoring contrast and direction information. In addition, for surmounting another major drawback of LBP such as locality which can result in the lack of shape and space expression of the holistic texture image, Zernike moment features are fused into the improved LBP texture features in the proposed method because they comprise orthogonal and rotation invariant property and can be easily and rapidly calculated to an arbitrary high order. Experimental results show that the proposed method can be remarkably superior to the other state-of-the-art methods when rotation invariant texture features are extracted and classified.

  1. Planar optical integrated circuits based on UV-patternable sol-gel technology

    NASA Astrophysics Data System (ADS)

    Sabattie, Jean-Marc; MacCraith, Brian D.; Mongey, Karen; Charmet, Jerome; O'Dwyer, Kieran; Pez, Mathias M.; Quentel, Francois; Thierry, Dean

    2003-03-01

    Planar lightwave circuits (PLCs) made from photo-patternable sol-gel materials are attracting considerable R&D interest. This is due to the advantages they offer for applications in optical telecommunications and their compatibility with existing silicon technology process equipment. In particular, the ability to produce devices compatible with silica optical fibres using a straightforward, environmentally friendly, photolithographic process is very attractive. The approach is now well-established in the literature and typically involves the incorporation of an acrylate moiety in the sol-gel precursor mixture, thereby providing a photo-polymerisability function. In this work, we report on the fabrication of passive optical components and devices designed for datacomms applications using visible diode lasers or the 1st telecom window. Silica-based sol-gel waveguides have been integrated in an opto-electronic multichip module (OE-MCM) demonstrator for optical interconnect applications. We have fabricated an 8-channel transmitter module for parallel optical interconnects (POI) based on 2 sub-modules: (a) an optical interface sub-assembly based on photo-patterned sol-gel optical waveguides, and (b) an optoelectronic component sub-module comprising an array of VCSELs. We describe here the fabrication, characterization and performance of the optical components and a POI Transmitter chip.

  2. Voltage-dependent switching of sensorimotor integration by a lobster central pattern generator.

    PubMed

    Nargeot, Romuald

    2003-06-15

    Behavioral adaptations and the underlying neural plasticity may not simply result from peripheral information conveyed by sensory inputs. Central neuronal networks often spontaneously generate neuronal activity patterns that may also contribute to sensorimotor integration and behavioral adaptations. The present study explored a novel form of sensory-induced plasticity by which the resulting changes in motor output depend essentially on the preexisting functional state of an identified neuron of an endogenously active central network. In the isolated lobster stomatogastric nervous system, electrical stimulation of a mechanosensory nerve transiently inactivated rhythmic spike bursting in the lateral pyloric (LP) neuron of the pyloric motor pattern-generating network. Repeated sensory nerve stimulation gradually and long-lastingly strengthened the bursting of the LP neuron to the detriment of sensory-elicited inactivation. This strengthening of pyloric-timed rhythmic activity was enhanced by experimental depolarization of the neuron. Conversely, when the LP neuron was hyperpolarized, the same sensory stimulation paradigm now gradually increased the susceptibility of the pyloric-timed bursting of the network neuron to sensory-elicited inactivation. Modulation of depolarization-activated and hyperpolarization-activated ionic conductances that underlie the intrinsic bursting properties of the LP neuron may contribute via differential voltage-dependent recruitment and effects to the respective adaptive processes. These data therefore suggest a novel state-dependent mechanism by which an endogenously active central network can decrease or increase its responsiveness to the same sensory input.

  3. Integration of growth and specification in chick wing digit-patterning.

    PubMed

    Towers, Matthew; Mahood, Ruth; Yin, Yili; Tickle, Cheryll

    2008-04-17

    In the classical model of chick wing digit-patterning, the polarizing region--a group of cells at the posterior margin of the early bud--produces a morphogen gradient, now known to be based on Sonic hedgehog (Shh), that progressively specifies anteroposterior positional identities in the posterior digit-forming region. Here we add an integral growth component to this model by showing that Shh-dependent proliferation of prospective digit progenitor cells is essential for specifying the complete pattern of digits across the anteroposterior axis. Inhibiting Shh signalling in early wing buds reduced anteroposterior expansion, and posterior digits were lost because all prospective digit precursors formed anterior structures. Inhibiting proliferation also irreversibly reduced anteroposterior expansion, but instead anterior digits were lost because all prospective digit precursors formed posterior structures. When proliferation recovered in such wings, Shh transcription was maintained for longer than normal, suggesting that duration of Shh expression is controlled by a mechanism that measures proliferation. Rescue experiments confirmed that Shh-dependent proliferation controls digit number during a discrete time-window in which Shh-dependent specification normally occurs. Our findings that Shh signalling has dual functions that can be temporally uncoupled have implications for understanding congenital and evolutionary digit reductions.

  4. Phenotypic integration between antipredator behavior and camouflage pattern in juvenile sticklebacks.

    PubMed

    Kim, Sin-Yeon; Velando, Alberto

    2015-03-01

    Predation is a strong selective force that promotes the evolution of antipredator behaviors and camouflage in prey animals. However, the independent evolution of single traits cannot explain how observed phenotypic variations of these traits are maintained within populations. We studied genetic and phenotypic correlations between antipredator behaviors (shoaling and risk-taking) and morphology traits (pigmentation and size) in juvenile three-spined sticklebacks by using pedigree-based quantitative genetic analysis to test phenotypic integration (or complex phenotype) as an evolutionary response to predation risk. Individuals with strongly melanized (i.e., camouflaged) phenotype and genotype were less sociable to conspecifics, but bolder during foraging under predation risk. Individuals with faster growing phenotype and genotype were bolder, and those with lager eyes were more fearful. These phenotypic integrations were not confounded with correlated plastic responses to predation risk because the phenotypes were measured in naïve fish born in the laboratory, but originated from a natural population with predation pressure. Consistent selection for particular combinations of traits under predation pressure or pleiotropic genes might influence the maintenance of the genetic (co)variations and polymorphism in melanin color, growth trajectory, and behavior patterns.

  5. Temporal integration of sequential auditory events: silent period in sound pattern activates human planum temporale.

    PubMed

    Mustovic, Henrietta; Scheffler, Klaus; Di Salle, Francesco; Esposito, Fabrizio; Neuhoff, John G; Hennig, Jürgen; Seifritz, Erich

    2003-09-01

    Temporal integration is a fundamental process that the brain carries out to construct coherent percepts from serial sensory events. This process critically depends on the formation of memory traces reconciling past with present events and is particularly important in the auditory domain where sensory information is received both serially and in parallel. It has been suggested that buffers for transient auditory memory traces reside in the auditory cortex. However, previous studies investigating "echoic memory" did not distinguish between brain response to novel auditory stimulus characteristics on the level of basic sound processing and a higher level involving matching of present with stored information. Here we used functional magnetic resonance imaging in combination with a regular pattern of sounds repeated every 100 ms and deviant interspersed stimuli of 100-ms duration, which were either brief presentations of louder sounds or brief periods of silence, to probe the formation of auditory memory traces. To avoid interaction with scanner noise, the auditory stimulation sequence was implemented into the image acquisition scheme. Compared to increased loudness events, silent periods produced specific neural activation in the right planum temporale and temporoparietal junction. Our findings suggest that this area posterior to the auditory cortex plays a critical role in integrating sequential auditory events and is involved in the formation of short-term auditory memory traces. This function of the planum temporale appears to be fundamental in the segregation of simultaneous sound sources.

  6. Visit Patterns for Severe Mental Illness with Implementation of Integrated Care: A Pilot Retrospective Cohort Study

    PubMed Central

    Fondow, Meghan; Pandhi, Nancy; Ricco, Jason; Zeidler Schreiter, Elizabeth; Fahey, Lauren; Serrano, Neftali; Burns, Marguerite; Jacobs, Elizabeth A.

    2016-01-01

    There is increasing interest in models that integrate behavioral health services into primary care. For patients with severe mental illness, a population with disproportionate morbidity and mortality, little is known about the impact of such models on primary care clinic utilization and provider panels. We performed a retrospective cohort pilot study examining visit patterns for 1,105 patients with severe mental illness (SMI), overall and by provider, before and after the implementation of a primary care behavioral health model which had a ramp up period from 5/06-8/07. We used 2003-2012 electronic health record data from two clinics of a Federally Qualified Health Center and conducted interrupted time series and chi-square analyses. During the intervention period there was a significant increase in the proportion of visits per month to the clinic for patient with SMI relative to overall visits (0.27; 95% CI 0.22-0.32). After the intervention period, this rate declined (-0.23; -0.19-0.28) but remained above the pre-intervention period. After integration of behavioral health into our primary care clinics, there was a sharp increase in the number of patients with severe mental illness, suggesting patient willingness to explore receiving care under this model. Clinics looking to adopt the model should be mindful of potential changes in patient subpopulations and proactively manage this transition. PMID:27398391

  7. Integrated local binary pattern texture features for classification of breast tissue imaged by optical coherence microscopy.

    PubMed

    Wan, Sunhua; Lee, Hsiang-Chieh; Huang, Xiaolei; Xu, Ting; Xu, Tao; Zeng, Xianxu; Zhang, Zhan; Sheikine, Yuri; Connolly, James L; Fujimoto, James G; Zhou, Chao

    2017-03-08

    This paper proposes a texture analysis technique that can effectively classify different types of human breast tissue imaged by Optical Coherence Microscopy (OCM). OCM is an emerging imaging modality for rapid tissue screening and has the potential to provide high resolution microscopic images that approach those of histology. OCM images, acquired without tissue staining, however, pose unique challenges to image analysis and pattern classification. We examined multiple types of texture features and found Local Binary Pattern (LBP) features to perform better in classifying tissues imaged by OCM. In order to improve classification accuracy, we propose novel variants of LBP features, namely average LBP (ALBP) and block based LBP (BLBP). Compared with the classic LBP feature, ALBP and BLBP features provide an enhanced encoding of the texture structure in a local neighborhood by looking at intensity differences among neighboring pixels and among certain blocks of pixels in the neighborhood. Fourty-six freshly excised human breast tissue samples, including 27 benign (e.g. fibroadenoma, fibrocystic disease and usual ductal hyperplasia) and 19 breast carcinoma (e.g. invasive ductal carcinoma, ductal carcinoma in situ and lobular carcinoma in situ) were imaged with large field OCM with an imaging area of 10 × 10 mm(2) (10, 000 × 10, 000 pixels) for each sample. Corresponding H&E histology was obtained for each sample and used to provide ground truth diagnosis. 4310 small OCM image blocks (500 × 500 pixels) each paired with corresponding H&E histology was extracted from large-field OCM images and labeled with one of the five different classes: adipose tissue (n = 347), fibrous stroma (n = 2,065), breast lobules (n = 199), carcinomas (pooled from all sub-types, n = 1,127), and background (regions outside of the specimens, n = 572). Our experiments show that by integrating a selected set of LBP and the two new variant (ALBP and BLBP) features at multiple scales, the

  8. Damascene patterned metal/adhesive wafer bonding for three-dimensional integration

    NASA Astrophysics Data System (ADS)

    McMahon, J. Jay

    Wafer bonding of damascene patterned metal/adhesive surfaces is explored for a new three-dimensional (3D) integration technology platform. By bonding a pair of damascene patterned metal/adhesive layers, high density micron-sized vias can be formed for interconnection of fully fabricated integrated circuit (IC) dies at the wafer-level. Such via dimensions increase the areal interconnect density by at least two orders of magnitude over current package and die-stacking approaches to 3D integration. The adhesive field-dielectric produces a high critical adhesion energy bond and has the potential to produce void-free bonded interfaces. This new technology platform has been demonstrated by fabricating and characterizing inter-wafer via-chains on 200 mm diameter Si wafers. Copper and partially cured divinylsiloxane bis-benzocyclobutene (BCB) are selected as the metal and adhesive, respectively, and unit processes for this demonstration are described. Typical alignment tolerance is ˜2 mum, and baseline bonding conditions include vacuum of 5x10-4 mbar, bonding force of 10 kN, and two step bonding temperature of 250°C for 60 min followed by 350°C for 60 min. Integration issues associated with the damascene patterning and the wafer bonding processes are discussed, particularly the resulting topography of damascene patterned Cu/BCB. Cross-sectional investigation of bonded and annealed inter-wafer interconnections provides insight into the Cu-Cu and BCB-BCB bonding interfaces. Inter-wafer specific contact resistance is measured to be on the order of 10-7 O-cm 2 for these via-chains. Several material characterization techniques have been explored to evaluate partially cured BCB as an adhesive field-dielectric. To investigate the critical adhesion energy, Gc, four-point bending is utilized to compare surfaces bonded after chemical-mechanical planarization (CMP) and various post-CMP treatments. The Gc of bonded 50% partially cured BCB is measured to be in the range of 32--44 J

  9. Spatial integration by MT pattern neurons: a closer look at pattern-to-component effects and the role of speed tuning.

    PubMed

    Perrone, John A; Krauzlis, Richard J

    2008-07-02

    The primate visual system faces a difficult problem whenever it encounters the motion of an object moving over a patch of the retina. Objects typically contain a number of edges at different orientations and so a range of image velocities are generated within the receptive field of a neuron processing the object movement. It is still a mystery as to how these different velocities are combined into one unified and correct velocity. Neurons in area MT (V5) are considered to be the neural substrate for this motion integration process. Some MT neurons (pattern type) respond selectively to the correct global motion of an object, whereas others respond primarily to the individual components making up the pattern (component type). Recent findings from MT pattern cells tested with small patches of motion (N. J. Majaj, M. Carandini, & J. A. Movshon, 2007) have put further constraints on the possible mechanisms underlying MT pattern motion integration. We tested and refined an existing model of MT pattern neurons (J. A. Perrone, 2004) using these same small patch stimuli and found that it can accommodate these new findings. We also discovered that the speed of the test stimuli may have had an impact on the N. J. Majaj et al. (2007) results and that MT direction and speed tuning may be more closely linked than previously thought.

  10. The classification of the Weyl conformal tensor in 4-dimensional manifolds of neutral signature

    NASA Astrophysics Data System (ADS)

    Hall, Graham

    2017-01-01

    This paper presents a simple account of the algebraic classification of the Weyl conformal tensor on a 4-dimensional manifold with metric g of neutral signature (+ , + , - , -) . The classification is algebraically similar to the well-known Petrov classification in the Lorentz case and the various algebraic types and corresponding canonical forms are obtained. Criteria concerning principal, totally null 2-spaces are explored and which lead to principal null directions similar to those of L. Bel in the Lorentz case. The uniqueness, or otherwise, of the tetrads in which the canonical forms appear are investigated and some topological and differentiability properties of the algebraic types are also established.

  11. Groundwater flow pattern and related environmental phenomena in complex geologic setting based on integrated model construction

    NASA Astrophysics Data System (ADS)

    Tóth, Ádám; Havril, Tímea; Simon, Szilvia; Galsa, Attila; Monteiro Santos, Fernando A.; Müller, Imre; Mádl-Szőnyi, Judit

    2016-08-01

    Groundwater flow, driven, controlled and determined by topography, geology and climate, is responsible for several natural surface manifestations and affected by anthropogenic processes. Therefore, flowing groundwater can be regarded as an environmental agent. Numerical simulation of groundwater flow could reveal the flow pattern and explain the observed features. In complex geologic framework, where the geologic-hydrogeologic knowledge is limited, the groundwater flow model could not be constructed based solely on borehole data, but geophysical information could aid the model building. The integrated model construction was presented via the case study of the Tihany Peninsula, Hungary, with the aims of understanding the background and occurrence of groundwater-related environmental phenomena, such as wetlands, surface water-groundwater interaction, slope instability, and revealing the potential effect of anthropogenic activity and climate change. The hydrogeologic model was prepared on the basis of the compiled archive geophysical database and the results of recently performed geophysical measurements complemented with geologic-hydrogeologic data. Derivation of different electrostratigraphic units, revealing fracturing and detecting tectonic elements was achieved by systematically combined electromagnetic geophysical methods. The deduced information can be used as model input for groundwater flow simulation concerning hydrostratigraphy, geometry and boundary conditions. The results of numerical modelling were interpreted on the basis of gravity-driven regional groundwater flow concept and validated by field mapping of groundwater-related phenomena. The 3D model clarified the hydraulic behaviour of the formations, revealed the subsurface hydraulic connection between groundwater and wetlands and displayed the groundwater discharge pattern, as well. The position of wetlands, their vegetation type, discharge features and induced landslides were explained as

  12. Effect of Practice Integration between Urologists and Radiation Oncologists on Prostate Cancer Treatment Patterns

    PubMed Central

    Bekelman, Justin E.; Suneja, Gita; Guzzo, Thomas; Evan Pollack, Craig; Armstrong, Katrina; Epstein, Andrew J.

    2013-01-01

    Purpose National attention has focused on whether urology-radiation oncology practice integration – known as integrated prostate cancer centers (IPCCs) – contributes to use of intensity-modulated radiation therapy (IMRT), a common and expensive treatment for prostate cancer. Methods We examined prostate cancer treatment patterns pre- and post-conversion of a urology practice to an IPCC in July, 2006. Using the SEER-Medicare database, we identified patients age ≥ 65 years diagnosed in one state-wide registry with non-metastatic prostate cancer between 2004 and 2007 and classified patients into 3 groups: (1) those seen by IPCC physicians (exposure group); (2) those living in the same hospital referral region (HRR) and not seen by IPCC physicians (HRR-control group); and (3) those living elsewhere in the state (state-control group). We compared changes in treatment among the 3 groups, adjusting for patient, clinical, and socio-economic factors. Results Compared with the 8.1 percentage point (ppt) increase in adjusted IMRT use in the state-control group, IMRT increased 20.3 ppts (95% confidence interval [CI] 13.4, 27.1) in the IPCC group and 19.2 ppts (95% CI 9.6, 28.9) in the HRR-control group. Androgen-deprivation therapy (ADT), for which Medicare reimbursement declined sharply, decreased similarly in the IPCC and HRR-control groups. Prostatectomy declined significantly in the IPCC group. Conclusions Coincident with the conversion of a urology group practice to an IPCC, we observed increases in IMRT and decreases in ADT among patients seen by IPCC physicians and those seen in the surrounding healthcare market that were not observed in the remainder of the state. PMID:23399652

  13. Overview and development of EDA tools for integration of DSA into patterning solutions

    NASA Astrophysics Data System (ADS)

    Torres, J. Andres; Fenger, Germain; Khaira, Daman; Ma, Yuansheng; Granik, Yuri; Kapral, Chris; Mitra, Joydeep; Krasnova, Polina; Ait-Ferhat, Dehia

    2017-03-01

    Directed Self-Assembly is the method by which a self-assembly polymer is forced to follow a desired geometry defined or influenced by a guiding pattern. Such guiding pattern uses surface potentials, confinement or both to achieve polymer configurations that result in circuit-relevant topologies, which can be patterned onto a substrate. Chemo, and grapho epitaxy of lines and space structures are now routinely inspected at full wafer level to understand the defectivity limits of the materials and their maximum resolution. In the same manner, there is a deeper understanding about the formation of cylinders using grapho-epitaxy processes. Academia has also contributed by developing methods that help reduce the number of masks in advanced nodes by "combining" DSA-compatible groups, thus reducing the total cost of the process. From the point of view of EDA, new tools are required when a technology is adopted, and most technologies are adopted when they show a clear cost-benefit over alternative techniques. In addition, years of EDA development have led to the creation of very flexible toolkits that permit rapid prototyping and evaluation of new process alternatives. With the development of high-chi materials, and by moving away of the well characterized PS-PMMA systems, as well as novel integrations in the substrates that work in tandem with diblock copolymer systems, it is necessary to assess any new requirements that may or may not need custom tools to support such processes. Hybrid DSA processes (which contain both chemo and grapho elements), are currently being investigated as possible contenders for sub-5nm process techniques. Because such processes permit the re-distribution of discontinuities in the regular arrays between the substrate and a cut operation, they have the potential to extend the number of applications for DSA. This paper illustrates the reason as to why some DSA processes can be supported by existing rules and technology, while other processes

  14. Patterns of correlation of facial shape with physiological measurements are more integrated than patterns of correlation with ratings.

    PubMed

    Windhager, S; Bookstein, F L; Millesi, E; Wallner, B; Schaefer, K

    2017-03-28

    This article exploits a method recently incorporated in the geometric morphometric toolkit that complements previous approaches to quantifying the facial features associated with specific body characteristics and trait attribution during social perception. The new method differentiates more globally encoded from more locally encoded information by a summary scaling dimension that is estimated by fitting a line to the plot of log bending energy against log variance explained, partial warp by partial warp, for some sample of varying shapes. In the present context these variances come from the regressions of shape on some exogenous cause or effect of form. We work an example involving data from male faces. Here the regression slopes are steepest, and the sums of explained variances over the uniform component, partial warp 1 and partial warp 2 are greatest, for the conventional body mass index, followed by cortisol and, lastly, perceived health. This suggests that physiological characteristics may be represented at larger scale (global patterns), whereas cues in perception are of smaller scale (local patterns). Such a polarity within psychomorphospace, the global versus the focal, now has a metric by which patterns of morphology can be modeled in both biological and psychological studies.

  15. Patterns of correlation of facial shape with physiological measurements are more integrated than patterns of correlation with ratings

    PubMed Central

    Windhager, S.; Bookstein, F. L.; Millesi, E.; Wallner, B.; Schaefer, K.

    2017-01-01

    This article exploits a method recently incorporated in the geometric morphometric toolkit that complements previous approaches to quantifying the facial features associated with specific body characteristics and trait attribution during social perception. The new method differentiates more globally encoded from more locally encoded information by a summary scaling dimension that is estimated by fitting a line to the plot of log bending energy against log variance explained, partial warp by partial warp, for some sample of varying shapes. In the present context these variances come from the regressions of shape on some exogenous cause or effect of form. We work an example involving data from male faces. Here the regression slopes are steepest, and the sums of explained variances over the uniform component, partial warp 1 and partial warp 2 are greatest, for the conventional body mass index, followed by cortisol and, lastly, perceived health. This suggests that physiological characteristics may be represented at larger scale (global patterns), whereas cues in perception are of smaller scale (local patterns). Such a polarity within psychomorphospace, the global versus the focal, now has a metric by which patterns of morphology can be modeled in both biological and psychological studies. PMID:28349947

  16. Integrated Analysis of Alzheimer's Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learning and Memory.

    PubMed

    Li, Wen-Xing; Dai, Shao-Xing; Liu, Jia-Qian; Wang, Qian; Li, Gong-Hua; Huang, Jing-Fei

    2016-01-01

    Alzheimer's disease (AD) and schizophrenia (SZ) are both accompanied by impaired learning and memory functions. This study aims to explore the expression profiles of learning or memory genes between AD and SZ. We downloaded 10 AD and 10 SZ datasets from GEO-NCBI for integrated analysis. These datasets were processed using RMA algorithm and a global renormalization for all studies. Then Empirical Bayes algorithm was used to find the differentially expressed genes between patients and controls. The results showed that most of the differentially expressed genes were related to AD whereas the gene expression profile was little affected in the SZ. Furthermore, in the aspects of the number of differentially expressed genes, the fold change and the brain region, there was a great difference in the expression of learning or memory related genes between AD and SZ. In AD, the CALB1, GABRA5, and TAC1 were significantly downregulated in whole brain, frontal lobe, temporal lobe, and hippocampus. However, in SZ, only two genes CRHBP and CX3CR1 were downregulated in hippocampus, and other brain regions were not affected. The effect of these genes on learning or memory impairment has been widely studied. It was suggested that these genes may play a crucial role in AD or SZ pathogenesis. The different gene expression patterns between AD and SZ on learning and memory functions in different brain regions revealed in our study may help to understand the different mechanism between two diseases.

  17. Sensory processing patterns predict the integration of information held in visual working memory.

    PubMed

    Lowe, Matthew X; Stevenson, Ryan A; Wilson, Kristin E; Ouslis, Natasha E; Barense, Morgan D; Cant, Jonathan S; Ferber, Susanne

    2016-02-01

    Given the limited resources of visual working memory, multiple items may be remembered as an averaged group or ensemble. As a result, local information may be ill-defined, but these ensemble representations provide accurate diagnostics of the natural world by combining gist information with item-level information held in visual working memory. Some neurodevelopmental disorders are characterized by sensory processing profiles that predispose individuals to avoid or seek-out sensory stimulation, fundamentally altering their perceptual experience. Here, we report such processing styles will affect the computation of ensemble statistics in the general population. We identified stable adult sensory processing patterns to demonstrate that individuals with low sensory thresholds who show a greater proclivity to engage in active response strategies to prevent sensory overstimulation are less likely to integrate mean size information across a set of similar items and are therefore more likely to be biased away from the mean size representation of an ensemble display. We therefore propose the study of ensemble processing should extend beyond the statistics of the display, and should also consider the statistics of the observer. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  18. Drawing on mind's canvas: differences in cortical integration patterns between artists and non-artists.

    PubMed

    Bhattacharya, Joydeep; Petsche, Hellmuth

    2005-09-01

    Our primary question was to learn whether mentally composing drawings of their own choice produce different brain electric features in artists and laymen. To this purpose, we studied multichannel electroencephalograph (EEG) signals from two broad groups (all participants were females): artists (professionally trained in visual arts) and non-artists (without any training in art). To assess the underlying synchronization, which is assumed to be the platform for general cognitive integration between different cortical regions, three measures inspired by nonlinear dynamical system theory were applied as follows: (1) index based on generalized synchronization; (2) index based on mean phase coherence; and (3) index of phase synchrony based on entropy. Results consistent over all three measures were as follows: comparing the tasks to rest, the artists showed significantly stronger short- and long-range delta band synchronization, whereas the non-artists showed enhancement in short-range beta and gamma band synchronization primarily in frontal regions; comparing the two groups during the tasks, the artists showed significantly stronger delta band synchronization and alpha band desynchronization than did the non-artists. Strong right hemispheric dominance in terms of synchronization was found in the artists. In artists, the higher synchrony in the low-frequency band is possibly due to the involvement of a more advanced long-term visual art memory and to extensive top-down processing. The results demonstrate that in artists, patterns of functional cooperation between cortical regions during mental creation of drawings were significantly different from those in non-artists.

  19. Recovery patterns, histological observations and genetic integrity in Malus shoot tips cryopreserved using droplet vitrification and encapsulation-dehydration procedures

    USDA-ARS?s Scientific Manuscript database

    A droplet-vitrification procedure is described for cryopreservation of Malus shoot tips. Survival patterns, recovery types, histological observations, and genetic integrity were compared for Malus shoot tips cryopreserved using this droplet-vitrification procedure and an encapsulation-dehydration pr...

  20. 4-Dimensional MRI and Attenuation Map Generation in PET/MRI with 4-Dimensional PET-Derived Deformation Matrices: Study of Feasibility for Lung Cancer Applications.

    PubMed

    Fayad, Hadi; Schmidt, Holger; Küstner, Thomas; Visvikis, Dimitris

    2017-05-01

    Respiratory motion may reduce accuracy in the fusion of functional and anatomic images from combined PET/MRI systems. Methodologies for the correction of respiratory motion in PET acquisitions with such systems are mostly based on the use of respiration-synchronized MRI acquisitions to derive motion fields. Existing approaches based on tagging acquisitions may introduce artifacts in MR images, whereas motion model approaches require the acquisition of training datasets. The objective of this work was to investigate the possibility of generating 4-dimensional (4D) MR images and associated attenuation maps (AMs) from the combination of a single static MR image and motion fields obtained from simultaneously acquired 4D non-attenuation-corrected (NAC) PET images. Methods: Four-dimensional PET/MRI datasets were acquired for 11 patients on a simultaneous PET/MRI system. The 4D PET datasets were retrospectively binned into 4 motion amplitude frames corresponding to the simultaneously acquired T1-weighted 4D MR images. A T1-weighted 3-dimensional MRI sequence with Dixon-based fat and water separation was also acquired at the end of expiration for PET attenuation correction purposes. All reconstructed 4D NAC PET images were then elastically registered to the single end-of-expiration NAC PET image. The derived motion fields were subsequently applied to the end-of-expiration frame of the acquired 4D MRI volume and the AM derived from the Dixon MR image to generate respiration-synchronized MR images and corresponding AMs. Results: The accuracy of the proposed method was assessed by comparing the generated and acquired images according to metrics such as overall correlation coefficients and differences in distances of anatomic landmarks on the generated and acquired MRI datasets. High correlation coefficients (mean ± SD: 0.93 ± 0.03) and small differences (2.69 ± 0.5 mm) were obtained. Moreover, small tissue classification differences (2.23% ± 0.68%) between generated and 4

  1. Evaluation of 4-dimensional Computed Tomography to 4-dimensional Cone-Beam Computed Tomography Deformable Image Registration for Lung Cancer Adaptive Radiation Therapy

    SciTech Connect

    Balik, Salim; Weiss, Elisabeth; Jan, Nuzhat; Roman, Nicholas; Sleeman, William C.; Fatyga, Mirek; Christensen, Gary E.; Zhang, Cheng; Murphy, Martin J.; Lu, Jun; Keall, Paul; Williamson, Jeffrey F.; Hugo, Geoffrey D.

    2013-06-01

    Purpose: To evaluate 2 deformable image registration (DIR) algorithms for the purpose of contour mapping to support image-guided adaptive radiation therapy with 4-dimensional cone-beam CT (4DCBCT). Methods and Materials: One planning 4D fan-beam CT (4DFBCT) and 7 weekly 4DCBCT scans were acquired for 10 locally advanced non-small cell lung cancer patients. The gross tumor volume was delineated by a physician in all 4D images. End-of-inspiration phase planning 4DFBCT was registered to the corresponding phase in weekly 4DCBCT images for day-to-day registrations. For phase-to-phase registration, the end-of-inspiration phase from each 4D image was registered to the end-of-expiration phase. Two DIR algorithms—small deformation inverse consistent linear elastic (SICLE) and Insight Toolkit diffeomorphic demons (DEMONS)—were evaluated. Physician-delineated contours were compared with the warped contours by using the Dice similarity coefficient (DSC), average symmetric distance, and false-positive and false-negative indices. The DIR results are compared with rigid registration of tumor. Results: For day-to-day registrations, the mean DSC was 0.75 ± 0.09 with SICLE, 0.70 ± 0.12 with DEMONS, 0.66 ± 0.12 with rigid-tumor registration, and 0.60 ± 0.14 with rigid-bone registration. Results were comparable to intraobserver variability calculated from phase-to-phase registrations as well as measured interobserver variation for 1 patient. SICLE and DEMONS, when compared with rigid-bone (4.1 mm) and rigid-tumor (3.6 mm) registration, respectively reduced the average symmetric distance to 2.6 and 3.3 mm. On average, SICLE and DEMONS increased the DSC to 0.80 and 0.79, respectively, compared with rigid-tumor (0.78) registrations for 4DCBCT phase-to-phase registrations. Conclusions: Deformable image registration achieved comparable accuracy to reported interobserver delineation variability and higher accuracy than rigid-tumor registration. Deformable image registration

  2. Synchrotron 4-dimensional imaging of two-phase flow through porous media

    PubMed Central

    Kim, F.H.; Penumadu, D.; Patel, P.; Xiao, X.; Garboczi, E.J.; Moylan, S.P.; Donmez, M.A.

    2016-01-01

    Near real-time visualization of complex two-phase flow in a porous medium was demonstrated with dynamic 4-dimensional (4D) (3D + time) imaging at the 2-BM beam line of the Advanced Photon Source (APS) at Argonne National Laboratory. Advancing fluid fronts through tortuous flow paths and their interactions with sand grains were clearly captured, and formations of air bubbles and capillary bridges were visualized. The intense X-ray photon flux of the synchrotron facility made 4D imaging possible, capturing the dynamic evolution of both solid and fluid phases. Computed Tomography (CT) scans were collected every 12 s with a pixel size of 3.25 µm. The experiment was carried out to improve understanding of the physics associated with two-phase flow. The results provide a source of validation data for numerical simulation codes such as Lattice-Boltzmann, which are used to model multi-phase flow through porous media. PMID:27891248

  3. Service Utilization Patterns as Predictors of Response to Trauma-Informed Integrated Treatment for Women With Co-occurring Disorders

    PubMed Central

    Gilbert, Allison R.; Morrissey, Joseph P.; Domino, Marisa E.

    2012-01-01

    Objective The current study examined whether clinical responses to an integrated treatment intervention among women with co-occurring disorders and histories of abuse varied according to their service use patterns at baseline. Methods Data were from a national, multi-site, integrated treatment intervention study in 1998-2003. Analyses included 999 study participants assigned to the integrated treatment group and who were symptomatic at baseline. Participants’ baseline service use activity was characterized according to five distinct baseline service use clusters. Logistic regression models estimated study participants’ odds of good clinical responses to integrated treatment at 12 months across the five service clusters. Results Participants with high levels of psychotropic medication and medical care use at baseline had significantly lower odds than low-intensity service users of having a good response to integrated treatment at 12 months on mental health, alcohol addiction, and posttraumatic stress measures. A majority of women in this group had serious medical illness or disability and were more likely than their counterparts with other service use patterns to have used homeless or domestic violence shelters. Conclusions Women who used high levels of medication and medical services appear to have faced especially difficult barriers in responding well to integrated treatment. Careful assessments of their mental health, trauma, and medical treatment needs may be required as part of integrated treatment in an effort to improve their response to integrated treatment, clinical outcomes and well-being. This information can also be used to target integrated treatment to women who are likely to respond positively and achieve meaningful improvements in their functioning. PMID:22368532

  4. Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models

    SciTech Connect

    Moler, Edward J.; Mian, I.S.

    2000-03-01

    How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss

  5. Determination of Internal Target Volume for Radiation Treatment Planning of Esophageal Cancer by Using 4-Dimensional Computed Tomography (4DCT)

    SciTech Connect

    Chen, Xiaojian; Lu, Haijun; Tai, An; Johnstone, Candice; Gore, Elizabeth; Li, X. Allen

    2014-09-01

    Purpose: To determine an efficient strategy for the generation of the internal target volume (ITV) for radiation treatment planning for esophageal cancer using 4-dimensional computed tomography (4DCT). Methods and Materials: 4DCT sets acquired for 20 patients with esophageal carcinoma were analyzed. Each of the 4DCT sets was binned into 10 respiratory phases. For each patient, the gross tumor volume (GTV) was delineated on the 4DCT set at each phase. Various strategies to derive ITV were explored, including the volume from the maximum intensity projection (MIP; ITV{sub M}IP), unions of the GTVs from selected multiple phases ITV2 (0% and 50% phases), ITV3 (ITV2 plus 80%), and ITV4 (ITV3 plus 60%), as well as the volumes expanded from ITV2 and ITV3 with a uniform margin. These ITVs were compared to ITV10 (the union of the GTVs for all 10 phases) and the differences were measured with the overlap ratio (OR) and relative volume ratio (RVR) relative to ITV10 (ITVx/ITV10). Results: For all patients studied, the average GTV from a single phase was 84.9% of ITV10. The average ORs were 91.2%, 91.3%, 94.5%, and 96.4% for ITV{sub M}IP, ITV2, ITV3, and ITV4, respectively. Low ORs were associated with irregular breathing patterns. ITV3s plus 1 mm uniform margins (ITV3+1) led to an average OR of 98.1% and an average RVR of 106.4%. Conclusions: The ITV generated directly from MIP underestimates the range of the respiration motion for esophageal cancer. The ITV generated from 3 phases (ITV3) may be used for regular breathers, whereas the ITV generated from 4 phases (ITV4) or ITV3 plus a 1-mm uniform margin may be applied for irregular breathers.

  6. [Impact of the Infrared Monitor Signal Pattern on Accuracy of Target Imaging in 4-dimensional Cone-beam Computed Tomography].

    PubMed

    Usui, Keisuke; Hara, Naoya; Isobe, Akira; Inoue, Tatsuya; Kurokawa, Chie; Sugimoto, Satoru; Sasai, Keisuke; Ogawa, Kouichi

    2016-06-01

    To realize the high precision radiotherapy, localized radiation field of the moving target is very important, and visualization of a temporal location of the target can help to improve the accuracy of the target localization. However, conditions of the breathing and the patient's own motion differ from the situation of the treatment planning. Therefore, positions of the tumor are affected by these changes. In this study, we implemented a method to reconstruct target motions obtained with the 4D CBCT using the sorted projection data according to the phase and displacement of the extracorporeal infrared monitor signal, and evaluated the proposed method with a moving phantom. In this method, motion cycles and positions of the marker were sorted to reconstruct the image, and evaluated the image quality affected by changes in the cycle, phase, and positions of the marker. As a result, we realized the visualization of the moving target using the sorted projection data according to the infrared monitor signal. This method was based on the projection binning, in which the signal of the infrared monitor was surrogate of the tumor motion. Thus, further major efforts are needed to ensure the accuracy of the infrared monitor signal.

  7. Interpretation of Integrated Water Vapor Patterns in Oceanic Midlatitude Cyclones Derived from the Scanning Multichannel Microwave Radiometer

    NASA Astrophysics Data System (ADS)

    McMurdie, Lynn Alison

    The interpretation of the integrated water vapor fields in midlatitude oceanic cyclones and how vapor patterns evolve and relate to storm intensity is the focus of this work. The integrated water vapor fields are derived from the Seasat and Nimbus 7 Scanning Multichannel Microwave Radiometers (SMMR). Averages of the typical water vapor distributions in storms occurring in specific regions and seasons are constructed. The average maximum and minimum water vapor content in storms occurring in the North Atlantic are significantly higher than in storms in the North Pacific for both warm and cold seasons. In addition, North Pacific storms have higher maximum and minimum water vapor content than Southern Ocean storms for both seasons. These differences are attributed to average differences in sea surface temperature and the amount of moisture transported poleward by the cyclones. Gridded meterological information is used to investigate the relationship between SMMR water vapor patterns and trajectories. Storms with higher than normal water vapor content have parcel trajectories that originated in low latitudes and experience significant upward motion. If a storm has an increase in water vapor with time, then the parcel trajectories at the later time originated from lower latitudes and experienced more lift than at the earlier time. A relationship between storm intensity, as defined by synoptic-scale vertical motion and surface pressure tendency, and integrated water vapor content was examined. SMMR water vapor patterns did not relate strongly to storm intensity. The usefulness of atmospheric water derived from SMMR, in the form of integrated water vapor and rainfall intensity, in indicating rapid cyclogenesis in the North Atlantic is explored. Unfortunately, unique features in the integrated water vapor patterns for storms that deepen rapidly could not be identified. However, large areas of high rain intensity are often present during the incipient stage of a rapidly

  8. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots

    PubMed Central

    Muraro, Daniele; Mellor, Nathan; Pound, Michael P.; Help, Hanna; Lucas, Mikaël; Chopard, Jérôme; Byrne, Helen M.; Godin, Christophe; Hodgman, T. Charlie; King, John R.; Pridmore, Tony P.; Helariutta, Ykä; Bennett, Malcolm J.; Bishopp, Anthony

    2014-01-01

    As multicellular organisms grow, positional information is continually needed to regulate the pattern in which cells are arranged. In the Arabidopsis root, most cell types are organized in a radially symmetric pattern; however, a symmetry-breaking event generates bisymmetric auxin and cytokinin signaling domains in the stele. Bidirectional cross-talk between the stele and the surrounding tissues involving a mobile transcription factor, SHORT ROOT (SHR), and mobile microRNA species also determines vascular pattern, but it is currently unclear how these signals integrate. We use a multicellular model to determine a minimal set of components necessary for maintaining a stable vascular pattern. Simulations perturbing the signaling network show that, in addition to the mutually inhibitory interaction between auxin and cytokinin, signaling through SHR, microRNA165/6, and PHABULOSA is required to maintain a stable bisymmetric pattern. We have verified this prediction by observing loss of bisymmetry in shr mutants. The model reveals the importance of several features of the network, namely the mutual degradation of microRNA165/6 and PHABULOSA and the existence of an additional negative regulator of cytokinin signaling. These components form a plausible mechanism capable of patterning vascular tissues in the absence of positional inputs provided by the transport of hormones from the shoot. PMID:24381155

  9. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots.

    PubMed

    Muraro, Daniele; Mellor, Nathan; Pound, Michael P; Help, Hanna; Lucas, Mikaël; Chopard, Jérôme; Byrne, Helen M; Godin, Christophe; Hodgman, T Charlie; King, John R; Pridmore, Tony P; Helariutta, Ykä; Bennett, Malcolm J; Bishopp, Anthony

    2014-01-14

    As multicellular organisms grow, positional information is continually needed to regulate the pattern in which cells are arranged. In the Arabidopsis root, most cell types are organized in a radially symmetric pattern; however, a symmetry-breaking event generates bisymmetric auxin and cytokinin signaling domains in the stele. Bidirectional cross-talk between the stele and the surrounding tissues involving a mobile transcription factor, SHORT ROOT (SHR), and mobile microRNA species also determines vascular pattern, but it is currently unclear how these signals integrate. We use a multicellular model to determine a minimal set of components necessary for maintaining a stable vascular pattern. Simulations perturbing the signaling network show that, in addition to the mutually inhibitory interaction between auxin and cytokinin, signaling through SHR, microRNA165/6, and PHABULOSA is required to maintain a stable bisymmetric pattern. We have verified this prediction by observing loss of bisymmetry in shr mutants. The model reveals the importance of several features of the network, namely the mutual degradation of microRNA165/6 and PHABULOSA and the existence of an additional negative regulator of cytokinin signaling. These components form a plausible mechanism capable of patterning vascular tissues in the absence of positional inputs provided by the transport of hormones from the shoot.

  10. Optimizing 4-Dimensional Magnetic Resonance Imaging Data Sampling for Respiratory Motion Analysis of Pancreatic Tumors

    SciTech Connect

    Stemkens, Bjorn; Tijssen, Rob H.N.; Senneville, Baudouin D. de

    2015-03-01

    Purpose: To determine the optimum sampling strategy for retrospective reconstruction of 4-dimensional (4D) MR data for nonrigid motion characterization of tumor and organs at risk for radiation therapy purposes. Methods and Materials: For optimization, we compared 2 surrogate signals (external respiratory bellows and internal MRI navigators) and 2 MR sampling strategies (Cartesian and radial) in terms of image quality and robustness. Using the optimized protocol, 6 pancreatic cancer patients were scanned to calculate the 4D motion. Region of interest analysis was performed to characterize the respiratory-induced motion of the tumor and organs at risk simultaneously. Results: The MRI navigator was found to be a more reliable surrogate for pancreatic motion than the respiratory bellows signal. Radial sampling is most benign for undersampling artifacts and intraview motion. Motion characterization revealed interorgan and interpatient variation, as well as heterogeneity within the tumor. Conclusions: A robust 4D-MRI method, based on clinically available protocols, is presented and successfully applied to characterize the abdominal motion in a small number of pancreatic cancer patients.

  11. Design and implementation of integrated solid wastes management pattern in industrial zones, case study of Shahroud, Iran.

    PubMed

    Saeid, Nazemi; Roudbari, Aliakbar; Yaghmaeian, Kamyar

    2014-01-14

    The aim of the study was to design and implementation of integrated solid wastes management pattern in Shahroud industrial zone, evaluates the results and determine possible performance problems. This cross - sectional study was carried out for 4 years in Shahroud industrial zone and the implementation process included:1- Qualitative and quantitative analysis of all solid waste generated in the city, 2- determine the current state of solid waste management in the zone and to identify programs conducted, 3- Design and implementation of integrated solid wastes management pattern including design and implementation of training programs, laws, penalties and incentives and explain and implement programs for all factories and 4- The monitoring of the implementation process and determine the results. Annually, 1,728 tons of solid wastes generated in the town including 1603 tons of industrial wastes and 125 tons of municipal wastes. By implementing this pattern, the two separated systems of collection and recycling of domestic and industrial wastes was launched in this zone. Also consistent with the goals, the amount of solid wastes generated and disposed in 2009 was 51.5 and 28.6 kg per 100 million Rials production, respectively. Results showed that implementation of pattern of separated collection, training programs, capacity building, providing technical services, completing chain of industries and strengthening the cooperation between industrial estate management and industrial units could greatly reduce the waste management problems.

  12. Design and implementation of integrated solid wastes management pattern in industrial zones, case study of Shahroud, Iran

    PubMed Central

    2014-01-01

    Background The aim of the study was to design and implementation of integrated solid wastes management pattern in Shahroud industrial zone, evaluates the results and determine possible performance problems. This cross - sectional study was carried out for 4 years in Shahroud industrial zone and the implementation process included:1- Qualitative and quantitative analysis of all solid waste generated in the city, 2- determine the current state of solid waste management in the zone and to identify programs conducted, 3- Design and implementation of integrated solid wastes management pattern including design and implementation of training programs, laws, penalties and incentives and explain and implement programs for all factories and 4- The monitoring of the implementation process and determine the results. Results Annually, 1,728 tons of solid wastes generated in the town including 1603 tons of industrial wastes and 125 tons of municipal wastes. By implementing this pattern, the two separated systems of collection and recycling of domestic and industrial wastes was launched in this zone. Also consistent with the goals, the amount of solid wastes generated and disposed in 2009 was 51.5 and 28.6 kg per 100 million Rials production, respectively. Conclusion Results showed that implementation of pattern of separated collection, training programs, capacity building, providing technical services, completing chain of industries and strengthening the cooperation between industrial estate management and industrial units could greatly reduce the waste management problems. PMID:24423020

  13. Identification of human papillomavirus (HPV) 16 DNA integration and the ensuing patterns of methylation in HPV-associated head and neck squamous cell carcinoma cell lines.

    PubMed

    Hatano, Takashi; Sano, Daisuke; Takahashi, Hideaki; Hyakusoku, Hiroshi; Isono, Yasuhiro; Shimada, Shoko; Sawakuma, Kae; Takada, Kentaro; Oikawa, Ritsuko; Watanabe, Yoshiyuki; Yamamoto, Hiroyuki; Itoh, Fumio; Myers, Jeffrey N; Oridate, Nobuhiko

    2017-04-01

    Recent studies showed that human papillomavirus (HPV) integration contributes to the genomic instability seen in HPV-associated head and neck squamous cell carcinoma (HPV-HNSCC). However, the epigenetic alterations induced after HPV integration remains unclear. To identify the molecular details of HPV16 DNA integration and the ensuing patterns of methylation in HNSCC, we performed next-generation sequencing using a target-enrichment method for the effective identification of HPV16 integration breakpoints as well as the characterization of genomic sequences adjacent to HPV16 integration breakpoints with three HPV16-related HNSCC cell lines. The DNA methylation levels of the integrated HPV16 genome and that of the adjacent human genome were also analyzed by bisulfite pyrosequencing. We found various integration loci, including novel integration sites. Integration loci were located predominantly in the intergenic region, with a significant enrichment of the microhomologous sequences between the human and HPV16 genomes at the integration breakpoints. Furthermore, various levels of methylation within both the human genome and the integrated HPV genome at the integration breakpoints in each integrant were observed. Allele-specific methylation analysis suggested that the HPV16 integrants remained hypomethylated when the flanking host genome was hypomethylated. After integration into highly methylated human genome regions, however, the HPV16 DNA became methylated. In conclusion, we found novel integration sites and methylation patterns in HPV-HNSCC using our unique method. These findings may provide insights into understanding of viral integration mechanism and virus-associated carcinogenesis of HPV-HNSCC.

  14. Design strategy for integrating DSA via patterning in sub-7 nm interconnects

    NASA Astrophysics Data System (ADS)

    Karageorgos, Ioannis; Ryckaert, Julien; Tung, Maryann C.; Wong, H.-S. P.; Gronheid, Roel; Bekaert, Joost; Karageorgos, Evangelos; Croes, Kris; Vandenberghe, Geert; Stucchi, Michele; Dehaene, Wim

    2016-03-01

    In recent years, major advancements have been made in the directed self-assembly (DSA) of block copolymers (BCPs). As a result, the insertion of DSA for IC fabrication is being actively considered for the sub-7nm nodes. At these nodes the DSA technology could alleviate costs for multiple patterning and limit the number of litho masks that would be required per metal layer. One of the most straightforward approaches for DSA implementation would be for via patterning through templated DSA, where hole patterns are readily accessible through templated confinement of cylindrical phase BCP materials. Our in-house studies show that decomposition of via layers in realistic circuits below the 7nm node would require at least many multi-patterning steps (or colors), using 193nm immersion lithography. Even the use of EUV might require double patterning in these dimensions, since the minimum via distance would be smaller than EUV resolution. The grouping of vias through templated DSA can resolve local conflicts in high density areas. This way, the number of required colors can be significantly reduced. For the implementation of this approach, a DSA-aware mask decomposition is required. In this paper, our design approach for DSA via patterning in sub-7nm nodes is discussed. We propose options to expand the list of DSA-compatible via patterns (DSA letters) and we define matching cost formulas for the optimal DSA-aware layout decomposition. The flowchart of our proposed approach tool is presented.

  15. Integrated Remote Sensing and Wavelet Analyses for Screening Short-term Teleconnection Patterns in Northeast America

    EPA Science Inventory

    Global sea surface temperature (SST) anomalies have a demonstrable effect on vegetation dynamics and precipitation patterns throughout the continental U.S. SST variations have been correlated with greenness (vegetation densities) and precipitation via ocean-atmospheric interactio...

  16. Integrated Remote Sensing and Wavelet Analyses for Screening Short-term Teleconnection Patterns in Northeast America

    EPA Science Inventory

    Global sea surface temperature (SST) anomalies have a demonstrable effect on vegetation dynamics and precipitation patterns throughout the continental U.S. SST variations have been correlated with greenness (vegetation densities) and precipitation via ocean-atmospheric interactio...

  17. Integrative analysis of lung development-cancer expression associations reveals the roles of signatures with inverse expression patterns.

    PubMed

    Zhang, Chunlong; Li, Chunquan; Xu, Yanjun; Feng, Li; Shang, Desi; Yang, Xinmiao; Han, Junwei; Sun, Zeguo; Li, Yixue; Li, Xia

    2015-05-01

    Recent studies have focused on exploring the associations between organ development and malignant tumors; however, the clinical relevance of the development signatures was inadequately addressed in lung cancer. In this study, we explored the associations between lung development and lung cancer progression by analyzing a total of two development and seven cancer datasets. We identified representative expression patterns (continuously up- and down-regulated) from development and cancer profiles, and inverse pattern associations were observed at both the gene and functional levels. Furthermore, we dissected the biological processes dominating the associations, and found that proliferation and immunity were respectively involved in the two inverse development-cancer expression patterns. Through sub-pathway analysis of the signatures with inverse expression patterns, we finally identified a 13-gene risk signature from the cell cycle sub-pathway, and evaluated its predictive performance for lung cancer patient clinical outcome using independent cohorts. Our findings indicated that the integrative analysis of development and cancer expression patterns provided a framework for identifying effective molecular signatures for clinical utility.

  18. Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins.

    PubMed

    Pérez-Claros, Juan Antonio; Jiménez-Arenas, Juan Manuel; Palmqvist, Paul

    2015-01-01

    The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.

  19. Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins

    PubMed Central

    Pérez-Claros, Juan Antonio; Jiménez-Arenas, Juan Manuel; Palmqvist, Paul

    2015-01-01

    The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups. PMID:26177535

  20. Spatial Self-Organization of Ecosystems: Integrating Multiple Mechanisms of Regular-Pattern Formation.

    PubMed

    Pringle, Robert M; Tarnita, Corina E

    2017-01-31

    Large-scale regular vegetation patterns are common in nature, but their causes are disputed. Whereas recent theory focuses on scale-dependent feedbacks as a potentially universal mechanism, earlier studies suggest that many regular spatial patterns result from territorial interference competition between colonies of social-insect ecosystem engineers, leading to hexagonally overdispersed nest sites and associated vegetation. Evidence for this latter mechanism is scattered throughout decades of disparate literature and lacks a unified conceptual framework, fueling skepticism about its generality in debates over the origins of patterned landscapes. We review these mechanisms and debates, finding evidence that spotted and gapped vegetation patterns generated by ants, termites, and other subterranean animals are globally widespread, locally important for ecosystem functioning, and consistent with models of intraspecific territoriality. Because these and other mechanisms of regular-pattern formation are not mutually exclusive and can coexist and interact at different scales, the prevailing theoretical outlook on spatial self-organization in ecology must expand to incorporate the dynamic interplay of multiple processes.

  1. Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis.

    PubMed

    De Rybel, Bert; Adibi, Milad; Breda, Alice S; Wendrich, Jos R; Smit, Margot E; Novák, Ondřej; Yamaguchi, Nobutoshi; Yoshida, Saiko; Van Isterdael, Gert; Palovaara, Joakim; Nijsse, Bart; Boekschoten, Mark V; Hooiveld, Guido; Beeckman, Tom; Wagner, Doris; Ljung, Karin; Fleck, Christian; Weijers, Dolf

    2014-08-08

    Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue. Copyright © 2014, American Association for the Advancement of Science.

  2. Impact of the transition from a conventional to an integrated contextual medical curriculum on students' learning patterns: a longitudinal study.

    PubMed

    Van der Veken, J; Valcke, M; De Maeseneer, J; Derese, A

    2009-05-01

    Until now, most research studying the impact of curriculum innovations on student learning patterns was restricted to short term or cross-sectional research. Studying longitudinal changes in student learning patterns parallel to the implementation of a curriculum innovation from a discipline based to an integrated contextual medical curriculum (ICMC). A post hoc study applying General Linear Model ANOVA one-way repeated-measures. The inventory of learning styles(126-item version) is used to determine changes in student learning patterns. Though not all hypotheses could be accepted, the results suggest a significant impact of the ICMC on learning processing strategies; regulation strategies; and on learning orientations. The clear build-up of the curriculum and vertical and horizontal integration of subject knowledge seem to have significantly reduced lack of regulation and promoted at an earlier stage structuring, relating, critical processing and vocational-orientation. The effect on use of sources of knowledge, self-regulation of learning content and certificate-orientation was less important than expected. It was yet not possible to confirm the hypothesis that ICMC students become better in translating study topics into their own phrasing or expressions; and neither the expected impact on vocation-orientation could be confirmed. There is little doubt that the present results are important to curriculum (re)designers and those interested in the evaluation of curriculum reforms.

  3. Manipulation of micro-particles through optical interference patterns generated by integrated photonic devices.

    PubMed

    Hsu, Li-Chung; Chen, Te-Chang; Yang, Yao-Tsu; Huang, Chieh-Yang; Shen, Da-Wei; Chen, Ya-Tzu; Lee, Ming-Chang M

    2013-03-21

    Micro-particle transport and switch governed by guided-wave optical interference are presented. The optical interference, occurring in a directional coupler and a multi-mode interferometer made by inverted rib waveguides, results in a specific evanescent field dependent on wavelength. Through a detailed theoretical analysis, the field of induced optical force shows a correlative pattern associated with the evanescent field. Experimental results demonstrate that 10 μm polystyrene beads are propelled with a trajectory subject to the interference pattern accordingly. By launching different wavelengths, the polystyrene beads can be delivered to different output waveguide ports. Massive micro-particle manipulation is applicable.

  4. Investigation of the Dynamical Structure and Diffusion in a System of Hamiltonian Type: 4-Dimensional Symplectic Map

    NASA Astrophysics Data System (ADS)

    Todorovic, N.

    2009-09-01

    The Nekhoroshev theorem (Nekhoroshev 1977) is one of the most important theorems in modern Hamiltonian dynamics. This theorem applies to quasi integrable Hamiltonian systems of type H(I,\\varphi)=h(I)+\\varepsilon f (I, \\varphi), where h(I) is the integrable approximation, f(I, \\varphi) the perturbing function, \\varepsilon is a small perturbing parameter, Iin R^n are the actions and \\varphi in T^n the angles of the system. With some additional geometrical and analytical properties, the theorem provides the stability of actions in exponentially long times. In recent years it has been shown that with some modifications the Nekhoroshev theorem can be applied to the problems in Solar system dynamics (Morbidelli and Guzzo 1997, Guzzo et al 2002, Efthymiopoulos and Sándor 2105, Pavlović and Guzzo 2008). In this work, we are interested to observe numerically a Nekhoroshev like behavior on a model given with a 4-dimensional symplectic map. The model is not in the quasi-integrable form, i.e. independently from the perturbation it contains some additional hyperbolic structures (they appear in the model as primary resonances). Since the hyperbolic structures exist even for zero perturbation, the system will belong to the class of the so called a priori unstable systems. The main numerical tool used here was the Fast Lyapunov Indicator- FLI, introduced in (Froschlé et al. 1997, 2000). As an indicator of chaotic motion, FLI gives very precise and fast information about the chaoticity of an orbit. Also, among regular orbits, FLI is able to differentiate resonant from nonresonant motions. This property of FLI allows us to visualize the studied system and to obtain the Arnold web of the model (Froschlé et al. 2000). In such a way it was possible to observe the transition from a stable Nekhoroshev like structure (regular orbits dominate) to a globally chaotic system where resonances overlap, also known as Chirikov regime. Numerically, this transition happens when between 50

  5. Accessibility patterns and community integration among previously homeless adults: a Geographic Information Systems (GIS) approach.

    PubMed

    Chan, Dara V; Gopal, Sucharita; Helfrich, Christine A

    2014-11-01

    Although a desired rehabilitation goal, research continues to document that community integration significantly lags behind housing stability success rates for people of a variety of ages who used to be homeless. While accessibility to resources is an environmental factor that may promote or impede integration activity, there has been little empirical investigation into the impact of proximity of community features on resource use and integration. Using a Geographic Information Systems (GIS) approach, the current study examines how accessibility or proximity to community features in Boston, United States related to the types of locations used and the size of an individual's "activity space," or spatial presence in the community. Significant findings include an inverse relationship between activity space size and proximity to the number and type of community features in one's immediate area. Specifically, larger activity spaces were associated with neighborhoods with less community features, and smaller activity spaces corresponded with greater availability of resources within one's immediate area. Activity space size also varied, however, based on proximity to different types of resources, namely transportation and health care. Greater community function, or the ability to navigate and use community resources, was associated with better accessibility and feeling part of the community. Finally, proximity to a greater number of individual identified preferred community features was associated with better social integration. The current study suggests the ongoing challenges of successful integration may vary not just based on accessibility to, but relative importance of, specific community features and affinity with one's surroundings. Community integration researchers and housing providers may need to attend to the meaning attached to resources, not just presence or use in the community.

  6. An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments

    PubMed Central

    Torres-Sánchez, Alejandro; Gómez-Gardeñes, Jesús; Falo, Fernando

    2015-01-01

    Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model. PMID:25816286

  7. Metropolitan expansion and population density patterns in third world supercities as indicated by integration of space and ground data

    NASA Astrophysics Data System (ADS)

    Eyre, L. A.

    Monitoring of the urbanization process in the less developed countries of the world is limited by the inadequacy of ground data such as censuses and by their explosive rates of population growth and spatial expansion. By integrating Landsat satellite imagery and available population data, more accurate analyses are possible than by using either medium alone. Using this technique, built-up area, population and patterns of population density for the year 1978 are quantified for six Third World supercities with population in excess of six million: Calcutta, Shanghai, Cairo, Mexico City, Sao Paulo and Rio de Janeiro. Significant differences in density patterns between these cities appear to be related to economic level and culture.

  8. The adenovirus type 12 - mouse cell system: permissivity and analysis of integration patterns of viral DNA in tumor cells.

    PubMed Central

    Starzinski-Powitz, A; Schulz, M; Esche, H; Mukai, N; Doerfler, W

    1982-01-01

    The integration patterns of persisting adenovirus type 12 (Ad12) DNA were analyzed in two Ad12-induced tumors of Balb/c and CBA/J mice and in one tumor cell line derived from an Ad12-induced retinoblastoma of C3H origin. In all three tumors the Ad12 genome was integrated colinearly and various copy numbers of viral DNA were found. Analysis of the Ad12 integration patterns revealed relatively simple offsize band patterns regardless of Ad12 copy numbers. The degree of methylation at the 5'-CCGG-3' sites in the inserted Ad12 genome was determined using the isoschizomeric restriction endonuclease pair HpaII and MspI. Methylation was rather incomplete in the primary tumor tissues but almost complete in the retinoblastoma line carried in culture for many passages. The levels of expression of the viral genome in the Balb/c tumor and in the retinoblastoma line were determined by in vitro translation of RNA isolated from these cells and selected with appropriate restriction endonuclease fragments of Ad12 DNA. In both instances the 59 K, 19 K, and 17 K proteins of the E1b region were expressed. Proteins of the E1a region appeared very faint in the size class between 22 K and 42 K. The permissivity of Ad12 and the replication of Ad12 DNA in mouse cells were investigated by blotting restricted DNA from cells soon after, and a long time after, infection and by hybridization with 32P-labeled Ad12 DNA. Neither primary mouse kidney cells nor the established L929 mouse cell line supported viral DNA replication. These results raise the question to what extent host cell factors determine Ad12 DNA replication in mammalian cells. Images Fig. 2. Fig. 3. Fig. 4. PMID:7188349

  9. Integrative Motivation: How Perceptions of the Target Language Country Influence Students' Motivational Pattern

    ERIC Educational Resources Information Center

    Nikitina, Larisa; Furuoka, Fumitaka

    2006-01-01

    Motivation has been recognized by both psychologists and educators as one of the key elements for a successful learning outcome. In research on motivation in language learning, it is customary to view the construct as a dyadic unity of integrative and instrumental motivation. The former includes the learners' attitudes towards the culture and…

  10. Integrative Life Planning. Critical Tasks for Career Development and Changing Life Patterns.

    ERIC Educational Resources Information Center

    Hansen, L. Sunny

    This book presents an integrative life planning (ILP) model for career professionals/counselors to use in helping their clients develop career and life pathways responsive to their own economic, family, spiritual, and cultural needs and also to community needs. Discussed in chapters 1-2, which introduce the ILP model as a new way of thinking about…

  11. Five year outcomes of hypofractionated simultaneous integrated boost irradiation in breast conserving therapy; patterns of recurrence.

    PubMed

    Bantema-Joppe, Enja J; Vredeveld, Eline J; de Bock, Geertruida H; Busz, Dianne M; Woltman-van Iersel, Marleen; Dolsma, Wil V; van der Laan, Hans Paul; Langendijk, Johannes A; Maduro, John H

    2013-08-01

    In 2005, we introduced hypofractionated 3-dimensional conformal radiotherapy with a simultaneous integrated boost (3D-CRT-SIB) technique after breast conserving surgery. In a consecutive series of 752 consecutive female invasive breast cancer patients (stages I-III) the 5-year actuarial rate for local control was 98.9%. This new technique gives excellent 5-year local control.

  12. SU-E-T-267: Proton Pencil Beam Scanning for Mediastinal Lymphoma: 4-Dimensional Feasibility Study

    SciTech Connect

    Zeng, C; Plastaras, J; Tochner, Z; Hill-Kayser, C; Hahn, S; Both, S

    2014-06-01

    Purpose: To assess the feasibility of proton pencil beam scanning (PBS) for the treatment of mediastinal lymphoma. Methods: A group of 6 patients were planned using an anterior field with PBS. Spots with ∼5 mm σ were used for all patients, while large spots (∼10 mm σ) were employed for patients with motion perpendicular to the beam (≥5 mm). We considered volumetric repainting such that, in each fraction, the same field would be delivered twice. Four-dimensional dose was calculated on initial and verification 4-dimensional computed tomography (4D-CT) scans (2—3) based on respiratory trace and beam delivery sequence. This was implemented by binning the spots into separate plans on each 4D-CT phase respectively. Four starting phases were sampled for each painting and 4 energy switching times (0.5 s, 1 s, 3 s, and 5 s) were tested, resulting in 2560 dose distributions for the cohort. Plan robustness was measured for target and critical structures in terms of the percentage difference between delivered dose and planned dose. Results: For 5 of the 6 patients, the ITV (internal target volume) D98% was degraded by <3% (standard deviations ∼ 0.1%) when averaged over the whole course (up to 5% per fraction). Deviations of mean lung dose, heart maximum dose, and cord maximum dose were within 5% of prescribed dose. For one patient with motion perpendicular to the beam (up to 5 mm), the degradation of ITV D98% was 9% over the whole course (12% per fraction), which was mitigated to 1% (3% per fraction) by employing large spots and repainting. No significant difference in coverage was observed for different energy switching times. Conclusion: This feasibility study demonstrates that, for mediastinal lymphoma, the PBS plan robustness can be maintained during delivery when target motion is measured and volumetric repainting and/or large spots are employed. This work was supported by Ion Beam Application.

  13. Visualization and Quantification of Olivine Carbonation Using 4-dimensional Synchrotron Microtomography

    NASA Astrophysics Data System (ADS)

    Xing, T.; Zhu, W.; Lisabeth, H. P.; Fusseis, F.

    2016-12-01

    Olivine carbonation reaction, in which CO2 is chemically incorporated to form carbonate, results in a solid volume increase. It is proposed that the excess solids could fracture the host rock, create new reactive surfaces and propel the reaction to completion. However, how fracturing takes place during reactions is still elusive. We conducted in-situ dynamic microtomography experiments to investigate the evolution of pore structure of olivine aggregate undergoing mineral carbonation. Sintered San Carlos olivine samples with initial porosities of 10-15% were reacted with a NaHCO3 aqueous solution at 200°C, under a constant confining pressure of 15 MPa and pore pressure of 10 MPa. Using the synchrotron-based X-ray microtomography, 3-dimensional pore structure was documented over 7 days without interrupting the reaction. The resulting 4-dimensional (3-dimension + time) dataset permits a detailed investigation of the reaction process at a spatial resolution of 0.65 micron. The data shows that the surface morphology of olivine is constantly changing. At the beginning, a volume reduction of olivine is observed, which is consistent with the vigorous dissolution suggested in other studies. As the reaction proceeds, the growth of idiomorphic magnesite crystals on the surface of the olivine grains becomes easily recognizable. The circumference of magnesite shows a constant growth throughout the experiment, with no indication of self-limiting. Porosity analysis reveals that, after an initial porosity increase of 2-4% (as a consequence of the rapid dissolution), the porosity of the sample interior decreases continuously. In contrast, porosity of surface layers continues to increase or stays constant. This difference indicates a non-uniform precipitation of reaction products within the sample. Such non-uniformity leads to a larger volume expansion of the sample interior. Stretching due to volume mismatch initiates tensile cracks. Crack coalescence to form large fractures and

  14. Management of Respiration-Induced Motion With 4-Dimensional Computed Tomography (4DCT) for Pancreas Irradiation

    SciTech Connect

    Tai, An; Liang, Zhiwen; Erickson, Beth; Li, X. Allen

    2013-08-01

    Purpose: The purposes of this study were to quantify respiration-induced organ motions for pancreatic cancer patients and to explore strategies to account for these motions. Methods and Materials: Both 3-dimensional computed tomography (3DCT) and 4-dimensional computed tomography (4DCT) scans were acquired sequentially for 15 pancreatic cancer patients, including 10 randomly selected patients and 5 patients selected from a subgroup of patients with large tumor respiratory motions. 3DCTs were fused with 2 sets of 4DCT data at the end of exhale phase (50%) and the end of inhale phase (0%). The target was delineated on the 50% and 0% phase CT sets, and the organs at risk were drawn on the 3DCT. These contours were populated to the CT sets at other respiratory phases based on deformable image registration. Internal target volumes (ITV) were generated by tracing the target contours of all phases (ITV{sub 10}), 3 phases of 0%, 20% and 50% (ITV{sub 3}), and 2 phases of 0% and 50% (ITV{sub 2}). ITVs generated from phase images were compared using percentage of volume overlap, Dice coefficient, geometric centers, and average surface distance. Results: Volume variations of pancreas, kidneys, and liver as a function of respiratory phases were small (<5%) during respiration. For the 10 randomly selected patients, peak-to-peak amplitudes of liver, left kidney, right kidney, and the target along the superior-inferior (SI) direction were 7.9 ± 3.2 mm, 7.1 ± 3.1 mm, 5.7 ± 3.2 mm, and 5.9 ± 2.8 mm, respectively. The percentage of volume overlap and Dice coefficient were 92% ± 1% and 96% ± 1% between ITV{sub 10} and ITV{sub 2} and 96% ± 1% and 98% ± 1% between ITV{sub 10} and ITV{sub 3}, respectively. The percentage of volume overlap between ITV{sub 10} and ITV{sub 3} was 93.6 ± 1.1 for patients with tumor motion >8 mm. Conclusions: Appropriate motion management strategies are proposed for radiation treatment planning of pancreatic tumors based on magnitudes of tumor

  15. Modeling Pancreatic Tumor Motion Using 4-Dimensional Computed Tomography and Surrogate Markers

    SciTech Connect

    Huguet, Florence; Yorke, Ellen D.; Davidson, Margaret; Zhang, Zhigang; Jackson, Andrew; Mageras, Gig S.; Wu, Abraham J.; Goodman, Karyn A.

    2015-03-01

    Purpose: To assess intrafractional positional variations of pancreatic tumors using 4-dimensional computed tomography (4D-CT), their impact on gross tumor volume (GTV) coverage, the reliability of biliary stent, fiducial seeds, and the real-time position management (RPM) external marker as tumor surrogates for setup of respiratory gated treatment, and to build a correlative model of tumor motion. Methods and Materials: We analyzed the respiration-correlated 4D-CT images acquired during simulation of 36 patients with either a biliary stent (n=16) or implanted fiducials (n=20) who were treated with RPM respiratory gated intensity modulated radiation therapy for locally advanced pancreatic cancer. Respiratory displacement relative to end-exhalation was measured for the GTV, the biliary stent, or fiducial seeds, and the RPM marker. The results were compared between the full respiratory cycle and the gating interval. Linear mixed model was used to assess the correlation of GTV motion with the potential surrogate markers. Results: The average ± SD GTV excursions were 0.3 ± 0.2 cm in the left-right direction, 0.6 ± 0.3 cm in the anterior-posterior direction, and 1.3 ± 0.7 cm in the superior-inferior direction. Gating around end-exhalation reduced GTV motion by 46% to 60%. D95% was at least the prescribed 56 Gy in 76% of patients. GTV displacement was associated with the RPM marker, the biliary stent, and the fiducial seeds. The correlation was better with fiducial seeds and with biliary stent. Conclusions: Respiratory gating reduced the margin necessary for radiation therapy for pancreatic tumors. GTV motion was well correlated with biliary stent or fiducial seed displacements, validating their use as surrogates for daily assessment of GTV position during treatment. A patient-specific internal target volume based on 4D-CT is recommended both for gated and not-gated treatment; otherwise, our model can be used to predict the degree of GTV motion.

  16. A laser-assisted process to produce patterned growth of vertically aligned nanowire arrays for monolithic microwave integrated devices.

    PubMed

    Kerckhoven, Vivien Van; Piraux, Luc; Huynen, Isabelle

    2016-06-10

    An experimental process for the fabrication of microwave devices made of nanowire arrays embedded in a dielectric template is presented. A pulse laser process is used to produce a patterned surface mask on alumina templates, defining precisely the wire growing areas during electroplating. This technique makes it possible to finely position multiple nanowire arrays in the template, as well as produce large areas and complex structures, combining transmission line sections with various nanowire heights. The efficiency of this process is demonstrated through the realisation of a microstrip electromagnetic band-gap filter and a substrate-integrated waveguide.

  17. Hydrologic Sensitivity to Climate Change of Precipitation Patterns via Integrated Modeling

    NASA Astrophysics Data System (ADS)

    Daniels, B. K.

    2011-12-01

    Understanding the impacts of climate change on water resources is critical to ecosystems and to human well being. Most previous work has involved coupling hydrologic models to global and regional climate models. While there is impressive agreement among climate models on temperature increase, unfortunately precipitation estimates present "wildly diverging pictures" [Schiermeier, Nature 2010]. In the IPCC AR4 WG1 SPM on page 16 one sees for most of the mid-latitudes that more than 1/3 of the models disagree with the majority on even the sign of any precipitation change and significant agreement of 90% is typically only found in the polar reaches [Oreskes, Philosophy of Science 2010]. Since precipitation is the primary driver of hydrology, therefore coupling of these climate models to hydrology can only yield projections that are highly uncertain. This work instead offers basic insight into the connections between all sorts of climate possibilities and hydrology. The observational climate inputs to GSFLOW basin models have been tweaked to compute the sensitivity of hydrological components to change in many climate variables. Impacts were evaluated from individual changes from a precipitation pattern such as total amounts, event intensities, event rates, durations, frequencies, and season lengths. By considering each precipitation pattern separately, we separate the confounding factors when all are changing at the same time and can then observe the impact of each factor by itself. Sensitivities have been computed for some 20 hydrologic flow components, such as runoff, infiltration, soil ET, interflow, recharge, baseflow, and streamflows. This hydrological system is highly non-linear and so a single set of computed hydrologic sensitivity values only describes the hydrologic partitioning for a single environmental condition. For a more complete picture, hydrological sensitivities have been computed over wide ranges of climate variables, such as a warmer to a colder

  18. Ontology Design Patterns: Bridging the Gap Between Local Semantic Use Cases and Large-Scale, Long-Term Data Integration

    NASA Astrophysics Data System (ADS)

    Shepherd, Adam; Arko, Robert; Krisnadhi, Adila; Hitzler, Pascal; Janowicz, Krzysztof; Chandler, Cyndy; Narock, Tom; Cheatham, Michelle; Schildhauer, Mark; Jones, Matt; Raymond, Lisa; Mickle, Audrey; Finin, Tim; Fils, Doug; Carbotte, Suzanne; Lehnert, Kerstin

    2015-04-01

    Integrating datasets for new use cases is one of the common drivers for adopting semantic web technologies. Even though linked data principles enables this type of activity over time, the task of reconciling new ontological commitments for newer use cases can be daunting. This situation was faced by the Biological and Chemical Oceanography Data Management Office (BCO-DMO) as it sought to integrate its existing linked data with other data repositories to address newer scientific use cases as a partner in the GeoLink Project. To achieve a successful integration with other GeoLink partners, BCO-DMO's metadata would need to be described using the new ontologies developed by the GeoLink partners - a situation that could impact semantic inferencing, pre-existing software and external users of BCO-DMO's linked data. This presentation describes the process of how GeoLink is bridging the gap between local, pre-existing ontologies to achieve scientific metadata integration for all its partners through the use of ontology design patterns. GeoLink, an NSF EarthCube Building Block, brings together experts from the geosciences, computer science, and library science in an effort to improve discovery and reuse of data and knowledge. Its participating repositories include content from field expeditions, laboratory analyses, journal publications, conference presentations, theses/reports, and funding awards that span scientific studies from marine geology to marine ecology and biogeochemistry to paleoclimatology. GeoLink's outcomes include a set of reusable ontology design patterns (ODPs) that describe core geoscience concepts, a network of Linked Data published by participating repositories using those ODPs, and tools to facilitate discovery of related content in multiple repositories.

  19. Pattern recognition applied to presidential elections in the United States, 1860-1980: Role of integral social, economic, and political traits

    PubMed Central

    Lichtman, A. J.; Keilis-Borok, V. I.

    1981-01-01

    The outcome of American presidential elections in 1860-1980 follows certain regular patterns which can be described phenomenologically by simple integral parameters of “common sense” type. PMID:16593125

  20. Integrating satellite actual evapotranspiration patterns into distributed model parametrization and evaluation for a mesoscale catchment

    NASA Astrophysics Data System (ADS)

    Demirel, M. C.; Mai, J.; Stisen, S.; Mendiguren González, G.; Koch, J.; Samaniego, L. E.

    2016-12-01

    Distributed hydrologic models are traditionally calibrated and evaluated against observations of streamflow. Spatially distributed remote sensing observations offer a great opportunity to enhance spatial model calibration schemes. For that it is important to identify the model parameters that can change spatial patterns before the satellite based hydrologic model calibration. Our study is based on two main pillars: first we use spatial sensitivity analysis to identify the key parameters controlling the spatial distribution of actual evapotranspiration (AET). Second, we investigate the potential benefits of incorporating spatial patterns from MODIS data to calibrate the mesoscale Hydrologic Model (mHM). This distributed model is selected as it allows for a change in the spatial distribution of key soil parameters through the calibration of pedo-transfer function parameters and includes options for using fully distributed daily Leaf Area Index (LAI) directly as input. In addition the simulated AET can be estimated at the spatial resolution suitable for comparison to the spatial patterns observed using MODIS data. We introduce a new dynamic scaling function employing remotely sensed vegetation to downscale coarse reference evapotranspiration. In total, 17 parameters of 47 mHM parameters are identified using both sequential screening and Latin hypercube one-at-a-time sampling methods. The spatial patterns are found to be sensitive to the vegetation parameters whereas streamflow dynamics are sensitive to the PTF parameters. The results of multi-objective model calibration show that calibration of mHM against observed streamflow does not reduce the spatial errors in AET while they improve only the streamflow simulations. We will further examine the results of model calibration using only multi spatial objective functions measuring the association between observed AET and simulated AET maps and another case including spatial and streamflow metrics together.

  1. Pitch doubling through dual-patterning lithography challenges in integration and litho budgets

    NASA Astrophysics Data System (ADS)

    Dusa, Mircea; Quaedackers, John; Larsen, Olaf F. A.; Meessen, Jeroen; van der Heijden, Eddy; Dicker, Gerald; Wismans, Onno; de Haas, Paul; van Ingen Schenau, Koen; Finders, Jo; Vleeming, Bert; Storms, Geert; Jaenen, Patrick; Cheng, Shaunee; Maenhoudt, Mireille

    2007-03-01

    We present results from investigating critical challenges of pitch doubling through Double Patterning to meet manufacturing requirements for 32nm 1/ II pitch on 1.2NA lithography system. Simulations of lithography alternatives identified manufacturable Dose-Focus latitudes for a dual-line positive process option which led to an experimental setup based on a single hardmask process. Key challenges of the selected process relate to the presence or absence of the hardmask layer during 1 st or 2 nd patterning step. This has an effect on wafer topography, process setup, etch bias and wafer litho-to-etch CDU offsets, which will create two final CDU populations. Therefore, there are two metrology challenges, separation between the two CD populations and overlay-at-resolution using CDSEM. They were addressed by designing appropriate CD and overlay targets and by implementing an adequate dense sampling allowing modeling of wafer and field CD distributions. We introduced a new CDU model to calculate double patterning budgets based on defining CD from its edges and pooling CD variance from two adjacent patterns within 2*Pitch distance. For a single line and 1.35NA system, the model predicted 3.1nm variance with mask CDU and etch bias being the major contributors. We achieved an experimental resolution of 32-nm 1/ II pitch on 1.2NA system, which equals 0.20k1. Experimental results at 32-nm resolution were confirmed in a pre-manufacturing environment on a full lot of 24 wafers, with raw CDU of 6nm (3s). After modeling and correcting for interfield (wafer) and intrafield spatial distributions, CDU was improved to 2.5nm (3s). Best overlay results equaled scanner SMO capability of ~7nm (mean+3s).

  2. From spinal central pattern generators to cortical network: integrated BCI for walking rehabilitation.

    PubMed

    Cheron, G; Duvinage, M; De Saedeleer, C; Castermans, T; Bengoetxea, A; Petieau, M; Seetharaman, K; Hoellinger, T; Dan, B; Dutoit, T; Sylos Labini, F; Lacquaniti, F; Ivanenko, Y

    2012-01-01

    Success in locomotor rehabilitation programs can be improved with the use of brain-computer interfaces (BCIs). Although a wealth of research has demonstrated that locomotion is largely controlled by spinal mechanisms, the brain is of utmost importance in monitoring locomotor patterns and therefore contains information regarding central pattern generation functioning. In addition, there is also a tight coordination between the upper and lower limbs, which can also be useful in controlling locomotion. The current paper critically investigates different approaches that are applicable to this field: the use of electroencephalogram (EEG), upper limb electromyogram (EMG), or a hybrid of the two neurophysiological signals to control assistive exoskeletons used in locomotion based on programmable central pattern generators (PCPGs) or dynamic recurrent neural networks (DRNNs). Plantar surface tactile stimulation devices combined with virtual reality may provide the sensation of walking while in a supine position for use of training brain signals generated during locomotion. These methods may exploit mechanisms of brain plasticity and assist in the neurorehabilitation of gait in a variety of clinical conditions, including stroke, spinal trauma, multiple sclerosis, and cerebral palsy.

  3. From Spinal Central Pattern Generators to Cortical Network: Integrated BCI for Walking Rehabilitation

    PubMed Central

    Cheron, G.; Duvinage, M.; De Saedeleer, C.; Castermans, T.; Bengoetxea, A.; Petieau, M.; Seetharaman, K.; Hoellinger, T.; Dan, B.; Dutoit, T.; Sylos Labini, F.; Lacquaniti, F.; Ivanenko, Y.

    2012-01-01

    Success in locomotor rehabilitation programs can be improved with the use of brain-computer interfaces (BCIs). Although a wealth of research has demonstrated that locomotion is largely controlled by spinal mechanisms, the brain is of utmost importance in monitoring locomotor patterns and therefore contains information regarding central pattern generation functioning. In addition, there is also a tight coordination between the upper and lower limbs, which can also be useful in controlling locomotion. The current paper critically investigates different approaches that are applicable to this field: the use of electroencephalogram (EEG), upper limb electromyogram (EMG), or a hybrid of the two neurophysiological signals to control assistive exoskeletons used in locomotion based on programmable central pattern generators (PCPGs) or dynamic recurrent neural networks (DRNNs). Plantar surface tactile stimulation devices combined with virtual reality may provide the sensation of walking while in a supine position for use of training brain signals generated during locomotion. These methods may exploit mechanisms of brain plasticity and assist in the neurorehabilitation of gait in a variety of clinical conditions, including stroke, spinal trauma, multiple sclerosis, and cerebral palsy. PMID:22272380

  4. Sensing Urban Land-Use Patterns by Integrating Google Tensorflow and Scene-Classification Models

    NASA Astrophysics Data System (ADS)

    Yao, Y.; Liang, H.; Li, X.; Zhang, J.; He, J.

    2017-09-01

    With the rapid progress of China's urbanization, research on the automatic detection of land-use patterns in Chinese cities is of substantial importance. Deep learning is an effective method to extract image features. To take advantage of the deep-learning method in detecting urban land-use patterns, we applied a transfer-learning-based remote-sensing image approach to extract and classify features. Using the Google Tensorflow framework, a powerful convolution neural network (CNN) library was created. First, the transferred model was previously trained on ImageNet, one of the largest object-image data sets, to fully develop the model's ability to generate feature vectors of standard remote-sensing land-cover data sets (UC Merced and WHU-SIRI). Then, a random-forest-based classifier was constructed and trained on these generated vectors to classify the actual urban land-use pattern on the scale of traffic analysis zones (TAZs). To avoid the multi-scale effect of remote-sensing imagery, a large random patch (LRP) method was used. The proposed method could efficiently obtain acceptable accuracy (OA = 0.794, Kappa = 0.737) for the study area. In addition, the results show that the proposed method can effectively overcome the multi-scale effect that occurs in urban land-use classification at the irregular land-parcel level. The proposed method can help planners monitor dynamic urban land use and evaluate the impact of urban-planning schemes.

  5. Pattern Representation and Evaluation of Data through Integration Correlation, and Transformation

    DTIC Science & Technology

    2014-02-01

    iterative process to translate the CWA results into requirements for prototype visualizations. Mockup visualizations were developed for an integrated...stream (Milestone 2) as will be detailed later in this report. The results of the cognitive work analysis (reportable outcome 1) and prototype mockups ...reportable outcome 2) are detailed below. Each mockup underwent a series of design iterations to ensure that the visualizations made sense for the

  6. Influences of upland and riparian land use patterns on stream biotic integrity

    USGS Publications Warehouse

    Snyder, C.D.; Young, J.A.; Villella, R.; Lemarie, D.P.

    2003-01-01

    We explored land use, fish assemblage structure, and stream habitat associations in 20 catchments in Opequon Creek watershed, West Virginia. The purpose was to determine the relative importance of urban and agriculture land use on stream biotic integrity, and to evaluate the spatial scale (i.e., whole-catchment vs riparian buffer) at which land use effects were most pronounced. We found that index of biological integrity (IBI) scores were strongly associated with extent of urban land use in individual catchments. Sites that received ratings of poor or very poor based on IBI scores had > 7% of urban land use in their respective catchments. Habitat correlations suggested that urban land use disrupted flow regime, reduced water quality, and altered stream channels. In contrast, we found no meaningful relationship between agricultural land use and IBI at either whole-catchment or riparian scales despite strong correlations between percent agriculture and several important stream habitat measures, including nitrate concentrations, proportion of fine sediments in riffles, and the abundance of fish cover. We also found that variation in gradient (channel slope) influenced responses of fish assemblages to land use. Urban land use was more disruptive to biological integrity in catchments with steeper channel slopes. Based on comparisons of our results in the topographically diverse Opequon Creek watershed with results from watersheds in flatter terrains, we hypothesize that the potential for riparian forests to mitigate effects of deleterious land uses in upland portions of the watershed is inversely related to gradient.

  7. A Fully Integrated and Miniaturized Heavy-metal-detection Sensor Based on Micro-patterned Reduced Graphene Oxide

    PubMed Central

    Xuan, Xing; Hossain, Md. Faruk; Park, Jae Yeong

    2016-01-01

    For this paper, a fully integrated and highly miniaturized electrochemical sensor was designed and fabricated on a silicon substrate. A solvothermal-assisted reduced graphene oxide named “TRGO” was then successfully micro-patterned using a lithography technique, followed by the electrodeposition of bismuth (Bi) on the surface of the micro-patterned TRGO for the electrochemical detection of heavy metal ions. The fully integrated electrochemical micro-sensor was then measured and evaluated for the detection of cadmium and lead-heavy metal ions in an acetic-acid buffered solution using the square wave anodic stripping voltammetry (SWASV) technique. The fabricated micro-sensor exhibited a linear detection range of 1.0 μg L−1 to 120.0 μg L−1 for both of the metal ions, and detection limits of 0.4 μg L−1 and 1.0 μg L−1 were recorded for the lead and cadmium (S/N = 3), respectively. Drinking-water samples were used for the practical assessment of the fabricated micro-sensor, and it showed an acceptable detection performance regarding the metal ions. PMID:27616629

  8. A Fully Integrated and Miniaturized Heavy-metal-detection Sensor Based on Micro-patterned Reduced Graphene Oxide

    NASA Astrophysics Data System (ADS)

    Xuan, Xing; Hossain, Md. Faruk; Park, Jae Yeong

    2016-09-01

    For this paper, a fully integrated and highly miniaturized electrochemical sensor was designed and fabricated on a silicon substrate. A solvothermal-assisted reduced graphene oxide named “TRGO” was then successfully micro-patterned using a lithography technique, followed by the electrodeposition of bismuth (Bi) on the surface of the micro-patterned TRGO for the electrochemical detection of heavy metal ions. The fully integrated electrochemical micro-sensor was then measured and evaluated for the detection of cadmium and lead-heavy metal ions in an acetic-acid buffered solution using the square wave anodic stripping voltammetry (SWASV) technique. The fabricated micro-sensor exhibited a linear detection range of 1.0 μg L‑1 to 120.0 μg L‑1 for both of the metal ions, and detection limits of 0.4 μg L‑1 and 1.0 μg L‑1 were recorded for the lead and cadmium (S/N = 3), respectively. Drinking-water samples were used for the practical assessment of the fabricated micro-sensor, and it showed an acceptable detection performance regarding the metal ions.

  9. A Fully Integrated and Miniaturized Heavy-metal-detection Sensor Based on Micro-patterned Reduced Graphene Oxide.

    PubMed

    Xuan, Xing; Hossain, Md Faruk; Park, Jae Yeong

    2016-09-12

    For this paper, a fully integrated and highly miniaturized electrochemical sensor was designed and fabricated on a silicon substrate. A solvothermal-assisted reduced graphene oxide named "TRGO" was then successfully micro-patterned using a lithography technique, followed by the electrodeposition of bismuth (Bi) on the surface of the micro-patterned TRGO for the electrochemical detection of heavy metal ions. The fully integrated electrochemical micro-sensor was then measured and evaluated for the detection of cadmium and lead-heavy metal ions in an acetic-acid buffered solution using the square wave anodic stripping voltammetry (SWASV) technique. The fabricated micro-sensor exhibited a linear detection range of 1.0 μg L(-1) to 120.0 μg L(-1) for both of the metal ions, and detection limits of 0.4 μg L(-1) and 1.0 μg L(-1) were recorded for the lead and cadmium (S/N = 3), respectively. Drinking-water samples were used for the practical assessment of the fabricated micro-sensor, and it showed an acceptable detection performance regarding the metal ions.

  10. Closing the Loop: Integrating Body, Muscle and Environment with Locomotion Central Pattern Generators

    DTIC Science & Technology

    2013-06-30

    optimal feedback control, central pattern generator, lamprey , locomotion, neural control Tim Kiemel, Kathleen Hoffman University of Maryland - College Park...between the neural circuitry, body, and fluid environment for swimming locomotion, where the lamprey serves as a model system1,2,3,4,5,6,7,8. Our...have done for a simple plant model of lamprey swimming (§2.2). In our CPG-based approach (§2.3), we have combined a simple CPG model with the plant model

  11. Evaluating Outcomes in Patients with Overactive Bladder within an Integrated Healthcare Delivery System Using a Treatment Patterns Analyzer

    PubMed Central

    Ng, Daniel B.; McCart, Melissa; Klein, Christopher; Campbell, Chelsey; Schoenhaus, Robert; Berner, Todd

    2016-01-01

    Background Overactive bladder (OAB) is a relatively common disease that has been linked to a variety of comorbidities, reductions in quality of life, and increased healthcare costs. Antimuscarinic agents are the standard of care among pharmacologic treatments for OAB, but these drugs are linked to high levels of anticholinergic burden, especially in the elderly. Objective To demonstrate how efficient data analysis can be used to identify gaps in care as a result of improvement strategies for OAB within an integrated healthcare delivery system setting. Methods We developed an OAB treatment patterns analyzer, a clinical outcomes software analysis program, to identify gaps in care, high anticholinergic burden, and potential quality improvement initiatives. Deidentified pharmacy and medical claims data from an integrated delivery network were imported into the OAB treatment patterns analyzer. Patients with a diagnosis of OAB who were continuously enrolled in the network between January 1, 2009, and December 31, 2013, were identified and were imported into the analyzer. The analyzer used National Drug Code; International Classification of Diseases, Ninth Edition, Clinical Modification; Current Procedural Terminology; and UB-92 codes to measure treatment patterns, comorbid conditions, anticholinergic burden, concomitant use with anticholinesterases, costs, and healthcare resource utilization. Results Of 157,710 members in the integrated delivery network population, 7309 patients met the study eligibility criteria. Of patients taking medications for OAB, 85% were nonadherent and 73% discontinued treatment within 1 year. Among 1147 patients in the integrated healthcare delivery system who were using medications for OAB, 39 (3.4%) patients were concomitantly taking anticholinesterase drugs and an antimuscarinic agent. The per-month plan-paid cost per member was $318.67. Of all the patients with OAB within the population, the rates of all-cause office visits, emergency

  12. Integrated input protection against discharges for Micro Pattern Gas Detectors readout ASICs

    NASA Astrophysics Data System (ADS)

    Fiutowski, T.; Dąbrowski, W.; Koperny, S.; Wiącek, P.

    2017-02-01

    Immunity against possible random discharges inside active detector volume of MPGDs is one of the key aspects that should be addressed in the design of the front-end electronics. This issue becomes particularly critical for systems with high channel counts and high density readout employing the front-end electronics built as multichannel ASICs implemented in modern CMOS technologies, for which the breakdown voltages are in the range of a few Volts. The paper presents the design of various input protection structures integrated in the ASIC manufactured in a 350 nm CMOS process and test results using an electrical circuit to mimic discharges in the detectors.

  13. Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis and maintenance of axial patterning.

    PubMed

    Lin, Alexander Y T; Pearson, Bret J

    2014-03-01

    During adult homeostasis and regeneration, the freshwater planarian must accomplish a constant balance between cell proliferation and cell death, while also maintaining proper tissue and organ size and patterning. How these ordered processes are precisely modulated remains relatively unknown. Here we show that planarians use the downstream effector of the Hippo signaling cascade, yorkie (yki; YAP in vertebrates) to control a diverse set of pleiotropic processes in organ homeostasis, stem cell regulation, regeneration and axial patterning. We show that yki functions to maintain the homeostasis of the planarian excretory (protonephridial) system and to limit stem cell proliferation, but does not affect the differentiation process or cell death. Finally, we show that Yki acts synergistically with WNT/β-catenin signaling to repress head determination by limiting the expression domains of posterior WNT genes and that of the WNT-inhibitor notum. Together, our data show that yki is a key gene in planarians that integrates stem cell proliferation control, organ homeostasis, and the spatial patterning of tissues.

  14. Patterns of morphological integration between parietal and temporal areas in the human skull.

    PubMed

    Bruner, Emiliano; Pereira-Pedro, Ana Sofia; Bastir, Markus

    2017-10-01

    Modern humans have evolved bulging parietal areas and large, projecting temporal lobes. Both changes, largely due to a longitudinal expansion of these cranial and cerebral elements, were hypothesized to be the result of brain evolution and cognitive variations. Nonetheless, the independence of these two morphological characters has not been evaluated. Because of structural and functional integration among cranial elements, changes in the position of the temporal poles can be a secondary consequence of parietal bulging and reorientation of the head axis. In this study, we use geometric morphometrics to test the correlation between parietal shape and the morphology of the endocranial base in a sample of adult modern humans. Our results suggest that parietal proportions show no correlation with the relative position of the temporal poles within the spatial organization of the endocranial base. The vault and endocranial base are likely to be involved in distinct morphogenetic processes, with scarce or no integration between these two districts. Therefore, the current evidence rejects the hypothesis of reciprocal morphological influences between parietal and temporal morphology, suggesting that evolutionary spatial changes in these two areas may have been independent. However, parietal bulging exerts a visible effect on the rotation of the cranial base, influencing head position and orientation. This change can have had a major relevance in the reorganization of the head functional axis. © 2017 Wiley Periodicals, Inc.

  15. Revertants of Adenovirus Type 12-Transformed Hamster Cell Line T637 as Tools in the Analysis of Integration Patterns

    PubMed Central

    Eick, Dirk; Stabel, Silvia; Doerfler, Walter

    1980-01-01

    Spontaneously arising morphological revertants of the adenovirus type 12 (Ad12)-transformed hamster cell line T637 had been previously isolated, and it had been demonstrated that in these revertants varying amounts of the integrated Ad12 genome were eliminated from the host genome. In this report, the patterns of persistence of the viral genome in the revertants were analyzed in detail. In some of the revertant cell lines, F10, TR3, and TR7, all copies of Ad12 DNA integrated in line T637 were lost. In lines TR1, -2, -4 to -6, -8 to -10, and -13 to -16, only the right-hand portion of one Ad12 genome was preserved; it consisted of the intact right segment of Ad12 DNA and was integrated at the same site as in line T637. In revertant lines G12, TR11, and TR12, one Ad12 DNA and varying parts of a second viral DNA molecule persisted in the host genome. These patterns of persistence of Ad12 DNA molecules in different revertants supported a model for a mode of integration of Ad12 DNA in T637 hamster cells in which multiple (20 to 22) copies of the entire Ad12 DNA were serially arranged, separated from each other by stretches of cellular DNA. The occurrence of such revertants demonstrated that foreign DNA sequences could not only be acquired but could also be lost from eucaryotic genomes. There was very little, if any, expression of Ad12-specific DNA sequences in the revertant lines TR7 and TR12. Moreover, Ad12 DNA sequences which were found to be undermethylated in line T637 were completely methylated in the revertant cell lines G12, TR11, TR12, and TR2. These findings were consistent with the absence of T antigen from the revertant lines reported earlier. Hence it was conceivable that the expression of integrated viral DNA sequences was somehow dependent on their positions in the cellular genome. In cell line TR637, the early segments of Ad12 DNA were expressed and undermethylated; conversely, in the revertant lines G12, TR11, TR12, and TR2, the same segments appeared to

  16. Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels

    NASA Astrophysics Data System (ADS)

    Zhang, Chenchu; Hu, Yanlei; Du, Wenqiang; Wu, Peichao; Rao, Shenglong; Cai, Ze; Lao, Zhaoxin; Xu, Bing; Ni, Jincheng; Li, Jiawen; Zhao, Gang; Wu, Dong; Chu, Jiaru; Sugioka, Koji

    2016-09-01

    Rapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices.

  17. Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels.

    PubMed

    Zhang, Chenchu; Hu, Yanlei; Du, Wenqiang; Wu, Peichao; Rao, Shenglong; Cai, Ze; Lao, Zhaoxin; Xu, Bing; Ni, Jincheng; Li, Jiawen; Zhao, Gang; Wu, Dong; Chu, Jiaru; Sugioka, Koji

    2016-09-13

    Rapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices.

  18. Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels

    PubMed Central

    Zhang, Chenchu; Hu, Yanlei; Du, Wenqiang; Wu, Peichao; Rao, Shenglong; Cai, Ze; Lao, Zhaoxin; Xu, Bing; Ni, Jincheng; Li, Jiawen; Zhao, Gang; Wu, Dong; Chu, Jiaru; Sugioka, Koji

    2016-01-01

    Rapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices. PMID:27619690

  19. Integrated remote sensing and wavelet analyses for screening short-term teleconnection patterns in northeast America

    NASA Astrophysics Data System (ADS)

    Mullon, Lee; Chang, Ni-Bin; Jeffrey Yang, Y.; Weiss, Jason

    2013-08-01

    Global sea surface temperature (SST) anomalies have an inherent effect on vegetation dynamics and precipitation processes throughout the continental United States (U.S.). SST variations have been correlated with precipitation patterns via ocean-atmospheric interactions known as climate teleconnections. Prior research has demonstrated that understanding excitation mechanisms of the teleconnection patterns can be instrumental for climate prediction across a wide region at sub-continental scales, yet these studies tend to have large uncertainties in estimates by assuming linearity when examining teleconnection signals. The co-existence of non-stationary and nonlinear signals embedded in SST anomalies makes the identification of the teleconnection patterns difficult at the local scale. This study explores the short-term (10-year) frequencies (i.e., interannual and seasonal ) embedded in the non-stationary teleconnection signals between SST at the North Atlantic and North Pacific oceans and the responses of terrestrial greenness and precipitation along multiple pristine sites in northeast U.S., including (1) White Mountain National Forest - Pemigewasset Wilderness, (2) Green Mountain National Forest - Lye Brook Wilderness, and (3) Adirondack State Park - Siamese Ponds Wilderness. Each site was selected to avoid anthropogenic influences that may otherwise mask climate teleconnection signals. Lagged pixel-wise linear teleconnection analysis based on remote sensing satellite images across anomalous global SST datasets found significant correlation regions between SST and these terrestrial sites. With the aid of wavelet analyses including continuous wavelet transform, cross-wavelet analysis, and wavelet coherency analysis, nonlinear and non-stationary signals exhibit salient covariations at biennial and triennial frequencies between terrestrial responses and SST anomalies across oceanic regions in agreement with the El Nino Southern Oscillation (ENSO) and North Atlantic

  20. The DebugIT core ontology: semantic integration of antibiotics resistance patterns.

    PubMed

    Schober, Daniel; Boeker, Martin; Bullenkamp, Jessica; Huszka, Csaba; Depraetere, Kristof; Teodoro, Douglas; Nadah, Nadia; Choquet, Remy; Daniel, Christel; Schulz, Stefan

    2010-01-01

    Antibiotics resistance development poses a significant problem in today's hospital care. Massive amounts of clinical data are being collected and stored in proprietary and unconnected systems in heterogeneous format. The DebugIT EU project promises to make this data geographically and semantically interoperable for case-based knowledge analysis approaches aiming at the discovery of patterns that help to align antibiotics treatment schemes. The semantic glue for this endeavor is DCO, an application ontology that enables data miners to query distributed clinical information systems in a semantically rich and content driven manner. DCO will hence serve as the core component of the interoperability platform for the DebugIT project. Here we present DCO and an approach thet uses the semantic web query language SPARQL to bind and ontologically query hospital database content using DCO and information model mediators. We provide a query example that indicates that ontological querying over heterogeneous information models is feasible via SPARQL construct- and resource mapping queries.

  1. Pattern recognition of concrete surface cracks and defects using integrated image processing algorithms

    NASA Astrophysics Data System (ADS)

    Balbin, Jessie R.; Hortinela, Carlos C.; Garcia, Ramon G.; Baylon, Sunnycille; Ignacio, Alexander Joshua; Rivera, Marco Antonio; Sebastian, Jaimie

    2017-06-01

    Pattern recognition of concrete surface crack defects is very important in determining stability of structure like building, roads or bridges. Surface crack is one of the subjects in inspection, diagnosis, and maintenance as well as life prediction for the safety of the structures. Traditionally determining defects and cracks on concrete surfaces are done manually by inspection. Moreover, any internal defects on the concrete would require destructive testing for detection. The researchers created an automated surface crack detection for concrete using image processing techniques including Hough transform, LoG weighted, Dilation, Grayscale, Canny Edge Detection and Haar Wavelet Transform. An automatic surface crack detection robot is designed to capture the concrete surface by sectoring method. Surface crack classification was done with the use of Haar trained cascade object detector that uses both positive samples and negative samples which proved that it is possible to effectively identify the surface crack defects.

  2. Measuring the IMF and Detailed Abundance Patterns from the Integrated Light of Old Stellar Systems

    NASA Astrophysics Data System (ADS)

    Conroy, Charlie

    The spectral energy distributions (SEDs) of unresolved stellar systems holds key information regarding the detailed abundance pattern, star formation history, dust properties, and initial mass function (IMF) of the underlying stellar population(s). This information can only be extracted with the aid of stellar population synthesis (SPS) models. Such models have been employed to estimate basic properties such as the star formation rate, metallicity (Z, and in certain contexts, alpha-enhancement), and total stellar mass (assuming an IMF). However, much more information is available in the SED than can be extracted by the current generation of SPS models because existing models are plagued by incomplete and poorly calibrated ingredients. The proposers request funds to develop a next generation SPS model capable of measuring the IMF and detailed abundance patterns from the SEDs of composite stellar systems. In particular, we intend to develop an SPS model that makes accurate predictions for the SEDs (from 0.1-3mu m at a resolving power of ~5,000) of composite systems as a function of the IMF, stellar age, metallicity, and individual elemental abundances (including C, N, O, Na, Mg, Ca, Ti, Cr, Mn, Fe, Sr, and Ba). This will require the construction of a new synthetic stellar spectral library and a new isochrone library. This new model will be the first to make predictions for the full SED shape as a function of individual abundance ratios, age, and the IMF. We will extensively calibrate the model predictions against data on individual stars and globular clusters. The new model will be essential for interpreting optical-NIR spectra obtained from the James Webb Space Telescope as well as both present and future ground-based facilities.

  3. Ecological hierarchies and self-organisation - Pattern analysis, modelling and process integration across scales

    USGS Publications Warehouse

    Reuter, H.; Jopp, F.; Blanco-Moreno, J. M.; Damgaard, C.; Matsinos, Y.; DeAngelis, D.L.

    2010-01-01

    A continuing discussion in applied and theoretical ecology focuses on the relationship of different organisational levels and on how ecological systems interact across scales. We address principal approaches to cope with complex across-level issues in ecology by applying elements of hierarchy theory and the theory of complex adaptive systems. A top-down approach, often characterised by the use of statistical techniques, can be applied to analyse large-scale dynamics and identify constraints exerted on lower levels. Current developments are illustrated with examples from the analysis of within-community spatial patterns and large-scale vegetation patterns. A bottom-up approach allows one to elucidate how interactions of individuals shape dynamics at higher levels in a self-organisation process; e.g., population development and community composition. This may be facilitated by various modelling tools, which provide the distinction between focal levels and resulting properties. For instance, resilience in grassland communities has been analysed with a cellular automaton approach, and the driving forces in rodent population oscillations have been identified with an agent-based model. Both modelling tools illustrate the principles of analysing higher level processes by representing the interactions of basic components.The focus of most ecological investigations on either top-down or bottom-up approaches may not be appropriate, if strong cross-scale relationships predominate. Here, we propose an 'across-scale-approach', closely interweaving the inherent potentials of both approaches. This combination of analytical and synthesising approaches will enable ecologists to establish a more coherent access to cross-level interactions in ecological systems. ?? 2010 Gesellschaft f??r ??kologie.

  4. Integration of Optical Coherence Tomography Scan Patterns to Augment Clinical Data Suite

    NASA Technical Reports Server (NTRS)

    Mason, S.; Patel, N.; Van Baalen, M.; Tarver, W.; Otto, C.; Samuels, B.; Koslovsky, M.; Schaefer, C.; Taiym, W.; Wear, M.; hide

    2018-01-01

    Vision changes identified in long duration spaceflight astronauts has led Space Medicine at NASA to adopt a more comprehensive clinical monitoring protocol. Optical Coherence Tomography (OCT) was recently implemented at NASA, including on board the International Space Station in 2013. NASA is collaborating with Heidelberg Engineering to increase the fidelity of the current OCT data set by integrating the traditional circumpapillary OCT image with radial and horizontal block images at the optic nerve head. The retinal nerve fiber layer was segmented by two experienced individuals. Intra-rater (N=4 subjects and 70 images) and inter-rater (N=4 subjects and 221 images) agreement was performed. The results of this analysis and the potential benefits will be presented.

  5. Patterns of preoperative consultation and surgical specialty in an integrated healthcare system.

    PubMed

    Thilen, Stephan R; Bryson, Christopher L; Reid, Robert J; Wijeysundera, Duminda N; Weaver, Edward M; Treggiari, Miriam M

    2013-05-01

    Many patients scheduled for elective surgery are referred for a preoperative medical consultation. Only limited data are available on factors associated with preoperative consultations. The authors hypothesized that surgical specialty contributes to variation in referrals for preoperative consultations. This is a cohort study using data from Group Health Cooperative, an integrated healthcare system. The authors included 13,673 patients undergoing a variety of common procedures-primarily low-risk surgeries-representing six surgical specialties, in 2005-2006. The authors identified consultations by family physicians, general internists, pulmonologists, or cardiologists in the 42 days preceding surgery. Multivariable logistic regression was used to estimate the association between surgical specialty and consultation, adjusting for potential confounders including the revised cardiac risk index, age, gender, Deyo comorbidity index, number of prescription medications, and 11 medication classes. The authors found that 3,063 (22%) of all patients had preoperative consultations, with significant variation by surgical specialty. Patients having ophthalmologic, orthopedic, or urologic surgery were more likely to have consultations compared with those having general surgery-adjusted odds ratios (95% CI) of 3.8 (3.3-4.2), 1.5 (1.3-1.7), and 2.3 (1.8-2.8), respectively. Preoperative consultations were more common in patients with lower revised cardiac risk scores. There is substantial practice variation among surgical specialties with regard to the use of preoperative consultations in this integrated healthcare system. Given the large number of consultations provided for patients with low cardiac risk and for patients presenting for low-risk surgeries, their indications, the financial burden, and cost-effectiveness of consultations deserve further study.

  6. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

    PubMed Central

    Hekkala, Evon R.; Platt, Steven G.; Thorbjarnarson, John B.; Rainwater, Thomas R.; Tessler, Michael; Cunningham, Seth W.; Twomey, Christopher; Amato, George

    2015-01-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet’s crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062

  7. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize.

    PubMed

    Hekkala, Evon R; Platt, Steven G; Thorbjarnarson, John B; Rainwater, Thomas R; Tessler, Michael; Cunningham, Seth W; Twomey, Christopher; Amato, George

    2015-09-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research.

  8. Patterns of genomic integration of nuclear chloroplast DNA fragments in plant species.

    PubMed

    Yoshida, Takanori; Furihata, Hazuka Y; Kawabe, Akira

    2014-01-01

    The transfer of organelle DNA fragments to the nuclear genome is frequently observed in eukaryotes. These transfers are thought to play an important role in gene and genome evolution of eukaryotes. In plants, such transfers occur from plastid to nuclear [nuclear plastid DNAs (NUPTs)] and mitochondrial to nuclear (nuclear mitochondrial DNAs) genomes. The amount and genomic organization of organelle DNA fragments have been studied in model plant species, such as Arabidopsis thaliana and rice. At present, publicly available genomic data can be used to conduct such studies in non-model plants. In this study, we analysed the amount and genomic organization of NUPTs in 17 plant species for which genome sequences are available. The amount and distribution of NUPTs varied among the species. We also estimated the distribution of NUPTs according to the time of integration (relative age) by conducting sequence similarity analysis between NUPTs and the plastid genome. The age distributions suggested that the present genomic constitutions of NUPTs could be explained by the combination of the rapidly eliminated deleterious parts and few but constantly existing less deleterious parts.

  9. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

    PubMed Central

    Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita

    2016-01-01

    We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution. PMID:27803195

  10. Turbiditic minibasin infill patterns: Insights from a novel integrated modeling approach

    NASA Astrophysics Data System (ADS)

    Luthi, Stefan; Hodgson, David; Wang, Xiaoxi; Groenenberg, Remco

    2017-04-01

    The seafloor bathymetry of intraslope minibasins on continental margins is known to play a significant role in controlling turbidity current pathways and the resulting sediment distribution. To investigate the governing processes, we combine laboratory analogue modelling of intraslope minibasin formation with numerical flow simulations of multi-event turbidity currents, an approach that allows an improved understanding of evolving flow-bathymetry-deposit interactions and the resulting internal stacking patterns of the minibasin infills. The bathymetry includes a shelf-to-slope channel followed by an upper minibasin, which are separated by a confining ridge from two lower minibasins that compares well with analogous bathymetries reported from various natural settings. A series of 100 consecutive flows is here reported in detail. They are released into the top of the channel and upon reaching the upper minibasin they follow a series of stages from short initial ponding, filling-and-spilling and an extended transition to long retrogradational ponding. Upon reaching the upper minibasin floor the currents undergo a hydraulic jump, causing much sediment to be deposited in the central part of the minibasin and on the counterslope. This modifies the bathymetry such that during the fill-and-spill stage, flow stripping and grain size partitioning cause some finer sediment to be transported across the confining ridge into the lower minibasins. Throughout the basin infill process the deposits retrograde upstream accompanied by lateral switching into locally formed depressions in the upper minibasin. After the fill-and-spill stage, significant deposition occurs in the channel where cyclic steps with wavelengths of 1-2 km develop as a function of pulsating flow behaviour that switches repeatedly between sub- to supercritical flow conditions. These results are at variance with conventional schemes that emphasise sequential downstream minibasin filling through ponding dominated by

  11. Differences in HTLV-I integration patterns between skin lesions and peripheral blood lymphocytes of HTLV-I seropositive patients with cutaneous lymphoproliferative disorders.

    PubMed

    Hamada, T; Setoyama, M; Katahira, Y; Furuno, T; Fujiyoshi, T; Sonoda, S; Tashiro, M

    1992-09-01

    We examined HTLV-I integration patterns in nine cases of HTLV-I-seropositive patients with cutaneous lymphoproliferative disorders. The Southern blot on EcoRI digests of DNA revealed a discrete band of HTLV-I provirus (monoclonal integration) in either skin lesions or peripheral blood lymphocytes (PBL). Four cases showed the monoclonal integration of HTLV-I provirus only in skin lesions: one case showed only in PBL and two cases showed in both skin and PBL. The Southern blot on PstI digests of DNA revealed a 2.4 Kb band of the internal construct of HTLV-I provirus (polyclonal integration) in the PBL of EcoRI-negative samples. The difference in HTLV-I integration patterns between skin lesions and PBL in these cases suggests that the monoclonal outgrowth of HTLV-I-infected cells in the skin is causatively associated with the pathogenesis of cutaneous ATL.

  12. Statistical monitoring of spatial patterns of environmental indices for integrated ecosystem assessment: Application to the Bay of Biscay pelagic zone

    NASA Astrophysics Data System (ADS)

    Woillez, Mathieu; Petitgas, Pierre; Huret, Martin; Struski, Caroline; Léger, Fabien

    2010-10-01

    Monitoring the environment of fish is a key component of the ecosystem approach to fisheries management. Here, we propose a methodology to statistically monitor time series of maps of environmental indices. These maps were derived from a 37-year hindcast of a coupled physical-biogeochemical model. The space-time variability in the maps was decomposed using empirical orthogonal functions into time-invariant spatial patterns and time-varying amplitudes for these patterns. A statistical process control chart was then applied to the time series of the amplitudes. In that way, changes were detected with known statistical performance. The monitoring system also specified how long the changes lasted and which years, seasons and zones were affected. Results for all indices were assembled in an integrative dashboard of the detected deviations. For illustration, the procedure was applied to the Bay of Biscay pelagic zone. The selected environmental indices characterized the evolution of hydrological structures such as fronts and river plumes, as well as changes in temperature, water column stratification, horizontal current flow and primary production. A major result was that, in the last decade, sea surface temperature showed repeated significant shifts towards warming, which were largest in the northern half of the Bay, while the spatial extension of river plumes over the shelf alternated between wet and dry years. From 2005, several other indices showed repeated significant deviations: increase in sea bottom temperature, increase in the depth of the pycnocline and changes in coastal currents. The procedure provided an integrated view of ecosystem variability and change for all its components and their spatial organization.

  13. TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

    SciTech Connect

    Chen, H; Tan, J; Kavanaugh, J; Dolly, S; Gay, H; Thorstad, W; Anastasio, M; Altman, M; Mutic, S; Li, H

    2014-06-15

    Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-time and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding

  14. Real-Time fMRI Pattern Decoding and Neurofeedback Using FRIEND: An FSL-Integrated BCI Toolbox

    PubMed Central

    Sato, João R.; Basilio, Rodrigo; Paiva, Fernando F.; Garrido, Griselda J.; Bramati, Ivanei E.; Bado, Patricia; Tovar-Moll, Fernanda; Zahn, Roland; Moll, Jorge

    2013-01-01

    The demonstration that humans can learn to modulate their own brain activity based on feedback of neurophysiological signals opened up exciting opportunities for fundamental and applied neuroscience. Although EEG-based neurofeedback has been long employed both in experimental and clinical investigation, functional MRI (fMRI)-based neurofeedback emerged as a promising method, given its superior spatial resolution and ability to gauge deep cortical and subcortical brain regions. In combination with improved computational approaches, such as pattern recognition analysis (e.g., Support Vector Machines, SVM), fMRI neurofeedback and brain decoding represent key innovations in the field of neuromodulation and functional plasticity. Expansion in this field and its applications critically depend on the existence of freely available, integrated and user-friendly tools for the neuroimaging research community. Here, we introduce FRIEND, a graphic-oriented user-friendly interface package for fMRI neurofeedback and real-time multivoxel pattern decoding. The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI BOLD level and functional connectivity) and brain decoding-based feedback using SVM. FRIEND delivers an intuitive graphic interface with flexible processing pipelines involving optimized procedures embedding widely validated packages, such as FSL and libSVM. In addition, a user-defined visual neurofeedback module allows users to easily design and run fMRI neurofeedback experiments using ROI-based or multivariate classification approaches. FRIEND is open-source and free for non-commercial use. Processing tutorials and extensive documentation are available. PMID:24312569

  15. Spike patterning in oxytocin neurons: Capturing physiological behaviour with Hodgkin-Huxley and integrate-and-fire models.

    PubMed

    Leng, Trystan; Leng, Gareth; MacGregor, Duncan J

    2017-01-01

    Integrate-and-fire (IF) models can provide close matches to the discharge activity of neurons, but do they oversimplify the biophysical properties of the neurons? A single compartment Hodgkin-Huxley (HH) model of the oxytocin neuron has previously been developed, incorporating biophysical measurements of channel properties obtained in vitro. A simpler modified integrate-and-fire model has also been developed, which can match well the characteristic spike patterning of oxytocin neurons as observed in vivo. Here, we extended the HH model to incorporate synaptic input, to enable us to compare spike activity in the model with experimental data obtained in vivo. We refined the HH model parameters to closely match the data, and then matched the same experimental data with a modified IF model, using an evolutionary algorithm to optimise parameter matching. Finally we compared the properties of the modified HH model with those of the IF model to seek an explanation for differences between spike patterning in vitro and in vivo. We show that, with slight modifications, the original HH model, like the IF model, is able to closely match both the interspike interval (ISI) distributions of oxytocin neurons and the observed variability of spike firing rates in vivo and in vitro. This close match of both models to data depends on the presence of a slow activity-dependent hyperpolarisation (AHP); this is represented in both models and the parameters used in the HH model representation match well with optimal parameters of the IF model found by an evolutionary algorithm. The ability of both models to fit data closely also depends on a shorter hyperpolarising after potential (HAP); this is explicitly represented in the IF model, but in the HH model, it emerges from a combination of several components. The critical elements of this combination are identified.

  16. Real-time fMRI pattern decoding and neurofeedback using FRIEND: an FSL-integrated BCI toolbox.

    PubMed

    Sato, João R; Basilio, Rodrigo; Paiva, Fernando F; Garrido, Griselda J; Bramati, Ivanei E; Bado, Patricia; Tovar-Moll, Fernanda; Zahn, Roland; Moll, Jorge

    2013-01-01

    The demonstration that humans can learn to modulate their own brain activity based on feedback of neurophysiological signals opened up exciting opportunities for fundamental and applied neuroscience. Although EEG-based neurofeedback has been long employed both in experimental and clinical investigation, functional MRI (fMRI)-based neurofeedback emerged as a promising method, given its superior spatial resolution and ability to gauge deep cortical and subcortical brain regions. In combination with improved computational approaches, such as pattern recognition analysis (e.g., Support Vector Machines, SVM), fMRI neurofeedback and brain decoding represent key innovations in the field of neuromodulation and functional plasticity. Expansion in this field and its applications critically depend on the existence of freely available, integrated and user-friendly tools for the neuroimaging research community. Here, we introduce FRIEND, a graphic-oriented user-friendly interface package for fMRI neurofeedback and real-time multivoxel pattern decoding. The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI BOLD level and functional connectivity) and brain decoding-based feedback using SVM. FRIEND delivers an intuitive graphic interface with flexible processing pipelines involving optimized procedures embedding widely validated packages, such as FSL and libSVM. In addition, a user-defined visual neurofeedback module allows users to easily design and run fMRI neurofeedback experiments using ROI-based or multivariate classification approaches. FRIEND is open-source and free for non-commercial use. Processing tutorials and extensive documentation are available.

  17. HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data.

    PubMed

    Dennis, Ann M; Hué, Stéphane; Pasquale, Dana; Napravnik, Sonia; Sebastian, Joseph; Miller, William C; Eron, Joseph J

    2015-10-01

    Latinos represent a growing proportion of HIV cases in North Carolina (NC). Understanding how immigrants are involved in local HIV transmission is important to guide interventions. We used phylogenetics to characterize Latino involvement in local HIV transmission chains. Transmission clusters were identified from maximum-likelihood phylogenies constructed with HIV pol sequences from 177 Latinos and 1,496 non-Latinos receiving care in NC. Highly supported clusters involving one or more Latinos were characterized. Migration data were obtained from interviews and chart review. Factors associated with cluster membership were identified using log-binomial regression. Most Latinos were male (76%), immigrants (83%), and had HIV-1B (99%). Immigrants were more likely to report heterosexual risk (67% vs. 23%) than U.S.-born Latinos (p < 0.01). We identified 32 clusters that included one or more Latinos; these involved 53 Latinos (30%) and 41 non-Latinos. Immigrant and U.S.-born Latinos were equally likely to be in clusters, but immigrants were more likely to be in clusters with another Latino (78% vs. 29%; p = 0.02). Cluster composition by ethnicity and risk behavior varied by cluster size; larger clusters contained fewer immigrants and more men who have sex with men (MSM). Factors associated with immigrant membership in local transmission clusters included age <30 years [RR 2.34 (95% CI 1.47-3.73)], Mexican origin [RR 2.55 (95% CI 1.29-6.88)], and residing in the United States longer before diagnosis [RR 1.53 (95% CI 1.09-2.15), per 10 years]. While some Latinos immigrate with HIV infection, many immigrants are involved in transmission networks after arrival, particularly MSM. HIV testing and prevention interventions must consider this heterogeneity and may be better targeted by integrating phylogenetic analyses.

  18. HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data

    PubMed Central

    Hué, Stéphane; Pasquale, Dana; Napravnik, Sonia; Sebastian, Joseph; Miller, William C.; Eron, Joseph J.

    2015-01-01

    Abstract Latinos represent a growing proportion of HIV cases in North Carolina (NC). Understanding how immigrants are involved in local HIV transmission is important to guide interventions. We used phylogenetics to characterize Latino involvement in local HIV transmission chains. Transmission clusters were identified from maximum-likelihood phylogenies constructed with HIV pol sequences from 177 Latinos and 1,496 non-Latinos receiving care in NC. Highly supported clusters involving one or more Latinos were characterized. Migration data were obtained from interviews and chart review. Factors associated with cluster membership were identified using log-binomial regression. Most Latinos were male (76%), immigrants (83%), and had HIV-1B (99%). Immigrants were more likely to report heterosexual risk (67% vs. 23%) than U.S.-born Latinos (p < 0.01). We identified 32 clusters that included one or more Latinos; these involved 53 Latinos (30%) and 41 non-Latinos. Immigrant and U.S.-born Latinos were equally likely to be in clusters, but immigrants were more likely to be in clusters with another Latino (78% vs. 29%; p = 0.02). Cluster composition by ethnicity and risk behavior varied by cluster size; larger clusters contained fewer immigrants and more men who have sex with men (MSM). Factors associated with immigrant membership in local transmission clusters included age <30 years [RR 2.34 (95% CI 1.47–3.73)], Mexican origin [RR 2.55 (95% CI 1.29–6.88)], and residing in the United States longer before diagnosis [RR 1.53 (95% CI 1.09–2.15), per 10 years]. While some Latinos immigrate with HIV infection, many immigrants are involved in transmission networks after arrival, particularly MSM. HIV testing and prevention interventions must consider this heterogeneity and may be better targeted by integrating phylogenetic analyses. PMID:26214548

  19. 4-dimensional functional profiling in the convulsant-treated larval zebrafish brain.

    PubMed

    Winter, Matthew J; Windell, Dylan; Metz, Jeremy; Matthews, Peter; Pinion, Joe; Brown, Jonathan T; Hetheridge, Malcolm J; Ball, Jonathan S; Owen, Stewart F; Redfern, Will S; Moger, Julian; Randall, Andrew D; Tyler, Charles R

    2017-07-26

    Functional neuroimaging, using genetically-encoded Ca(2+) sensors in larval zebrafish, offers a powerful combination of high spatiotemporal resolution and higher vertebrate relevance for quantitative neuropharmacological profiling. Here we use zebrafish larvae with pan-neuronal expression of GCaMP6s, combined with light sheet microscopy and a novel image processing pipeline, for the 4D profiling of chemoconvulsant action in multiple brain regions. In untreated larvae, regions associated with autonomic functionality, sensory processing and stress-responsiveness, consistently exhibited elevated spontaneous activity. The application of drugs targeting different convulsant mechanisms (4-Aminopyridine, Pentylenetetrazole, Pilocarpine and Strychnine) resulted in distinct spatiotemporal patterns of activity. These activity patterns showed some interesting parallels with what is known of the distribution of their respective molecular targets, but crucially also revealed system-wide neural circuit responses to stimulation or suppression. Drug concentration-response curves of neural activity were identified in a number of anatomically-defined zebrafish brain regions, and in vivo larval electrophysiology, also conducted in 4dpf larvae, provided additional measures of neural activity. Our quantification of network-wide chemoconvulsant drug activity in the whole zebrafish brain illustrates the power of this approach for neuropharmacological profiling in applications ranging from accelerating studies of drug safety and efficacy, to identifying pharmacologically-altered networks in zebrafish models of human neurological disorders.

  20. Gene Set-Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer.

    PubMed

    Chang, Chia-Ming; Chuang, Chi-Mu; Wang, Mong-Lien; Yang, Yi-Ping; Chuang, Jen-Hua; Yang, Ming-Jie; Yen, Ming-Shyen; Chiou, Shih-Hwa; Chang, Cheng-Chang

    2016-08-05

    Clear cell (CCC), endometrioid (EC), mucinous (MC) and high-grade serous carcinoma (SC) are the four most common subtypes of epithelial ovarian carcinoma (EOC). The widely accepted dualistic model of ovarian carcinogenesis divided EOCs into type I and II categories based on the molecular features. However, this hypothesis has not been experimentally demonstrated. We carried out a gene set-based analysis by integrating the microarray gene expression profiles downloaded from the publicly available databases. These quantified biological functions of EOCs were defined by 1454 Gene Ontology (GO) term and 674 Reactome pathway gene sets. The pathogenesis of the four EOC subtypes was investigated by hierarchical clustering and exploratory factor analysis. The patterns of functional regulation among the four subtypes containing 1316 cases could be accurately classified by machine learning. The results revealed that the ERBB and PI3K-related pathways played important roles in the carcinogenesis of CCC, EC and MC; while deregulation of cell cycle was more predominant in SC. The study revealed that two different functional regulation patterns exist among the four EOC subtypes, which were compatible with the type I and II classifications proposed by the dualistic model of ovarian carcinogenesis.

  1. [Integrity].

    PubMed

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  2. Properties and application of a multichannel integrated circuit for low-artifact, patterned electrical stimulation of neural tissue

    PubMed Central

    Hottowy, Paweł; Skoczeń, Andrzej; Gunning, Deborah E.; Kachiguine, Sergei; Mathieson, Keith; Sher, Alexander; Wiącek, Piotr; Litke, Alan M.; Dąbrowski, Władysław

    2012-01-01

    Objective Modern multielectrode array (MEA) systems can record the neuronal activity from thousands of electrodes, but their ability to provide spatio-temporal patterns of electrical stimulation is very limited. Furthermore, the stimulus-related artifacts significantly limit the ability to record the neuronal responses to the stimulation. To address these issues, we designed a multichannel integrated circuit for patterned MEA-based electrical stimulation and evaluated its performance in experiments with isolated mouse and rat retina. Approach The Stimchip includes 64 independent stimulation channels. Each channel comprises an internal digital-to-analog converter that can be configured as a current or voltage source. The shape of the stimulation waveform is defined independently for each channel by the real-time data stream. In addition, each channel is equipped with circuitry for reduction of the stimulus artifact. Main results Using a high-density MEA stimulation/recording system, we effectively stimulated individual retinal ganglion cells (RGCs) and recorded the neuronal responses with minimal distortion, even on the stimulating electrodes. We independently stimulated a population of RGCs in rat retina and, using a complex spatio-temporal pattern of electrical stimulation pulses, we replicated visually-evoked spiking activity of a subset of these cells with high fidelity. Significance Compared with current state-of-the-art MEA systems, the Stimchip is able to stimulate neuronal cells with much more complex sequences of electrical pulses and with significantly reduced artifacts. This opens up new possibilities for studies of neuronal responses to electrical stimulation, both in the context of neuroscience research and in the development of neuroprosthetic devices. PMID:23160018

  3. Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes: Probable Transmissions between Other Primates and Chimpanzees†

    PubMed Central

    Jern, Patric; Sperber, Göran O.; Blomberg, Jonas

    2006-01-01

    The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line. PMID:16415014

  4. Identification of spatiotemporal nutrient patterns in a coastal bay via an integrated k-means clustering and gravity model.

    PubMed

    Chang, Ni-Bin; Wimberly, Brent; Xuan, Zhemin

    2012-03-01

    This study presents an integrated k-means clustering and gravity model (IKCGM) for investigating the spatiotemporal patterns of nutrient and associated dissolved oxygen levels in Tampa Bay, Florida. By using a k-means clustering analysis to first partition the nutrient data into a user-specified number of subsets, it is possible to discover the spatiotemporal patterns of nutrient distribution in the bay and capture the inherent linkages of hydrodynamic and biogeochemical features. Such patterns may then be combined with a gravity model to link the nutrient source contribution from each coastal watershed to the generated clusters in the bay to aid in the source proportion analysis for environmental management. The clustering analysis was carried out based on 1 year (2008) water quality data composed of 55 sample stations throughout Tampa Bay collected by the Environmental Protection Commission of Hillsborough County. In addition, hydrological and river water quality data of the same year were acquired from the United States Geological Survey's National Water Information System to support the gravity modeling analysis. The results show that the k-means model with 8 clusters is the optimal choice, in which cluster 2 at Lower Tampa Bay had the minimum values of total nitrogen (TN) concentrations, chlorophyll a (Chl-a) concentrations, and ocean color values in every season as well as the minimum concentration of total phosphorus (TP) in three consecutive seasons in 2008. The datasets indicate that Lower Tampa Bay is an area with limited nutrient input throughout the year. Cluster 5, located in Middle Tampa Bay, displayed elevated TN concentrations, ocean color values, and Chl-a concentrations, suggesting that high values of colored dissolved organic matter are linked with some nutrient sources. The data presented by the gravity modeling analysis indicate that the Alafia River Basin is the major contributor of nutrients in terms of both TP and TN values in all seasons

  5. All ASD complex and real 4-dimensional Einstein spaces with Λ≠0 admitting a nonnull Killing vector

    NASA Astrophysics Data System (ADS)

    Chudecki, Adam

    2016-12-01

    Anti-self-dual (ASD) 4-dimensional complex Einstein spaces with nonzero cosmological constant Λ equipped with a nonnull Killing vector are considered. It is shown that any conformally nonflat metric of such spaces can be always brought to a special form and the Einstein field equations can be reduced to the Boyer-Finley-Plebański equation (Toda field equation). Some alternative forms of the metric are discussed. All possible real slices (neutral, Euclidean and Lorentzian) of ASD complex Einstein spaces with Λ≠0 admitting a nonnull Killing vector are found.

  6. [New theory of holistic integrative physiology and medicine. III: New insight of neurohumoral mechanism and pattern of control and regulation for core axe of respiration, circulation and metabolism].

    PubMed

    Sun, Xing-guo

    2015-07-01

    Systemic mechanism of neurohumoral control and regulation for human is limited. We used the new theory of holistic integrative physiology and medicine to approach the mechanism and pattern of neurohumoral control and regulation for life. As the core of human life, there are two core axes of functions. The first one is the common goal of respiration and circulation to transport oxygen and carbon dioxide for cells, and the second one is the goal of gastrointestinal tract and circulation to transport energy material and metabolic product for cells. These two core axes maintain the metabolism. The neurohumoral regulation is holistically integrated and unified for all functions in human body. We simplified explain the mechanism of neurohumoral control and regulation life (respiration and circulation) as the example pattern of sound system. Based upon integrated regulation of life, we described the neurohumoral pattern to control respiration and circulation.

  7. Integration

    ERIC Educational Resources Information Center

    Kalyn, Brenda

    2006-01-01

    Integrated learning is an exciting adventure for both teachers and students. It is not uncommon to observe the integration of academic subjects such as math, science, and language arts. However, educators need to recognize that movement experiences in physical education also can be linked to academic curricula and, may even lead the…

  8. 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation

    PubMed Central

    Lee, Juhyun; Fei, Peng; Packard, René R. Sevag; Kang, Hanul; Xu, Hao; Baek, Kyung In; Jen, Nelson; Chen, Junjie; Yen, Hilary; Chi, Neil C.; Ho, Chih-Ming; Hsiai, Tzung K.

    2016-01-01

    Hemodynamic shear forces are intimately linked with cardiac development, during which trabeculae form a network of branching outgrowths from the myocardium. Mutations that alter Notch signaling also result in trabeculation defects. Here, we assessed whether shear stress modulates trabeculation to influence contractile function. Specifically, we acquired 4D (3D + time) images with light sheets by selective plane illumination microscopy (SPIM) for rapid scanning and deep axial penetration during zebrafish morphogenesis. Reduction of blood viscosity via gata1a morpholino oligonucleotides (MO) reduced shear stress, resulting in downregulation of Notch signaling and attenuation of trabeculation. Arrest of cardiomyocyte contraction either by troponin T type 2a (tnnt2a) MO or in weak atriumm58 (wea) mutants resulted in reduced shear stress and downregulation of Notch signaling and trabeculation. Integrating 4D SPIM imaging with synchronization algorithm demonstrated that coinjection of neuregulin1 mRNA with gata1 MO rescued trabeculation to restore contractile function in association with upregulation of Notch-related genes. Crossbreeding of Tg(flk:mCherry) fish, which allows visualization of the vascular system with the Tg(tp1:gfp) Notch reporter line, revealed that shear stress–mediated Notch activation localizes to the endocardium. Deleting endocardium via the clochesk4 mutants downregulated Notch signaling, resulting in nontrabeculated ventricle. Subjecting endothelial cells to pulsatile flow in the presence of the ADAM10 inhibitor corroborated shear stress–activated Notch signaling to modulate trabeculation. PMID:27018592

  9. 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation.

    PubMed

    Lee, Juhyun; Fei, Peng; Packard, René R Sevag; Kang, Hanul; Xu, Hao; Baek, Kyung In; Jen, Nelson; Chen, Junjie; Yen, Hilary; Kuo, C-C Jay; Chi, Neil C; Ho, Chih-Ming; Li, Rongsong; Hsiai, Tzung K

    2016-05-02

    Hemodynamic shear forces are intimately linked with cardiac development, during which trabeculae form a network of branching outgrowths from the myocardium. Mutations that alter Notch signaling also result in trabeculation defects. Here, we assessed whether shear stress modulates trabeculation to influence contractile function. Specifically, we acquired 4D (3D + time) images with light sheets by selective plane illumination microscopy (SPIM) for rapid scanning and deep axial penetration during zebrafish morphogenesis. Reduction of blood viscosity via gata1a morpholino oligonucleotides (MO) reduced shear stress, resulting in downregulation of Notch signaling and attenuation of trabeculation. Arrest of cardiomyocyte contraction either by troponin T type 2a (tnnt2a) MO or in weak atriumm58 (wea) mutants resulted in reduced shear stress and downregulation of Notch signaling and trabeculation. Integrating 4D SPIM imaging with synchronization algorithm demonstrated that coinjection of neuregulin1 mRNA with gata1 MO rescued trabeculation to restore contractile function in association with upregulation of Notch-related genes. Crossbreeding of Tg(flk:mCherry) fish, which allows visualization of the vascular system with the Tg(tp1:gfp) Notch reporter line, revealed that shear stress-mediated Notch activation localizes to the endocardium. Deleting endocardium via the clochesk4 mutants downregulated Notch signaling, resulting in nontrabeculated ventricle. Subjecting endothelial cells to pulsatile flow in the presence of the ADAM10 inhibitor corroborated shear stress-activated Notch signaling to modulate trabeculation.

  10. Gene expression patterns regulating embryogenesis based on the integrated de novo transcriptome assembly of the Japanese flounder.

    PubMed

    Fu, Yuanshuai; Jia, Liang; Shi, Zhiyi; Zhang, Junling; Li, Wenjuan

    2017-06-01

    The Japanese flounder (Paralichthys olivaceus) is one of the most important commercial and biological marine fishes. However, the molecular biology involved during embryogenesis and early development of the Japanese flounder remains largely unknown due to a lack of genomic resources. A comprehensive and integrated transcriptome is necessary to study the molecular mechanisms of early development and to allow for the detailed characterization of gene expression patterns during embryogenesis; this approach is critical to understanding the processes that occur prior to mesectoderm formation during early embryonic development. In this study, more than 117.8 million 100bp PE reads were generated from pooled RNA extracted from unfertilized eggs to 41dph (days post-hatching) embryos and were sequenced using Illumina pair-end sequencing technology. In total, 121,513 transcripts (≥200bp) were obtained using de novo assembly. A sequence similarity search indicated that 52,338 transcripts show significant similarity to 22,462 known proteins from the NCBI non-redundant database and the Swiss-Prot protein database and were annotated using Blast2GO. GO terms were assigned to 44,627 transcripts with 12,006 functional terms, and 10,024 transcripts were assigned to 133 KEGG pathways. Furthermore, gene expression differences between the unfertilized egg and the gastrula embryo were analysed using Illumina RNA-Seq with single-read sequencing technology, and 24,837 differentially and specifically expressed transcripts were identified and included 5,286 annotated transcripts and 19,569 non-annotated transcripts. All of the expressed transcripts in the unfertilized egg and gastrula embryo were further classified as maternal, zygotic, or maternal-zygotic transcripts, which may help us to understand the roles of these transcripts during the embryonic development of the Japanese flounder. Thus, the results will contribute to an improved understanding of the gene expression patterns and

  11. Integration of Scale Invariant Generator Technique and S-A Technique for Characterizing 2-D Patterns for Information Retrieve

    NASA Astrophysics Data System (ADS)

    Cao, L.; Cheng, Q.

    2004-12-01

    The scale invariant generator technique (SIG) and spectrum-area analysis technique (S-A) were developed independently relevant to the concept of the generalized scale invariance (GSI). The former was developed for characterizing the parameters involved in the GSI for characterizing and simulating multifractal measures whereas the latter was for identifying scaling breaks for decomposition of superimposed multifractal measures caused by multiple geophysical processes. A natural integration of these two techniques may yield a new technique to serve two purposes, on the one hand, that can enrich the power of S-A by increasing the interpretability of decomposed patterns in some applications of S-A and, on the other hand, that can provide a mean to test the uniqueness of multifractality of measures which is essential for application of SIG technique in more complicated environment. The implementation of the proposed technique has been done as a Dynamic Link Library (DLL) in Visual C++. The program can be friendly used for method validation and application in different fields.

  12. Patterns of sperm damage in Chernobyl passerine birds suggest a trade-off between sperm length and integrity.

    PubMed

    Hermosell, Ignacio G; Laskemoen, Terje; Rowe, Melissah; Møller, Anders P; Mousseau, Timothy A; Albrecht, Tomás; Lifjeld, Jan T

    2013-10-23

    Interspecific variation in sperm size is enigmatic, but generally assumed to reflect species-specific trade-offs in selection pressures. Among passerine birds, sperm length varies sevenfold, and sperm competition risk seems to drive the evolution of longer sperm. However, little is known about factors favouring short sperm or constraining the evolution of longer sperm. Here, we report a comparative analysis of sperm head abnormalities among 11 species of passerine bird in Chernobyl, presumably resulting from chronic irradiation following the 1986 accident. Frequencies of sperm abnormalities varied between 15.7 and 77.3% among species, more than fourfold higher than in uncontaminated areas. Nonetheless, species ranked similarly in sperm abnormalities in unpolluted areas as in Chernobyl, pointing to intrinsic factors underlying variation in sperm damage among species. Scanning electron microscopy of abnormal spermatozoa revealed patterns of acrosome damage consistent with premature acrosome reaction. Sperm length, but not sperm competition risk explained variation in sperm damage among species. This suggests that longer spermatozoa are more susceptible to premature acrosome reaction. Therefore, we hypothesize a trade-off between sperm length and sperm integrity affecting sperm evolution in passerine birds.

  13. Patterns of sperm damage in Chernobyl passerine birds suggest a trade-off between sperm length and integrity

    PubMed Central

    Hermosell, Ignacio G.; Laskemoen, Terje; Rowe, Melissah; Møller, Anders P.; Mousseau, Timothy A.; Albrecht, Tomáš; Lifjeld, Jan T.

    2013-01-01

    Interspecific variation in sperm size is enigmatic, but generally assumed to reflect species-specific trade-offs in selection pressures. Among passerine birds, sperm length varies sevenfold, and sperm competition risk seems to drive the evolution of longer sperm. However, little is known about factors favouring short sperm or constraining the evolution of longer sperm. Here, we report a comparative analysis of sperm head abnormalities among 11 species of passerine bird in Chernobyl, presumably resulting from chronic irradiation following the 1986 accident. Frequencies of sperm abnormalities varied between 15.7 and 77.3% among species, more than fourfold higher than in uncontaminated areas. Nonetheless, species ranked similarly in sperm abnormalities in unpolluted areas as in Chernobyl, pointing to intrinsic factors underlying variation in sperm damage among species. Scanning electron microscopy of abnormal spermatozoa revealed patterns of acrosome damage consistent with premature acrosome reaction. Sperm length, but not sperm competition risk explained variation in sperm damage among species. This suggests that longer spermatozoa are more susceptible to premature acrosome reaction. Therefore, we hypothesize a trade-off between sperm length and sperm integrity affecting sperm evolution in passerine birds. PMID:24088561

  14. Metabolomic Analysis of Diet-Induced Type 2 Diabetes Using UPLC/MS Integrated with Pattern Recognition Approach

    PubMed Central

    Sun, Hui; Zhang, Shuxiang; Zhang, Aihua; Yan, Guangli; Wu, Xiuhong; Han, Ying; Wang, Xijun

    2014-01-01

    Metabolomics represents an emerging discipline concerned with comprehensive assessment of small molecule endogenous metabolites in biological systems and provides a powerful approach insight into the mechanisms of diseases. Type 2 diabetes (T2D), called the burden of the 21st century, is growing with an epidemic rate. However, its precise molecular mechanism has not been comprehensively explored. In this study, we applied urinary metabolomics based on the UPLC/MS integrated with pattern recognition approaches to discover differentiating metabolites, to characterize and explore metabolic pathway disruption in an experimental model for high-fat-diet induced T2D. Six differentiating urinary metabolites were found in the negative mode, and two (2-(4-hydroxy-3-methoxy-phenyl) acetaldehyde sulfate, 2-phenylethanol glucuronide) of which were identified involving the key metabolic pathways linked to pentose and glucuronate interconversions, starch, sucrose metabolism and tyrosine metabolism. Our study provides new insight into pathophysiologic mechanisms and may enhance the understanding of T2D pathogenesis. PMID:24671089

  15. Determining the critical effective temperature and heat dispersal pattern in monopolar radiofrequency ablation using temperature-time integration

    PubMed Central

    TSENG, HOW; LIN, SEY-EN; CHANG, YEN-LIANG; CHEN, MING-HSU; HUNG, SHIH-HAN

    2016-01-01

    The radiofrequency ablation (RFA) lesion size is posited to be disproportionate to the total delivered energy, and temperature-time integration (TTI) may have a more critical effect on lesion size. The present study aimed to evaluate this hypothesis by determining the temperature threshold and temperature distribution over tissues during the RFA lesioning process. Using an ex vivo chicken tissue model and an in vivo rabbit model with RFA applied for 2 min under various target temperature settings, the resultant lesions were evaluated histologically using Masson's trichrome stain. The temperature distribution over the tissue during the RFA lesioning process was also determined using a VT02 Visual IR Thermometer. It was revealed that the thermal injury threshold for RFA in the chicken tissues was ~65°C, but that it ranged from 55–65°C in mammals. Using infra-red thermal imaging, the temperature gradient (from the center to the periphery) during the RFA lesioning process demonstrated a uniform heat diffusion pattern. This data supports the proposed hypothesis that TTI is a critical parameter in determining RFA lesion size and can be applied clinically using the following equation: [Target temperature − 55 (°C)] × time (sec) is proportional to RFA lesion size. PMID:26997990

  16. Turbulent Kinetic Energy Assessed by Multipoint 4-Dimensional Flow Magnetic Resonance Imaging Provides Additional Information Relative to Echocardiography for the Determination of Aortic Stenosis Severity.

    PubMed

    Binter, Christian; Gotschy, Alexander; Sündermann, Simon H; Frank, Michelle; Tanner, Felix C; Lüscher, Thomas F; Manka, Robert; Kozerke, Sebastian

    2017-06-01

    Turbulent kinetic energy (TKE), assessed by 4-dimensional (4D) flow magnetic resonance imaging, is a measure of energy loss in disturbed flow as it occurs, for instance, in aortic stenosis (AS). This work investigates the additional information provided by quantifying TKE for the assessment of AS severity in comparison to clinical echocardiographic measures. Fifty-one patients with AS (67±15 years, 20 female) and 10 healthy age-matched controls (69±5 years, 5 female) were prospectively enrolled to undergo multipoint 4D flow magnetic resonance imaging. Patients were split into 2 groups (severe and mild/moderate AS) according to their echocardiographic mean pressure gradient. TKE values were integrated over the aortic arch to obtain peak TKE. Integrating over systole yielded total TKEsys and by normalizing for stroke volume, normalized TKEsys was obtained. Mean pressure gradient and TKE correlated only weakly (R(2)=0.26 for peak TKE and R(2)=0.32 for normalized TKEsys) in the entire study population including control subjects, while no significant correlation was observed in the AS patient group. In the patient population with dilated ascending aorta, both peak TKE and total TKEsys were significantly elevated (P<0.01), whereas mean pressure gradient was significantly lower (P<0.05). Patients with bicuspid aortic valves also showed significantly increased TKE metrics (P<0.01), although no significant difference was found for mean pressure gradient. Elevated TKE levels imply higher energy losses associated with bicuspid aortic valves and dilated ascending aortic geometries that are not assessable by current echocardiographic measures. These findings indicate that TKE may provide complementary information to echocardiography, helping to distinguish within the heterogeneous population of patients with moderate to severe AS. © 2017 American Heart Association, Inc.

  17. Improved estimates of the dynamical state of the North Pacific Ocean from a 4 dimensional variational data assimilation

    NASA Astrophysics Data System (ADS)

    Masuda, Shuhei; Awaji, Toshiyuki; Sugiura, Nozomi; Ishikawa, Yoichi; Baba, Kinji; Horiuchi, Kazutoshi; Komori, Nobumasa

    2003-08-01

    A 4-dimensional variational data assimilation system has been used to better define the mean seasonal state of the North Pacific. The synthesis of available observational records and a sophisticated general circulation model produces a dynamically consistent time-varying dataset which exhibits realistic features of the global ocean circulation and requires no artificial sources or sinks for the temperature and salinity fields. The dataset enables us to clarify the water mass formation and movement processes. A sensitivity experiment using our system reveals that the origin of the North Pacific Intermediate Water can be traced back to the Okhotsk and Bering Seas in the subarctic region and to the subtropical Kuroshio region further south, consistent with recent observational findings. This result illustrates that the ocean state derived from our data assimilation has greater information and forecast potential than that obtained from earlier methods.

  18. Utilization of 4-Dimensional Data Visualization Modeling to Evaluate Burial Ground Contaminants at the Paducah Gaseous Diffusion Plant, Paducah, Kentucky

    SciTech Connect

    Brindley, T. L.; Tarantino, J. J.; Locke, A. L.; Dollins, D. W.

    2006-07-01

    This paper describes how 4-Dimensional (4D) Data Visualization Modeling was used to evaluate historical data and to help guide the decisions for the sampling necessary to complete a Remedial Investigation/Feasibility Study (RI/FS) for the burial ground sites at the Department of Energy (DOE) Paducah Gaseous Diffusion Plant (PGDP). DOE at the Paducah Site is primarily involved in environmental cleanup and landlord activities. The scope of this project was to prepare a work plan for identifying the data available and the data required to conduct an RI/FS for the Burial Ground Operable Unit (BGOU) located within and near PGDP. The work plan focuses on collecting existing information about contamination in and around the burial grounds and determining what additional data are required to support an assessment of risks to human health and the environment and to support future decisions regarding actions to reduce these risks. (authors)

  19. Quantitative volumetric analysis of gliomas with sequential MRI and ¹¹C-methionine PET assessment: patterns of integration in therapy planning.

    PubMed

    Arbizu, Javier; Tejada, S; Marti-Climent, J M; Diez-Valle, R; Prieto, E; Quincoces, G; Vigil, C; Idoate, M A; Zubieta, J L; Peñuelas, I; Richter, J A

    2012-05-01

    The aim of the study was to evaluate the volumetric integration patterns of standard MRI and (11)C-methionine positron emission tomography (PET) images in the surgery planning of gliomas and their relationship to the histological grade. We studied 23 patients with suspected or previously treated glioma who underwent preoperative (11)C-methionine PET because MRI was imprecise in defining the surgical target contour. Images were transferred to the treatment planning system, coregistered and fused (BrainLAB). Tumour delineation was performed by (11)C-methionine PET thresholding (vPET) and manual segmentation over MRI (vMRI). A 3-D volumetric study was conducted to evaluate the contribution of each modality to tumour target volume. All cases were surgically treated and histological classification was performed according to WHO grades. Additionally, several biopsy samples were taken according to the results derived either from PET or from MRI and analysed separately. Fifteen patients had high-grade tumours [ten glioblastoma multiforme (GBM) and five anaplastic), whereas eight patients had low-grade tumours. Biopsies from areas with high (11)C-methionine uptake without correspondence in MRI showed tumour proliferation, including infiltrative zones, distinguishing them from dysplasia and radionecrosis. Two main PET/MRI integration patterns emerged after analysis of volumetric data: pattern vMRI-in-vPET (11/23) and pattern vPET-in-vMRI (9/23). Besides, a possible third pattern with differences in both directions (vMRI-diff-vPET) could also be observed (3/23). There was a statistically significant association between the tumour classification and integration patterns described above (p < 0.001, κ = 0.72). GBM was associated with pattern vMRI-in-vPET (9/10), low-grade with pattern vPET-in-vMRI (7/8) and anaplastic with pattern vMRI-diff-vPET (3/5). The metabolically active tumour volume observed in (11)C-methionine PET differs from the volume of MRI by showing areas

  20. 3D Rheological Modeling of NW Intraplate Europe, Deciphering Spatial Integrated strength patterns, Mechanical Strong Layering and EET

    NASA Astrophysics Data System (ADS)

    Beekman, F.; Hardebol, N.; Cloetingh, S.; Tesauro, M.

    2006-12-01

    Better understanding of 3D rheological heterogeneity of the European Lithosphere provide the key to tie the recorded intraplate deformation pattern to stress fields transmitted into plate interior from plate boundary forces. The first order strain patterns result from stresses transmitted through the European lithosphere that is marked by a patchwork of high strength variability from inherited structural and compositional heterogeneities and upper mantle thermal perturbations. As the lithospheric rheology depends primarily on its spatial structure, composition and thermal estate, the 3D strength model for the European lithosphere relies on a 3D compositional model that yields the compositional heterogeneities and an iteratively calculated thermal cube using Fouriers law for heat conduction. The accurate appraisal of spatial strength variability results from proper mapping and integration of the geophysical compositional and thermal input parameters. Therefore, much attention has been paid to a proper description of first order structural and tectonic features that facilitate compilation of the compositional and thermal input models. As such, the 3D strength model reflects the thermo-mechanical structure inherited from the Europeans polyphase deformation history. Major 3D spatial mechanical strength variability has been revealed. The East-European and Fennoscandian Craton to the NE exhibit high strength (30-50 1012 N/m) from low mantle temperatures and surface heatflow of 35-60 mW/m2 while central and western Europe reflect a polyphase Phanerozoic thermo- tectonic history. Here, regions with high rigidity are formed primarily by patches of thermally stabilized Variscan Massifs (e.g. Rhenish, Armorican, Bohemian, and Iberian Massif) with low heatflow and lithospheric thickness values (50-65 mW/m2; 110-150 km) yielding strengths of ~15-25 1012 N/m. In contrast, major axis of weakened lithosphere coincides with Cenozoic Rift System (e.g. Upper and Lower Rhine Grabens

  1. [Assessment of the impacts of soil erosion on water environment based on the integration of soil erosion process and landscape pattern].

    PubMed

    Liu, Yu; Wu, Bing-Fang; Zeng, Yuan; Zhang, Lei

    2013-09-01

    The integration of the effects of landscape pattern to the assessment of the impacts of soil erosion on eco-environmental is of practical significance in methodological prospect, being able to provide an approach for identifying water body's sediment source area, assessing the potential risks of sediment export of on-site soil erosion to the target water body, and evaluating the capacity of regional landscape pattern in preventing soil loss. In this paper, the RUSLE model was applied to simulate the on-site soil erosion rate. With the consideration of the soil retention potential of vegetation cover and topography, a quantitative assessment was conducted on the impacts of soil erosion in the water source region of the middle route for South-to-North Water Transfer Project on rivers and reservoirs by delineating landscape pattern at point (or cell) scale and sub-watershed level. At point (or grid cell) scale, the index of soil erosion impact intensity (I) was developed as an indicator of the potential risk of sediment export to the water bodies. At sub-watershed level, the landscape leakiness index (LI) was employed to indicate the sediment retention capacity of a given landscape pattern. The results revealed that integrating the information of landscape pattern and the indices of soil erosion process could spatially effectively reflect the impact intensity of in situ soil erosion on water bodies. The LI was significantly exponentially correlated to the mean sediment retention capacity of landscape and the mean vegetation coverage of watershed, and the sediment yield at sub-watershed scale was significantly correlated to the LI in an exponential regression. It could be concluded that the approach of delineating landscape pattern based on soil erosion process and the integration of the information of landscape pattern with its soil retention potential could provide a new approach for the risk evaluation of soil erosion.

  2. Ethnic differences in maternal dietary patterns are largely explained by socio-economic score and integration score: a population-based study

    PubMed Central

    Sommer, Christine; Sletner, Line; Jenum, Anne K.; Mørkrid, Kjersti; Andersen, Lene F.; Birkeland, Kåre I.; Mosdøl, Annhild

    2013-01-01

    Background The impact of socio-economic position and integration level on the observed ethnic differences in dietary habits has received little attention. Objectives To identify and describe dietary patterns in a multi-ethnic population of pregnant women, to explore ethnic differences in odds ratio (OR) for belonging to a dietary pattern, when adjusted for socio-economic status and integration level and to examine whether the dietary patterns were reflected in levels of biomarkers related to obesity and hyperglycaemia. Design This cross-sectional study was a part of the STORK Groruddalen study. In total, 757 pregnant women, of whom 59% were of a non-Western origin, completed a food frequency questionnaire in gestational week 28±2. Dietary patterns were extracted through cluster analysis using Ward's method. Results Four robust clusters were identified where cluster 4 was considered the healthier dietary pattern and cluster 1 the least healthy. All non-European women as compared to Europeans had higher OR for belonging to the unhealthier dietary patterns 1–3 vs. cluster 4. Women from the Middle East and Africa had the highest OR, 21.5 (95% CI 10.6–43.7), of falling into cluster 1 vs. 4 as compared to Europeans. The ORs decreased substantially after adjusting for socio-economic score and integration score. A non-European ethnic origin, low socio-economic and integration scores, conduced higher OR for belonging to clusters 1, 2, and 3 as compared to cluster 4. Significant differences in fasting and 2-h glucose, fasting insulin, glycosylated haemoglobin (HbA1c), insulin resistance (HOMA-IR), and total cholesterol were observed across the dietary patterns. After adjusting for ethnicity, differences in fasting insulin (p=0.015) and HOMA-IR (p=0.040) across clusters remained significant, despite low power. Conclusion The results indicate that socio-economic and integration level may explain a large proportion of the ethnic differences in dietary patterns. PMID

  3. An integrated geochemical and geological approach for determining hydrocarbon generation-migration patterns: Central Gulf Coast Basin

    SciTech Connect

    Echols, J.B.; Zimmerman, R.K.; Goddard, D.A.

    1994-12-31

    New geochemical, geological, and well-production data indicate a Mesozoic hydrocarbon source for many younger reservoirs in central Louisiana and southwest Mississippi. A Jurassic source has been determined for several Cretaceous reservoirs in oil and gas fields of northeast Louisiana. The characteristic Wilcox, Sparta, and Frio biomarker, Bisnorhopane, identified in Austin Chalk oils from southwest Mississippi, links these Mesozoic and Tertiary oils. Cross-plots of {delta}{sup 13}C{sub AROM} versus {delta}{sup 13}C{sub SAT} indicate an Upper Jurassic (Smackover) and Lower Cretaceous source for certain Upper Cretaceous and Tertiary oils. However, the pristane/C{sub 17} ratio versus {delta}{sup 13}C{sub SAT} cross-plot indicates Wilcox and Sparta oils are heavily biodegraded Mesozoic (Lower Cretaceous) oils. There is an absence of gas accumulations in central Louisiana and southwest Mississippi in Midway, Wilcox, and Sparta reservoirs updip from coeval gas-prone source rocks. This is an indication of (1) a sealing regional fault system and/or stratigraphic migration barrier paralleling the Paleocene-Eocene shelf edge or (2) an earlier selective escape via vertical migration pathways. Vertical migration of hydrocarbons in northeast Louisiana, central Louisiana, and southwest Mississippi was accomplished primarily through fracture systems caused by wrench faulting; to the south and west, salt tectonics and related normal faulting played significant roles in the process. In onshore and offshore south Louisiana, normal faulting and salt-related tectonics created primary migration pathways. Regional hydrocarbon generation-migration patterns differ conceptually from those illustrated in previous models employing long-range migration based primarily on geochemical considerations. This new interpretation integrates geochemical, geological, and production data useful in identifying new exploration plays in north and central Louisiana and in southwest Mississippi.

  4. An integrated geochemical and geological approach for determining hydrocarbon generation-migration patterns: Central Gulf Coast Basin

    SciTech Connect

    Echols, J.B.; Zimmerman, R.K.; Goddard, D.A.

    1994-09-01

    New geochemical, geological, and well-production data indicate a Mesozoic hydrocarbon source for many younger reservoirs in central Louisiana and southwest Mississippi. A Jurassic source has been determined for several oil and gas fields in northeast Louisiana. The characteristic Wilcox and Sparta biomarker, bisnorhopane, identified in Austin Chalk oils from southwest Mississippi, links these Mesozoic and Tertiary oils. Cross-plots of {delta}{sup 13}C{sub AROM} vs. {delta}{sup 13}C{sub SAT} indicate a lower Cretaceous source for certain upper Cretaceous and Tertiary oils, while crossplots of pristane/nC{sub 17} ratio vs. {delta}{sup 13}C{sub SAT} crossplots indicate that Wilcox and Sparta oils are heavily biodegraded Mesozoic (lower Cretaceous) oils. There is an absence of gas accumulations in central Louisiana and southwest Mississippi in Midway, Wilcox, and Sparta reservoirs updip from coeval gas-prone source rocks. This is an indication of a sealing regional fault system and/or stratigraphic migration barrier paralleling the Paleocene-Eocene shelf edge. Vertical migration of hydrocarbons in northeast Louisiana, central Louisiana, and southwest Mississippi was accomplished primarily through fracture systems caused by wrench faulting; to the south and west, salt tectonics and related normal faulting played significant roles in the process. In onshore and offshore south Louisiana, normal faulting and salt-related tectonics created primary migration pathways. Regional hydrocarbon generation-migration patterns differ conceptually from those illustrated in previous models employing long-range migration based primarily on geochemical considerations. This new interpretation integrates geochemical, geological, and production data especially useful in identifying new exploration plays in north and central Louisiana and in southwest Mississippi.

  5. Bombyx mori and Aedes aegypti form multi-functional immune complexes that integrate pattern recognition, melanization, coagulants, and hemocyte recruitment

    PubMed Central

    Phillips, Dennis R.

    2017-01-01

    The innate immune system of insects responds to wounding and pathogens by mobilizing multiple pathways that provide both systemic and localized protection. Key localized responses in hemolymph include melanization, coagulation, and hemocyte encapsulation, which synergistically seal wounds and envelop and destroy pathogens. To be effective, these pathways require a targeted deposition of their components to provide protection without compromising the host. Extensive research has identified a large number of the effectors that comprise these responses, but questions remain regarding their post-translational processing, function, and targeting. Here, we used mass spectrometry to demonstrate the integration of pathogen recognition proteins, coagulants, and melanization components into stable, high-mass, multi-functional Immune Complexes (ICs) in Bombyx mori and Aedes aegypti. Essential proteins common to both include phenoloxidases, apolipophorins, serine protease homologs, and a serine protease that promotes hemocyte recruitment through cytokine activation. Pattern recognition proteins included C-type Lectins in B. mori, while A. aegypti contained a protein homologous to Plasmodium-resistant LRIM1 from Anopheles gambiae. We also found that the B. mori IC is stabilized by extensive transglutaminase-catalyzed cross-linking of multiple components. The melanization inhibitor Egf1.0, from the parasitoid wasp Microplitis demolitor, blocked inclusion of specific components into the IC and also inhibited transglutaminase activity. Our results show how coagulants, melanization components, and hemocytes can be recruited to a wound surface or pathogen, provide insight into the mechanism by which a parasitoid evades this immune response, and suggest that insects as diverse as Lepidoptera and Diptera utilize similar defensive mechanisms. PMID:28199361

  6. Microfluidic-integrated patterned ITO immunosensor for rapid detection of prostate-specific membrane antigen biomarker in prostate cancer.

    PubMed

    Seenivasan, Rajesh; Singh, Chandra K; Warrick, Jay W; Ahmad, Nihal; Gunasekaran, Sundaram

    2017-09-15

    An optically transparent patterned indium tin oxide (ITO) three-electrode sensor integrated with a microfluidic channel was designed for label-free immunosensing of prostate-specific membrane antigen (PSMA), a prostate cancer (PCa) biomarker, expressed on prostate tissue and circulating tumor cells but also found in serum. The sensor relies on cysteamine capped gold nanoparticles (N-AuNPs) covalently linked with anti-PSMA antibody (Ab) for target specificity. A polydimethylsiloxane (PDMS) microfluidic channel is used to efficiently and reproducibly introduce sample containing soluble proteins/cells to the sensor. The PSMA is detected and quantified by measuring the change in differential pulse voltammetry signal of a redox probe ([Fe(CN)6](3-)/[Fe(CN)6](4-)) that is altered upon binding of PSMA with PSMA-Ab immobilized on N-AuNPs/ITO. Detection of PSMA expressing cells and soluble PSMA was tested. The limit of detection (LOD) of the sensor for PSMA-based PCa cells is 6/40µL (i.e., 150 cells/mL) (n=3) with a linear range of 15-400 cells/40µL (i.e., 375-10,000 cells/mL), and for the soluble PSMA is 0.499ng/40µL (i.e., 12.5ng/mL) (n=3) with the linear range of 0.75-250ng/40µL (i.e., 19-6250ng/mL), both with an incubation time of 10min. The results indicate that the sensor has a suitable sensitivity and dynamic range for routine detection of PCa circulating tumor cells and can be adapted to detect other biomarkers/cancer cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Bombyx mori and Aedes aegypti form multi-functional immune complexes that integrate pattern recognition, melanization, coagulants, and hemocyte recruitment.

    PubMed

    Phillips, Dennis R; Clark, Kevin D

    2017-01-01

    The innate immune system of insects responds to wounding and pathogens by mobilizing multiple pathways that provide both systemic and localized protection. Key localized responses in hemolymph include melanization, coagulation, and hemocyte encapsulation, which synergistically seal wounds and envelop and destroy pathogens. To be effective, these pathways require a targeted deposition of their components to provide protection without compromising the host. Extensive research has identified a large number of the effectors that comprise these responses, but questions remain regarding their post-translational processing, function, and targeting. Here, we used mass spectrometry to demonstrate the integration of pathogen recognition proteins, coagulants, and melanization components into stable, high-mass, multi-functional Immune Complexes (ICs) in Bombyx mori and Aedes aegypti. Essential proteins common to both include phenoloxidases, apolipophorins, serine protease homologs, and a serine protease that promotes hemocyte recruitment through cytokine activation. Pattern recognition proteins included C-type Lectins in B. mori, while A. aegypti contained a protein homologous to Plasmodium-resistant LRIM1 from Anopheles gambiae. We also found that the B. mori IC is stabilized by extensive transglutaminase-catalyzed cross-linking of multiple components. The melanization inhibitor Egf1.0, from the parasitoid wasp Microplitis demolitor, blocked inclusion of specific components into the IC and also inhibited transglutaminase activity. Our results show how coagulants, melanization components, and hemocytes can be recruited to a wound surface or pathogen, provide insight into the mechanism by which a parasitoid evades this immune response, and suggest that insects as diverse as Lepidoptera and Diptera utilize similar defensive mechanisms.

  8. A method to integrate patterned electrospun fibers with microfluidic systems to generate complex microenvironments for cell culture applications

    PubMed Central

    Wallin, Patric; Zandén, Carl; Carlberg, Björn; Hellström Erkenstam, Nina; Liu, Johan; Gold, Julie

    2012-01-01

    The properties of a cell’s microenvironment are one of the main driving forces in cellular fate processes and phenotype expression invivo. The ability to create controlled cell microenvironments invitro becomes increasingly important for studying or controlling phenotype expression in tissue engineering and drug discovery applications. This includes the capability to modify material surface properties within well-defined liquid environments in cell culture systems. One successful approach to mimic extra cellular matrix is with porous electrospun polymer fiber scaffolds, while microfluidic networks have been shown to efficiently generate spatially and temporally defined liquid microenvironments. Here, a method to integrate electrospun fibers with microfluidic networks was developed in order to form complex cell microenvironments with the capability to vary relevant parameters. Spatially defined regions of electrospun fibers of both aligned and random orientation were patterned on glass substrates that were irreversibly bonded to microfluidic networks produced in poly-dimethyl-siloxane. Concentration gradients obtained in the fiber containing channels were characterized experimentally and compared with values obtained by computational fluid dynamic simulations. Velocity and shear stress profiles, as well as vortex formation, were calculated to evaluate the influence of fiber pads on fluidic properties. The suitability of the system to support cell attachment and growth was demonstrated with a fibroblast cell line. The potential of the platform was further verified by a functional investigation of neural stem cell alignment in response to orientation of electrospun fibers versus a microfluidic generated chemoattractant gradient of stromal cell-derived factor 1 alpha. The described method is a competitive strategy to create complex microenvironments invitro that allow detailed studies on the interplay of topography, substrate surface properties, and soluble

  9. Integration of plasma-assisted surface chemical modification, soft lithography, and protein surface activation for single-cell patterning

    NASA Astrophysics Data System (ADS)

    Cheng, Q.; Komvopoulos, K.

    2010-07-01

    Surface patterning for single-cell culture was accomplished by combining plasma-assisted surface chemical modification, soft lithography, and protein-induced surface activation. Hydrophilic patterns were produced on Parylene C films deposited on glass substrates by oxygen plasma treatment through the windows of polydimethylsiloxane shadow masks. After incubation first with Pluronic F108 solution and then serum medium overnight, surface seeding with mesenchymal stem cells in serum medium resulted in single-cell patterning. The present method provides a means of surface patterning with direct implications in single-cell culture.

  10. Micro-patterning of NdFeB and SmCo magnet films for integration into micro-electro-mechanical-systems

    NASA Astrophysics Data System (ADS)

    Walther, A.; Marcoux, C.; Desloges, B.; Grechishkin, R.; Givord, D.; Dempsey, N. M.

    2009-03-01

    The integration of high-performance RE-TM (NdFeB and SmCo) hard magnetic films into micro-electro-mechanical-systems (MEMS) requires their patterning at the micron scale. In this paper we report on the applicability of standard micro-fabrication steps (film deposition onto topographically patterned substrates, wet etching and planarization) to the patterning of 5-8 μm thick RE-TM films. While NdFeB comprehensively fills micron-scaled trenches in patterned substrates, SmCo deposits are characterized by poor filling of the trench corners, which poses a problem for further processing by planarization. The magnetic hysteresis loops of both the NdFeB and SmCo patterned films are comparable to those of non-patterned films prepared under the same deposition/annealing conditions. A micron-scaled multipole magnetic field pattern is directly produced by the unidirectional magnetization of the patterned films. NdFeB and SmCo show similar behavior when wet etched in an amorphous state: etch rates of approximately 1.25 μm/min and vertical side walls which may be attributed to a large lateral over-etch of typically 20 μm. Chemical-mechanical-planarization (CMP) produced material removal rates of 0.5-3 μm/min for amorphous NdFeB. Ar ion etching of such films followed by the deposition of a Ta layer prior to film crystallization prevented degradation in magnetic properties compared to non-patterned films.

  11. Understanding the relationship between image quality and motion velocity in gated computed tomography: preliminary work for 4-dimensional musculoskeletal imaging.

    PubMed

    Tay, Shian Chao; Primak, Andrew N; Fletcher, Joel G; Schmidt, Bernhard; An, Kai-Nan; McCollough, Cynthia H

    2008-01-01

    To study the effect of motion velocity on image quality to determine the requirements for 4-dimensional (4D; ie, 3D + time) musculoskeletal computed tomographic (CT) imaging. A phantom with resolution targets in both axial (x-y) and coronal (x-z) planes was attached to a motion device and scanned with 64-slice CT using a retrospectively gated CT protocol with pitch values of 0.1 and 0.2. Data were acquired with the phantom at rest and while moving periodically along the x axis at several velocities. Spatial resolution and motion artifacts were assessed both for the axial and coronal targets. A linear relationship was found between motion artifact severity and phantom velocity. Spatial resolution was better preserved in the coronal target. However, coronal images displayed banding artifacts, with band displacements being linearly related to motion velocity. The 4D CT imaging of periodically moving objects with velocities up to 20 mm/s is feasible using a pitch value of 0.1 and a motion frequency of 30 cycles per minute.

  12. Multistability, local pattern formation, and global collective firing in a small-world network of nonleaky integrate-and-fire neurons.

    PubMed

    Rothkegel, Alexander; Lehnertz, Klaus

    2009-03-01

    We investigate numerically the collective dynamical behavior of pulse-coupled nonleaky integrate-and-fire neurons that are arranged on a two-dimensional small-world network. To ensure ongoing activity, we impose a probability for spontaneous firing for each neuron. We study network dynamics evolving from different sets of initial conditions in dependence on coupling strength and rewiring probability. Besides a homogeneous equilibrium state for low coupling strength, we observe different local patterns including cyclic waves, spiral waves, and turbulentlike patterns, which-depending on network parameters-interfere with the global collective firing of the neurons. We attribute the various network dynamics to distinct regimes in the parameter space. For the same network parameters different network dynamics can be observed depending on the set of initial conditions only. Such a multistable behavior and the interplay between local pattern formation and global collective firing may be attributable to the spatiotemporal dynamics of biological networks.

  13. Multistability, local pattern formation, and global collective firing in a small-world network of nonleaky integrate-and-fire neurons

    NASA Astrophysics Data System (ADS)

    Rothkegel, Alexander; Lehnertz, Klaus

    2009-03-01

    We investigate numerically the collective dynamical behavior of pulse-coupled nonleaky integrate-and-fire neurons that are arranged on a two-dimensional small-world network. To ensure ongoing activity, we impose a probability for spontaneous firing for each neuron. We study network dynamics evolving from different sets of initial conditions in dependence on coupling strength and rewiring probability. Besides a homogeneous equilibrium state for low coupling strength, we observe different local patterns including cyclic waves, spiral waves, and turbulentlike patterns, which—depending on network parameters—interfere with the global collective firing of the neurons. We attribute the various network dynamics to distinct regimes in the parameter space. For the same network parameters different network dynamics can be observed depending on the set of initial conditions only. Such a multistable behavior and the interplay between local pattern formation and global collective firing may be attributable to the spatiotemporal dynamics of biological networks.

  14. Patterns and trends of postpartum family planning in Ethiopia, Malawi, and Nigeria: evidence of missed opportunities for integration.

    PubMed

    Hounton, Sennen; Winfrey, William; Barros, Aluisio J D; Askew, Ian

    2015-01-01

    Background The first 12 months following childbirth are a period when a subsequent pregnancy holds the greatest risk for mother and baby, but also when there are numerous contacts with the healthcare system for postnatal care for mother and baby (immunisation, nutrition, etc.). The benefits and importance of postpartum family planning are well documented. They include a reduction in risk of miscarriage, as well as mitigation of (or protection against) low birth weight, neonatal and maternal death, preterm birth, and anaemia. Objectives The objectives of this paper are to assess patterns and trends in the use of postpartum family planning at the country level, to determine whether postpartum family planning is associated with birth interval and parity, and to identify the health services most closely associated with postpartum family planning after adjusting for socio-economic characteristics. Design Data were used from Demographic and Health Surveys that contain a reproductive calendar, carried out within the last 10 years, from Ethiopia, Malawi, and Nigeria. All women for whom the calendar was completed and who gave birth between 57 and 60 months prior to data collection were included in the analysis. For each of the births, we merged the reproductive calendar with the birth record into a survey for each country reflecting the previous 60 months. The definition of the postpartum period in this paper is based on a period of 3 months postpartum. We used this definition to assess early adoption of postpartum family planning. We assessed variations in postpartum family planning according to demographic and socio-economic variables, as well as its association with various contact opportunities with the health system [antenatal care (ANC), childbirth in facilities, immunisation, etc.]. We did simple descriptive analysis with tabular, graphic, and 'equiplot' displays and a logistic regression controlling for important background characteristics. Results Overall

  15. Patterns and trends of postpartum family planning in Ethiopia, Malawi, and Nigeria: evidence of missed opportunities for integration.

    PubMed

    Hounton, Sennen; Winfrey, William; Barros, Aluisio J D; Askew, Ian

    2015-01-01

    The first 12 months following childbirth are a period when a subsequent pregnancy holds the greatest risk for mother and baby, but also when there are numerous contacts with the healthcare system for postnatal care for mother and baby (immunisation, nutrition, etc.). The benefits and importance of postpartum family planning are well documented. They include a reduction in risk of miscarriage, as well as mitigation of (or protection against) low birth weight, neonatal and maternal death, preterm birth, and anaemia. The objectives of this paper are to assess patterns and trends in the use of postpartum family planning at the country level, to determine whether postpartum family planning is associated with birth interval and parity, and to identify the health services most closely associated with postpartum family planning after adjusting for socio-economic characteristics. Data were used from Demographic and Health Surveys that contain a reproductive calendar, carried out within the last 10 years, from Ethiopia, Malawi, and Nigeria. All women for whom the calendar was completed and who gave birth between 57 and 60 months prior to data collection were included in the analysis. For each of the births, we merged the reproductive calendar with the birth record into a survey for each country reflecting the previous 60 months. The definition of the postpartum period in this paper is based on a period of 3 months postpartum. We used this definition to assess early adoption of postpartum family planning. We assessed variations in postpartum family planning according to demographic and socio-economic variables, as well as its association with various contact opportunities with the health system [antenatal care (ANC), childbirth in facilities, immunisation, etc.]. We did simple descriptive analysis with tabular, graphic, and 'equiplot' displays and a logistic regression controlling for important background characteristics. Overall, variation in postpartum use of modern

  16. Patterns and trends of postpartum family planning in Ethiopia, Malawi, and Nigeria: evidence of missed opportunities for integration

    PubMed Central

    Hounton, Sennen; Winfrey, William; Barros, Aluisio J. D.; Askew, Ian

    2015-01-01

    Background The first 12 months following childbirth are a period when a subsequent pregnancy holds the greatest risk for mother and baby, but also when there are numerous contacts with the healthcare system for postnatal care for mother and baby (immunisation, nutrition, etc.). The benefits and importance of postpartum family planning are well documented. They include a reduction in risk of miscarriage, as well as mitigation of (or protection against) low birth weight, neonatal and maternal death, preterm birth, and anaemia. Objectives The objectives of this paper are to assess patterns and trends in the use of postpartum family planning at the country level, to determine whether postpartum family planning is associated with birth interval and parity, and to identify the health services most closely associated with postpartum family planning after adjusting for socio-economic characteristics. Design Data were used from Demographic and Health Surveys that contain a reproductive calendar, carried out within the last 10 years, from Ethiopia, Malawi, and Nigeria. All women for whom the calendar was completed and who gave birth between 57 and 60 months prior to data collection were included in the analysis. For each of the births, we merged the reproductive calendar with the birth record into a survey for each country reflecting the previous 60 months. The definition of the postpartum period in this paper is based on a period of 3 months postpartum. We used this definition to assess early adoption of postpartum family planning. We assessed variations in postpartum family planning according to demographic and socio-economic variables, as well as its association with various contact opportunities with the health system [antenatal care (ANC), childbirth in facilities, immunisation, etc.]. We did simple descriptive analysis with tabular, graphic, and ‘equiplot’ displays and a logistic regression controlling for important background characteristics. Results Overall

  17. Patterns of integration in the canine skull: an inside view into the relationship of the skull modules of domestic dogs and wolves.

    PubMed

    Curth, Stefan; Fischer, Martin S; Kupczik, Kornelius

    2017-08-17

    The skull shape variation in domestic dogs exceeds that of grey wolves by far. The artificial selection of dogs has even led to breeds with mismatching upper and lower jaws and maloccluded teeth. For that reason, it has been advocated that their skulls (including the teeth) can be divided into more or less independent modules on the basis of genetics, development or function. In this study, we investigated whether the large diversity of dog skulls and the frequent occurrence of orofacial disproportions can be explained by a lower integration strength between the modules of the skull and by deviations in their covariation pattern when compared to wolves. For that purpose, we employed geometric morphometric methods on the basis of 99 3D-landmarks representing the cranium (subdivided into rostrum and braincase), the mandible (subdivided into ramus and corpus), and the upper and lower tooth rows. These were taken from CT images of 196 dog and wolf skulls. First, we calculated the shape disparity of the mandible and the cranium in dogs and wolves. Then we tested whether the integration strength (measured by RV coefficient) and the covariation pattern (as analysed by partial least squares analysis) of the modules subordinate to the cranium and the mandible can explain differing disparity results. We show, contrary to our expectations, that the higher skull shape diversity in dogs is not explained by less integrated skull modules. Also, the pattern of their covariation in the dog skull can be traced back to similar patterns in the wolf. This shows that existing differences between wolves and dogs are at the utmost a matter of degree and not absolute. Copyright © 2017 Elsevier GmbH. All rights reserved.

  18. First identification of sub- and supercritical convection patterns from ‘GeoFlow’, the geophysical flow simulation experiment integrated in Fluid Science Laboratory

    NASA Astrophysics Data System (ADS)

    Futterer, B.; Egbers, C.; Dahley, N.; Koch, S.; Jehring, L.

    2010-01-01

    Physical mechanisms of thermally driven rotating fluids are important for a large number of geophysical problems, e.g. to explain the convection of the Earth's liquid outer core. Objective of the 'GeoFlow' experiment is to study stability, pattern formation, and transition to chaos of thermal convection in fluid-filled concentric, co-axially rotating spheres. This experiment is integrated in the Fluid Science Laboratory of the European COLUMBUS module on International Space Station. Fluid dynamics of the experiment was predicted with numerical simulations by means of a spectral code. In the non-rotating case the onset of convection bifurcated into steady fluid flow. Here patterns of convection showed co-existing states with axisymmetric, cubic and pentagonal modes. Transition to chaos was in the form of sudden onset. For the thermal convection in rotating spheres the onset of first instability showed an increase of modes for higher parameter regime. Transition was from steady via periodic to chaotic behaviour. Convection patterns of the experiment are observed with the Wollaston shearing interferometry. Images are in terms of interferograms with fringe patterns corresponding to special convective flows. A first glance at the images showed the classification of sub- and supercritical flow regimes. Aligned with numerical data a shift between experiment and numerical simulation was identified. Identification of convection patterns in interferograms was demonstrated for the example of a supercritical flow.

  19. Comparative Assessment of Liver Tumor Motion Using Cine–Magnetic Resonance Imaging Versus 4-Dimensional Computed Tomography

    SciTech Connect

    Fernandes, Annemarie T.; Apisarnthanarax, Smith; Yin, Lingshu; Zou, Wei; Rosen, Mark; Plastaras, John P.; Ben-Josef, Edgar; Metz, James M.; Teo, Boon-Keng

    2015-04-01

    Purpose: To compare the extent of tumor motion between 4-dimensional CT (4DCT) and cine-MRI in patients with hepatic tumors treated with radiation therapy. Methods and Materials: Patients with liver tumors who underwent 4DCT and 2-dimensional biplanar cine-MRI scans during simulation were retrospectively reviewed to determine the extent of target motion in the superior–inferior, anterior–posterior, and lateral directions. Cine-MRI was performed over 5 minutes. Tumor motion from MRI was determined by tracking the centroid of the gross tumor volume using deformable image registration. Motion estimates from 4DCT were performed by evaluation of the fiducial, residual contrast (or liver contour) positions in each CT phase. Results: Sixteen patients with hepatocellular carcinoma (n=11), cholangiocarcinoma (n=3), and liver metastasis (n=2) were reviewed. Cine-MRI motion was larger than 4DCT for the superior–inferior direction in 50% of patients by a median of 3.0 mm (range, 1.5-7 mm), the anterior–posterior direction in 44% of patients by a median of 2.5 mm (range, 1-5.5 mm), and laterally in 63% of patients by a median of 1.1 mm (range, 0.2-4.5 mm). Conclusions: Cine-MRI frequently detects larger differences in hepatic intrafraction tumor motion when compared with 4DCT most notably in the superior–inferior direction, and may be useful when assessing the need for or treating without respiratory management, particularly in patients with unreliable 4DCT imaging. Margins wider than the internal target volume as defined by 4DCT were required to encompass nearly all the motion detected by cine-MRI for some of the patients in this study.

  20. Levator hiatus dimensions in late pregnancy and the process of labor: a 3- and 4-dimensional transperineal ultrasound study.

    PubMed

    Siafarikas, Franziska; Stær-Jensen, Jette; Hilde, Gunvor; Bø, Kari; Ellström Engh, Marie

    2014-05-01

    The objectives of the investigation were to study the association between levator hiatus dimensions in late pregnancy and both the length of second stage of labor and also the delivery mode in women delivering their first child. In this cohort study, 231 nulliparous women were examined with 3- and 4-dimensional transperineal ultrasonography at 37 weeks of gestation. The anteroposterior, transverse diameter, and the area of levator hiatus were measured at rest, during levator ani muscle contraction, and during Valsalva maneuver. The second stage of labor was divided into passive and active second stage and delivery modes into normal vaginal or instrumental deliveries. Spearman correlation coefficient, independent-sample t test, and standard logistic regression were used for analysis. Larger levator hiatus dimensions at rest and during contraction at 37 weeks of gestation correlated with a shorter duration of the active second stage in women with normal vaginal delivery (Spearman correlation coefficient, -0.13 to -0.35, P ≤ .08). Women having normal vaginal deliveries had significantly larger transverse diameter at rest, during contraction, and during Valsalva maneuver compared with women having instrumental deliveries (mean difference, 0.29; 95% confidence interval (CI), 0.16-0.41; mean difference, 0.33; 95% CI, 0.21-0.44 and mean difference, 0.24; 95% CI, 0.06-0.42; P < .05). The same was true for the levator hiatus area at rest and during contraction (mean difference, 1.22; 95% CI, 0.37-2.07 and mean difference, 0.84; 95% CI, 0.22-1.46; P < .01). These estimates were unchanged by adjustments in the logistic regression analysis. Larger levator hiatus dimensions in late pregnancy had a significant association with a shorter active second stage of labor and normal vaginal delivery. Copyright © 2014 Mosby, Inc. All rights reserved.

  1. Comparative assessment of liver tumor motion using cine-magnetic resonance imaging versus 4-dimensional computed tomography.

    PubMed

    Fernandes, Annemarie T; Apisarnthanarax, Smith; Yin, Lingshu; Zou, Wei; Rosen, Mark; Plastaras, John P; Ben-Josef, Edgar; Metz, James M; Teo, Boon-Keng

    2015-04-01

    To compare the extent of tumor motion between 4-dimensional CT (4DCT) and cine-MRI in patients with hepatic tumors treated with radiation therapy. Patients with liver tumors who underwent 4DCT and 2-dimensional biplanar cine-MRI scans during simulation were retrospectively reviewed to determine the extent of target motion in the superior-inferior, anterior-posterior, and lateral directions. Cine-MRI was performed over 5 minutes. Tumor motion from MRI was determined by tracking the centroid of the gross tumor volume using deformable image registration. Motion estimates from 4DCT were performed by evaluation of the fiducial, residual contrast (or liver contour) positions in each CT phase. Sixteen patients with hepatocellular carcinoma (n=11), cholangiocarcinoma (n=3), and liver metastasis (n=2) were reviewed. Cine-MRI motion was larger than 4DCT for the superior-inferior direction in 50% of patients by a median of 3.0 mm (range, 1.5-7 mm), the anterior-posterior direction in 44% of patients by a median of 2.5 mm (range, 1-5.5 mm), and laterally in 63% of patients by a median of 1.1 mm (range, 0.2-4.5 mm). Cine-MRI frequently detects larger differences in hepatic intrafraction tumor motion when compared with 4DCT most notably in the superior-inferior direction, and may be useful when assessing the need for or treating without respiratory management, particularly in patients with unreliable 4DCT imaging. Margins wider than the internal target volume as defined by 4DCT were required to encompass nearly all the motion detected by cine-MRI for some of the patients in this study. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. HPVbase – a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas

    PubMed Central

    Kumar Gupta, Amit; Kumar, Manoj

    2015-01-01

    Human papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis. PMID:26205472

  3. HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas.

    PubMed

    Kumar Gupta, Amit; Kumar, Manoj

    2015-07-24

    Human papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis.

  4. Mutation of the zebrafish glass onion locus causes early cell-nonautonomous loss of neuroepithelial integrity followed by severe neuronal patterning defects in the retina.

    PubMed

    Pujic, Z; Malicki, J

    2001-06-15

    Mutation of the glass onion locus causes drastic neuronal patterning defects in the zebrafish retina and brain. The precise stratified appearance of the wild-type retina is absent in the mutants. The glass onion phenotype is first visible shortly after the formation of optic primordia and is characterized by the rounding of cells and disruption of the ventricular surface in the eye and brain neuroepithelia. With exception of the dorsal- and ventral-most regions of the brain, neuroepithelial cells lose their integrity and begin to distribute ectopically. At later stages, the laminar patterning of retinal neurons is severely disrupted. Despite the lack of lamination, individual retinal cell classes differentiate in the glass onion retina. Mosaic analysis reveals that the glass onion mutation acts cell nonautonomously within the retina and brain, as neuroepithelial cell morphology and polarity in these tissues are normal when mutant cells develop in wild-type hosts. We conclude that the glass onion mutation affects cell-cell signaling event(s) involved in the maintenance of the neuroepithelial cell layer shortly after its formation. The disruption of neuroepithelial integrity may be the cause of the neuronal patterning defects following neurogenesis. In addition, the expression of the glass onion phenotype in a subset of neuroepithelial cells as well as its onset following the initial formation of the neuroepithelial sheets indicate the presence of genetically distinct temporal and spatial subdivisions in the development of this histologically uniform tissue.

  5. Integrated polymer solar cells in serial architecture with patterned charge-transporting MoOx for miniature high-voltage sources

    NASA Astrophysics Data System (ADS)

    Cho, Seong-Min; Keum, Chang-Min; Park, Hea-Lim; Kim, Min-Hoi; Bae, Jin-Hyuk; Lee, Sin-Doo

    2014-04-01

    We develop miniature high-voltage sources from polymer solar cells (PSCs) with charge-transporting molybdenum oxide (MoOx) integrated in a serial architecture through sacrificial layer (SL)-assisted patterning. The MoOx layer, being patterned by the lift-off process of the SL of a hydrophobic fluorinated-polymer, as a hole transporting layer plays a critical role on the reduction of the dark current and the increase of a high open circuit voltage of an integrated PSC array. The underlying mechanism lies primarily on the elimination of the lateral charge pathways in the MoOx layer in the presence of the electrode interconnection. Two miniature voltage sources consisting of 20 PSCs and 50 PSCs are demonstrated in the operation of a liquid crystal display and an organic field-effect transistor, respectively. Our SL-assisted integration approach will be directly applicable for implementing the self-power sources made of the PSCs into a wide range of the electronic and optoelectronic devices.

  6. Relation between the contrast in time integrated dynamic speckle patterns an the power spectral density of their temporal intensity fluctuations.

    PubMed

    Draijer, Matthijs J; Hondebrink, Erwin; Larsson, Marcus; van Leeuwen, Ton G; Steenbergen, Wiendelt

    2010-10-11

    Scattering fluid flux can be quantified with coherent light, either from the contrast of speckle patterns, or from the moments of the power spectrum of intensity fluctuations. We present a theory connecting these approaches for the general case of mixed static-dynamic patterns of boiling speckles without prior assumptions regarding the particle dynamics. An expression is derived and tested relating the speckle contrast to the intensity power spectrum. Our theory demonstrates that in speckle contrast the concentration of moving particles dominates over the contribution of speed to the particle flux. Our theory provides a basis for comparison of both approaches when used for studying tissue perfusion.

  7. Migration patterns in Central America seen in the context of economic integration and the need for sustainable development.

    PubMed

    Stein, E

    1993-08-01

    This exploratory discussion of migration policy in Central America focuses on actual procedures in a multisectoral framework that assumes economic integration and sustainable development. The article follows the following format: the author's perspective and general approach to the problems of migration policy and integrated development, an analysis and review of the inadequacies of concepts and methodologies and the need for strengthening Central America's policies, arguments for changing present development strategies, and suggestions for regional economic integration. New policies must be equitable, sustainable, and suitable for agricultural frontier areas at the present level of economic integration. The further development of practical and concrete solutions in the region is based on the current groundwork. New policies should emphasize community participation, a grassroots approach rather than a top-down one, and an alternative model. An alternative system which promotes and facilitates the vertical development of small and medium farmers needs both a Rural Communal Financing System and a System for Communal Marketing to eliminate all speculative economic practices which impede small farmers from making a profit. Buffer zones in the frontier agricultural areas are required. Small farms need to gradually improve farming practices rather than to transfer miraculous technologies. A number of forest products could be collected and commercialized for various purposes, if the knowledgeable indigenous population is informed and involved in participatory research on the technical and ethnological culture and action programs. Many sectors are involved, problems are complex, and the speed of change is very rapid in the region. An approach that seeks to relate sustainable development, economic integration, and migration policy must incorporate the perspective of integrated development and a structural analysis of poverty. The approach suggested in this article would

  8. The widely used Nicotiana benthamiana 16c line has an unusual T-DNA integration pattern including a transposon sequence.

    PubMed

    Philips, Joshua G; Naim, Fatima; Lorenc, Michał T; Dudley, Kevin J; Hellens, Roger P; Waterhouse, Peter M

    2017-01-01

    Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site. Therefore, using next generation sequencing, genome mapping and local alignment, we identified the location and characteristics of the integrated T-DNA. As suggested from previous molecular hybridisation and inheritance data, the transgenic line contains a single GFP-expressing locus. However, the GFP coding sequence differs from that originally reported. Furthermore, a 3.2 kb portion of a transposon, appears to have co-integrated with the T-DNA. The location of the integration mapped to a region of the genome represented by Nbv0.5scaffold4905 in the www.benthgenome.com assembly, and with less integrity to Niben101Scf03641 in the www.solgenomics.net assembly. The transposon is not endogenous to laboratory strains of N. benthamiana or Agrobacterium tumefaciens strain GV3101 (MP90), which was reportedly used in the generation of line 16c. However, it is present in the popular LBA4404 strain. The integrated transposon sequence includes its 5' terminal repeat and a transposase gene, and is immediately adjacent to the GFP gene. This unexpected genetic arrangement may contribute to the characteristics that have made the 16c line such a popular research tool and alerts researchers, taking transgenic plants to commercial release, to be aware of this genomic hitchhiker.

  9. The widely used Nicotiana benthamiana 16c line has an unusual T-DNA integration pattern including a transposon sequence

    PubMed Central

    Lorenc, Michał T.; Dudley, Kevin J.; Hellens, Roger P.

    2017-01-01

    Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site. Therefore, using next generation sequencing, genome mapping and local alignment, we identified the location and characteristics of the integrated T-DNA. As suggested from previous molecular hybridisation and inheritance data, the transgenic line contains a single GFP-expressing locus. However, the GFP coding sequence differs from that originally reported. Furthermore, a 3.2 kb portion of a transposon, appears to have co-integrated with the T-DNA. The location of the integration mapped to a region of the genome represented by Nbv0.5scaffold4905 in the www.benthgenome.com assembly, and with less integrity to Niben101Scf03641 in the www.solgenomics.net assembly. The transposon is not endogenous to laboratory strains of N. benthamiana or Agrobacterium tumefaciens strain GV3101 (MP90), which was reportedly used in the generation of line 16c. However, it is present in the popular LBA4404 strain. The integrated transposon sequence includes its 5’ terminal repeat and a transposase gene, and is immediately adjacent to the GFP gene. This unexpected genetic arrangement may contribute to the characteristics that have made the 16c line such a popular research tool and alerts researchers, taking transgenic plants to commercial release, to be aware of this genomic hitchhiker. PMID:28231340

  10. Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools

    PubMed Central

    Huang, Zhenzhen; Duan, Huilong; Li, Haomin

    2015-01-01

    Several large-scale human cancer genomics projects such as TCGA offered huge genomic and clinical data for researchers to obtain meaningful genomics alterations which intervene in the development and metastasis of the tumor. A web-based TCGA data analysis platform called TCGA4U was developed in this study. TCGA4U provides a visualization solution for this study to illustrate the relationship of these genomics alternations with clinical data. A whole genome screening of the survival related gene expression patterns in breast cancer was studied. The gene list that impacts the breast cancer patient survival was divided into two patterns. Gene list of each of these patterns was separately analyzed on DAVID. The result showed that mitochondrial ribosomes play a more crucial role in the cancer development. We also reported that breast cancer patients with low HSPA2 expression level had shorter overall survival time. This is widely different to findings of HSPA2 expression pattern in other cancer types. TCGA4U provided a new perspective for the TCGA datasets. We believe it can inspire more biomedical researchers to study and explain the genomic alterations in cancer development and discover more targeted therapies to help more cancer patients. PMID:26576432

  11. Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools.

    PubMed

    Huang, Zhenzhen; Duan, Huilong; Li, Haomin

    2015-01-01

    Several large-scale human cancer genomics projects such as TCGA offered huge genomic and clinical data for researchers to obtain meaningful genomics alterations which intervene in the development and metastasis of the tumor. A web-based TCGA data analysis platform called TCGA4U was developed in this study. TCGA4U provides a visualization solution for this study to illustrate the relationship of these genomics alternations with clinical data. A whole genome screening of the survival related gene expression patterns in breast cancer was studied. The gene list that impacts the breast cancer patient survival was divided into two patterns. Gene list of each of these patterns was separately analyzed on DAVID. The result showed that mitochondrial ribosomes play a more crucial role in the cancer development. We also reported that breast cancer patients with low HSPA2 expression level had shorter overall survival time. This is widely different to findings of HSPA2 expression pattern in other cancer types. TCGA4U provided a new perspective for the TCGA datasets. We believe it can inspire more biomedical researchers to study and explain the genomic alterations in cancer development and discover more targeted therapies to help more cancer patients.

  12. Reduction of a grid moire pattern by integrating a carbon-interspaced high precision x-ray grid with a digital radiographic detector

    SciTech Connect

    Yoon, Jai-Woong; Park, Young-Guk; Park, Chun-Joo; Kim, Do-Il; Lee, Jin-Ho; Chung, Nag-Kun; Choe, Bo-Young; Suh, Tae-Suk; Lee, Hyoung-Koo

    2007-11-15

    The stationary grid commonly used with a digital x-ray detector causes a moire interference pattern due to the inadequate sampling of the grid shadows by the detector pixels. There are limitations with the previous methods used to remove the moire such as imperfect electromagnetic interference shielding and the loss of image information. A new method is proposed for removing the moire pattern by integrating a carbon-interspaced high precision x-ray grid with high grid line uniformity with the detector for frequency matching. The grid was aligned to the detector by translating and rotating the x-ray grid with respect to the detector using microcontrolled alignment mechanism. The gap between the grid and the detector surface was adjusted with micrometer precision to precisely match the projected grid line pitch to the detector pixel pitch. Considering the magnification of the grid shadows on the detector plane, the grids were manufactured such that the grid line frequency was slightly higher than the detector sampling frequency. This study examined the factors that affect the moire pattern, particularly the line frequency and displacement. The frequency of the moire pattern was found to be sensitive to the angular displacement of the grid with respect to the detector while the horizontal translation alters the phase but not the moire frequency. The frequency of the moire pattern also decreased with decreasing difference in frequency between the grid and the detector, and a moire-free image was produced after complete matching for a given source to detector distance. The image quality factors including the contrast, signal-to-noise ratio and uniformity in the images with and without the moire pattern were investigated.

  13. Reduction of a grid moiré pattern by integrating a carbon-interspaced high precision x-ray grid with a digital radiographic detector.

    PubMed

    Yoon, Jai-Woong; Park, Young-Guk; Park, Chun-Joo; Kim, Do-Il; Lee, Jin-Ho; Chung, Nag-Kun; Choe, Bo-Young; Suh, Tae-Suk; Lee, Hyoung-Koo

    2007-11-01

    The stationary grid commonly used with a digital x-ray detector causes a moiré interference pattern due to the inadequate sampling of the grid shadows by the detector pixels. There are limitations with the previous methods used to remove the moiré such as imperfect electromagnetic interference shielding and the loss of image information. A new method is proposed for removing the moiré pattern by integrating a carbon-interspaced high precision x-ray grid with high grid line uniformity with the detector for frequency matching. The grid was aligned to the detector by translating and rotating the x-ray grid with respect to the detector using microcontrolled alignment mechanism. The gap between the grid and the detector surface was adjusted with micrometer precision to precisely match the projected grid line pitch to the detector pixel pitch. Considering the magnification of the grid shadows on the detector plane, the grids were manufactured such that the grid line frequency was slightly higher than the detector sampling frequency. This study examined the factors that affect the moiré pattern, particularly the line frequency and displacement. The frequency of the moiré pattern was found to be sensitive to the angular displacement of the grid with respect to the detector while the horizontal translation alters the phase but not the moiré frequency. The frequency of the moiré pattern also decreased with decreasing difference in frequency between the grid and the detector, and a moiré-free image was produced after complete matching for a given source to detector distance. The image quality factors including the contrast, signal-to-noise ratio and uniformity in the images with and without the moiré pattern were investigated.

  14. 4-Dimensionally Guided 3-Dimensional Color-Doppler Ultrasonography Quantifies Carotid Artery Stenosis With High Reproducibility and Accuracy.

    PubMed

    Macharzina, Roland Richard; Kocher, Sascha; Messé, Steven R; Rutkowski, Thomas; Hoffmann, Fabian; Vogt, Matthias; Vach, Werner; Fan, Nian; Rastan, Aljoscha; Neumann, Franz-Josef; Zeller, Thomas

    2017-07-13

    The purpose was to analyze the agreement and binary accuracy of the degree of internal carotid artery stenosis (ICAS) as determined by 4-dimensionally (4D) real-time gray-scale guided 3-dimensional (3D) color-Doppler ultrasonography (3DC-US) (4D/3DC-US) compared with catheter angiography (CA) and duplex ultrasonography (DUS). This study hypothesized that 4D/3DC-US is noninferior to CA and DUS in grading ICAS in selected patients. Clinical stratification in patients with ICAS largely depends on a patient's symptomatic status and the degree of stenosis. Screening with 4D/3DC-US was prospectively performed in 93 study patients (with 122 ICASs), thus yielding 80 patients for analysis (with 103 ICASs) after excluding patients with insufficient image quality, previous revascularization, and contraindications to CA. The ultrasound examination (10 MHz) consisted of consensus conform DUS examination and independent real-time 4D-guided gray-scale views for orientation followed by static 3DC-US NASCET (North American Symptomatic Carotid Endarterectomy Trial) percent stenosis quantification using off-line multiplanar rendering. Multiplanar selective CA of the same ICASs was quantified with dedicated software in a blinded fashion. Quantitative CA of 103 stenoses with a mean degree of 65 ± 17% was compared with 4D/3DC-US, with a resulting concordance correlation coefficient of 0.89 and a standard deviation of differences (SDD) of 8.1% at a bias of +1.7%. Binary 50% and 70% stenosis detection with 4D/3DC-US revealed a sensitivity of 97% and 87%, respectively, and a specificity of 92% and 84%, respectively. Interobserver SDD for CA of 52 stenoses (7.2%) did not differ from SDD for 4D/3DC-US and CA (p = 0.274). Accuracy of 50% stenosis detection by 4D/3DC-US was tendentially higher compared with DUS (96% vs. 91%). The 4D/3DC-US method provides reliable and accurate stenosis quantification and binary classification with good diagnostic accuracy compared with CA and DUS. Copyright

  15. On Darboux's approach to R-separability of variables. Classification of conformally flat 4-dimensional binary metrics

    NASA Astrophysics Data System (ADS)

    Szereszewski, A.; Sym, A.

    2015-09-01

    are binary metrics. In this paper we solve the following problem: to classify all conformally flat (of arbitrary signature) 4-dimensional binary metrics. Among them there are 1) those that are separable in the sense of SRE metrics Kalnins-Miller (1978 Trans. Am. Math. Soc. 244 241-61 1982 J. Phys. A: Math. Gen. 15 2699-709 1984 Adv. Math. 51 91-106 1983 SIAM J. Math. Anal. 14 126-37) and 2) new examples of non-Stäckel R-separability in 4 dimensions.

  16. Integrating a Hive Triangle Pattern with Subpixel Analysis for Noncontact Measurement of Structural Dynamic Response by Using a Novel Image Processing Scheme

    PubMed Central

    Hung, Shih-Lin

    2014-01-01

    This work presents a digital image processing approach with a unique hive triangle pattern by integrating subpixel analysis for noncontact measurement of structural dynamic response data. Feasibility of proposed approach is demonstrated based on numerical simulation of a photography experiment. According to those results, the measured time-history displacement of simulated image correlates well with the numerical solution. A small three-story frame is then mounted on a small shaker table, and a linear variation differential transformation (LVDT) is set on the second floor. Experimental results indicate that the relative error between data from LVDT and analyzed data from digital image correlation is below 0.007%, 0.0205 in terms of frequency and displacement, respectively. Additionally, the appropriate image block affects the estimation accuracy of the measurement system. Importantly, the proposed approach for evaluating pattern center and size is highly promising for use in assigning the adaptive block for a digital image correlation method. PMID:24955396

  17. Patterns and processes in complex landscapes: testing alternative biogeographical hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i.

    PubMed

    Eldon, Jon; Price, Jonathan P; Magnacca, Karl; Price, Donald K

    2013-07-01

    The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age and geographical isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study, we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet-forest-restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that probably reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographical model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographical systems. © 2013 John Wiley & Sons Ltd.

  18. Integrating Emerging Topics through Online Team Design in a Hybrid Communication Networks Course: Interaction Patterns and Impact of Prior Knowledge

    ERIC Educational Resources Information Center

    Reisslein, Jana; Seeling, Patrick; Reisslein, Martin

    2005-01-01

    An important challenge in the introductory communication networks course in electrical and computer engineering curricula is to integrate emerging topics, such as wireless Internet access and network security, into the already content-intensive course. At the same time it is essential to provide students with experiences in online collaboration,…

  19. Integrative analysis of gene expression patterns predicts specific modulations of defined cell functions by estrogen and tamoxifen in MCF7 breast cancer cells.

    PubMed

    Gadal, F; Starzec, A; Bozic, C; Pillot-Brochet, C; Malinge, S; Ozanne, V; Vicenzi, J; Buffat, L; Perret, G; Iris, F; Crepin, M

    2005-02-01

    To explore the mechanisms whereby estrogen and antiestrogen (tamoxifen (TAM)) can regulate breast cancer cell growth, we investigated gene expression changes in MCF7 cells treated with 17beta-estradiol (E2) and/or with 4-OH-TAM. The patterns of differential expression were determined by the ValiGen Gene IDentification (VGID) process, a subtractive hybridization approach combined with microarray validation screening. Their possible biologic consequences were evaluated by integrative data analysis. Over 1000 cDNA inserts were isolated and subsequently cloned, sequenced and analyzed against nucleotide and protein databases (NT/NR/EST) with BLAST software. We revealed that E2 induced differential expression of 279 known and 28 unknown sequences, whereas TAM affected the expression of 286 known and 14 unknown sequences. Integrative data analysis singled out a set of 32 differentially expressed genes apparently involved in broad cellular mechanisms. The presence of E2 modulated the expression patterns of 23 genes involved in anchors and junction remodeling; extracellular matrix (ECM) degradation; cell cycle progression, including G1/S check point and S-phase regulation; and synthesis of genotoxic metabolites. In tumor cells, these four mechanisms are associated with the acquisition of a motile and invasive phenotype. TAM partly reversed the E2-induced differential expression patterns and consequently restored most of the biologic functions deregulated by E2, except the mechanisms associated with cell cycle progression. Furthermore, we found that TAM affects the expression of nine additional genes associated with cytoskeletal remodeling, DNA repair, active estrogen receptor formation and growth factor synthesis, and mitogenic pathways. These modulatory effects of E2 and TAM upon the gene expression patterns identified here could explain some of the mechanisms associated with the acquisition of a more aggressive phenotype by breast cancer cells, such as E2-independent

  20. Identification of heat risk patterns in the U.S. National Capital Region by integrating heat stress and related vulnerability.

    PubMed

    Aubrecht, Christoph; Özceylan, Dilek

    2013-06-01

    The increase in the number and severity of weather extremes (including excessive heat) potentially associated with climate change has highlighted the needs for research into risk assessment and risk reduction measures. Extreme heat events, the focus of this paper, have been consistently reported as the leading cause of weather-related mortality in the United States in recent years. In order to fully understand impact potentials and analyze risk in its individual components both the spatially and temporally varying patterns of heat and the multidimensional characteristics of vulnerability have to be considered. In this paper we present a composite index aggregating these factors to assess heat related risk for the U.S. National Capital Region in 2010. The study reveals how risk patterns are in part driven by the geographic variations of vulnerability, generally showing a clear difference between high-risk urban areas and wide areas of low risk in the suburban and rural environments. This pattern is particularly evident for the core center of the study area around the District of Columbia, which is largely characterized by high index values despite not having experienced the peak of the heat stress as compared to other regions in the metropolitan area. The article aims to set a framework for local-level heat stress risk assessment that can provide valuable input and decision support for climate adaptation planning as well as emergency managers aiming at risk reduction and optimization of resource distribution. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. UV lithography-based protein patterning on silicon: Towards the integration of bioactive surfaces and CMOS electronics

    NASA Astrophysics Data System (ADS)

    Lenci, S.; Tedeschi, L.; Pieri, F.; Domenici, C.

    2011-08-01

    A simple and fast methodology for protein patterning on silicon substrates is presented, providing an insight into possible issues related to the interaction between biological and microelectronic technologies. The method makes use of standard photoresist lithography and is oriented towards the implementation of biosensors containing Complementary Metal-Oxide-Semiconductor (CMOS) conditioning circuitry. Silicon surfaces with photoresist patterns were prepared and hydroxylated by means of resist- and CMOS backend-compatible solutions. Subsequent aminosilane deposition and resist lift-off in organic solvents resulted into well-controlled amino-terminated geometries. The discussion is focused on resist- and CMOS-compatibility problems related to the used chemicals. Some samples underwent gold nanoparticle (Au NP) labeling and Scanning Electron Microscopy (SEM) observation, in order to investigate the quality of the silane layer. Antibodies were immobilized on other samples, which were subsequently exposed to a fluorescently labeled antigen. Fluorescence microscopy observation showed that this method provides spatially selective immobilization of protein layers onto APTES-patterned silicon samples, while preserving protein reactivity inside the desired areas and low non-specific adsorption elsewhere. Strong covalent biomolecule binding was achieved, giving stable protein layers, which allows stringent binding conditions and a good binding specificity, really useful for biosensing.

  2. Pulmonary Ventilation Imaging Based on 4-Dimensional Computed Tomography: Comparison With Pulmonary Function Tests and SPECT Ventilation Images

    SciTech Connect

    Yamamoto, Tokihiro; Kabus, Sven; Lorenz, Cristian; Mittra, Erik; Hong, Julian C.; Chung, Melody; Eclov, Neville; To, Jacqueline; Diehn, Maximilian; Loo, Billy W.; Keall, Paul J.

    2014-10-01

    Purpose: 4-dimensional computed tomography (4D-CT)-based pulmonary ventilation imaging is an emerging functional imaging modality. The purpose of this study was to investigate the physiological significance of 4D-CT ventilation imaging by comparison with pulmonary function test (PFT) measurements and single-photon emission CT (SPECT) ventilation images, which are the clinical references for global and regional lung function, respectively. Methods and Materials: In an institutional review board–approved prospective clinical trial, 4D-CT imaging and PFT and/or SPECT ventilation imaging were performed in thoracic cancer patients. Regional ventilation (V{sub 4DCT}) was calculated by deformable image registration of 4D-CT images and quantitative analysis for regional volume change. V{sub 4DCT} defect parameters were compared with the PFT measurements (forced expiratory volume in 1 second (FEV{sub 1}; % predicted) and FEV{sub 1}/forced vital capacity (FVC; %). V{sub 4DCT} was also compared with SPECT ventilation (V{sub SPECT}) to (1) test whether V{sub 4DCT} in V{sub SPECT} defect regions is significantly lower than in nondefect regions by using the 2-tailed t test; (2) to quantify the spatial overlap between V{sub 4DCT} and V{sub SPECT} defect regions with Dice similarity coefficient (DSC); and (3) to test ventral-to-dorsal gradients by using the 2-tailed t test. Results: Of 21 patients enrolled in the study, 18 patients for whom 4D-CT and either PFT or SPECT were acquired were included in the analysis. V{sub 4DCT} defect parameters were found to have significant, moderate correlations with PFT measurements. For example, V{sub 4DCT}{sup HU} defect volume increased significantly with decreasing FEV{sub 1}/FVC (R=−0.65, P<.01). V{sub 4DCT} in V{sub SPECT} defect regions was significantly lower than in nondefect regions (mean V{sub 4DCT}{sup HU} 0.049 vs 0.076, P<.01). The average DSCs for the spatial overlap with SPECT ventilation defect regions were only moderate (V

  3. Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts.

    PubMed

    Flores-Rentería, Lluvia; Rymer, Paul D; Riegler, Markus

    2017-03-01

    Reticulate evolution by hybridization is considered a common process shaping the evolution of many plant species, however, reticulation could also be due to incomplete lineage sorting in biodiverse systems. For our study we selected a group of closely related plant taxa with contrasting yet partially overlapping geographic distributions and different population sizes, to distinguish between reticulated patterns due to hybridization and incomplete lineage sorting. We predicted that sympatric or proximal populations of different species are more likely to have gene flow than geographically distant populations of the same widespread species. Furthermore, for species with restricted distributions, and therefore, small effective population sizes, we predicted complete lineage sorting. Eastern grey box eucalypt species (Eucalyptus supraspecies Moluccanae) provide an ideal system to explore patterns of reticulate evolution. They form a diverse, recently evolved and phylogenetically undefined group within Eucalyptus, with overlapping morphological features and hybridization in nature. We used a multi-faceted approach, combining analyses of chloroplast and nuclear DNA, as well as seedling morphology, flowering time and ecological spatial differentiation in order to test for species delimitation and reticulate evolution in this group. The multiple layers of results were consistent and suggested a lack of monophyly at different hierarchical levels due to multidirectional gene flow among several species, challenging species delimitation. Chloroplast and nuclear haplotypes were shared among different species in geographic proximity, consistent with hybridization zones. Furthermore, species with restricted distributions appeared better resolved due to lineage sorting in the absence of hybridization. We conclude that a combination of molecular, morphological and ecological approaches is required to disentangle patterns of reticulate evolution in the box eucalypts. Published by

  4. Monolithic integration of optical grade GaAs on Si (001) substrates deeply patterned at a micron scale

    SciTech Connect

    Bietti, Sergio; Scaccabarozzi, Andrea; Bonera, Emiliano; Miglio, Leo; Sanguinetti, Stefano; Frigeri, Cesare; Falub, Claudiu V.; Känel, Hans von

    2013-12-23

    Dense arrays of micrometric crystals, with areal filling up to 93%, are obtained by depositing GaAs in a mask-less molecular beam epitaxy process onto Si substrates. The substrates are patterned into tall, micron sized pillars. Faceted high aspect ratio GaAs crystals are achieved by tuning the Ga adatom for short surface diffusion lengths. The crystals exhibit bulk-like optical quality due to defect termination at the sidewalls. Simultaneously, the thermal strain induced by different thermal expansion parameters of GaAs and Si is fully relieved. This opens the route to thick film applications without crack formation and wafer bowing.

  5. Comparing Integrated and Disciplinary Clinical Training Patterns for Dental Interns: Advantages, Disadvantages, and Effect on Students' Self-Confidence.

    PubMed

    Wu, Junrong; Feng, Xiaoli; Chen, Aijie; Zhang, Yanli; Liu, Qi; Shao, Longquan

    2016-03-01

    In China, the five-year program of undergraduate education for stomatology consists of four years of lecture courses and one year of internship focused on clinical training. Dental schools provide this clinical training either in their own clinics (referred to as the one-stage pattern because all forms of practice are completed together) or by placing students in external clinics usually at non-affiliated hospitals (referred to as the three-stage program because the three primary areas are taught separately). The aims of this study were to investigate differences in teaching effect between the one-stage and the three-stage patterns and to evaluate advantages and disadvantages of the two patterns. A three-section, 31-item questionnaire was designed to assess basic and clinic information about the interns' training and their self-confidence in performing clinical procedures. The survey was administered to graduates who finished the fifth-year internship in 2012-14. Of the 356 individuals invited to participate, 303 graduates who spent their intern years in 43 academic dental institutions returned completed surveys (response rate of 85%). The one-stage group (n=121) reported longer independent operation time than the three-stage group (n=182) (p<0.01). No significant difference was found between the groups for assessment of clinic infrastructure (p=0.121). The interns were most confident in oral hygiene instruction and scale and polish (overall median=5), but showed low confidence in rubber dam placement and four other procedures (overall median=2). The one-stage group rated their confidence level higher than the three-stage group on comprehensive skills such as arranging appointments and managing patients and procedures needing long treatment periods such as molar endodontics. The three-stage group showed higher confidence on more specialized procedures such as surgical extractions and suturing. This study found that both of the two intern patterns had advantages and

  6. Evaluating the effect of human activity patterns on air pollution exposure using an integrated field-based and agent-based modelling framework

    NASA Astrophysics Data System (ADS)

    Schmitz, Oliver; Beelen, Rob M. J.; de Bakker, Merijn P.; Karssenberg, Derek

    2015-04-01

    Constructing spatio-temporal numerical models to support risk assessment, such as assessing the exposure of humans to air pollution, often requires the integration of field-based and agent-based modelling approaches. Continuous environmental variables such as air pollution are best represented using the field-based approach which considers phenomena as continuous fields having attribute values at all locations. When calculating human exposure to such pollutants it is, however, preferable to consider the population as a set of individuals each with a particular activity pattern. This would allow to account for the spatio-temporal variation in a pollutant along the space-time paths travelled by individuals, determined, for example, by home and work locations, road network, and travel times. Modelling this activity pattern requires an agent-based or individual based modelling approach. In general, field- and agent-based models are constructed with the help of separate software tools, while both approaches should play together in an interacting way and preferably should be combined into one modelling framework, which would allow for efficient and effective implementation of models by domain specialists. To overcome this lack in integrated modelling frameworks, we aim at the development of concepts and software for an integrated field-based and agent-based modelling framework. Concepts merging field- and agent-based modelling were implemented by extending PCRaster (http://www.pcraster.eu), a field-based modelling library implemented in C++, with components for 1) representation of discrete, mobile, agents, 2) spatial networks and algorithms by integrating the NetworkX library (http://networkx.github.io), allowing therefore to calculate e.g. shortest routes or total transport costs between locations, and 3) functions for field-network interactions, allowing to assign field-based attribute values to networks (i.e. as edge weights), such as aggregated or averaged

  7. Foam patterns

    DOEpatents

    Chaudhry, Anil R; Dzugan, Robert; Harrington, Richard M; Neece, Faurice D; Singh, Nipendra P; Westendorf, Travis

    2013-11-26

    A method of creating a foam pattern comprises mixing a polyol component and an isocyanate component to form a liquid mixture. The method further comprises placing a temporary core having a shape corresponding to a desired internal feature in a cavity of a mold and inserting the mixture into the cavity of the mold so that the mixture surrounds a portion of the temporary core. The method optionally further comprises using supporting pins made of foam to support the core in the mold cavity, with such pins becoming integral part of the pattern material simplifying subsequent processing. The method further comprises waiting for a predetermined time sufficient for a reaction from the mixture to form a foam pattern structure corresponding to the cavity of the mold, wherein the foam pattern structure encloses a portion of the temporary core and removing the temporary core from the pattern independent of chemical leaching.

  8. Modeling change-pattern-value dynamics on land use: an integrated GIS and artificial neural networks approach.

    PubMed

    Dai, Erfu; Wu, Shaohong; Shi, Wenzhong; Cheung, Chui-Kwan; Shaker, Ahmed

    2005-10-01

    The use of spatial methods to detect and characterize changes in land use has been attracting increasing attention from researchers. The objectives of this article were to formulate the dynamics of land use on the temporal and spatial dimensions from the perspectives of the Change-Pattern-Value (CPV) and driving mechanism, based on multitemporal remote sensing data and socioeconomic data. The Artificial Neural Networks were used to identify the factors driving changes in land use. The Pearl River Delta Region of southeast China, which was experiencing rapid economic growth and widespread land conversion, has been selected as the study region. The results show that from 1985 to 2000 in the study region (1) the most prominent characteristics of change in land use were the expansion of the urban land at the expense of farmland, forests, and grasslands, (2) the land-use pattern was being optimized during this period, (3) in an analysis of value, built-up land can yield a return of more than 30 times that of farmland, water area, and forests lands, and (4) rapid economic development, growth in population, and the development of an infrastructure were major driving factors behind ecological land loss and the nonecological land expansion.

  9. Within-team Patterns of Communication and Referral in Multimodal Treatment of Chronic Low Back Pain Patients by an Integrative Care Team

    PubMed Central

    O'Connor, Bonnie B.; Eisenberg, David M.; Buring, Julie E.; Liang, Catherine L.; Osypiuk, Kamila; Levy, Donald B.

    2015-01-01

    Background: Nonspecific chronic low back pain (CLBP) is a highly prevalent and costly public health problem with few treatment options that provide consistent and greater than modest benefits. Treatment of CLBP is shifting from unimodal to multimodal and multidisciplinary approaches, including biopsychosocially-based complementary and integrative care. Multidisciplinary approaches require unique levels of communication and coordination amongst clinicians; however, to date few studies have evaluated patterns of communication and decision making amongst clinicians collaborating in the care of challenging patients with CLBP. Methods: As part of an observational study evaluating the effectiveness and cost-effectiveness of an integrative, team-based care model for the treatment of CLBP, we used multiple qualitative research methods to characterize within-team cross-referral and communication amongst jointly-trained practitioners representing diverse biomedical and complementary disciplines. Patterns of communication and coordinated care are summarized for 3 cases of CLBP treated by multiple members (≥3) of an integrative medical team embedded within an academic hospital. Results: Patients were aged from 36 to 88 years with varied comorbidities. Qualitative content analysis revealed 5 emergent themes regarding integrative patient care and treatment decision in this clinic: (1) the fundamental importance of the clinic's formal teamwork training; (2) the critical communicative and collaborative function of regular team meetings; (3) the importance to patient care goals of having the varied disciplines practicing “under one roof”; (4) a universal commitment to understanding and treating patients as whole persons; and (5) a shared philosophy of helping patients to help themselves. These key themes are all interconnected and form the foundation of the clinic's culture. Conclusions: Our qualitative findings provide context for current trends in enhancing patient

  10. Deterministic patterned growth of high-mobility large-crystal graphene: a path towards wafer scale integration

    NASA Astrophysics Data System (ADS)

    Miseikis, Vaidotas; Bianco, Federica; David, Jérémy; Gemmi, Mauro; Pellegrini, Vittorio; Romagnoli, Marco; Coletti, Camilla

    2017-06-01

    We demonstrate rapid deterministic (seeded) growth of large single-crystals of graphene by chemical vapour deposition (CVD) utilising pre-patterned copper substrates with chromium nucleation sites. Arrays of graphene single-crystals as large as several hundred microns are grown with a periodicity of up to 1 mm. The graphene is transferred to target substrates using aligned and contamination- free semi-dry transfer. The high quality of the synthesised graphene is confirmed by Raman spectroscopy and transport measurements, demonstrating room-temperature carrier mobility of 21 000 cm2 V-1 s-1 when transferred on top of hexagonal boron nitride. By tailoring the nucleation of large single-crystals according to the desired device geometry, it will be possible to produce complex device architectures based on single-crystal graphene, thus paving the way to the adoption of CVD graphene in wafer-scale fabrication.

  11. Integrating nap and night-time sleep into sleep patterns reveals differential links to health-relevant outcomes.

    PubMed

    Devine, Jaime K; Wolf, Jutta M

    2016-04-01

    Both night-time sleep and nap behaviour have been linked consistently to health outcomes. Although reasons for napping are usually tied to night-time sleep, the majority of studies assess their effects independently. The current study thus aimed to examine the health relevance of patterns of sleep behaviour that take into account both night-time and daytime sleep habits. Night-time sleep, recorded during 7 days via actigraphy from 313 participants (aged 34-82 years) of the Midlife in the United States II Biomarker study, was assessed. Blood and urine specimens were assayed for noradrenaline, interleukin-6 and C-reactive protein. Participants self-reported nap behaviour, depressive symptoms, perceived chronic stress and the presence of medical symptoms and conditions. Overall, nappers (n = 208) showed elevated waist-hip ratios, C-reactive protein and interleukin-6 levels compared to non-nappers and reported more physiological symptoms and conditions (all P ≤ 0.019). Within nappers, cluster analysis revealed three patterns of sleep behaviour-infrequent nappers with good night-time sleep, frequent nappers with good night-time sleep and nappers with poor night-time sleep. Nappers with poor night-time sleep thereby exhibited elevated noradrenaline levels, depressive symptoms and perceived stress scores compared to other groups (all P ≤ 0.041). These findings support the idea that nap-health relationships are complex, in that frequency of napping and accumulation of nap sleep is not related linearly to health consequences. Assessing nap behaviour in conjunction with night-time sleep behaviour appeared crucial to elucidate further the health relevance of napping, particularly in terms of psychological health outcomes, including chronic stress and depressive symptoms.

  12. Oasis dynamics change and its influence on landscape pattern on Jinta oasis in arid China from 1963a to 2010a: Integration of multi-source satellite images

    NASA Astrophysics Data System (ADS)

    Xie, Yuchu; Gong, Jie; Sun, Peng; Gou, Xiaohua

    2014-12-01

    As one of the vital research highlights of global land use and cover change, oasis change and its interaction with landscape pattern have been regarded as an important content of regional environmental change research in arid areas. Jinta oasis, a typical agricultural oasis characterized by its dramatic exploitation and use of water and land resources in Hexi corridor, northwest arid region in China, was selected as a case to study the spatiotemporal oasis change and its effects on oasis landscape pattern. Based on integration of Keyhole satellite photographs, KATE-200 photographs, Landsat MSS, TM and ETM+ images, we evaluated and analyzed the status, trend and spatial pattern change of Jinta oasis and the characteristics of landscape pattern change by a set of mathematical models and combined this information with landscape metrics and community surveys. During the period of 1963a-2010a, Jinta oasis expanded gradually with an area increase of 219.15 km2, and the conversion between oasis and desert was frequent with a state of “imbalance-balance-extreme imbalance conditions”. Moreover, most of the changes took place in the ecotone between oasis and desert and the interior of oasis due to the reclamation of abandoned land, such as Yangjingziwan and Xiba townships. Furthermore, the area, size and spatial distribution of oasis were influenced by human activities and resulted in fundamental changes of oasis landscape pattern. The fractal characteristics, dispersion degree and fragmentation of Jinta oasis decreased and the oasis landscape tended to be simple and uniform. Oasis change trajectories and its landscape pattern were mainly influenced by water resource utilization, policies (especially land policies), demographic factors, technological advancements, as well as regional economic development. We found that time series analysis of multi-source remote sensing images and the application of an oasis change model provided a useful approach to monitor oasis change

  13. Biodegradation pattern and tissue integration of native and cross-linked porcine collagen soft tissue augmentation matrices – an experimental study in the rat

    PubMed Central

    2014-01-01

    Introduction Within the last decades, collagen types I and III have been established as a sufficient biomaterial for GBR and GTR procedures. They might also be an adequate matrix for soft tissue augmentations. However, collagen materials differ significantly regarding resorption time, biodegradation pattern and the invasion of inflammatory cells. The aim of the present study was to compare the biodegradation and tissue integration of native, differently processed and cross-linked collagen scaffolds in rats. Methods Four experimental porcine collagen matrices of 1.0 mm thickness, developed for soft tissue augmentation procedures, were tested. Based on the same native dermal Type I and III collagen, native (ND, Mucoderm® prototype), specifically defatted (DD), ethylene dioxide cross-linked (ECL) and dehydrothermally cross-linked (DCL) dermis collagen (AAP/Botiss Biomaterials, Berlin, Germany) were evaluated. Two specimens of 1 × 1 cm were fixed around a non-absorbable spacer using non-absorbable sutures. After rehydration, specimens (N = 8) were randomly allocated in unconnected subcutaneous pouches on the back of 40 Wistar rats. Rats were divided into five groups (1, 2, 4, 8 and 12 weeks), including eight animals each. After each period, eight rats were sacrificed and explanted specimens were prepared for histological analysis. The following parameters were evaluated: membrane thickness as a sign of biodegradation and volume stability, cell ingrowth, vascularization, tissue integration and foreign body reaction. Results Biodegradation pattern of the non cross-linked collagen scaffolds differed only slightly in terms of presence of inflammatory cells and cell invasion into the matrix. In terms of biodegradation, ECL displayed a considerable slower resorption than ND, DCL and DD. Chemical cross-linking using ethylene dioxide showed a significant higher invasion of inflammatory cells. Conclusion Within the limits of the present study it was concluded that the

  14. NeuroCa: integrated framework for systematic analysis of spatiotemporal neuronal activity patterns from large-scale optical recording data

    PubMed Central

    Jang, Min Jee; Nam, Yoonkey

    2015-01-01

    Abstract. Optical recording facilitates monitoring the activity of a large neural network at the cellular scale, but the analysis and interpretation of the collected data remain challenging. Here, we present a MATLAB-based toolbox, named NeuroCa, for the automated processing and quantitative analysis of large-scale calcium imaging data. Our tool includes several computational algorithms to extract the calcium spike trains of individual neurons from the calcium imaging data in an automatic fashion. Two algorithms were developed to decompose the imaging data into the activity of individual cells and subsequently detect calcium spikes from each neuronal signal. Applying our method to dense networks in dissociated cultures, we were able to obtain the calcium spike trains of ∼1000 neurons in a few minutes. Further analyses using these data permitted the quantification of neuronal responses to chemical stimuli as well as functional mapping of spatiotemporal patterns in neuronal firing within the spontaneous, synchronous activity of a large network. These results demonstrate that our method not only automates time-consuming, labor-intensive tasks in the analysis of neural data obtained using optical recording techniques but also provides a systematic way to visualize and quantify the collective dynamics of a network in terms of its cellular elements. PMID:26229973

  15. Progressive glucose stimulation of islet beta cells reveals a transition from segregated to integrated modular functional connectivity patterns

    NASA Astrophysics Data System (ADS)

    Markovič, Rene; Stožer, Andraž; Gosak, Marko; Dolenšek, Jurij; Marhl, Marko; Rupnik, Marjan Slak

    2015-01-01

    Collective beta cell activity in islets of Langerhans is critical for the supply of insulin within an organism. Even though individual beta cells are intrinsically heterogeneous, the presence of intercellular coupling mechanisms ensures coordinated activity and a well-regulated exocytosis of insulin. In order to get a detailed insight into the functional organization of the syncytium, we applied advanced analytical tools from the realm of complex network theory to uncover the functional connectivity pattern among cells composing the intact islet. The procedure is based on the determination of correlations between long temporal traces obtained from confocal functional multicellular calcium imaging of beta cells stimulated in a stepwise manner with a range of physiological glucose concentrations. Our results revealed that the extracted connectivity networks are sparse for low glucose concentrations, whereas for higher stimulatory levels they become more densely connected. Most importantly, for all ranges of glucose concentration beta cells within the islets form locally clustered functional sub-compartments, thereby indicating that their collective activity profiles exhibit a modular nature. Moreover, we show that the observed non-linear functional relationship between different network metrics and glucose concentration represents a well-balanced setup that parallels physiological insulin release.

  16. An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates

    PubMed Central

    Sun, Ping; Clamp, John; Xu, Dapeng; Huang, Bangqin; Shin, Mann Kyoon

    2016-01-01

    Peritrichs are a major group of ciliates with worldwide distribution. Yet, its internal phylogeny remains unresolved owing to limited sampling. Additionally, ecological distributions of peritrichs are poorly known. We performed substantially expanded phylogenetic analyses of peritrichs that incorporated SSU rDNA sequences of samples collected from three continents, revealing a number of new relationships between and within major lineages that greatly challenged the classic view of the group. Interrogation of a dataset comprising new environmental sequences from an estuary and the open ocean generated with high throughput sequencing and clone libraries plus putative environmental peritrich sequences at Genbank, produced a comprehensive tree of peritrichs from a variety of habitats and revealed unique ecological distribution patterns of several lineages for the first time. Also, evidence of adaptation to extreme environments in the Astylozoidae clade greatly broadened the phylogenetic range of peritrichs capable of living in extreme environments. Reconstruction of ancestral states revealed that peritrichs may have transitioned repeatedly from freshwater to brackish/marine/hypersaline environments. This work establishes a phylogenetic framework for more mature investigations of peritrichs in the future, and the approach used here provides a model of how to elucidate evolution in the context of ecological niches in any lineage of microbial eukaryotes. PMID:26880590

  17. An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates.

    PubMed

    Sun, Ping; Clamp, John; Xu, Dapeng; Huang, Bangqin; Shin, Mann Kyoon

    2016-02-16

    Peritrichs are a major group of ciliates with worldwide distribution. Yet, its internal phylogeny remains unresolved owing to limited sampling. Additionally, ecological distributions of peritrichs are poorly known. We performed substantially expanded phylogenetic analyses of peritrichs that incorporated SSU rDNA sequences of samples collected from three continents, revealing a number of new relationships between and within major lineages that greatly challenged the classic view of the group. Interrogation of a dataset comprising new environmental sequences from an estuary and the open ocean generated with high throughput sequencing and clone libraries plus putative environmental peritrich sequences at Genbank, produced a comprehensive tree of peritrichs from a variety of habitats and revealed unique ecological distribution patterns of several lineages for the first time. Also, evidence of adaptation to extreme environments in the Astylozoidae clade greatly broadened the phylogenetic range of peritrichs capable of living in extreme environments. Reconstruction of ancestral states revealed that peritrichs may have transitioned repeatedly from freshwater to brackish/marine/hypersaline environments. This work establishes a phylogenetic framework for more mature investigations of peritrichs in the future, and the approach used here provides a model of how to elucidate evolution in the context of ecological niches in any lineage of microbial eukaryotes.

  18. Selective filling for patterning in microfluidic channels and integration of chromatography in "lab-on-a-chip" devices using sol-gel technology

    NASA Astrophysics Data System (ADS)

    Jindal, Rohit

    The last decade has seen tremendous advancement in the development of miniaturized chemical analysis system also known as "lab-on-a-chip". It is believed that the true potential of these devices will be achieved by integrating various functions such as separation, reaction, sensing, mixing, pumping, injection and detection onto a single chip. The ability to pattern different functionalities is indispensable for the development of highly integrated devices. In this work, a simple method based on the concept of selective filling is described for patterning in the microfluidic channels. It is based on the difference in the free energy of filling between an open and a covered part of the channel. This method was used for the integration of chromatography in the microfluidic devices. A chromatographic column was realized by utilizing sol-gel as an immobilization matrix for entrapping reversed phase chromatographic particles. Localization of the stationary phase was achieved using the selective filling technique. Channels were fabricated in quartz using photolithography and wet etching. Electroosmotic flow was used for manipulating fluid movement in the channels. Cross channel design was used for making a pulse injection of the solutes in the separation channel. An optical fiber setup was developed for carrying out on-chip UV absorbance detection. Stationary phase was created under different sol-gel synthesis conditions. It was established that the sol-gel synthesis carried out under acidic conditions provides the optimum synthesis conditions for creating separation column. Chromatographic performance of the stationary phase material was demonstrated by separating peptides present in a mixture. The sol-gel immobilization method was extended for the integration of micropump in the chip. The micropump enables pumping of the fluid in field free channels. Preliminary results, demonstrating the potential of carbon nanotubes as a support material in the microfluidic channels

  19. Self-Patterning of Silica/Epoxy Nanocomposite Underfill by Tailored Hydrophilic-Superhydrophobic Surfaces for 3D Integrated Circuit (IC) Stacking.

    PubMed

    Tuan, Chia-Chi; James, Nathan Pataki; Lin, Ziyin; Chen, Yun; Liu, Yan; Moon, Kyoung-Sik; Li, Zhuo; Wong, C P

    2017-03-15

    As microelectronics are trending toward smaller packages and integrated circuit (IC) stacks nowadays, underfill, the polymer composite filled in between the IC chip and the substrate, becomes increasingly important for interconnection reliability. However, traditional underfills cannot meet the requirements for low-profile and fine pitch in high density IC stacking packages. Post-applied underfills have difficulties in flowing into the small gaps between the chip and the substrate, while pre-applied underfills face filler entrapment at bond pads. In this report, we present a self-patterning underfilling technology that uses selective wetting of underfill on Cu bond pads and Si3N4 passivation via surface energy engineering. This novel process, fully compatible with the conventional underfilling process, eliminates the issue of filler entrapment in typical pre-applied underfilling process, enabling high density and fine pitch IC die bonding.

  20. An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants

    PubMed Central

    Zhang, Li; Wang, Shi-Bo; Li, Qi-Gang; Song, Jian; Hao, Yu-Qi; Zhou, Ling; Zheng, Huan-Quan; Dunwell, Jim M.; Zhang, Yuan-Ming

    2016-01-01

    Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content. PMID:27159078

  1. Quantitative glycome analysis of N-glycan patterns in bladder cancer vs normal bladder cells using an integrated strategy.

    PubMed

    Yang, Ganglong; Tan, Zengqi; Lu, Wei; Guo, Jia; Yu, Hanjie; Yu, Jingmin; Sun, Chengwen; Qi, Xiaowei; Li, Zheng; Guan, Feng

    2015-02-06

    Diagnosis of bladder cancer, one of the most common types of human cancer, at an early (nonmuscle-invasive) stage is the best way to reduce the mortality rate. Tumor malignancy in general is closely associated with alterations of glycan expression. Glycosylation status, particularly global glycomes, in bladder cancer has not been well studied. We integrated lectin microarray and mass spectrometry (MS) methods to quantitatively analyze and compare glycan expression in four bladder cancer cell lines (KK47, YTS1, J82, T24) and one normal bladder mucosa cell line (HCV29). Glycopattern alterations were analyzed using lectin microarray analysis and confirmed by lectin staining and lectin blotting. Associations of glycopatterns with diverging stages were evaluated by lectin histochemistry on tissue microarrays. N-Glycans were derivatized by amidation of sialylated glycans with acetohydrazide and reductive amination with the stable isotope tags [(12)C6]- and [(13)C6]-aniline, and were quantitatively analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). N-Glycan biosynthesis-associated proteins were quantitatively analyzed by a stable isotope labeling by amino acids in cell culture (SILAC) proteomics method, which revealed significant differences in expression of 13 glycosyltransferases and 4 glycosidases. Our findings indicate that sialyl Lewis X (sLe(x)), terminal GalNAc and Gal, and high mannose-type N-glycans were more highly expressed in bladder cancer cells and tissues than in normal cells. Bladder cancer cells showed high expression of core-fucosylated N-glycans but low expression of terminally fucosylated N-glycans. Each of these glycome changes may be directly related to bladder cancer progression.

  2. Spatial and temporal patterns of water storage in hydropedological units in northern headwaters: integrating isotopic and hydrometric approaches

    NASA Astrophysics Data System (ADS)

    Geris, J.; Tetzlaff, D.; McDonnell, J. J.; Soulsby, C.

    2013-12-01

    high storage capacity of the wetter catchment soils. The integration of hydrometric data and soil water stable isotopes across soil profiles has been invaluable for differentiating the functional soil water dynamics of the different hydropedological-vegetation assemblages.

  3. Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data.

    PubMed

    Miller, A D; van Rooyen, A; Rašić, G; Ierodiaconou, D A; Gorfine, H K; Day, R; Wong, C; Hoffmann, A A; Weeks, A R

    2016-08-01

    Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

  4. Diffuse nitrogen loss simulation and impact assessment of stereoscopic agriculture pattern by integrated water system model and consideration of multiple existence forms

    NASA Astrophysics Data System (ADS)

    Zhang, Yongyong; Gao, Yang; Yu, Qiang

    2017-09-01

    Agricultural nitrogen loss becomes an increasingly important source of water quality deterioration and eutrophication, even threatens water safety for humanity. Nitrogen dynamic mechanism is still too complicated to be well captured at watershed scale due to its multiple existence forms and instability, disturbance of agricultural management practices. Stereoscopic agriculture is a novel agricultural planting pattern to efficiently use local natural resources (e.g., water, land, sunshine, heat and fertilizer). It is widely promoted as a high yield system and can obtain considerable economic benefits, particularly in China. However, its environmental quality implication is not clear. In our study, Qianyanzhou station is famous for its stereoscopic agriculture pattern of Southern China, and an experimental watershed was selected as our study area. Regional characteristics of runoff and nitrogen losses were simulated by an integrated water system model (HEQM) with multi-objective calibration, and multiple agriculture practices were assessed to find the effective approach for the reduction of diffuse nitrogen losses. Results showed that daily variations of runoff and nitrogen forms were well reproduced throughout watershed, i.e., satisfactory performances for ammonium and nitrate nitrogen (NH4-N and NO3-N) loads, good performances for runoff and organic nitrogen (ON) load, and very good performance for total nitrogen (TN) load. The average loss coefficient was 62.74 kg/ha for NH4-N, 0.98 kg/ha for NO3-N, 0.0004 kg/ha for ON and 63.80 kg/ha for TN. The dominating form of nitrogen losses was NH4-N due to the applied fertilizers, and the most dramatic zones aggregated in the middle and downstream regions covered by paddy and orange orchard. In order to control diffuse nitrogen losses, the most effective practices for Qianyanzhou stereoscopic agriculture pattern were to reduce farmland planting scale in the valley by afforestation, particularly for orchard in the

  5. Identification of volatile and semivolatile compounds in chemical ionization GC-MS using a mass-to-structure (MTS) Search Engine with integral isotope pattern ranking.

    PubMed

    Liao, Wenta; Draper, William M

    2013-02-21

    The mass-to-structure or MTS Search Engine is an Access 2010 database containing theoretical molecular mass information for 19,438 compounds assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. This database, which contains no experimental mass spectral data, was developed as an aid to identification of compounds in atmospheric pressure ionization (API)-LC-MS. This paper describes a powerful upgrade to this database, a fully integrated utility for filtering or ranking candidates based on isotope ratios and patterns. The new MTS Search Engine is applied here to the identification of volatile and semivolatile compounds including pesticides, nitrosoamines and other pollutants. Methane and isobutane chemical ionization (CI) GC-MS spectra were obtained from unit mass resolution mass spectrometers to determine MH(+) masses and isotope ratios. Isotopes were measured accurately with errors of <4% and <6%, respectively, for A + 1 and A + 2 peaks. Deconvolution of interfering isotope clusters (e.g., M(+) and [M - H](+)) was required for accurate determination of the A + 1 isotope in halogenated compounds. Integrating the isotope data greatly improved the speed and accuracy of the database identifications. The database accurately identified unknowns from isobutane CI spectra in 100% of cases where as many as 40 candidates satisfied the mass tolerance. The paper describes the development and basic operation of the new MTS Search Engine and details performance testing with over 50 model compounds.

  6. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 1-Model formulation and biological data assimilation twin experiments

    NASA Astrophysics Data System (ADS)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A quadratic formulation for an incremental lognormal 4-dimensional variational assimilation method (incremental L4DVar) is introduced for assimilation of biogeochemical observations into a 3-dimensional ocean circulation model. L4DVar assumes that errors in the model state are lognormally rather than Gaussian distributed, and implicitly ensures that state estimates are positive definite, making this approach attractive for biogeochemical variables. The method is made practical for a realistic implementation having a large state vector through linear assumptions that render the cost function quadratic and allow application of existing minimization techniques. A simple nutrient-phytoplankton-zooplankton-detritus (NPZD) model is coupled to the Regional Ocean Modeling System (ROMS) and configured for the California Current System. Quadratic incremental L4DVar is evaluated in a twin model framework in which biological fields only are in error and compared to G4DVar which assumes Gaussian distributed errors. Five-day assimilation cycles are used and statistics from four years of model integration analyzed. The quadratic incremental L4DVar results in smaller root-mean-squared errors and better statistical agreement with reference states than G4DVar while maintaining a positive state vector. The additional computational cost and implementation effort are trivial compared to the G4DVar system, making quadratic incremental L4DVar a practical and beneficial option for realistic biogeochemical state estimation in the ocean.

  7. Comparison of 4-Dimensional Computed Tomography Ventilation With Nuclear Medicine Ventilation-Perfusion Imaging: A Clinical Validation Study

    SciTech Connect

    Vinogradskiy, Yevgeniy; Koo, Phillip J.; Castillo, Richard; Castillo, Edward; Guerrero, Thomas; Gaspar, Laurie E.; Miften, Moyed; Kavanagh, Brian D.

    2014-05-01

    on a regional level. Our study presents an important step for the integration of 4DCT-ventilation into thoracic clinical practice.

  8. Comparison of 4-dimensional computed tomography ventilation with nuclear medicine ventilation-perfusion imaging: a clinical validation study.

    PubMed

    Vinogradskiy, Yevgeniy; Koo, Phillip J; Castillo, Richard; Castillo, Edward; Guerrero, Thomas; Gaspar, Laurie E; Miften, Moyed; Kavanagh, Brian D

    2014-05-01

    step for the integration of 4DCT-ventilation into thoracic clinical practice. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Integrated Science.

    ERIC Educational Resources Information Center

    Rainey, Larry; Miller, Roxanne Greitz

    1997-01-01

    Describes the Integrated Science program that integrates biology, earth/space science, chemistry, and physics over a three-year, spiraling sequence arranged around broad themes such as cycles, changes, patterns, and waves. Includes weekly telecasts via public television and satellite, teacher manuals, student handbooks, e-mail connections, staff…

  10. Combining temporally-integrated heat stress duration and frequency with multi-dimensional vulnerability characteristics to derive local-level risk patterns

    NASA Astrophysics Data System (ADS)

    Özceylan, Dilek; Aubrecht, Christoph

    2013-04-01

    The observed changing in the nature of climate related events and the increase in the number and severity of extreme weather events has been changing risk patterns and puts more people at risk. In recent years extreme heat events caused excess mortality and public concerns in many regions of the world (e.g., 2003 and 2006 Western European heat waves, 2007 and 2010 Asian heat waves, 2006 and most recent 2010-2012 North American heat waves). In the United States extreme heat events have been consistently reported as the leading cause of weather- related mortality and have attracted the attention of the international scientific community regarding the critical importance of risk assessment and decoding its components for risk reduction. In order to understand impact potentials and analyze risk in its individual components both the spatially and temporally varying patterns of heat stress and the multidimensional characteristics of vulnerability have to be considered. In this study we present a composite risk index aggregating these factors and implement that for the U.S. National Capital Region on a high level of spatial detail. The applied measure of assessing heat stress hazard is a novel approach of integrating magnitude, duration, and frequency over time in the assessment and is opposed to the study of single extreme events and the analysis of mere absolute numbers of heat waves that are independent of the length of the respective events. On the basis of heat related vulnerability conceptualization, we select various population and land cover characteristics in our study area and define a composite vulnerability index based on aggregation of three groups of indicators related to demographic, socio-economic, and environmental factors. The study reveals how risk patterns seem to be driven by the vulnerability distribution, generally showing a clear difference between high-risk urban areas and wide areas of low risk in the sub-urban and rural environments. This is

  11. Observations and Modeling of Low Level Moisture Convergence Patterns in the Southern Appalachians during the Integrated Precipitation and Hydrology Experiment (IPHEx) Extended Observing Period

    NASA Astrophysics Data System (ADS)

    Wilson, Anna M.; Barros, Ana P.

    2015-04-01

    Accurate fields of precipitation accumulations and intensity at high spatial resolution in regions of complex terrain are largely unavailable. This is due to first, a lack of existing in situ observations, both because of the challenge in having high enough density in the instrument placement to represent the large spatial heterogeneity in rainfall patterns in these regions and because of the remote, harsh nature of the terrain that makes it difficult to install and maintain instrumentation and second, obstacles to remote sensing such as beam blockage and ground clutter that are caused by the complex orography. In this study we leverage observations from two sources: 1) a high-elevation, high-density tipping bucket rain gauge network that has been recording precipitation observations for over six years along ridgelines in the Pigeon River Basin, a small watershed in the Southern Appalachians, and 2) the 4-D database of observations collected in 2014 in support of the Global Precipitation Mission (GPM) during the first field campaign after the launch of the GPM satellite, the Integrated Precipitation and Hydrology Experiment (IPHEx), to learn about formation and maintenance mechanisms for fog and low cloud in this region and the resulting impact on the precipitation regime. The observations focused on here are those at the near surface, within 2 kilometers of the ground level. This presentation will focus on process-based modeling studies using the Advanced Research Weather and Forecasting Model conducted based upon observations made during this campaign. Case studies will be presented for real events simulated during the IPHEx campaign. These case studies occurred with different synoptic conditions, but include observational evidence of orographic enhancement. The case studies are simulated and analyzed in order to investigate how the topography modulates the regional, diurnal patterns of moisture convergence and fog and low cloud formation, as well as the mid

  12. Taming the Mighty Mississippi: Integrating paleo-flood data and modeling to understand the patterns and causes of extreme floods on a major river system

    NASA Astrophysics Data System (ADS)

    Munoz, Samuel; Giosan, Liviu; Jeffrey, Donnelly; Dee, Sylvia; Shen, Zhixiong

    2016-04-01

    The Mississippi River is an economic artery of the United States that is heavily managed to provide flood control and maintain a navigable shipping channel. The current system of levees and spillway structures was conceived in the early 20th century, but the ability of this system to withstand the altered hydroclimatic conditions projected for the next century is poorly understood. Here, we present initial results from a project that integrates new sedimentary records from floodplain lakes with analyses of sediment geochemistry and climate model simulations to better understand the causes of extreme floods on the lower Mississippi River. In our sedimentary paleoflood records, flood event beds are characterized by an upward fining sequence from deposition of the bedload and suspended load during overbank floods, identified here using high-resolution laser particle-size analysis and elemental composition (XRF), and dated using radioisotopes (137Cs, 210Pb, 14C) and optically-stimulated luminescence (OSL) on quartz. Grain-size descriptors and elemental ratios of Zr/Fe and Fe/Rb are highly correlated, and are used alongside historical discharge records to develop a statistical model for reconstructing flood magnitude in prehistoric contexts. Geochemical analyses of sediments from the floodplains of major tributaries of the Mississippi are used to assess the systematics of 87Sr/86Sr, 143Nd/144Nd, 206Pb/204Pb, and 208Pb/204Pb across the basin, enabling identification of the synoptic patterns of individual paleo-flood events. We investigate the dynamical drivers of past floods on the lower Mississippi using both reanalysis data and the last millennium simulation from NCAR model CESM1 to find that increased likelihoods of extreme floods on the lower Mississippi River are associated with enhanced moisture flux over midcontinental North America that is controlled by the interaction of seasonally variable soil moisture over major tributaries with inter-annual (e.g., ENSO) and

  13. A high performance P(VDF-TrFE) nanogenerator with self-connected and vertically integrated fibers by patterned EHD pulling

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoliang; Tian, Hongmiao; Li, Xiangming; Shao, Jinyou; Ding, Yucheng; An, Ningli; Zhou, Yaopei

    2015-07-01

    Piezoelectricity based energy harvesting from mechanical vibrations has attracted extensive attention for its potential application in powering wireless mobile electronics recently. Here, a patterned electrohydrodynamic (EHD) pulling technology was proposed to fabricate a new self-connected, piezoelectric fiber array vertically integrated P(VDF-TrFE) nanogenerator, with a molecular poling orientation fully aligned to the principal excitation for maximized conversion and a well-bridged electrode pair for efficient charge collection. The nanogenerator is fabricated in a novel way by applying a voltage across an electrode pair sandwiching an air gap and an array of shallow micropillars, during which the EHD force tends to pull the micropillars upward, generating a microfiber array finally in robust contact with the upper electrode. Such a thermoplastic and EHD deformation of the microfibers, featured simultaneously by an electric field and by a microfiber elongation dominantly vertical to the electrode, leads to a poling orientation of P(VDF-TrFE) well coincident with the principal strain for the generator excited by a force normal to the electrodes. The as-prepared piezoelectric device exhibits an enhanced output voltage up to 4.0 V and a current of 2.6 μA, therefore the piezoelectric voltage was enhanced to 5.4 times that from the bulk film. Under periodic mechanical impact, electric signals are repeatedly generated from the device and used to power a seven-segment indicator, RBGY colored light-emitting diodes, and a large-scale liquid crystal display screen. These results not only provide a tool for fabricating 3D piezoelectric polymers but offer a new type of self-connected nanogenerator for the next generation of self-powered electronics.Piezoelectricity based energy harvesting from mechanical vibrations has attracted extensive attention for its potential application in powering wireless mobile electronics recently. Here, a patterned electrohydrodynamic (EHD

  14. Changing practice patterns for breast cancer radiation therapy with clinical pathways: An analysis of hypofractionation in a large, integrated cancer center network.

    PubMed

    Rajagopalan, Malolan S; Flickinger, John C; Heron, Dwight E; Beriwal, Sushil

    2015-01-01

    Hypofractionated whole breast irradiation (HF-WBI) following breast conserving surgery has produced excellent outcomes, but utilization remains limited. We evaluated the impact of a clinical pathway in the adoption of HF-WBI in a large, integrated radiation oncology network. We identified patients aged ≥70 years treated for breast cancer or ductal carcinoma in situ. Patients treated with palliative intent, accelerated partial breast radiation, following mastectomy, or with axillary nodal, supraclavicular, or internal mammary fields were excluded. HF-WBI was defined as ≤20 fractions with a dose/fraction ≥2.5 Gy. Multivariate analysis identified variables associated with increased HF-WBI utilization. We identified 2426 patients meeting inclusion criteria. HF-WBI utilization increased significantly from 6.5% (22.0% academic, 2.0% community) before pathway modification to 33.8% afterwards (68.5% academic, 25.3% community, P<.001). For academic physicians, the relative risk of HF-WBI utilization was 3.8 following publication of the seminal HF-WBI trial and 10.6 following pathway modification (P < .001). For community physicians, the relative risk of HF-WBI utilization did not significantly change following publication but was 21.0 following pathway modification (P < .001). The increased adoption of HF-WBI saved an estimated $154,000 annually in our network. We found that our implementation of clinical pathways substantially increased adoption of HF-WBI for breast cancer. We found no significant change in utilization of HF-WBI among community physicians following publication of a seminal trial for HF-WBI until after clinical pathway implementation, which increased the use of HF-WBI by 20-fold. Clinical pathways may be effective in changing practice patterns, disseminating evidence, and realizing health care savings. Copyright © 2015 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

  15. Transcriptional Profiling of Newly Generated Dentate Granule Cells Using TU Tagging Reveals Pattern Shifts in Gene Expression during Circuit Integration1,2

    PubMed Central

    Chatzi, Christina; Shen, Rongkun; Goodman, Richard H.

    2016-01-01

    Abstract Despite representing only a small fraction of hippocampal granule cells, adult-generated newborn granule cells have been implicated in learning and memory (Aimone et al., 2011). Newborn granule cells undergo functional maturation and circuit integration over a period of weeks. However, it is difficult to assess the accompanying gene expression profiles in vivo with high spatial and temporal resolution using traditional methods. Here we used a novel method [“thiouracil (TU) tagging”] to map the profiles of nascent mRNAs in mouse immature newborn granule cells compared with mature granule cells. We targeted a nonmammalian uracil salvage enzyme, uracil phosphoribosyltransferase, to newborn neurons and mature granule cells using retroviral and lentiviral constructs, respectively. Subsequent injection of 4-TU tagged nascent RNAs for analysis by RNA sequencing. Several hundred genes were significantly enhanced in the retroviral dataset compared with the lentiviral dataset. We compared a selection of the enriched genes with steady-state levels of mRNAs using quantitative PCR. Ontology analysis revealed distinct patterns of nascent mRNA expression, with newly generated immature neurons showing enhanced expression for genes involved in synaptic function, and neural differentiation and development, as well as genes not previously associated with granule cell maturation. Surprisingly, the nascent mRNAs enriched in mature cells were related to energy homeostasis and metabolism, presumably indicative of the increased energy demands of synaptic transmission and their complex dendritic architecture. The high spatial and temporal resolution of our modified TU-tagging method provides a foundation for comparison with steady-state RNA analyses by traditional transcriptomic approaches in defining the functional roles of newborn neurons. PMID:27011954

  16. A high performance P(VDF-TrFE) nanogenerator with self-connected and vertically integrated fibers by patterned EHD pulling.

    PubMed

    Chen, Xiaoliang; Tian, Hongmiao; Li, Xiangming; Shao, Jinyou; Ding, Yucheng; An, Ningli; Zhou, Yaopei

    2015-07-21

    Piezoelectricity based energy harvesting from mechanical vibrations has attracted extensive attention for its potential application in powering wireless mobile electronics recently. Here, a patterned electrohydrodynamic (EHD) pulling technology was proposed to fabricate a new self-connected, piezoelectric fiber array vertically integrated P(VDF-TrFE) nanogenerator, with a molecular poling orientation fully aligned to the principal excitation for maximized conversion and a well-bridged electrode pair for efficient charge collection. The nanogenerator is fabricated in a novel way by applying a voltage across an electrode pair sandwiching an air gap and an array of shallow micropillars, during which the EHD force tends to pull the micropillars upward, generating a microfiber array finally in robust contact with the upper electrode. Such a thermoplastic and EHD deformation of the microfibers, featured simultaneously by an electric field and by a microfiber elongation dominantly vertical to the electrode, leads to a poling orientation of P(VDF-TrFE) well coincident with the principal strain for the generator excited by a force normal to the electrodes. The as-prepared piezoelectric device exhibits an enhanced output voltage up to 4.0 V and a current of 2.6 μA, therefore the piezoelectric voltage was enhanced to 5.4 times that from the bulk film. Under periodic mechanical impact, electric signals are repeatedly generated from the device and used to power a seven-segment indicator, RBGY colored light-emitting diodes, and a large-scale liquid crystal display screen. These results not only provide a tool for fabricating 3D piezoelectric polymers but offer a new type of self-connected nanogenerator for the next generation of self-powered electronics.

  17. Recovery patterns, histological observations and genetic integrity in Malus shoot tips cryopreserved using droplet-vitrification and encapsulation-dehydration procedures.

    PubMed

    Li, Bai-Quan; Feng, Chao-Hong; Wang, Min-Rui; Hu, Ling-Yun; Volk, Gayle; Wang, Qiao-Chun

    2015-11-20

    A droplet-vitrification procedure is described for cryopreservation of Malus shoot tips. Survival patterns, recovery types, histological observations, and genetic integrity were compared for Malus shoot tips cryopreserved using this droplet-vitrification procedure and an encapsulation-dehydration procedure that was previously reported by us. In both procedures, three types of shoot tip recovery were observed following cryopreservation: callus formation without shoot regrowth, leaf formation without shoot regrowth, and shoot regrowth. Three categories of histological observations were also identified in cross-sections of shoot tips recovered after cryopreservation using the two cryogenic procedures. In category 1, almost all of the cells (94-95%) in the apical dome (AD) were damaged or killed and only some cells (30-32%) in the leaf primordia (LPs) survived. In category 2, only a few cells (18-20%) in the AD and some cells (30-31%) in the LPs survived. In category 3, majority of the cells (60-62%) in the AD and some cells (30-33%) in the LPs survived. These data suggest that shoot regrowth is correlated to the presence of a majority of surviving cells in the AD after liquid nitrogen exposure. No polymorphic bands were detected by inter-simple sequence repeats or by random amplified polymorphic DNA assessments, and ploidy levels analyzed by flow cytometry were unchanged when plants recovered after cryoexposure were compared to controls. The droplet-vitrification procedure appears to be robust since seven genotypes representing four Malus species and one hybrid recovered shoots following cryopreservation. Mean shoot regrowth levels of these seven genotypes were 48% in the droplet-vitrification method, which were lower than those (61%) in the encapsulation-dehydration procedure reported in our previous study, suggesting the latter may be preferred for routine cryobanking applications for Malus shoot tips. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Patterns of Broken Patterns

    NASA Astrophysics Data System (ADS)

    Field, R. W.; Park, G. B.; Changala, P. B.; Baraban, J. H.; Stanton, J. F.; Merer, A. J.

    2013-06-01

    Spectroscopy - it is all about patterns. Some patterns look so indescribably complicated that, unlike pornography, you do not know one when you see one. It is tempting to say that, at high vibrational excitation, interactions among normal mode basis states are so strong and widespread that all patterns are obliterated. But this is not true. When normal mode frequencies are in near integer multiple ratios, polyads emerge. A polyad is a robust pattern often comprising many vibrational eigenstates. Each such pattern might span many hundreds of cm^{-1}, and it is inevitable that several unrelated polyad patterns overlap. When polyads overlap, it might seem impossible to disentangle them. However, the key to disentanglement is that polyads come in families in which successive generations are related by harmonic oscillator matrix element selection and scaling rules. Families of polyads are described by families of scaling-based effective Hamiltonian matrices, {H}^{{eff}}. No matter how complex and overlapped, the polyad {H}^{{eff}} serves as a magic decoder for picking out the polyad pattern. Sometimes the polyad patterns are systematically broken (a meta-pattern), owing to proximity to an isomerization barrier, as occurs in highly excited bending levels of the S_{1} state of HCCH, which encode the trans-cis minimum energy isomerization path. Quantum Chemists often dismiss {H}^{{eff}} models, precisely because they are models that do not express the full dimensionality of the complete Hamiltonian. But an {H}^{{eff}} explains rather than describes. Shunning {H}^{{eff}}s is like throwing out the baby with the bath water. Don't do it!

  19. Time-Adjusted Internal Target Volume: A Novel Approach Focusing on Heterogeneity of Tumor Motion Based on 4-Dimensional Computed Tomography Imaging for Radiation Therapy Planning of Lung Cancer

    SciTech Connect

    Nishibuchi, Ikuno; Kimura, Tomoki; Nakashima, Takeo; Ochi, Yusuke; Takahashi, Ippei; Doi, Yoshiko; Kenjo, Masahiro; Kaneyasu, Yuko; Ozawa, Syuichi; Murakami, Yuji; Wadasaki, Koichi; Nagata, Yasushi

    2014-08-01

    Purpose: To consider nonuniform tumor motion within the internal target volume (ITV) by defining time-adjusted ITV (TTV), a volume designed to include heterogeneity of tumor existence on the basis of 4-dimensional computed tomography (4D-CT). Methods and Materials: We evaluated 30 lung cancer patients. Breath-hold CT (BH-CT) and free-breathing 4D-CT scans were acquired for each patient. The tumors were manually delineated using a lung CT window setting (window, 1600 HU; level, −300 HU). Tumor in BH-CT images was defined as gross tumor volume (GTV), and the sum of tumors in 4D-CT images was defined as ITV-4D. The TTV images were generated from the 4D-CT datasets, and the tumor existence probability within ITV-4D was calculated. We calculated the TTV{sub 80} value, which is the percentage of the volume with a tumor existence probability that exceeded 80% on ITV-4D. Several factors that affected the TTV{sub 80} value, such as the ITV-4D/GTV ratio or tumor centroid deviation, were evaluated. Results: Time-adjusted ITV images were acquired for all patients, and tumor respiratory motion heterogeneity was visualized. The median (range) ITV-4D/GTV ratio and median tumor centroid deviation were 1.6 (1.0-4.1) and 6.3 mm (0.1-30.3 mm), respectively. The median TTV{sub 80} value was 43.3% (2.9-98.7%). Strong correlations were observed between the TTV{sub 80} value and the ITV-4D/GTV ratio (R=−0.71) and tumor centroid deviation (R=−0.72). The TTV images revealed the tumor motion pattern features within ITV. Conclusions: The TTV images reflected nonuniform tumor motion, and they revealed the tumor motion pattern features, suggesting that the TTV concept may facilitate various aspects of radiation therapy planning of lung cancer while incorporating respiratory motion in the future.

  20. Verification of Planning Target Volume Settings in Volumetric Modulated Arc Therapy for Stereotactic Body Radiation Therapy by Using In-Treatment 4-Dimensional Cone Beam Computed Tomography

    SciTech Connect

    Takahashi, Wataru; Yamashita, Hideomi; Kida, Satoshi; Masutani, Yoshitaka; Sakumi, Akira; Ohtomo, Kuni; Nakagawa, Keiichi; Haga, Akihiro

    2013-07-01

    Purpose: To evaluate setup error and tumor motion during beam delivery by using 4-dimensional cone beam computed tomography (4D CBCT) and to assess the adequacy of the planning target volume (PTV) margin for lung cancer patients undergoing volumetric modulated arc therapy for stereotactic body radiation therapy (VMAT-SBRT). Methods and Materials: Fifteen lung cancer patients treated by single-arc VMAT-SBRT were selected in this analysis. All patients were treated with an abdominal compressor. The gross tumor volumes were contoured on maximum inspiration and maximum expiration CT datasets from 4D CT respiratory sorting and merged into internal target volumes (ITVs). The PTV margin was isotropically taken as 5 mm. Registration was automatically performed using “pre-3D” CBCT. Treatment was performed with a D95 prescription of 50 Gy delivered in 4 fractions. The 4D tumor locations during beam delivery were determined using in-treatment 4D CBCT images acquired in each fraction. Then, the discrepancy between the actual tumor location and the ITV was evaluated in the lateral, vertical, and longitudinal directions. Results: Overall, 55 4D CBCT sets during VMAT-SBRT were successfully obtained. The amplitude of tumor motion was less than 10 mm in all directions. The average displacements between ITV and actual tumor location during treatment were 0.41 ± 0.93 mm, 0.15 ± 0.58 mm, and 0.60 ± 0.99 mm for the craniocaudal, left-right, and anteroposterior directions, respectively. The discrepancy in each phase did not exceed 5 mm in any direction. Conclusions: With in-treatment 4D CBCT, we confirmed the required PTV margins when the registration for moving target was performed using pre-3D CBCT. In-treatment 4D CBCT is a direct method for quantitatively assessing the intrafractional location of a moving target.

  1. Verification of planning target volume settings in volumetric modulated arc therapy for stereotactic body radiation therapy by using in-treatment 4-dimensional cone beam computed tomography.

    PubMed

    Takahashi, Wataru; Yamashita, Hideomi; Kida, Satoshi; Masutani, Yoshitaka; Sakumi, Akira; Ohtomo, Kuni; Nakagawa, Keiichi; Haga, Akihiro

    2013-07-01

    To evaluate setup error and tumor motion during beam delivery by using 4-dimensional cone beam computed tomography (4D CBCT) and to assess the adequacy of the planning target volume (PTV) margin for lung cancer patients undergoing volumetric modulated arc therapy for stereotactic body radiation therapy (VMAT-SBRT). Fifteen lung cancer patients treated by single-arc VMAT-SBRT were selected in this analysis. All patients were treated with an abdominal compressor. The gross tumor volumes were contoured on maximum inspiration and maximum expiration CT datasets from 4D CT respiratory sorting and merged into internal target volumes (ITVs). The PTV margin was isotropically taken as 5 mm. Registration was automatically performed using "pre-3D" CBCT. Treatment was performed with a D95 prescription of 50 Gy delivered in 4 fractions. The 4D tumor locations during beam delivery were determined using in-treatment 4D CBCT images acquired in each fraction. Then, the discrepancy between the actual tumor location and the ITV was evaluated in the lateral, vertical, and longitudinal directions. Overall, 55 4D CBCT sets during VMAT-SBRT were successfully obtained. The amplitude of tumor motion was less than 10 mm in all directions. The average displacements between ITV and actual tumor location during treatment were 0.41 ± 0.93 mm, 0.15 ± 0.58 mm, and 0.60 ± 0.99 mm for the craniocaudal, left-right, and anteroposterior directions, respectively. The discrepancy in each phase did not exceed 5 mm in any direction. With in-treatment 4D CBCT, we confirmed the required PTV margins when the registration for moving target was performed using pre-3D CBCT. In-treatment 4D CBCT is a direct method for quantitatively assessing the intrafractional location of a moving target. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. A Pilot Evaluation of a 4-Dimensional Cone-Beam Computed Tomographic Scheme Based on Simultaneous Motion Estimation and Image Reconstruction

    SciTech Connect

    Dang, Jun; Gu, Xuejun; Pan, Tinsu; Wang, Jing

    2015-02-01

    Purpose: To evaluate the performance of a 4-dimensional (4-D) cone-beam computed tomographic (CBCT) reconstruction scheme based on simultaneous motion estimation and image reconstruction (SMEIR) through patient studies. Methods and Materials: The SMEIR algorithm contains 2 alternating steps: (1) motion-compensated CBCT reconstruction using projections from all phases to reconstruct a reference phase 4D-CBCT by explicitly considering the motion models between each different phase and (2) estimation of motion models directly from projections by matching the measured projections to the forward projection of the deformed reference phase 4D-CBCT. Four lung cancer patients were scanned for 4 to 6 minutes to obtain approximately 2000 projections for each patient. To evaluate the performance of the SMEIR algorithm on a conventional 1-minute CBCT scan, the number of projections at each phase was reduced by a factor of 5, 8, or 10 for each patient. Then, 4D-CBCTs were reconstructed from the down-sampled projections using Feldkamp-Davis-Kress, total variation (TV) minimization, prior image constrained compressive sensing (PICCS), and SMEIR. Using the 4D-CBCT reconstructed from the fully sampled projections as a reference, the relative error (RE) of reconstructed images, root mean square error (RMSE), and maximum error (MaxE) of estimated tumor positions were analyzed to quantify the performance of the SMEIR algorithm. Results: The SMEIR algorithm can achieve results consistent with the reference 4D-CBCT reconstructed with many more projections per phase. With an average of 30 to 40 projections per phase, the MaxE in tumor position detection is less than 1 mm in SMEIR for all 4 patients. Conclusion: The results from a limited number of patients show that SMEIR is a promising tool for high-quality 4D-CBCT reconstruction and tumor motion modeling.

  3. The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems . Part II - Performance and application to the California Current System

    NASA Astrophysics Data System (ADS)

    Moore, Andrew M.; Arango, Hernan G.; Broquet, Gregoire; Edwards, Chris; Veneziani, Milena; Powell, Brian; Foley, Dave; Doyle, James D.; Costa, Dan; Robinson, Patrick

    2011-10-01

    The Regional Ocean Modeling System (ROMS) 4-dimensional variational (4D-Var) data assimilation systems have been systematically applied to the mesoscale circulation environment of the California Current to demonstrate the performance and practical utility of the various components of ROMS 4D-Var. In particular, we present a comparison of three approaches to 4D-Var, namely: the primal formulation of the incremental strong constraint approach; the dual formulation “physical-space statistical analysis system”; and the dual formulation indirect representer approach. In agreement with theoretical considerations all three approaches converge to the same ocean circulation estimate when using the same observations and prior information. However, the rate of convergence of the dual formulation was found to be inferior to that of the primal formulation. Other aspects of the 4D-Var performance that relate to the use of multiple outer-loops, preconditioning, and the weak constraint are also explored. A systematic evaluation of the impact of the various components of the 4D-Var control vector (i.e. the initial conditions, surface forcing and open boundary conditions) is also presented. It is shown that correcting for uncertainties in the model initial conditions exerts the largest influence on the ability of the model to fit the available observations. Various important diagnostics of 4D-Var are also examined, including estimates of the posterior error, the information content of the observation array, and innovation-based consistency checks on the prior error assumptions. Using these diagnostic tools, we find that more than 90% of the observations assimilated into the model provide redundant information. This is a symptom of the large percentage of satellite data that are used and to some extent the nature of the data processing employed. This is the second in a series of three papers describing the ROMS 4D-Var systems.

  4. Prenatal screening for fetal face and clefting in a prospective study on low-risk population: can 3- and 4-dimensional ultrasound enhance visualization and detection rate?

    PubMed

    Tonni, Gabriele; Centini, Giovanni; Rosignoli, Lucia

    2005-10-01

    A study of 1856 second trimester low-risk pregnancies was conducted over a period of 12 months to evaluate the detection rate of cleft lip and palate by 3- and 4-dimensional (3D, 4D) ultrasonography. To image the fetal face and profile, a protocol regarding the use of external or internal hand stimulation or a repeated scan was followed, and the time taken to perform 3D scan was compared to that of a conventional 2D ultrasound. One case of unilateral right cleft lip and a cleft lip plus cleft palate were both identified, giving a prevalence of 1.1 per 1000 live births and a prenatal detection rate of 100%. The average imaging time for fetal face/profile view was significantly less with 3D when compared to 2D (5.33 vs 6.2 seconds, P < .001) and diagnosis at first scan without external or internal hand stimulation was feasible in 78% by 2D versus 87% by 3D technique (P < .0001). Cleft lip and palate were isolated prenatal findings and newborn karyotyping showed normal chromosomal maps in both cases. With the use of this standardized protocol, we were able to image the fetal face and profile view in all cases. We underline the critical role of sonographic expertise in screening for these anomalies and the great enhancement in imaging soft tissues and bone lesions by using 3D ultrasound. We advocate that screening for cleft lip and palate be included in future standard ultrasound examination in the second trimester of pregnancy.

  5. Integrated Warfighter Biodefense Program (IWBP)

    DTIC Science & Technology

    2012-02-01

    In addition, further work was done on developing Pattern Based Prediction by implementing a predictive analytics methodology based on stochastic...integrating Pattern Based Prediction (to enable Predictive Analytics ) with Pattern Based Discovery. FINANCIAL SUMMARY: Contract Activity QLI Contract

  6. Cone-Beam Computed Tomography Internal Motion Tracking Should Be Used to Validate 4-Dimensional Computed Tomography for Abdominal Radiation Therapy Patients.

    PubMed

    Rankine, Leith; Wan, Hanlin; Parikh, Parag; Maughan, Nichole; Poulsen, Per; DeWees, Todd; Klein, Eric; Santanam, Lakshmi

    2016-06-01

    To demonstrate that fiducial tracking during pretreatment Cone-Beam CT (CBCT) can accurately measure tumor motion and that this method should be used to validate 4-dimensional CT (4DCT) margins before each treatment fraction. For 31 patients with abdominal tumors and implanted fiducial markers, tumor motion was measured daily with CBCT and fluoroscopy for 202 treatment fractions. Fiducial tracking and maximum-likelihood algorithms extracted 3-dimensional fiducial trajectories from CBCT projections. The daily internal margin (IM) (ie, range of fiducial motion) was calculated for CBCT and fluoroscopy as the 5th-95th percentiles of displacement in each cardinal direction. The planning IM from simulation 4DCT (IM4DCT) was considered adequate when within ±1.2 mm (anterior-posterior, left-right) and ±3 mm (superior-inferior) of the daily measured IM. We validated CBCT fiducial tracking as an accurate predictive measure of intrafraction motion by comparing the daily measured IMCBCT with the daily IM measured by pretreatment fluoroscopy (IMpre-fluoro); these were compared with pre- and posttreatment fluoroscopy (IMfluoro) to identify those patients who could benefit from imaging during treatment. Four-dimensional CT could not accurately predict intrafractional tumor motion for ≥80% of fractions in 94% (IMCBCT), 97% (IMpre-fluoro), and 100% (IMfluoro) of patients. The IMCBCT was significantly closer to IMpre-fluoro than IM4DCT (P<.01). For patients with median treatment time t < 7.5 minutes, IMCBCT was in agreement with IMfluoro for 93% of fractions (superior-inferior), compared with 63% for the t > 7.5 minutes group, demonstrating the need for patient-specific intratreatment imaging. Tumor motion determined from 4DCT simulation does not accurately predict the daily motion observed on CBCT or fluoroscopy. Cone-beam CT could replace fluoroscopy for pretreatment verification of simulation IM4DCT, reducing patient setup time and imaging dose. Patients with

  7. TH-E-17A-06: Anatomical-Adaptive Compressed Sensing (AACS) Reconstruction for Thoracic 4-Dimensional Cone-Beam CT

    SciTech Connect

    Shieh, C; Kipritidis, J; OBrien, R; Cooper, B; Kuncic, Z; Keall, P

    2014-06-15

    Purpose: The Feldkamp-Davis-Kress (FDK) algorithm currently used for clinical thoracic 4-dimensional (4D) cone-beam CT (CBCT) reconstruction suffers from noise and streaking artifacts due to projection under-sampling. Compressed sensing theory enables reconstruction of under-sampled datasets via total-variation (TV) minimization, but TV-minimization algorithms such as adaptive-steepest-descent-projection-onto-convex-sets (ASD-POCS) often converge slowly and are prone to over-smoothing anatomical details. These disadvantages can be overcome by incorporating general anatomical knowledge via anatomy segmentation. Based on this concept, we have developed an anatomical-adaptive compressed sensing (AACS) algorithm for thoracic 4D-CBCT reconstruction. Methods: AACS is based on the ASD-POCS framework, where each iteration consists of a TV-minimization step and a data fidelity constraint step. Prior to every AACS iteration, four major thoracic anatomical structures - soft tissue, lungs, bony anatomy, and pulmonary details - were segmented from the updated solution image. Based on the segmentation, an anatomical-adaptive weighting was applied to the TV-minimization step, so that TV-minimization was enhanced at noisy/streaky regions and suppressed at anatomical structures of interest. The image quality and convergence speed of AACS was compared to conventional ASD-POCS using an XCAT digital phantom and a patient scan. Results: For the XCAT phantom, the AACS image represented the ground truth better than the ASD-POCS image, giving a higher structural similarity index (0.93 vs. 0.84) and lower absolute difference (1.1*10{sup 4} vs. 1.4*10{sup 4}). For the patient case, while both algorithms resulted in much less noise and streaking than FDK, the AACS image showed considerably better contrast and sharpness of the vessels, tumor, and fiducial marker than the ASD-POCS image. In addition, AACS converged over 50% faster than ASD-POCS in both cases. Conclusions: The proposed AACS

  8. Audio-Visual Biofeedback Does Not Improve the Reliability of Target Delineation Using Maximum Intensity Projection in 4-Dimensional Computed Tomography Radiation Therapy Planning

    SciTech Connect

    Lu, Wei; Neuner, Geoffrey A.; George, Rohini; Wang, Zhendong; Sasor, Sarah; Huang, Xuan; Regine, William F.; Feigenberg, Steven J.; D'Souza, Warren D.

    2014-01-01

    Purpose: To investigate whether coaching patients' breathing would improve the match between ITV{sub MIP} (internal target volume generated by contouring in the maximum intensity projection scan) and ITV{sub 10} (generated by combining the gross tumor volumes contoured in 10 phases of a 4-dimensional CT [4DCT] scan). Methods and Materials: Eight patients with a thoracic tumor and 5 patients with an abdominal tumor were included in an institutional review board-approved prospective study. Patients underwent 3 4DCT scans with: (1) free breathing (FB); (2) coaching using audio-visual (AV) biofeedback via the Real-Time Position Management system; and (3) coaching via a spirometer system (Active Breathing Coordinator or ABC). One physician contoured all scans to generate the ITV{sub 10} and ITV{sub MIP}. The match between ITV{sub MIP} and ITV{sub 10} was quantitatively assessed with volume ratio, centroid distance, root mean squared distance, and overlap/Dice coefficient. We investigated whether coaching (AV or ABC) or uniform expansions (1, 2, 3, or 5 mm) of ITV{sub MIP} improved the match. Results: Although both AV and ABC coaching techniques improved frequency reproducibility and ABC improved displacement regularity, neither improved the match between ITV{sub MIP} and ITV{sub 10} over FB. On average, ITV{sub MIP} underestimated ITV{sub 10} by 19%, 19%, and 21%, with centroid distance of 1.9, 2.3, and 1.7 mm and Dice coefficient of 0.87, 0.86, and 0.88 for FB, AV, and ABC, respectively. Separate analyses indicated a better match for lung cancers or tumors not adjacent to high-intensity tissues. Uniform expansions of ITV{sub MIP} did not correct for the mismatch between ITV{sub MIP} and ITV{sub 10}. Conclusions: In this pilot study, audio-visual biofeedback did not improve the match between ITV{sub MIP} and ITV{sub 10}. In general, ITV{sub MIP} should be limited to lung cancers, and modification of ITV{sub MIP} in each phase of the 4DCT data set is recommended.

  9. Spatiotemporal image correlation with spherical sampling and high-definition flow: new 4-dimensional method for assessment of tissue vascularization changes during the cardiac cycle: reproducibility analysis.

    PubMed

    Kudla, Marek J; Alcázar, Juan Luis

    2012-01-01

    To describe and assess the interobserver reproducibility of a new method for evaluation of ovarian vascularization using spatiotemporal image correlation-high definition flow (STIC-HDF). Stored 4-dimensional (4D) STIC-HDF volume data from 39 healthy pre-menopausal fertile women (aged <35 years) examined in the follicular part of the menstrual cycle by transvaginal sonography were assessed by two different examiners blinded from each other (one in Spain the other in Poland). Using 1-cm(3) spherical sampling, the vascularization index (VI) from the most vascularized part of the ovarian stroma was calculated at two different moments of the cardiac cycle (systole and diastole). System settings were kept constant for all patients (pulse repetition frequency, 0.6 kHz; gain, 0.2) with a depth of 40 mm. Analysis was performed offline using 4D software on a personal computer. On the basis of VI and vascularization-flow index (VFI) values during systole and diastole, 4 new 4D indices were defined: 4D systolic/diastolic volumetric index (4D-SDVI = VI(syst)/VI(diast)), 4D hemodynamic volumetric index (4D-HVI = [VI(syst) + VI(diast)]/[VI(syst) - VI(diast)]), 4D systolic/diastolic vascularization-flow index (4D-SDVFI = VFI(syst)/VFI(diast)), and 4D hemodynamic vascularization-flow index (4D-HVFI = [VFI(syst) + VFI(diast)]/[VFI(syst)- VFI(diast)]). Reproducibility of measurements was estimated by calculating the intraclass correlation coefficient (ICC). The systolic VI, diastolic VI, 4D-SDVI, 4D-HVI, systolic VFI, diastolic VFI, and 4D-HVFI showed good reproducibility (ICC, 0.992, 0.994, 0.879, 0.915, 0.995, 0.995, and 0.893, respectively). The 4D-SDVFI showed moderate reproducibility (ICC, 0.797). We describe 4 new 4D vascular indices for assessing tissue vascularization using STIC-HDF technology. Assessment of ovarian vascularization using this STIC-HDF spherical sampling is reliable. The calculation of these new indices is reproducible between two different examiners.

  10. Do Fourth Graders Integrate Text and Picture in Processing and Learning from an Illustrated Science Text? Evidence from Eye-Movement Patterns

    ERIC Educational Resources Information Center

    Mason, Lucia; Tornatora, Maria Caterina; Pluchino, Patrik

    2013-01-01

    This study used eye-tracking methodology in the school setting to examine fourth graders' online processing of text and graphics while reading an illustrated science text. We were interested in identifying patterns of visual behavior, which was examined considering individual differences in reading comprehension, prior knowledge, and spatial…

  11. Do Fourth Graders Integrate Text and Picture in Processing and Learning from an Illustrated Science Text? Evidence from Eye-Movement Patterns

    ERIC Educational Resources Information Center

    Mason, Lucia; Tornatora, Maria Caterina; Pluchino, Patrik

    2013-01-01

    This study used eye-tracking methodology in the school setting to examine fourth graders' online processing of text and graphics while reading an illustrated science text. We were interested in identifying patterns of visual behavior, which was examined considering individual differences in reading comprehension, prior knowledge, and spatial…

  12. Finite element model of surface acoustic wave method for mechanical characterization of patterned thin films of the ultra-large scaled integrated interconnect.

    PubMed

    Xiao, Xia; Shan, Xingmeng; Tao, Ye; Sun, Yuan; Kikkawa, Takamaro

    2013-02-01

    Surface acoustic waves (SAWs) technique is a promising method to determine the mechanical properties of thin low dielectric constant (low-k) dielectrics by matching the experimental dispersion curve with the theoretical dispersion curves. However, it is difficult to calculate the dispersion curves when SAWs propagate along patterned structure. In this paper, finite element method (FEM) is applied to obtain the numerical dispersion results of SAWs propagating on patterned film. Periodic boundary condition and plane-strain model is used to improve the computation speed. Four structures of bulk silicon, single layered low-k film, two layered Cu and SiO2 film, and patterned film, are simulated in this paper. The dispersion curves of single low-k films derived from the FEM simulation agree very well with those calculated by traditional method, which verifies the correct employment of the FEM approach. Dispersion curves of two patterned film structure of Cu and SiO2 with difference metal wire width are obtained. Effective Young's moduli are achieved by fitting the FEM simulated results with those of traditional theoretical calculation through least square error method.

  13. Integration of hydrologic and water allocation models in basin-scale water resources management considering crop pattern and climate change: Karkheh River Basin in Iran

    USDA-ARS?s Scientific Manuscript database

    The paradigm of integrated water resources management requires coupled analysis of hydrology and water resources in a river basin. Population growth and uncertainties due to climate change make historic data not a reliable source of information for future planning of water resources, hence necessit...

  14. Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia.

    PubMed

    Kavakiotis, Ioannis; Xochelli, Aliki; Agathangelidis, Andreas; Tsoumakas, Grigorios; Maglaveras, Nicos; Stamatopoulos, Kostas; Hadzidimitriou, Anastasia; Vlahavas, Ioannis; Chouvarda, Ioanna

    2016-06-06

    Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insight into the physiology and pathology of B cells, leading to strong prognostication markers for clinical outcome in chronic lymphocytic leukaemia (CLL), the most frequent adult B-cell malignancy. In this paper we present a methodology for integrating multiple immunogenetic and clinocobiological data sources in order to extract features and create high quality datasets for SHM analysis in IG receptors of CLL patients. This dataset is used as the basis for a higher level integration procedure, inspired form social choice theory. This is applied in the Towards Analysis, our attempt to investigate the potential ontogenetic transformation of genes belonging to specific stereotyped CLL subsets towards other genes or gene families, through SHM. The data integration process, followed by feature extraction, resulted in the generation of a dataset containing information about mutations occurring through SHM. The Towards analysis performed on the integrated dataset applying voting techniques, revealed the distinct behaviour of subset #201 compared to other subsets, as regards SHM related movements among gene clans, both in allele-conserved and non-conserved gene areas. With respect to movement between genes, a high percentage movement towards pseudo genes was found in all CLL subsets. This data integration and feature extraction process can set the basis for exploratory analysis or a fully automated computational data mining approach on many as yet unanswered, clinically relevant biological questions.

  15. Effect of Integrated Cognitive Therapy on Hippocampal Functional Connectivity Patterns in Stroke Patients with Cognitive Dysfunction: A Resting-State fMRI Study

    PubMed Central

    Yang, Shanli; Jiang, Cai; Ye, Haicheng; Tao, Jing; Huang, Jia; Gao, Yanling; Lin, Zhicheng; Chen, Lidian

    2014-01-01

    Objective. This study aimed to identify abnormal hippocampal functional connectivity (FC) following ischemic stroke using resting-state fMRI. We also explored whether abnormal hippocampal FC could be modulated by integrated cognitive therapy and tested whether these alterations were associated with cognitive performance. Methods. 18 right-handed cognitively impaired ischemic stroke patients and 18 healty control (HC) subjects were included in this study. Stroke subjects were scanned at baseline and after integrated cognitive therapy, while HCs were only scanned at baseline, to identify regions that show significant correlations with the seed region. Behavioral and cognitive assessments were obtained before each scan. Results. During the resting state, we found abnormal hippocampal FC associated with temporal regions, insular cortex, cerebellum, and prefrontal cortex in stroke patients compared to HCs. After integrated cognitive therapy, however, the stroke group showed increased hippocampal FC mainly located in the prefrontal gyrus and the default mode network (DMN). Altered hippocampal FC was associated with cognitive improvement. Conclusion. Resting-state fMRI may provide novel insight into the study of functional networks in the brain after stroke. Furthermore, altered hippocampal FC may be a compensatory mechanism for cognitive recovery after ischemic stroke. PMID:25548595

  16. Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior[W][OA

    PubMed Central

    Osorio, Sonia; Alba, Rob; Nikoloski, Zoran; Kochevenko, Andrej; Fernie, Alisdair R.; Giovannoni, James J.

    2012-01-01

    Integrative comparative analyses of transcript and metabolite levels from climacteric and nonclimacteric fruits can be employed to unravel the similarities and differences of the underlying regulatory processes. To this end, we conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato (Solanum lycopersicum; climacteric) and pepper (Capsicum chilense; nonclimacteric) fruits across development and ripening. Computational methods from multivariate and network-based analyses successfully revealed the difference between the covariance structures of the integrated data sets. Moreover, our results suggest that both fruits have similar ethylene-mediated signaling components; however, their regulation is different and may reflect altered ethylene sensitivity or regulators other than ethylene in pepper. Genes involved in ethylene biosynthesis were not induced in pepper fruits. Nevertheless, genes downstream of ethylene perception such as cell wall metabolism genes, carotenoid biosynthesis genes, and the never-ripe receptor were clearly induced in pepper as in tomato fruit. While signaling sensitivity or actual signals may differ between climacteric and nonclimacteric fruit, the evidence described here suggests that activation of a common set of ripening genes influences metabolic traits. Also, a coordinate regulation of transcripts and the accumulation of key organic acids, including malate, citrate, dehydroascorbate, and threonate, in pepper fruit were observed. Therefore, the integrated analysis allows us to uncover additional information for the comprehensive understanding of biological events relevant to metabolic regulation during climacteric and nonclimacteric fruit development. PMID:22685169

  17. Accuracy of Routine Treatment Planning 4-Dimensional and Deep-Inspiration Breath-Hold Computed Tomography Delineation of the Left Anterior Descending Artery in Radiation Therapy

    SciTech Connect

    White, Benjamin M.; Vennarini, Sabina; Lin, Lilie; Freedman, Gary; Santhanam, Anand; Low, Daniel A.; Both, Stefan

    2015-03-15

    Purpose: To assess the feasibility of radiation therapy treatment planning 4-dimensional computed tomography (4DCT) and deep-inspiration breath-hold (DIBH) CT to accurately contour the left anterior descending artery (LAD), a primary indicator of radiation-induced cardiac toxicity for patients undergoing radiation therapy. Methods and Materials: Ten subjects were prospectively imaged with a cardiac-gated MRI protocol to determine cardiac motion effects, including the displacement of a region of interest comprising the LAD. A series of planar views were obtained and resampled to create a 3-dimensional (3D) volume. A 3D optical flow deformable image registration algorithm determined tissue displacement during the cardiac cycle. The measured motion was then used as a spatial boundary to characterize motion blurring of the radiologist-delineated LAD structure for a cohort of 10 consecutive patients enrolled prospectively on a breast study including 4DCT and DIBH scans. Coronary motion–induced blurring artifacts were quantified by applying an unsharp filter to accentuate the LAD structure despite the presence of motion blurring. The 4DCT maximum inhalation and exhalation respiratory phases were coregistered to determine the LAD displacement during tidal respiration, as visualized in 4DCT. Results: The average 90th percentile heart motion for the region of interest was 0.7 ± 0.1 mm (left–right [LR]), 1.3 ± 0.6 mm (superior–inferior [SI]), and 0.6 ± 0.2 mm (anterior–posterior [AP]) in the cardiac-gated MRI cohort. The average relative increase in the number of voxels comprising the LAD contour was 69.4% ± 4.5% for the DIBH. The LAD volume overestimation had the dosimetric impact of decreasing the reported mean LAD dose by 23% ± 9% on average in the DIBH. During tidal respiration the average relative LAD contour increase was 69.3% ± 5.9% and 67.9% ± 4.6% for inhalation and exhalation respiratory phases, respectively. The average 90th

  18. Intraindividual quantitative and qualitative comparison of gadopentetate dimeglumine and gadobutrol in time-resolved contrast-enhanced 4-dimensional magnetic resonance angiography in minipigs.

    PubMed

    Hadizadeh, Dariusch Reza; Jost, Gregor; Pietsch, Hubertus; Weibrecht, Martin; Perkuhn, Michael; Boschewitz, Jack Maria; Keil, Vera Catharina; Träber, Frank; Kukuk, Guido Matthias; Schild, Hans Heinz; Willinek, Winfried Albert

    2014-07-01

    The concentration and relaxivities of contrast agents affect quantitative and qualitative image quality in contrast-enhanced time-resolved 4-dimensional magnetic resonance angiography (4D-MRA). Gadobutrol has a high relaxivity and is the only gadolinium (Gd)-based contrast agent approved for clinical use at a 1 M concentration. This promises to confer superior bolus characteristics by generating a steeper and shorter bolus with a higher peak Gd concentration. The purpose of this study was to quantitatively examine bolus characteristics of 1 M gadobutrol compared with 0.5 M gadopentetate dimeglumine and to evaluate image quality in thoracoabdominal 4D-MRA. A total of 7 Goettingen minipigs received dynamic computed tomography (CT) on a clinical 64-slice CT (transverse slices, 80 kV, 20 seconds, 0.3 s/dynamic frame) and 4D-MRA (time-resolved imaging with stochastic trajectories; 1. transverse slices, 30 seconds, 0.49 s/frame; 2. coronal slices, 70 seconds, 1.3 s/frame) on a 1.5-T clinical whole-body magnetic resonance imaging under general anesthesia using gadopentetate dimeglumine and gadobutrol in an intraindividual comparative study. Computed tomography attenuations were converted into Gd concentrations on the basis of previous phantom experiments. Quantitative analysis included measurements of the full width at half maximum, time-to-peak intervals, and peak of each bolus in dynamic CT and transverse 4D-MRA. These studies were carried out at equivalent contrast agent flow rates of 1 mL/s. Quantitative analysis (7 arteries and veins) and qualitative image analysis were performed on coronal thoracoabdominal 4D-MRA studies carried out at flow rates of 1 mL/s and, in the case of gadopentetate dimeglumine, also at molarity-adjusted flow rates of 2 mL/s. The bolus in both transverse 4D-MRA and dynamic CT was significantly narrower (full width at half maximum), earlier (time to peak), and higher (signal intensity enhancement in 4D-MRA, Gd concentration in dynamic CT) when

  19. Characterization of Growth and Reproduction Performance, Transgene Integration, Expression, and Transmission Patterns in Transgenic Pigs Produced by piggyBac Transposition-Mediated Gene Transfer.

    PubMed

    Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

    2016-10-01

    Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance and characterized the transgene insertion, transmission, and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression, and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favorable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition.

  20. Marangoni patterns

    NASA Astrophysics Data System (ADS)

    Thyagu, N. Nirmal; Strombom, Evelyn; Palumbo, Daniel; Caicedo, Carlos; Shinbrot, Troy

    2010-11-01

    We study Marangoni patterns that emerge when common food dye is dropped into a dish of shallow water. These patterns consist of tendrils and spots that sharpen over time before eventually fading. We demonstrate that the patterns can be modeled using coupled reaction-diffusion equations, where the "reaction" terms appear due to a nonlinear dependence of surface tension on dye concentration. We show using a spatio-temporal metric that these patterns are distinct from previously described Turing patterns.

  1. Microfluidic White Organic Light-Emitting Diode Based on Integrated Patterns of Greenish-Blue and Yellow Solvent-Free Liquid Emitters

    PubMed Central

    Kobayashi, Naofumi; Kasahara, Takashi; Edura, Tomohiko; Oshima, Juro; Ishimatsu, Ryoichi; Tsuwaki, Miho; Imato, Toshihiko; Shoji, Shuichi; Mizuno, Jun

    2015-01-01

    We demonstrated a novel microfluidic white organic light-emitting diode (microfluidic WOLED) based on integrated sub-100-μm-wide microchannels. Single-μm-thick SU-8-based microchannels, which were sandwiched between indium tin oxide (ITO) anode and cathode pairs, were fabricated by photolithography and heterogeneous bonding technologies. 1-Pyrenebutyric acid 2-ethylhexyl ester (PLQ) was used as a solvent-free greenish-blue liquid emitter, while 2,8-di-tert-butyl-5,11-bis(4-tert-butylphenyl)-6,12-diphenyltetracene (TBRb)-doped PLQ was applied as a yellow liquid emitter. In order to form the liquid white light-emitting layer, the greenish-blue and yellow liquid emitters were alternately injected into the integrated microchannels. The fabricated electro-microfluidic device successfully exhibited white electroluminescence (EL) emission via simultaneous greenish-blue and yellow emissions under an applied voltage of 100 V. A white emission with Commission Internationale de l’Declairage (CIE) color coordinates of (0.40, 0.42) was also obtained; the emission corresponds to warm-white light. The proposed device has potential applications in subpixels of liquid-based microdisplays and for lighting. PMID:26439164

  2. Microfluidic White Organic Light-Emitting Diode Based on Integrated Patterns of Greenish-Blue and Yellow Solvent-Free Liquid Emitters

    NASA Astrophysics Data System (ADS)

    Kobayashi, Naofumi; Kasahara, Takashi; Edura, Tomohiko; Oshima, Juro; Ishimatsu, Ryoichi; Tsuwaki, Miho; Imato, Toshihiko; Shoji, Shuichi; Mizuno, Jun

    2015-10-01

    We demonstrated a novel microfluidic white organic light-emitting diode (microfluidic WOLED) based on integrated sub-100-μm-wide microchannels. Single-μm-thick SU-8-based microchannels, which were sandwiched between indium tin oxide (ITO) anode and cathode pairs, were fabricated by photolithography and heterogeneous bonding technologies. 1-Pyrenebutyric acid 2-ethylhexyl ester (PLQ) was used as a solvent-free greenish-blue liquid emitter, while 2,8-di-tert-butyl-5,11-bis(4-tert-butylphenyl)-6,12-diphenyltetracene (TBRb)-doped PLQ was applied as a yellow liquid emitter. In order to form the liquid white light-emitting layer, the greenish-blue and yellow liquid emitters were alternately injected into the integrated microchannels. The fabricated electro-microfluidic device successfully exhibited white electroluminescence (EL) emission via simultaneous greenish-blue and yellow emissions under an applied voltage of 100 V. A white emission with Commission Internationale de l’Declairage (CIE) color coordinates of (0.40, 0.42) was also obtained; the emission corresponds to warm-white light. The proposed device has potential applications in subpixels of liquid-based microdisplays and for lighting.

  3. Net primary productivity, allocation pattern and carbon use efficiency in an apple orchard assessed by integrating eddy covariance, biometric and continuous soil chamber measurements

    NASA Astrophysics Data System (ADS)

    Zanotelli, D.; Montagnani, L.; Manca, G.; Tagliavini, M.

    2013-05-01

    Carbon use efficiency (CUE), the ratio of net primary production (NPP) over gross primary production (GPP), is a functional parameter that could possibly link the current increasingly accurate global GPP estimates with those of net ecosystem exchange, for which global predictors are still unavailable. Nevertheless, CUE estimates are actually available for only a few ecosystem types, while information regarding agro-ecosystems is scarce, in spite of the simplified spatial structure of these ecosystems that facilitates studies on allocation patterns and temporal growth dynamics. We combined three largely deployed methods, eddy covariance, soil respiration and biometric measurements, to assess monthly values of CUE, NPP and allocation patterns in different plant organs in an apple orchard during a complete year (2010). We applied a measurement protocol optimized for quantifying monthly values of carbon fluxes in this ecosystem type, which allows for a cross check between estimates obtained from different methods. We also attributed NPP components to standing biomass increments, detritus cycle feeding and lateral exports. We found that in the apple orchard, both net ecosystem production and gross primary production on a yearly basis, 380 ± 30 g C m-2 and 1263 ± 189 g C m-2 respectively, were of a magnitude comparable to those of natural forests growing in similar climate conditions. The largest differences with respect to forests are in the allocation pattern and in the fate of produced biomass. The carbon sequestered from the atmosphere was largely allocated to production of fruit: 49% of annual NPP was taken away from the ecosystem through apple production. Organic material (leaves, fine root litter, pruned wood and early fruit falls) contributing to the detritus cycle was 46% of the NPP. Only 5% was attributable to standing biomass increment, while this NPP component is generally the largest in forests. The CUE, with an annual average of 0.71 ± 0.12, was higher

  4. An integrated SOM-based multivariate approach for spatio-temporal patterns identification and source apportionment of pollution in complex river network.

    PubMed

    Yang, Yonghui; Wang, Cuiyu; Guo, Huaicheng; Sheng, Hu; Zhou, Feng

    2012-09-01

    In this study, three classification techniques (self-organizing maps, hierarchical cluster analysis and discriminant analysis) were applied to identify spatial water pollution levels, temporal water quality response delay phenomena (WQRDP), source pollution types (point, urban non-point, or agricultural non-point). Two models (principal components analysis (PCA), and positive matrix factorization (PMF)) were used to do the further quantitative source apportionment studying. The 27 inflow rivers in spatial were divided into three pollution levels (A, high; B, medium; C, low). The primary pollution pattern in spatial Clusters A, B, and C were point, urban non-point and agricultural non-point separately, in consideration of simultaneous land use types. Source apportionment results identified five typical factors in spatial Cluster A and six typical factors in spatial Cluster B and C as responsible for the data structure, explaining 80%-90% of the total variance of the dataset.

  5. Very Large Scale Integration of Nano-Patterned YBa2Cu3O7-delta Josephson Junctions in a Two-Dimensional Array

    SciTech Connect

    Cybart, Shane A; Anton, Steven; Wu, Stephen; Clarke, John; Dynes, Robert

    2009-09-01

    Very large scale integration of Josephson junctions in a two-dimensional series-parallel array has been achieved by ion irradiating a YBa{sub 2}Cu{sub 3}O{sub 7-{delta}} film through slits in a nano-fabricated mask created with electron beam lithography and reactive ion etching. The mask consisted of 15,820 high-aspect ratio (20:1), 35-nm wide slits that restricted the irradiation in the film below to form Josephson junctions. Characterizing each parallel segment k, containing 28 junctions, with a single critical current I{sub ck} we found a standard deviation in I{sub ck} of about 16%.

  6. How will Idaho's Agricultural Producers Adapt to Changing Precipitation Patterns? Evidence from an Integrated Hydrologic-Economic Model with Bayesian Updating

    NASA Astrophysics Data System (ADS)

    Beebe, G. L.; Flores, A. N.; Cobourn, K. M.

    2011-12-01

    Climate change is expected to alter the timing, duration, and quantity of natural precipitation. Changes in precipitation climatology will correspondingly impact the decisions made by agricultural producers, particularly with respect to which crops are grown and whether production is primarily rain fed or irrigated. In this study, we build an integrated hydro-economic simulation model in which adaptive management by agricultural producers is driven by a Bayesian learning process. We parameterize the model with soil and climate data from the Snake River Basin in Idaho to explore the dynamic adjustment of agricultural producers through a sequence of discrete and continuous land-use and input-use decisions. In the model, we evaluate the long-term dynamics of production in response to differing precipitation scenarios and comment on the way in which producer learning affects the economic impacts of climate change.

  7. Wnt5a Deficiency Leads to Anomalies in Ureteric Tree Development, Tubular Epithelial Cell Organization and Basement Membrane Integrity Pointing to a Role in Kidney Collecting Duct Patterning

    PubMed Central

    Pietilä, Ilkka; Prunskaite-Hyyryläinen, Renata; Kaisto, Susanna; Tika, Elisavet; van Eerde, Albertien M.; Salo, Antti M.; Garma, Leonardo; Miinalainen, Ilkka; Feitz, Wout F.; Bongers, Ernie M. H. F.; Juffer, André; Knoers, Nine V. A. M.; Renkema, Kirsten Y.; Myllyharju, Johanna; Vainio, Seppo J.

    2016-01-01

    The Wnts can be considered as candidates for the Congenital Anomaly of Kidney and Urinary Tract, CAKUT diseases since they take part in the control of kidney organogenesis. Of them Wnt5a is expressed in ureteric bud (UB) and its deficiency leads to duplex collecting system (13/90) uni- or bilateral kidney agenesis (10/90), hypoplasia with altered pattern of ureteric tree organization (42/90) and lobularization defects with partly fused ureter trunks (25/90) unlike in controls. The UB had also notably less tips due to Wnt5a deficiency being at E15.5 306 and at E16.5 765 corresponding to 428 and 1022 in control (p<0.02; p<0.03) respectively. These changes due to Wnt5a knock out associated with anomalies in the ultrastructure of the UB daughter epithelial cells. The basement membrane (BM) was malformed so that the BM thickness increased from 46.3 nm to 71.2 nm (p<0.01) at E16.5 in the Wnt5a knock out when compared to control. Expression of a panel of BM components such as laminin and of type IV collagen was also reduced due to the Wnt5a knock out. The P4ha1 gene that encodes a catalytic subunit of collagen prolyl 4-hydroxylase I (C-P4H-I) in collagen synthesis expression and the overall C-P4H enzyme activity were elevated by around 26% due to impairment in Wnt5a function from control. The compound Wnt5a+/-;P4ha1+/- embryos demonstrated Wnt5a-/- related defects, for example local hyperplasia in the UB tree. A R260H WNT5A variant was identified from renal human disease cohort. Functional studies of the consequence of the corresponding mouse variant in comparison to normal ligand reduced Wnt5a-signalling in vitro. Together Wnt5a has a novel function in kidney organogenesis by contributing to patterning of UB derived collecting duct development contributing putatively to congenital disease. PMID:26794322

  8. Study on the sediment characteristics of the snow in a typical residential community and its integrated biological treatment pattern in Harbin.

    PubMed

    Xue, Bin-Xia; Li, Tong-Yu; Li, Chun-Ying; Wei, Li; Hou, Xiao-He

    2017-09-17

    Winter cities have severe shortages of water resources. The effective classification and recycling of urban water resources that are available here are therefore significant for the sustainable utilization of water in winter cities, and snow is a potential water resource. In this research, the water quality of the snow and the pollutant composition in the vehicle roads of a typical residential community of Harbin are analyzed. It is concluded that there is a large amount of suspended substances, including chemical oxygen demand (COD), salt, ammonia, and oil in this snow. There are 27 main pollutants. The oily substances are dominated by hexadecane and are accompanied by toxic substances, including benzene, toluene, ethylbenzene, xylene (BTEX), and naphthalene. As snow is a carrier of pollutants, the underground space of the urban shallow green belt is proposed to be used to establish a snow-melting system that would integrate biological treatment devices. This method allows the year-round collection, storage, and utilization of rainwater for use in city planning and municipal technology, realizing multiple objectives and having a significant influence on further urban development.

  9. Mapping the spatial pattern of temperate forest above ground biomass by integrating airborne lidar with Radarsat-2 imagery via geostatistical models

    NASA Astrophysics Data System (ADS)

    Li, Wang; Niu, Zheng; Gao, Shuai; Wang, Cheng

    2014-11-01

    Light Detection and Ranging (LiDAR) and Synthetic Aperture Radar (SAR) are two competitive active remote sensing techniques in forest above ground biomass estimation, which is important for forest management and global climate change study. This study aims to further explore their capabilities in temperate forest above ground biomass (AGB) estimation by emphasizing the spatial auto-correlation of variables obtained from these two remote sensing tools, which is a usually overlooked aspect in remote sensing applications to vegetation studies. Remote sensing variables including airborne LiDAR metrics, backscattering coefficient for different SAR polarizations and their ratio variables for Radarsat-2 imagery were calculated. First, simple linear regression models (SLR) was established between the field-estimated above ground biomass and the remote sensing variables. Pearson's correlation coefficient (R2) was used to find which LiDAR metric showed the most significant correlation with the regression residuals and could be selected as co-variable in regression co-kriging (RCoKrig). Second, regression co-kriging was conducted by choosing the regression residuals as dependent variable and the LiDAR metric (Hmean) with highest R2 as co-variable. Third, above ground biomass over the study area was estimated using SLR model and RCoKrig model, respectively. The results for these two models were validated using the same ground points. Results showed that both of these two methods achieved satisfactory prediction accuracy, while regression co-kriging showed the lower estimation error. It is proved that regression co-kriging model is feasible and effective in mapping the spatial pattern of AGB in the temperate forest using Radarsat-2 data calibrated by airborne LiDAR metrics.

  10. Integration and relative value of biomarkers for prediction of MCI to AD progression: spatial patterns of brain atrophy, cognitive scores, APOE genotype and CSF biomarkers.

    PubMed

    Da, Xiao; Toledo, Jon B; Zee, Jarcy; Wolk, David A; Xie, Sharon X; Ou, Yangming; Shacklett, Amanda; Parmpi, Paraskevi; Shaw, Leslie; Trojanowski, John Q; Davatzikos, Christos

    2014-01-01

    This study evaluates the individual, as well as relative and joint value of indices obtained from magnetic resonance imaging (MRI) patterns of brain atrophy (quantified by the SPARE-AD index), cerebrospinal fluid (CSF) biomarkers, APOE genotype, and cognitive performance (ADAS-Cog) in progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD) within a variable follow-up period up to 6 years, using data from the Alzheimer's Disease Neuroimaging Initiative-1 (ADNI-1). SPARE-AD was first established as a highly sensitive and specific MRI-marker of AD vs. cognitively normal (CN) subjects (AUC = 0.98). Baseline predictive values of all aforementioned indices were then compared using survival analysis on 381 MCI subjects. SPARE-AD and ADAS-Cog were found to have similar predictive value, and their combination was significantly better than their individual performance. APOE genotype did not significantly improve prediction, although the combination of SPARE-AD, ADAS-Cog and APOE ε4 provided the highest hazard ratio estimates of 17.8 (last vs. first quartile). In a subset of 192 MCI patients who also had CSF biomarkers, the addition of Aβ1-42, t-tau, and p-tau181p to the previous model did not improve predictive value significantly over SPARE-AD and ADAS-Cog combined. Importantly, in amyloid-negative patients with MCI, SPARE-AD had high predictive power of clinical progression. Our findings suggest that SPARE-AD and ADAS-Cog in combination offer the highest predictive power of conversion from MCI to AD, which is improved, albeit not significantly, by APOE genotype. The finding that SPARE-AD in amyloid-negative MCI patients was predictive of clinical progression is not expected under the amyloid hypothesis and merits further investigation.

  11. Integrating geologic and satellite radar data for mapping dome-and-basin patterns in the In Ouzzal Terrane, Western Hoggar, Algeria

    NASA Astrophysics Data System (ADS)

    Deroin, Jean-Paul; Djemai, Safouane; Bendaoud, Abderrahmane; Brahmi, Boualem; Ouzegane, Khadidja; Kienast, Jean-Robert

    2014-11-01

    The In Ouzzal Terrane (IOT) located in the north-western part of the Tuareg Shield forms an elongated N-S trending block, more than 400 km long and 80 km wide. It involves an Archaean crust remobilized during a very high-temperature metamorphic event related to the Palaeoproterozoic orogeny. The IOT largely crops out in the rocky and sandy desert of Western Hoggar. It corresponds mainly to a flat area with some reliefs composed of Late Panafrican granites, dyke networks or Cambrian volcanic rocks. These flat areas are generally covered by thin sand veneers. They are favorable for discriminating bedrock geological units using imaging radar, backscattering measurements, and field checking, because the stony desert is particularly sensitive to the radar parameters such as wavelength or polarization. The main radar data used are those obtained with the ALOS-PALSAR sensor (L-band), in ScanSAR mode (large swath) and Fine Beam modes. The PALSAR sensor has been also compared to ENVISAT-ASAR and to optical imagery. Detailed mapping of some key areas indicates extensive Archaean dome-and-basin patterns. In certain parts, the supracrustal synforms and orthogneiss domes exhibit linear or circular features corresponding to shear zones or rolling structures, respectively. The geological mapping of these dome-and-basin structures, and more generally of the Archaean and Proterozoic lithological units, is more accurate with the SAR imagery, particularly when using the L-band, than with the optical imagery. A quantitative approach is carried out in order to estimate the backscatter properties of the main rock types. Due to the large variety of configurations, radar satellite imagery such as ALOS PALSAR represents a key tool for geological mapping in arid region at different scales from the largest (e.g., 1:500,000) to the smallest (e.g., 1:50,000).

  12. Coccolithophore and benthic foraminifera distribution patterns in the Gulf of Cadiz and Western Iberian Margin during Integrated Ocean Drilling Program (IODP) Expedition 339

    NASA Astrophysics Data System (ADS)

    Balestra, B.; Grunert, P.; Ausin, B.; Hodell, D.; Flores, J.-A.; Alvarez-Zarikian, C. A.; Hernandez-Molina, F. J.; Stow, D.; Piller, W. E.; Paytan, A.

    2017-06-01

    For the first time during an Integrated Ocean Drilling Program (IODP) Expedition (Exp. 339, Mediterranean Outflow) water samples for living coccolithophore distributions and mudline samples for coccoliths, benthic foraminifera, and geochemical analyses in the underlying surface sediments were collected. In total, 14 water samples (from 5 to 20 m water depth) and 7 mudline samples were gathered at the drill sites. Coccolithophore distributions show spatial variations in species diversity. In particular, assemblages that characterize the Western Iberian Margin differ from those in the Gulf of Cadiz, indicative of oceanographic and environmental controls on the community in the upper ocean (0-20 m depth). Comparison of the living assemblages to those in surface sediments shows differences in the presence of some species, suggesting the influence of post deposition sedimentary processes. Other factors such as the season of sampling and the limited sampling depth may also have a role in the differences recorded. Benthic foraminiferal assemblages seem to be primarily determined by source, quantity and quality of available food. Sites in the Gulf of Cadiz are bathed by Mediterranean Outflow Water (MOW) and characterized by a considerable amount of advected food particles. Elevated epibenthic foraminifera exploit this niche, while arborescent epifaunal and infaunal taxa thrive on food particles falling out of MOW. The combined data suggest different flow speeds and settling of MOW suspension load in the Gulf of Cadiz. In contrast, assemblages from the Western Iberian Margin located farthest from or outside of MOW are determined by local export productivity and mirror trophic conditions in the surface waters. Both assemblages reveal variation in the composition at intermediate and deep water depths along the southern and western Iberian Margins with distance from the Strait of Gibraltar.

  13. Use of a Corona Discharge to Selectively Pattern a Hydrophilic/Hydrophobic Interface for Integrating Segmented Flow with Microchip Electrophoresis and Electrochemical Detection

    PubMed Central

    Filla, Laura A.; Kirkpatrick, Douglas C.; Martin, R. Scott

    2011-01-01

    Segmented flow in microfluidic devices involves the use of droplets that are generated either on- or off-chip. When used with off-chip sampling methods, segmented flow has been shown to prevent analyte dispersion and improve temporal resolution by periodically surrounding an aqueous flow stream with an immiscible carrier phase as it is transferred to the microchip. To analyze the droplets by methods such as electrochemistry or electrophoresis, a method to “desegment” the flow into separate aqueous and immiscible carrier phase streams is needed. In this paper, a simple and straightforward approach for this desegmentation process was developed by first creating an air/water junction in natively hydrophobic and perpendicular PDMS channels. The air-filled channel was treated with a corona discharge electrode to create a hydrophilic/hydrophobic interface. When a segmented flow stream encounters this interface, only the aqueous sample phase enters the hydrophilic channel, where it can be subsequently analyzed by electrochemistry or microchip-based electrophoresis with electrochemical detection. It is shown that the desegmentation process does not significantly degrade the temporal resolution of the system, with rise times as low as 12 s reported after droplets are recombined into a continuous flow stream. This approach demonstrates significant advantages over previous studies in that the treatment process takes only a few minutes, fabrication is relatively simple, and reversible sealing of the microchip is possible. This work should enable future studies where off-chip processes such as microdialysis can be integrated with segmented flow and electrochemical-based detection. PMID:21718004

  14. Use of a corona discharge to selectively pattern a hydrophilic/hydrophobic interface for integrating segmented flow with microchip electrophoresis and electrochemical detection.

    PubMed

    Filla, Laura A; Kirkpatrick, Douglas C; Martin, R Scott

    2011-08-01

    Segmented flow in microfluidic devices involves the use of droplets that are generated either on- or off-chip. When used with off-chip sampling methods, segmented flow has been shown to prevent analyte dispersion and improve temporal resolution by periodically surrounding an aqueous flow stream with an immiscible carrier phase as it is transferred to the microchip. To analyze the droplets by methods such as electrochemistry or electrophoresis, a method to "desegment" the flow into separate aqueous and immiscible carrier phase streams is needed. In this paper, a simple and straightforward approach for this desegmentation process was developed by first creating an air/water junction in natively hydrophobic and perpendicular PDMS channels. The air-filled channel was treated with a corona discharge electrode to create a hydrophilic/hydrophobic interface. When a segmented flow stream encounters this interface, only the aqueous sample phase enters the hydrophilic channel, where it can be subsequently analyzed by electrochemistry or microchip-based electrophoresis with electrochemical detection. It is shown that the desegmentation process does not significantly degrade the temporal resolution of the system, with rise times as low as 12 s reported after droplets are recombined into a continuous flow stream. This approach demonstrates significant advantages over previous studies in that the treatment process takes only a few minutes, fabrication is relatively simple, and reversible sealing of the microchip is possible. This work should enable future studies in which off-chip processes such as microdialysis can be integrated with segmented flow and electrochemical-based detection.

  15. The integrative analysis of microRNA and mRNA expression in Apis mellifera following maze-based visual pattern learning.

    PubMed

    Qin, Qiu-Hong; Wang, Zi-Long; Tian, Liu-Qing; Gan, Hai-Yan; Zhang, Shao-Wu; Zeng, Zhi-Jiang

    2014-10-01

    The honeybee (Apis mellifera) is a social insect with strong sensory capacity and diverse behavioral repertoire and is recognized as a good model organism for studying the neurobiological basis of learning and memory. In this study, we analyzed the changes in microRNA (miRNA) and messenger RNA (mRNA) following maze-based visual learning using next-generation small RNA sequencing and Solexa/lllumina Digital Gene Expression tag profiling (DGE). For small RNA sequencing, we obtained 13 367 770 and 13 132 655 clean tags from the maze and control groups, respectively. A total of 40 differentially expressed known miRNAs were detected between these two samples, and all of them were up-regulated in the maze group compared to the control group. For DGE, 5 681 320 and 5 939 855 clean tags were detected from the maze and control groups, respectively. There were a total of 388 differentially expressed genes between these two samples, with 45 genes up-regulated and 343 genes down-regulated in the maze group, compared to the control group. Additionally, the expression levels of 10 differentially expressed genes were confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the expression trends of eight of them were consistent with the DGE result, although the degree of change was lower in amplitude. The integrative analysis of miRNA and mRNA expression showed that, among the 40 differentially expressed known miRNAs and 388 differentially expressed genes, 60 pairs of miRNA/mRNA were identified as co-expressed in our present study. These results suggest that both miRNA and mRNA may play a pivotal role in the process of learning and memory in honeybees. Our sequencing data provide comprehensive miRNA and gene expression information for maze-based visual learning, which will facilitate understanding of the molecular mechanisms of honeybee learning and memory.

  16. Evaluation of effects of changes in canal management and precipitation patterns on salinity in Biscayne Bay, Florida, using an integrated surface-water/groundwater model

    USGS Publications Warehouse

    Lohmann, Melinda A.; Swain, Eric D.; Wang, John D.; Dixon, Joann

    2012-01-01

    Biscayne National Park, located in Biscayne Bay in southeast Florida, is one of the largest marine parks in the country and sustains a large natural marine fishery where numerous threatened and endangered species reproduce. In recent years, the bay has experienced hypersaline conditions (salinity greater than 35 practical salinity units) of increasing magnitude and duration. Hypersalinity events were particularly pronounced during April to August 2004 in nearshore areas along the southern and middle parts of the bay. Prolonged hypersaline conditions can cause degradation of water quality and permanent damage to, or loss of, brackish nursery habitats for multiple species of fish and crustaceans as well as damage to certain types of seagrasses that are not tolerant of extreme changes in salinity. To evaluate the factors that contribute to hypersalinity events and to test the effects of possible changes in precipitation patterns and canal flows into Biscayne Bay on salinity in the bay, the U.S. Geological Survey constructed a coupled surface-water/groundwater numerical flow model. The model is designed to account for freshwater flows into Biscayne Bay through the canal system, leakage of salty bay water into the underlying Biscayne aquifer, discharge of fresh and salty groundwater from the Biscayne aquifer into the bay, direct effects of precipitation on bay salinity, indirect effects of precipitation on recharge to the Biscayne aquifer, direct effects of evapotranspiration (ET) on bay salinity, indirect effects of ET on recharge to the Biscayne aquifer, and maintenance of mass balance of both water and solute. The model was constructed using the Flow and Transport in a Linked Overland/Aquifer Density Dependent System (FTLOADDS) simulator, version 3.3, which couples the two-dimensional, surface-water flow and solute-transport simulator SWIFT2D with the density-dependent, groundwater flow an solute-transport simulator SEAWAT. The model was calibrated by a trial

  17. Accurate detection of coronary artery disease by integrated analysis of the ST-segment depression/heart rate patterns during the exercise and recovery phases of the exercise electrocardiography test.

    PubMed

    Lehtinen, R; Sievänen, H; Viik, J; Turjanmaa, V; Niemelä, K; Malmivuo, J

    1996-11-01

    In this comparative cross-sectional study, we evaluated whether a novel computerized diagnostic variable, ST-segment depression/heart rate ST/HR analysis during both the exercise and postexercise recovery phases of the exercise electrocardiography (ECG) test, can detect coronary artery disease more accurately than methods using either exercise or recovery phase alone. The study population comprised 347 clinical patients referred for a routine bicycle exercise ECG test at Tampere University Hospital, Finland. Of these, 127 had angiographically proven coronary artery disease, whereas 13 had no coronary artery disease according to angiography, 18 had no perfusion defect according to technetium-99m sestamibi single-photon emission computed tomography, and 189 were clinically normal with respect to cardiac diseases. For each patient, the maximum values of the ST/HR hysteresis, ST/HR index, end-exercise ST depression, and recovery ST depression were determined from the Mason-Likar modification of the standard 12-lead exercise electrocardiogram [aVL, aVR, and V1 excluded]. The diagnostic performance of these continuous diagnostic variables was compared by means of receiver-operating characteristic analysis. The area under the receiver-operating characteristic curve of the ST/HR hysteresis was 89%, which was significantly larger than that of the end-exercise ST depression (76%, p < or = 0.0001), recovery ST depression (84%, p = 0.0063), or ST/HR index (83%, p = 0.0023), indicating superior diagnostic performance of the ST/HR hysteresis independent of the partition value selection. In conclusion, computerized analysis of the HR-adjusted ST depression pattern during the exercise phase, integrated with the HR-adjusted ST depression pattern during the recovery phase after exercise, can significantly improve the diagnostic performance and clinical utility of the exercise ECG test for the detection of coronary artery disease.

  18. Pattern Formation

    NASA Astrophysics Data System (ADS)

    Hoyle, Rebecca

    2006-03-01

    From the stripes of a zebra and the spots on a leopard's back to the ripples on a sandy beach or desert dune, regular patterns arise everywhere in nature. The appearance and evolution of these phenomena has been a focus of recent research activity across several disciplines. This book provides an introduction to the range of mathematical theory and methods used to analyse and explain these often intricate and beautiful patterns. Bringing together several different approaches, from group theoretic methods to envelope equations and theory of patterns in large-aspect ratio-systems, the book also provides insight behind the selection of one pattern over another. Suitable as an upper-undergraduate textbook for mathematics students or as a fascinating, engaging, and fully illustrated resource for readers in physics and biology, Rebecca Hoyle's book, using a non-partisan approach, unifies a range of techniques used by active researchers in this growing field. Accessible description of the mathematical theory behind fascinating pattern formation in areas such as biology, physics and materials science Collects recent research for the first time in an upper level textbook Features a number of exercises - with solutions online - and worked examples

  19. Teaching Design Patterns through Computer Game Development

    ERIC Educational Resources Information Center

    Gestwicki, Paul; Sun, Fu-Shing

    2008-01-01

    We present an approach for teaching design patterns that emphasizes object-orientation and patterns integration. The context of computer game development is used to engage and motivate students, and it is additionally rich with design patterns. A case study is presented based on "EEClone," an arcade-style computer game implemented in Java. Our…

  20. A reduction for spiking integrate-and-fire network dynamics ranging from homogeneity to synchrony.

    PubMed

    Zhang, J W; Rangan, A V

    2015-04-01

    In this paper we provide a general methodology for systematically reducing the dynamics of a class of integrate-and-fire networks down to an augmented 4-dimensional system of ordinary-differential-equations. The class of integrate-and-fire networks we focus on are homogeneously-structured, strongly coupled, and fluctuation-driven. Our reduction succeeds where most current firing-rate and population-dynamics models fail because we account for the emergence of 'multiple-firing-events' involving the semi-synchronous firing of many neurons. These multiple-firing-events are largely responsible for the fluctuations generated by the network and, as a result, our reduction faithfully describes many dynamic regimes ranging from homogeneous to synchronous. Our reduction is based on first principles, and provides an analyzable link between the integrate-and-fire network parameters and the relatively low-dimensional dynamics underlying the 4-dimensional augmented ODE.

  1. Computing myocardial motion in 4-dimensional echocardiography.

    PubMed

    Mukherjee, Ryan; Sprouse, Chad; Pinheiro, Aurélio; Abraham, Theodore; Burlina, Philippe

    2012-07-01

    We describe a novel method for computing dense 3D myocardial motion with high accuracy in four-dimensional (4D) echocardiography (3 dimensions spatial plus time). The method is based on a classic variational optical flow technique but exploits modern developments in optical flow research to utilize the full capabilities of 4D echocardiography. Using a variety of metrics, we present an in-depth performance evaluation of the method on synthetic, phantom, and intraoperative 4D transesophageal echocardiographic data. When compared with state-of-the-art optical flow and speckle tracking techniques currently found in 4D echocardiography, the method we present shows notable improvements in error rates. We believe the performance improvements shown can have a positive impact when the method is used as input for various applications, such as strain computation, biomechanical modeling, and automated diagnostics.

  2. Effect of an integrated community-based package for maternal and newborn care on feeding patterns during the first 12 weeks of life: a cluster-randomized trial in a South African township.

    PubMed

    Ijumba, Petrida; Doherty, Tanya; Jackson, Debra; Tomlinson, Mark; Sanders, David; Swanevelder, Sonja; Persson, Lars-Åke

    2015-10-01

    To analyse the effect of community-based counselling on feeding patterns during the first 12 weeks after birth, and to study whether the effect differs by maternal HIV status, educational level or household wealth. Cluster-randomized trial with fifteen clusters in each arm to evaluate an integrated package providing two pregnancy and five postnatal home visits delivered by community health workers. Infant feeding data were collected using 24 h recall of nineteen food and fluid items. A township near Durban, South Africa. Pregnant women (1894 intervention and 2243 control) aged 17 years or more. Twelve weeks after birth, 1629 (intervention) and 1865 (control) mother-infant pairs were available for analysis. Socio-economic conditions differed slightly across intervention groups, which were considered in the analyses. There was no effect on early initiation of breast-feeding. At 12 weeks of age the intervention doubled exclusive breast-feeding (OR=2·29; 95 % CI 1·80, 2·92), increased exclusive formula-feeding (OR=1·70; 95 % CI 1·28, 2·27), increased predominant breast-feeding (OR=1·71; 95 % CI 1·34, 2·19), decreased mixed formula-feeding (OR=0·68; 95 % CI 0·55, 0·83) and decreased mixed breast-feeding (OR=0·54; 95 % CI 0·44, 0·67). The effect on exclusive breast-feeding at 12 weeks was stronger among HIV-negative mothers than HIV-positive mothers (P=0·01), while the effect on mixed formula-feeding was significant only among HIV-positive mothers (P=0·03). The effect on exclusive feeding was not different by household wealth or maternal education levels. A perinatal intervention package delivered by community health workers was effective in increasing exclusive breast-feeding, exclusive formula-feeding and decreasing mixed feeding.

  3. Effect of an integrated community-based package for maternal and newborn care on feeding patterns during the first 12 weeks of life: a cluster-randomized trial in a South African township

    PubMed Central

    Ijumba, Petrida; Doherty, Tanya; Jackson, Debra; Tomlinson, Mark; Sanders, David; Swanevelder, Sonja; Persson, Lars-Åke

    2015-01-01

    Objective To analyse the effect of community-based counselling on feeding patterns during the first 12 weeks after birth, and to study whether the effect differs by maternal HIV status, educational level or household wealth. Design Cluster-randomized trial with fifteen clusters in each arm to evaluate an integrated package providing two pregnancy and five postnatal home visits delivered by community health workers. Infant feeding data were collected using 24 h recall of nineteen food and fluid items. Setting A township near Durban, South Africa. Subjects Pregnant women (1894 intervention and 2243 control) aged 17 yearsor more. Results Twelve weeks after birth, 1629 (intervention) and 1865 (control) mother–infant pairs were available for analysis. Socio-economic conditions differed slightly across intervention groups, which were considered in the analyses. There was no effect on early initiation of breast-feeding. At 12 weeks of age the intervention doubled exclusive breast-feeding (OR=2·29; 95 % CI 1·80, 2·92), increased exclusive formula-feeding (OR=1·70; 95 % CI 1·28, 2·27), increased predominant breast-feeding (OR=1·71; 95 % CI 1·34, 2·19), decreased mixed formula-feeding (OR=0·68; 95 % CI 0·55, 0·83) and decreased mixed breast-feeding (OR=0·54; 95 % CI 0·44, 0·67). The effect on exclusive breast-feeding at 12 weeks was stronger among HIV-negative mothers than HIV-positive mothers (P=0·01), while the effect on mixed formula feeding was significant only among HIV-positive mothers (P=0·03). The effect on exclusive feeding was not different by household wealth or maternal education levels. Conclusions A perinatal intervention package delivered by community health workers was effective in increasing exclusive breast-feeding, exclusive formula feeding and decreasing mixed feeding. PMID:25660465

  4. Patterns of stress responses shift during seasonal life-history transitions: An analysis comparing baseline, maximal and integrated corticosterone in female red-sided garter snakes (Thamnophis sirtalis parietalis).

    PubMed

    Dayger, Catherine A; Lutterschmidt, Deborah I

    2017-05-15

    Glucocorticoids often rise and fall with a variety of external and internal cues and frequently vary among life-history stages. This suggests that changing glucocorticoids may coordinate life-history transitions. To explore this hypothesis, we asked if the time-course of stress-induced glucocorticoid levels differ between two life-history transitions (i.e., spring and fall migration) in female red-sided garter snakes (Thamnophis sirtalis parietalis). We collected non-migratory females from a communal den and migratory females from a road along the migration route and treated them with 4h of capture stress; plasma corticosterone was measured before, during and after capture stress. During the spring, den-collected females exhibited a stress-induced peak in corticosterone at an earlier sampling time than migrating, road-collected females. Because the pattern of corticosterone responses varied with migratory state, negative feedback on and/or sensitivity of the hypothalamus-pituitaryadrenal (HPA) axis may be linked to spring migration. During the fall, capture stress elicited an increase in corticosterone in den-collected females but not in migrating, road-collected females. Baseline corticosterone was higher and both maximal and integrated corticosterone responses were lower during the fall compared to spring, indicating that stress responses are smaller when baseline corticosterone is elevated, perhaps due to a "ceiling effect". These data suggest that HPA axis regulation changes during seasonal migration, possibly via altering negative feedback, HPA axis sensitivity, or some other mechanism. This study supports the hypothesis that glucocorticoids coordinate life-history events and suggests that examining a suite of stress response characteristics is most informative for understanding the function of HPA modulation. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Making digit patterns in the vertebrate limb.

    PubMed

    Tickle, Cheryll

    2006-01-01

    The vertebrate limb has been a premier model for studying pattern formation - a striking digit pattern is formed in human hands, with a thumb forming at one edge and a little finger at the other. Classic embryological studies in different model organisms combined with new sophisticated techniques that integrate gene-expression patterns and cell behaviour have begun to shed light on the mechanisms that control digit patterning, and stimulate re-evaluation of the current models.

  6. Desert Patterns

    NASA Image and Video Library

    2017-09-27

    Desert Patterns - April 13th, 2003 Description: Seen through the "eyes" of a satellite sensor, ribbons of Saharan sand dunes seem to glow in sunset colors. These patterned stripes are part of Erg Chech, a desolate sand sea in southwestern Algeria, Africa, where the prevailing winds create an endlessly shifting collage of large, linear sand dunes. The term "erg" is derived from an Arabic word for a field of sand dunes. Credit: USGS/NASA/Landsat 7 To learn more about the Landsat satellite go to: landsat.gsfc.nasa.gov/ NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Join us on Facebook

  7. Optical Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Yu, Francis T. S.; Jutamulia, Suganda

    1998-06-01

    This book provides a comprehensive review of optical pattern recognition, covering theoretical aspects as well as details of practical implementations and signal processing techniques. The first chapter is devoted to pattern recognition performed with optical correlators. Later chapters discuss new approaches based on neural networks, wavelet transforms, and the fractional Fourier transform. The book also covers nonlinear filter methods and optical-electronic hybrid systems. The final part deals with the devices and materials employed in modern systems, such as photorefractive crystals, microlasers, and liquid crystal spatial light modulators. The volume gives many examples of working systems that integrate optics, electronics, and computers, and it covers a range of new developments from mathematical theories to novel optical materials. It will be of great interest to graduate students and researchers in optical engineering and machine vision.

  8. Understanding taxi travel patterns

    NASA Astrophysics Data System (ADS)

    Cai, Hua; Zhan, Xiaowei; Zhu, Ji; Jia, Xiaoping; Chiu, Anthony S. F.; Xu, Ming

    2016-09-01

    Taxis play important roles in modern urban transportation systems, especially in mega cities. While providing necessary amenities, taxis also significantly contribute to traffic congestion, urban energy consumption, and air pollution. Understanding the travel patterns of taxis is thus important for addressing many urban sustainability challenges. Previous research has primarily focused on examining the statistical properties of passenger trips, which include only taxi trips occupied with passengers. However, unoccupied trips are also important for urban sustainability issues because they represent potential opportunities to improve the efficiency of the transportation system. Therefore, we need to understand the travel patterns of taxis as an integrated system, instead of focusing only on the occupied trips. In this study we examine GPS trajectory data of 11,880 taxis in Beijing, China for a period of three weeks. Our results show that taxi travel patterns share similar traits with travel patterns of individuals but also exhibit differences. Trip displacement distribution of taxi travels is statistically greater than the exponential distribution and smaller than the truncated power-law distribution. The distribution of short trips (less than 30 miles) can be best fitted with power-law while long trips follow exponential decay. We use radius of gyration to characterize individual taxi's travel distance and find that it does not follow a truncated power-law as observed in previous studies. Spatial and temporal regularities exist in taxi travels. However, with increasing spatial coverage, taxi trips can exhibit dual high probability density centers.

  9. Patterning and templating for nanoelectronics.

    PubMed

    Galatsis, Kosmas; Wang, Kang L; Ozkan, Mihri; Ozkan, Cengiz S; Huang, Yu; Chang, Jane P; Monbouquette, Harold G; Chen, Yong; Nealey, Paul; Botros, Youssry

    2010-02-09

    The semiconductor industry will soon be launching 32 nm complementary metal oxide semiconductor (CMOS) technology node using 193 nm lithography patterning technology to fabricate microprocessors with more than 2 billion transistors. To ensure the survival of Moore's law, alternative patterning techniques that offer advantages beyond conventional top-down patterning are aggressively being explored. It is evident that most alternative patterning techniques may not offer compelling advantages to succeed conventional top-down lithography for silicon integrated circuits, but alternative approaches may well indeed offer functional advantages in realising next-generation information processing nanoarchitectures such as those based on cellular, bioinsipired, magnetic dot logic, and crossbar schemes. This paper highlights and evaluates some patterning methods from the Center on Functional Engineered Nano Architectonics in Los Angeles and discusses key benchmarking criteria with respect to CMOS scaling.

  10. Data assimilation in a coupled physical-biogeochemical model of the California current system using an incremental lognormal 4-dimensional variational approach: Part 3-Assimilation in a realistic context using satellite and in situ observations

    NASA Astrophysics Data System (ADS)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A fully coupled physical and biogeochemical ocean data assimilation system is tested in a realistic configuration of the California Current System using the Regional Ocean Modeling System. In situ measurements for sea surface temperature and salinity as well as satellite observations for temperature, sea level and chlorophyll are used for the year 2000. Initial conditions of the combined physical and biogeochemical state are adjusted at the start of each 3-day assimilation cycle. Data assimilation results in substantial reduction of root-mean-square error (RMSE) over unconstrained model output. RMSE for physical variables is slightly lower when assimilating only physical variables than when assimilating both physical variables and surface chlorophyll. Surface chlorophyll RMSE is lowest when assimilating both physical variables and surface chlorophyll. Estimates of subsurface, nitrate and chlorophyll show modest improvements over the unconstrained model run relative to independent, unassimilated in situ data. Assimilation adjustments to the biogeochemical initial conditions are investigated within different regions of the California Current System. The incremental, lognormal 4-dimensional data assimilation method tested here represents a viable approach to coupled physical biogeochemical state estimation at practical computational cost.

  11. Gauge Integration

    DTIC Science & Technology

    2002-09-01

    convergence theorems. Lebesgue developed his theory of measure and integration to address these shortcomings. His integral is more powerful in the...This relatively recent integral possesses the intuitive description of the Riemann integral, with the power of the Lebesgue integral. The purpose of this...strong convergence theorems. Lebesgue developed his theory of measure and integration to address these shortcomings. His integral is more powerful in the

  12. Integrated Means Integrity

    ERIC Educational Resources Information Center

    Odegard, John D.

    1978-01-01

    Describes the operation of the Cessna Pilot Center (CPC) flight training systems. The program is based on a series of integrated activities involving stimulus, response, reinforcement and association components. Results show that the program can significantly reduce in-flight training time. (CP)

  13. Integrated Means Integrity

    ERIC Educational Resources Information Center

    Odegard, John D.

    1978-01-01

    Describes the operation of the Cessna Pilot Center (CPC) flight training systems. The program is based on a series of integrated activities involving stimulus, response, reinforcement and association components. Results show that the program can significantly reduce in-flight training time. (CP)

  14. Defrosting Patterns

    NASA Technical Reports Server (NTRS)

    2003-01-01

    MGS MOC Release No. MOC2-487, 18 September 2003

    This June 2003 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) picture shows patterns created by defrosting processes on the south polar seasonal ice cap. Seasonal cap refers to the part of the polar cap that comes and goes with the seasons, as opposed to the residual cap, which lasts throughout the summer. The area shown here, in summer, will have no frost. This picture was taken during southern spring. As the seasonal frost begins to sublime away, dark cracks form a polygon pattern, and wind blows material to form varied bright and dark streaks. What is unknown is whether the dark streaks consist of sand and silt from beneath the seasonal frost, or whether they, too, consist of frost that has been transformed into coarse-grained particles that can be mobilized by wind. Alternatively, the streaks represent erosion and removal of frost, rather than deposition of granular material. The bright streaks are most likely made of frost--whether they are water ice or carbon dioxide ice remains to be determined. The bulk of the frosted surface shown here is carbon dioxide ice. The image is located near 87.3oS, 192.4oW. The picture covers an area 3 km (1.9 mi) wide and is illuminated by sunlight from the upper left.

  15. Patterning flows and polymers

    NASA Astrophysics Data System (ADS)

    Stroock, Abraham Duncan

    This thesis presents the use of patterned surfaces for controlling fluid dynamics on a sub-millimeter scale, and for fabricating a new class of polymeric materials. In chapters 1--4, chemical and mechanical structures were used to control the form of flows of fluids in microchannels. This work was done in the context of the development of microfluidic technology for performing chemical tasks in portable, integrated devices. Chapter 1 reviews this work for an audience of chemists who are potential users of these techniques in the development of micro-analytical and micro-synthetic devices. Appendix 1 contains a more general review of microfluidics. Chapter 2 presents experimental results on the use of patterned surface charge density to create new electroosmotic (EO) flows in microchannels; the chapter includes a successful model of the observed flows. In Chapter 3, patterns of topography on the wall of a microchannel were used to generate recirculation in pressure-driven flows. The design and characterization of an efficient mixer based on these flows is presented. A theoretical treatment of these flows is given in Appendix 2. The experimental methods used for the work with both EO and pressure-driven flows are presented in Chapter 4. In Chapter 5, a pattern of asymmetrical grooves in a heated plate was used to perturb Marangoni-Benard (M-B) convection, a dynamic system that spontaneously forms patterned flows. The interaction of the imposed pattern and the inherent pattern of the M-B convection led to a net flow in the plane of convecting layer of fluid. The direction of this flow depended on the orientation of the asymmetrical grooves, the temperature difference across the layer, and the thickness of the layer. A phenomenological model is presented to explain this ratchet effect in which local recirculation was coupled into a global flow. In Chapter 6, surfaces patterned by microcontact printing were used as a workbench on which to build molecularly thin polymer

  16. Exponential Growth through Pattern Exploration

    ERIC Educational Resources Information Center

    Brown, Betty

    2005-01-01

    Participants at the Summer Institute Pattern Exploration: Integration Math and Science in the Middle Grades used and developed a method treat arithmetic, algebra and geometry as one entity. The use of iterative geometric constructions is seen to reinforce the concepts of exponents, ratios and algebraic expressions for the nth stage of the…

  17. Robustness of Embryonic Patterning

    NASA Astrophysics Data System (ADS)

    Barkai, Naama

    2002-03-01

    Developmental patterning proceeds reliably despite natural fluctuations in the expression levels of genes and changes in gene dosage. Patterning mechanisms that rely on morphogen gradients generally involve a network of feedback loops, which buffer against such perturbations. Although most components of the patterning networks have been identified and characterized, quantitative and mechanistic understanding of how their functions are integrated to achieve robustness is still missing. Here, we report a quantitative study of a morphogen gradient, determining cell fates in the fruit-fly embryo. We find that differential protein cleavage, coupled with selective diffusion, defines a robust system which can adjust to large variations in levels of the different protein components. The mechanism underlying robustness relies on the convergence of the signaling profile to a finite distribution, which in most regions is independent of physical boundary conditions such as production rates. An excess of signaling molecules is stored in a restricted spatial domain. This limiting profile property is exhibited by a class of reaction-diffusion equations, and may represent a general mechanism for achieving robustness in morphogen gradient systems. Experimental verification of model's predictions will be described.

  18. Integrating Technology with Architectural Needs

    ERIC Educational Resources Information Center

    Elmasry, Sarah

    2009-01-01

    Researchers at the Center of High Performance Learning Technologies (CHPLE), Virginia Tech, conducted a study investigating issues related to integration of learning technologies with architectural systems in contemporary learning environments. The study is qualitative in nature, and focuses on integration patterns of learning technologies with…

  19. Integrating Art.

    ERIC Educational Resources Information Center

    BCATA Journal for Art Teachers, 1991

    1991-01-01

    These articles focus on art as a component of interdisciplinary integration. (1) "Integrated Curriculum and the Visual Arts" (Anna Kindler) considers various aspects of integration and implications for art education. (2) "Integration: The New Literacy" (Tim Varro) illustrates how the use of technology can facilitate…

  20. Geometry Embedded in North American Quilt Patterns

    ERIC Educational Resources Information Center

    Wares, A.

    2006-01-01

    Quilts are an integral part of the North American culture. Most households in North America have quilts with intricate geometric patterns. These patterns symbolize different things to different groups of people in this part of the world. It is important for students to see how mathematics comes from what is done in day-to-day life, not from the…

  1. Throwing Patterns of the Mentally Retarded.

    ERIC Educational Resources Information Center

    Auxter, David

    This study explored developmental patterns in the acquisition of the gross motor skill of throwing among 110 educable, mentally retarded 7- to 12-year-olds. Each child was examined through cinematographic procedures to discover: a) variance in throwing patterns, b) elements composing throwing skills, and c) sequential integration of the elements…

  2. Generating Weighted Test Patterns for VLSI Chips

    NASA Technical Reports Server (NTRS)

    Siavoshi, Fardad

    1990-01-01

    Improved built-in self-testing circuitry for very-large-scale integrated (VLSI) digital circuits based on version of weighted-test-pattern-generation concept, in which ones and zeros in pseudorandom test patterns occur with probabilities weighted to enhance detection of certain kinds of faults. Requires fewer test patterns and less computation time and occupies less area on circuit chips. Easy to relate switching activity in outputs with fault-detection activity by use of probabilistic fault-detection techniques.

  3. Pattern collapse solution for asymmetric pattern

    NASA Astrophysics Data System (ADS)

    Tu, C. J.; Huang, C. H.; Yang, Elvis; Yang, T. H.; Chen, K. C.

    2017-03-01

    One of the most critical issues associate with decreasing photo-resist feature size is pattern collapse, and more serious pattern collapse can be easily observed especially in asymmetric pitch environment due to unbalanced capillary stress acting on photo-resist pattern during development rinse step. The pattern collapse would kill product yield in the worse condition. This work investigates the approaches of mitigating the asymmetric pattern collapse behavior, such as adjusting photoresist pattern aspect ratio, applying surfactant during development rinse to reduce the solution surface tension, and altering underlying anti-reflection coating and hard-mask combinations to tailor the photo-resist bottom profile as well as decreasing developer permeation into photo-resist interface. Pattern sizing to resist unbalanced capillary force is also explored in the asymmetric pattern region. Two novel layout methods to mitigate asymmetric dummy pattern collapse were demonstrated and both methods were confirmed to have higher immunity against pattern collapse in asymmetric pitch environment.

  4. Glass strengthening and patterning methods

    SciTech Connect

    Harper, David C; Wereszczak, Andrew A; Duty, Chad E

    2015-01-27

    High intensity plasma-arc heat sources, such as a plasma-arc lamp, are used to irradiate glass, glass ceramics and/or ceramic materials to strengthen the glass. The same high intensity plasma-arc heat source may also be used to form a permanent pattern on the glass surface--the pattern being raised above the glass surface and integral with the glass (formed of the same material) by use of, for example, a screen-printed ink composition having been irradiated by the heat source.

  5. Pattern, Growth and Control

    PubMed Central

    Lander, Arthur D.

    2011-01-01

    The view of biology as goal-directed engineering has deep historical roots in developmental biology, a field currently benefitting from an influx of ideas and methods from systems biology. Systems biology draws on non-biological paradigms to explain developmental mechanisms of control, the specific type of regulation that achieves or maintains a desired end. This review highlights some of the current efforts designed to elucidate basic design principles underlying the engineering objectives of robustness, precision, and scaling that are required during developmental control of growth and pattern formation. Examples from vertebrate and invertebrate development are used to illustrate general principles including the value of integral feedback in achieving set-point control; the usefulness of self-organizing behavior; the importance of recognizing and appropriately handling noise; and the No Free Lunch theory. Through the examination of such principles, systems biology offers a functional framework to make sense of the mechanistic complexity of organismal development. PMID:21414486

  6. Morphological Integration of the Modern Human Mandible during Ontogeny.

    PubMed

    Polanski, Joshua M

    2011-01-01

    Craniofacial integration is prevalent in anatomical modernity research. Little investigation has been done on mandibular integration. Integration patterns were quantified in a longitudinal modern human sample of mandibles. This integration pattern is one of modularization between the alveolar and muscle attachment regions, but with age-specific differences. The ascending ramus and nonalveolar portions of the corpus remain integrated throughout ontogeny. The alveolar region is dynamic, becoming modularized according to the needs of the mandible at a particular developmental stage. Early in ontogeny, this modularity reflects the need for space for the developing dentition; later, modularity is more reflective of mastication. The overall pattern of modern human mandibular integration follows the integration pattern seen in other mammals, including chimpanzees. Given the differences in craniofacial integration patterns between humans and chimpanzees, but the similarities in mandibular integration, it is likely that the mandible has played the more passive role in hominin skull evolution.

  7. Morphological Integration of the Modern Human Mandible during Ontogeny

    PubMed Central

    Polanski, Joshua M.

    2011-01-01

    Craniofacial integration is prevalent in anatomical modernity research. Little investigation has been done on mandibular integration. Integration patterns were quantified in a longitudinal modern human sample of mandibles. This integration pattern is one of modularization between the alveolar and muscle attachment regions, but with age-specific differences. The ascending ramus and nonalveolar portions of the corpus remain integrated throughout ontogeny. The alveolar region is dynamic, becoming modularized according to the needs of the mandible at a particular developmental stage. Early in ontogeny, this modularity reflects the need for space for the developing dentition; later, modularity is more reflective of mastication. The overall pattern of modern human mandibular integration follows the integration pattern seen in other mammals, including chimpanzees. Given the differences in craniofacial integration patterns between humans and chimpanzees, but the similarities in mandibular integration, it is likely that the mandible has played the more passive role in hominin skull evolution. PMID:21716741

  8. RG stability of integrable fishnet models

    NASA Astrophysics Data System (ADS)

    Mamroud, Ohad; Torrents, Genís

    2017-06-01

    We address the question of perturbative consistency in the scalar fishnet models presented by Caetano, Gürdoğan and Kazakov [1, 2]. We argue that their 3-dimensional ϕ 6 fishnet model becomes perturbatively stable under renormalization in the large N limit, in contrast to what happens in their 4-dimensional ϕ 4 fishnet model, in which double trace terms are known to be generated by the RG flow. We point out that there is a direct way to modify this second theory that protects it from such corrections. Additionally, we observe that the 6-dimensional ϕ 3 Lagrangian that spans an hexagonal integrable scalar fishnet is consistent at the perturbative level as well. The nontriviality and simplicity of this last model is illustrated by computing the anomalous dimensions of its tr ϕ i ϕ j operators to all perturbative orders.

  9. Different patterns of confabulation.

    PubMed

    Dalla Barba, G

    1993-12-01

    In this study we investigated the amnesic-confabulatory condition of two patients, M.B. and S.D., exhibiting different patterns of confabulation. Neuropsychological examination showed in M.B. a normal intellectual efficiency and a selective deficit of episodic memory, whereas S.D. was impaired in tests of intellectual efficiency, episodic memory, semantic knowledge and frontal functions. The relation of confabulation to retrieval conditions and the degree of impairment of the semantic memory system was investigated with a set of questions involving the retrieval of various kinds of information. In M.B. confabulation was restricted to episodic memory tasks, whereas in S.D. it also affected the retrieval of semantic information. S.D.'s confabulatory reports were 'semantically anomalous', whereas the semantic structure of M.B.'s confabulations was appropriate. Further investigation using the encoding specificity paradigm showed an interaction of encoding/retrieval conditions in M.B. but not in S.D. This pattern of results is discussed in terms of a different level of disruption of processes that normally monitor the retrieval of information. It is further argued that the confabulation content must be considered in terms of its semantic structure and relies on the level of integrity of semantic knowledge.

  10. Teaching Integrity

    ERIC Educational Resources Information Center

    Saunders, Sue; Butts, Jennifer Lease

    2011-01-01

    Integrity is one of those essential yet highly ambiguous concepts. For the purpose of this chapter, integrity is defined as that combination of both attributes and actions that makes entities appear to be whole and ethical, as well as consistent. Like the concepts of leadership or wisdom or community or collaboration, integrity is a key element of…

  11. Associative Pattern Recognition In Analog VLSI Circuits

    NASA Technical Reports Server (NTRS)

    Tawel, Raoul

    1995-01-01

    Winner-take-all circuit selects best-match stored pattern. Prototype cascadable very-large-scale integrated (VLSI) circuit chips built and tested to demonstrate concept of electronic associative pattern recognition. Based on low-power, sub-threshold analog complementary oxide/semiconductor (CMOS) VLSI circuitry, each chip can store 128 sets (vectors) of 16 analog values (vector components), vectors representing known patterns as diverse as spectra, histograms, graphs, or brightnesses of pixels in images. Chips exploit parallel nature of vector quantization architecture to implement highly parallel processing in relatively simple computational cells. Through collective action, cells classify input pattern in fraction of microsecond while consuming power of few microwatts.

  12. Associative Pattern Recognition In Analog VLSI Circuits

    NASA Technical Reports Server (NTRS)

    Tawel, Raoul

    1995-01-01

    Winner-take-all circuit selects best-match stored pattern. Prototype cascadable very-large-scale integrated (VLSI) circuit chips built and tested to demonstrate concept of electronic associative pattern recognition. Based on low-power, sub-threshold analog complementary oxide/semiconductor (CMOS) VLSI circuitry, each chip can store 128 sets (vectors) of 16 analog values (vector components), vectors representing known patterns as diverse as spectra, histograms, graphs, or brightnesses of pixels in images. Chips exploit parallel nature of vector quantization architecture to implement highly parallel processing in relatively simple computational cells. Through collective action, cells classify input pattern in fraction of microsecond while consuming power of few microwatts.

  13. Development and evaluation of a high-resolution reanalysis of the East Australian Current region using the Regional Ocean Modelling System (ROMS 3.4) and Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) data assimilation

    NASA Astrophysics Data System (ADS)

    Kerry, Colette; Powell, Brian; Roughan, Moninya; Oke, Peter

    2016-10-01

    As with other Western Boundary Currents globally, the East Australian Current (EAC) is highly variable making it a challenge to model and predict. For the EAC region, we combine a high-resolution state-of-the-art numerical ocean model with a variety of traditional and newly available observations using an advanced variational data assimilation scheme. The numerical model is configured using the Regional Ocean Modelling System (ROMS 3.4) and takes boundary forcing from the BlueLink ReANalysis (BRAN3). For the data assimilation, we use an Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) scheme, which uses the model dynamics to perturb the initial conditions, atmospheric forcing, and boundary conditions, such that the modelled ocean state better fits and is in balance with the observations. This paper describes the data assimilative model configuration that achieves a significant reduction of the difference between the modelled solution and the observations to give a dynamically consistent "best estimate" of the ocean state over a 2-year period. The reanalysis is shown to represent both assimilated and non-assimilated observations well. It achieves mean spatially averaged root mean squared (rms) residuals with the observations of 7.6 cm for sea surface height (SSH) and 0.4 °C for sea surface temperature (SST) over the assimilation period. The time-mean rms residual for subsurface temperature measured by Argo floats is a maximum of 0.9 °C between water depths of 100 and 300 m and smaller throughout the rest of the water column. Velocities at several offshore and continental shelf moorings are well represented in the reanalysis with complex correlations between 0.8 and 1 for all observations in the upper 500 m. Surface radial velocities from a high-frequency radar array are assimilated and the reanalysis provides surface velocity estimates with complex correlations with observed velocities of 0.8-1 across the radar footprint. A comparison with

  14. Integration, Resegregation and Integration Maintenance.

    ERIC Educational Resources Information Center

    Peterman, William A.

    Recent increases in black migration to the suburbs and the continuing existence of discrimination in housing have emphasized the issues of integration and resegregation in suburban municipalities. To prevent resegregation, many integrated municipalities have adopted integration maintenance measures such as efforts to inform people that racial…

  15. Capacitance enhancement via electrode patterning

    NASA Astrophysics Data System (ADS)

    Ho, Tuan A.; Striolo, Alberto

    2013-11-01

    The necessity of increasing the energy density in electric double layer capacitors to meet current demand is fueling fundamental and applied research alike. We report here molecular dynamics simulation results for aqueous electrolytes near model electrodes. Particular focus is on the effect of electrode patterning on the structure of interfacial electrolytes, and on the potential drop between the solid electrodes and the bulk electrolytes. The latter is estimated by numerically integrating the Poisson equation using the charge densities due to water and ions accumulated near the interface as input. We considered uniform and patterned electrodes, both positively and negatively charged. The uniformly charged electrodes are modeled as graphite. The patterned ones are obtained by removing carbon atoms from the top-most graphene layer, yielding nanoscopic squares and stripes patterns. For simplicity, the patterned electrodes are effectively simulated as insulators (the charge remains localized on the top-most layer of carbon atoms). Our simulations show that the patterns alter the structure of water and the accumulation of ions at the liquid-solid interfaces. Using aqueous NaCl solutions, we found that while the capacitance calculated for three positively charged electrodes did not change much, that calculated for the negatively charged electrodes significantly increased upon patterning. We find that both water structure and orientation, as well as ion accumulation affect the capacitance. As electrode patterning affects differently water structure and ion accumulation, it might be possible to observe ion-specific effects. These results could be useful for advancing our understanding of electric double layer capacitors, capacitive desalination processes, as well as of fundamental interfacial electrolytes properties.

  16. Capacitance enhancement via electrode patterning

    SciTech Connect

    Ho, Tuan A.; Striolo, Alberto

    2013-11-28

    The necessity of increasing the energy density in electric double layer capacitors to meet current demand is fueling fundamental and applied research alike. We report here molecular dynamics simulation results for aqueous electrolytes near model electrodes. Particular focus is on the effect of electrode patterning on the structure of interfacial electrolytes, and on the potential drop between the solid electrodes and the bulk electrolytes. The latter is estimated by numerically integrating the Poisson equation using the charge densities due to water and ions accumulated near the interface as input. We considered uniform and patterned electrodes, both positively and negatively charged. The uniformly charged electrodes are modeled as graphite. The patterned ones are obtained by removing carbon atoms from the top-most graphene layer, yielding nanoscopic squares and stripes patterns. For simplicity, the patterned electrodes are effectively simulated as insulators (the charge remains localized on the top-most layer of carbon atoms). Our simulations show that the patterns alter the structure of water and the accumulation of ions at the liquid-solid interfaces. Using aqueous NaCl solutions, we found that while the capacitance calculated for three positively charged electrodes did not change much, that calculated for the negatively charged electrodes significantly increased upon patterning. We find that both water structure and orientation, as well as ion accumulation affect the capacitance. As electrode patterning affects differently water structure and ion accumulation, it might be possible to observe ion-specific effects. These results could be useful for advancing our understanding of electric double layer capacitors, capacitive desalination processes, as well as of fundamental interfacial electrolytes properties.

  17. Vertebrate Embryonic Cleavage Pattern Determination.

    PubMed

    Hasley, Andrew; Chavez, Shawn; Danilchik, Michael; Wühr, Martin; Pelegri, Francisco

    2017-01-01

    The pattern of the earliest cell divisions in a vertebrate embryo lays the groundwork for later developmental events such as gastrulation, organogenesis, and overall body plan establishment. Understanding these early cleavage patterns and the mechanisms that create them is thus crucial for the study of vertebrate development. This chapter describes the early cleavage stages for species representing ray-finned fish, amphibians, birds, reptiles, mammals, and proto-vertebrate ascidians and summarizes current understanding of the mechanisms that govern these patterns. The nearly universal influence of cell shape on orientation and positioning of spindles and cleavage furrows and the mechanisms that mediate this influence are discussed. We discuss in particular models of aster and spindle centering and orientation in large embryonic blastomeres that rely on asymmetric internal pulling forces generated by the cleavage furrow for the previous cell cycle. Also explored are mechanisms that integrate cell division given the limited supply of cellular building blocks in the egg and several-fold changes of cell size during early development, as well as cytoskeletal specializations specific to early blastomeres including processes leading to blastomere cohesion. Finally, we discuss evolutionary conclusions beginning to emerge from the contemporary analysis of the phylogenetic distributions of cleavage patterns. In sum, this chapter seeks to summarize our current understanding of vertebrate early embryonic cleavage patterns and their control and evolution.

  18. The concept of pattern in craniofacial growth.

    PubMed

    Moyers, R E; Bookstein, F L; Guire, K E

    1979-08-01

    1. There are semantic and associated problems with the word pattern in biology, particularly in orthodontics and facial growth. 2. Pattern, as we use the term, is invariance of relationships--"a set of constraints operating to preserve the integration of parts under varying conditions and through time." 3. Craniofacial pattern can be described and quantified by the identification of craniofacial constants, measures that are relatively invariant. 4. Growth is change and is best identified by studying those measures of size and shape that vary most sensitively through time over development stages. 5. The many traditional cephalometric measures that represent well neither pattern nor growth (mixed) are of less clinical utility than either pure pattern indices or growth indices. 6. The analytical and conceptual separation of pattern and growth seems useful in analysis of morphology, analysis of growth, prediction of growth, and clinical treatment planning.

  19. Assuring structural integrity in Army systems

    NASA Technical Reports Server (NTRS)

    1985-01-01

    The object of this study was to recommend possible improvements in the manner in which structural integrity of Army systems is assured. The elements of a structural integrity program are described, and relevant practices used in various industries and government organizations are reviewed. Some case histories of Army weapon systems are examined. The mandatory imposition of a structural integrity program patterned after the Air Force Aircraft Structural Integrity Program is recommended and the benefits of such an action are identified.

  20. Integrated Learning

    ERIC Educational Resources Information Center

    Gnanakan, Ken

    2012-01-01

    This book upholds the idea of learning and education as a means to individual development and social empowerment. It presents a holistic picture, looking at learning as an integral part of one's social and physical life. Strongly differing from existing classroom perspectives, the book analyses integrated learning at its broadest possible…

  1. Integrated Networks.

    ERIC Educational Resources Information Center

    Robinovitz, Stewart

    1987-01-01

    A strategy for integrated data and voice networks implemented at the University of Michigan is described. These networks often use multi-technologies, multi-vendors, and multi-transmission media that will be fused into a single integrated network. Transmission media include twisted-pair wire, coaxial cable, fiber optics, and microwave. (Author/MLW)

  2. Integrated Learning

    ERIC Educational Resources Information Center

    Gnanakan, Ken

    2012-01-01

    This book upholds the idea of learning and education as a means to individual development and social empowerment. It presents a holistic picture, looking at learning as an integral part of one's social and physical life. Strongly differing from existing classroom perspectives, the book analyses integrated learning at its broadest possible…

  3. Integrative Education.

    ERIC Educational Resources Information Center

    Walker, Dean

    1995-01-01

    In contrast with subject-bound education, integrative education promotes the construction of broad "mental programs" that require students to use skills and information in new, realistic contexts. Early childhood education has long been a model of integrative education, emphasizing the whole child and offering a wide range of experiences that…

  4. Integrated Networks.

    ERIC Educational Resources Information Center

    Robinovitz, Stewart

    1987-01-01

    A strategy for integrated data and voice networks implemented at the University of Michigan is described. These networks often use multi-technologies, multi-vendors, and multi-transmission media that will be fused into a single integrated network. Transmission media include twisted-pair wire, coaxial cable, fiber optics, and microwave. (Author/MLW)

  5. Integrated care requires integrated supervision

    PubMed Central

    Ketelaars, Corry A.J

    2011-01-01

    Introduction Given recent developments in integrated care, it is becoming increasingly important for the Dutch Health Care Inspectorate to direct its supervision in a way that may help speed up the implementation of integrated care. Description of care practice Since the implementation of integrated care for chronic patients is facing obstacles, alternative methods are required to ensure that the implementation process does not run into any delays. By applying a risk-based approach to integrated care providers, the Inspectorate can analyse the care providers' performance by means of quality indicators and rank them. In order to be effective, appropriated supervision arrangements will be applied to the care providers of integrated care. Discussion With a ranking model transparency will be improved and this may encourage integrated care providers to strive for greater quality due to the competition inherent in the system. Supervision based on advice and encouragement might be helpful in the implementation of integrated care. Conclusion Integrated care also requires integrated supervision, which means the Inspectorate may have to reconsider its working methods and the composition of its inspection teams. PMID:21637707

  6. Ontology Design Patterns as Interfaces (invited)

    NASA Astrophysics Data System (ADS)

    Janowicz, K.

    2015-12-01

    In recent years ontology design patterns (ODP) have gained popularity among knowledge engineers. ODPs are modular but self-contained building blocks that are reusable and extendible. They minimize the amount of ontological commitments and thereby are easier to integrate than large monolithic ontologies. Typically, patterns are not directly used to annotate data or to model certain domain problems but are combined and extended to form data and purpose-driven local ontologies that serve the needs of specific applications or communities. By relying on a common set of patterns these local ontologies can be aligned to improve interoperability and enable federated queries without enforcing a top-down model of the domain. In previous work, we introduced ontological views as layer on top of ontology design patterns to ease the reuse, combination, and integration of patterns. While the literature distinguishes multiple types of patterns, e.g., content patterns or logical patterns, we propose to use them as interfaces here to guide the development of ontology-driven systems.

  7. Derivative Sign Patterns

    ERIC Educational Resources Information Center

    Clark, Jeffrey

    2011-01-01

    Analysis of the patterns of signs of infinitely differentiable real functions shows that only four patterns are possible if the function is required to exhibit the pattern at all points in its domain and that domain is the set of all real numbers. On the other hand all patterns are possible if the domain is a bounded open interval.

  8. Derivative Sign Patterns

    ERIC Educational Resources Information Center

    Clark, Jeffrey

    2011-01-01

    Analysis of the patterns of signs of infinitely differentiable real functions shows that only four patterns are possible if the function is required to exhibit the pattern at all points in its domain and that domain is the set of all real numbers. On the other hand all patterns are possible if the domain is a bounded open interval.

  9. Patterns of Enlisted Compensation

    DTIC Science & Technology

    2001-01-01

    we documented the patterns of enlisted compensation. Nor did we perform a behavioral analysis of these patterns-that is, we do not explain why the...patterns we observed exist. Rather, our documentation of the patterns is intended to be a baseline description that can serve to identify areas in which future behavioral analysis would be especially fruitful.

  10. Integrative psychotherapy.

    PubMed

    Kozarić-Kovacić, Dragica

    2008-09-01

    The main purposes of the article are to present the history of integration in psychotherapy, the reasons of the development integrative approaches, and the approaches to integration in psychotherapy. Three approaches to integration in psychotherapy exist: theoretical integration, theoretical eclecticism, and common factors in different psychotherapeutic trends. In integrative psychotherapy, the basic epistemology, theory, and clinical practice are based on the phenomenology, field theory, holism, dialogue, and co-creation of dialogue in the therapeutic relationship. The main criticism is that integrative psychotherapy suffers from confusion and many unresolved controversies. It is difficult to theoretically and methodologically define the clinically applied model that is based on such a different epistemological and theoretical presumptions. Integrative psychotherapy is a synthesis of humanistic psychotherapy, object relations theory, and psychoanalytical self psychology. It focuses on the dynamics and potentials of human relationships, with a goal of changing the relations and understanding internal and external resistances. The process of integrative psychotherapy is primarily focused on the developmental-relational model and co-creation of psychotherapeutic relationship as a single interactive event, which is not unilateral, but rather a joint endeavor by both the therapist and the patient/client. The need for a relationship is an important human need and represents a process of attunement that occurs as a response to the need for a relationship, a unique interpersonal contact between two people. If this need is not met, it manifests with the different feelings and various defenses. To meet this need, we need to have another person with whom we can establish a sensitive, attuned relationship. Thus, the therapist becomes this person who tries to supplement what the person did not receive. Neuroscience can be a source of integration through different therapies. We

  11. Scholarly Integrity.

    PubMed

    Francisco, Joseph S; Hahn, Ulrike; Schwarz, Helmut

    2017-04-03

    "… Scholarly integrity is not only the foundational bedrock of scientific inquiry, it is also the prerequisite for a positive image of scholarship … For individuals, integrity is an aspect of moral character and experience. For institutions, it is about creating an environment that promotes responsible conduct … In the first instance, research institutions must provide guidelines and codes of practice on scholarly integrity …" Read more in the Editorial by J. S. Francisco, U. Hahn, and H. Schwarz. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Integrative Oncology.

    PubMed

    Lopez, Gabriel; Mao, Jun J; Cohen, Lorenzo

    2017-09-01

    Integrative oncology helps support the health of patients with cancer and their caregivers through an evidence-informed approach to lifestyle and behavior modification and the use of complementary health therapies as part of conventional cancer care. Integrative approaches can provide patients relief from cancer and cancer treatment-related symptoms, leading to improvements in their physical and psychosocial health. An evidence-informed approach is important when recommending an integrative cancer plan. Efforts at enhancing communication between patients and health care providers, as well as between integrative practitioners and conventional health care teams, are critical to achieving optimal health and healing for patients with cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Gene Insertion Patterns and Sites

    NASA Astrophysics Data System (ADS)

    Vain, Philippe; Thole, Vera

    During the past 25 years, the molecular analysis of transgene insertion patterns and sites in plants has greatly contributed to our understanding of the mechanisms underlying transgene integration, expression, and stability in the nuclear genome. Molecular characterization is also an essential step in the safety assessment of genetically modified crops. This chapter describes the standard experimental procedures used to analyze transgene insertion patterns and loci in cereals and grasses transformed using Agrobacterium tumefaciens or direct transfer of DNA. Methods and protocols enabling the determination of the number and configuration of transgenic loci via a combination of inheritance studies, polymerase chain reaction, and Southern analyses are presented. The complete characterization of transgenic inserts in plants is, however, a holistic process relying on a wide variety of experimental approaches. In this chapter, these additional approaches are not detailed but references to relevant bibliographic records are provided.

  14. Theory of electrochemical pattern formation

    NASA Astrophysics Data System (ADS)

    Christoph, J.; Eiswirth, M.

    2002-03-01

    The spatial coupling in electrochemical systems is mediated by ion migration under the influence of the electric field. Since field effects spread very rapidly, every point of an electrode can communicate with every other one practically instantaneously through migration coupling. Based on mathematical potential theory we present the derivation of a generally applicable reaction-migration equation, which describes the coupling via an integral over the whole electrode area. The corresponding coupling function depends only on the geometry of the electrode setup and has been computed for commonly used electrode shapes (such as ring, disk, ribbon or rectangle). The pattern formation observed in electrochemical systems in the bistable, excitable and oscillatory regime can be reproduced in computer simulations, and the types of patterns occurring under different geometries can be rationalized.

  15. Integrated diagnostics

    NASA Technical Reports Server (NTRS)

    Hunthausen, Roger J.

    1988-01-01

    Recently completed projects in which advanced diagnostic concepts were explored and/or demonstrated are summarized. The projects begin with the design of integrated diagnostics for the Army's new gas turbine engines, and advance to the application of integrated diagnostics to other aircraft subsystems. Finally, a recent project is discussed which ties together subsystem fault monitoring and diagnostics with a more complete picture of flight domain knowledge.

  16. Feedback Integrators

    NASA Astrophysics Data System (ADS)

    Chang, Dong Eui; Jiménez, Fernando; Perlmutter, Matthew

    2016-12-01

    A new method is proposed to numerically integrate a dynamical system on a manifold such that the trajectory stably remains on the manifold and preserves the first integrals of the system. The idea is that given an initial point in the manifold we extend the dynamics from the manifold to its ambient Euclidean space and then modify the dynamics outside the intersection of the manifold and the level sets of the first integrals containing the initial point such that the intersection becomes a unique local attractor of the resultant dynamics. While the modified dynamics theoretically produces the same trajectory as the original dynamics, it yields a numerical trajectory that stably remains on the manifold and preserves the first integrals. The big merit of our method is that the modified dynamics can be integrated with any ordinary numerical integrator such as Euler or Runge-Kutta. We illustrate this method by applying it to three famous problems: the free rigid body, the Kepler problem and a perturbed Kepler problem with rotational symmetry. We also carry out simulation studies to demonstrate the excellence of our method and make comparisons with the standard projection method, a splitting method and Störmer-Verlet schemes.

  17. Functional Integration

    NASA Astrophysics Data System (ADS)

    Cartier, Pierre; DeWitt-Morette, Cecile

    2010-06-01

    Acknowledgements; List symbols, conventions, and formulary; Part I. The Physical and Mathematical Environment: 1. The physical and mathematical environment; Part II. Quantum Mechanics: 2. First lesson: gaussian integrals; 3. Selected examples; 4. Semiclassical expansion: WKB; 5. Semiclassical expansion: beyond WKB; 6. Quantum dynamics: path integrals and operator formalism; Part III. Methods from Differential Geometry: 7. Symmetries; 8. Homotopy; 9. Grassmann analysis: basics; 10. Grassmann analysis: applications; 11. Volume elements, divergences, gradients; Part IV. Non-Gaussian Applications: 12. Poisson processes in physics; 13. A mathematical theory of Poisson processes; 14. First exit time: energy problems; Part V. Problems in Quantum Field Theory: 15. Renormalization 1: an introduction; 16. Renormalization 2: scaling; 17. Renormalization 3: combinatorics; 18. Volume elements in quantum field theory Bryce DeWitt; Part VI. Projects: 19. Projects; Appendix A. Forward and backward integrals: spaces of pointed paths; Appendix B. Product integrals; Appendix C. A compendium of gaussian integrals; Appendix D. Wick calculus Alexander Wurm; Appendix E. The Jacobi operator; Appendix F. Change of variables of integration; Appendix G. Analytic properties of covariances; Appendix H. Feynman's checkerboard; Bibliography; Index.

  18. Discriminative Chemical Patterns: Automatic and Interactive Design.

    PubMed

    Bietz, Stefan; Schomburg, Karen T; Hilbig, Matthias; Rarey, Matthias

    2015-08-24

    The classification of molecules with respect to their inhibiting, activating, or toxicological potential constitutes a central aspect in the field of cheminformatics. Often, a discriminative feature is needed to distinguish two different molecule sets. Besides physicochemical properties, substructures and chemical patterns belong to the descriptors most frequently applied for this purpose. As a commonly used example of this descriptor class, SMARTS strings represent a powerful concept for the representation and processing of abstract chemical patterns. While their usage facilitates a convenient way to apply previously derived classification rules on new molecule sets, the manual generation of useful SMARTS patterns remains a complex and time-consuming process. Here, we introduce SMARTSminer, a new algorithm for the automatic derivation of discriminative SMARTS patterns from preclassified molecule sets. Based on a specially adapted subgraph mining algorithm, SMARTSminer identifies structural features that are frequent in only one of the given molecule classes. In comparison to elemental substructures, it also supports the consideration of general and specific SMARTS features. Furthermore, SMARTSminer is integrated into an interactive pattern editor named SMARTSeditor. This allows for an intuitive visualization on the basis of the SMARTSviewer concept as well as interactive adaption and further improvement of the generated patterns. Additionally, a new molecular matching feature provides an immediate feedback on a pattern's matching behavior across the molecule sets. We demonstrate the utility of the SMARTSminer functionality and its integration into the SMARTSeditor software in several different classification scenarios.

  19. ACTION TOWARD QUALITY INTEGRATED EDUCATION.

    ERIC Educational Resources Information Center

    New York City Board of Education, Brooklyn, NY.

    THE STEPS TAKEN TO IMPROVE INTEGRATED EDUCATION FOR CHILDREN IN NEW YORK CITY INCLUDED SENDING EIGHTH-GRADE PUPILS TO 10 JUNIOR HIGH SCHOOLS, CHANGING NEW COMMUNITY ZONING PLANS, CHANGING THE FEEDER PATTERNS IN THREE SETS OF JUNIOR HIGH SCHOOLS, CLOSING THE GIRLS HIGH SCHOOL IN BROOKLYN, CONTINUING THE FREE CHOICE TRANSFER PLAN, REDESIGNING THE…

  20. Integrative Pediatrics: Looking Forward

    PubMed Central

    McClafferty, Hilary

    2015-01-01

    Increase in the prevalence of disease and illness has dramatically altered the landscape of pediatrics. As a result, there is a demand for pediatricians with new skills and a sharper focus on preventative health. Patient demand and shifting pediatric illness patterns have accelerated research in the field of pediatric integrative medicine. This emerging field can be defined as healing-oriented medicine that considers the whole child, including all elements of lifestyle and family health. It is informed by evidence and carefully weighs all appropriate treatment options. This Special Issue of Children, containing a collection of articles written by expert clinicians, represents an important educational contribution to the field. The goal of the edition is to raise awareness about integrative topics with robust supporting evidence, and to identify areas where more research is needed. PMID:27417349

  1. Integrated optic biosensor

    NASA Astrophysics Data System (ADS)

    Boiarski, Anthony A.; Busch, James R.; Bhullar, Ballwant S.; Ridgway, Richard W.; Miller, Larry S.; Zulich, A. W.

    1993-05-01

    A micro-sized biosensor is formed using integrated-optic channel waveguides in a Mach- Zehnder interferometer configuration. The device measures refractive index changes on the waveguide surface, so it is called a biorefractometer. With an appropriate overlay or selective coating, the sensor can monitor proteins in blood or pollutants and bio-warfare agents in water. The waveguides are fabricated in a glass substrate using potassium ion exchange. A patterned glass buffer layer defines the interferometer's sensing and reference arms. A silicone-rubber cell arrangement brings sample analytes into contact with proteins immobilized on the integrated-optical waveguide surface. Data obtained for antigen-antibody binding of the proteins human Immunoglobulin-G and staph enterotoxin-B indicate that a 50 - 100 ng/ml concentration levels can be measured in less than ten minutes.

  2. Male pattern baldness (image)

    MedlinePlus

    Male pattern baldness is a sex-linked characteristic that is passed from mother to child. A man can more accurately predict his chances of developing male pattern baldness by observing his mother's father than by looking ...

  3. Pattern Formation in Materials

    NASA Astrophysics Data System (ADS)

    Karma, Alain

    2011-04-01

    Pattern formation is ubiquitous in nature, from sand ripples formed by wind to the development of a complex biological organism with different organs and a central nervous system. In the realm of materials, patterns are formed invariably when matter is transformed between different solid, liquid or gaseous states far from thermodynamic equilibrium. Material failure is itself mediated by the propagation of cracks that form intricate patterns. Understanding how patterns form and evolve is key to design materials with desired properties and to optimize their performance and safety. This talk will discuss recent progress made to understand three distinct class of patterns including the highly branched snow-flake-like dendritic patterns formed during the solidification process, polycrystalline patterns shaped by grain boundaries, and crack patterns.

  4. Pattern recognition technique

    NASA Technical Reports Server (NTRS)

    Hong, J. P.

    1971-01-01

    Technique operates regardless of pattern rotation, translation or magnification and successfully detects out-of-register patterns. It improves accuracy and reduces cost of various optical character recognition devices and page readers and provides data input to computer.

  5. Patterns of Change: Forces and Motion

    ERIC Educational Resources Information Center

    Phillips, Marianne; Jeffery, Tonya D.

    2016-01-01

    Patterns of Change: Forces and Motion is an integrated science lesson that uses the 5E lesson cycle to tie together science with language arts, mathematics, literature, technology, engineering and social studies in an engaging format applicable for young learners. This lesson has been uniquely designed for the purpose of providing elementary…

  6. Mining Collaborative Patterns in Tutorial Dialogues

    ERIC Educational Resources Information Center

    D'Mello, Sidney; Olney, Andrew; Person, Natalie

    2010-01-01

    We present a method to automatically detect collaborative patterns of student and tutor dialogue moves. The method identifies significant two-step excitatory transitions between dialogue moves, integrates the transitions into a directed graph representation, and generates and tests data-driven hypotheses from the directed graph. The method was…

  7. Patterned Video Sensors For Low Vision

    NASA Technical Reports Server (NTRS)

    Juday, Richard D.

    1996-01-01

    Miniature video cameras containing photoreceptors arranged in prescribed non-Cartesian patterns to compensate partly for some visual defects proposed. Cameras, accompanied by (and possibly integrated with) miniature head-mounted video display units restore some visual function in humans whose visual fields reduced by defects like retinitis pigmentosa.

  8. Patterns of Change: Forces and Motion

    ERIC Educational Resources Information Center

    Phillips, Marianne; Jeffery, Tonya D.

    2016-01-01

    Patterns of Change: Forces and Motion is an integrated science lesson that uses the 5E lesson cycle to tie together science with language arts, mathematics, literature, technology, engineering and social studies in an engaging format applicable for young learners. This lesson has been uniquely designed for the purpose of providing elementary…

  9. Pattern transfer of directed self-assembly patterns for CMOS device applications

    NASA Astrophysics Data System (ADS)

    Tsai, Hsin-Yu; Miyazoe, Hiroyuki; Engelmann, Sebastian; Liu, Chi-Chun; Gignac, Lynne; Bucchignano, James; Klaus, David; Breslin, Chris; Joseph, Eric; Cheng, Joy; Sanders, Daniel; Guillorn, Michael

    2013-10-01

    A study on the optimization of etch transfer processes using 200-mm-scale production type plasma etch tools for circuit relevant patterning in the sub-30-nm pitch regime using directed self-assembly (DSA) line-space patterning is presented. This work focuses on etch stack selection and process tuning, such as plasma power, chuck temperature, and end point strategy, to improve critical dimension control, pattern fidelity, and process window. Results from DSA patterning of gate structures featuring a high-k dielectric, a metal nitride and poly Si gate electrode, and a SiN capping layer are also presented. These results further establish the viability of DSA pattern generation as a potential method for Complementary metal-oxide-semiconductor (CMOS) integrated circuit patterning beyond the 10-nm node.

  10. Classical integrability

    NASA Astrophysics Data System (ADS)

    Torrielli, Alessandro

    2016-08-01

    We review some essential aspects of classically integrable systems. The detailed outline of the sections consists of: 1. Introduction and motivation, with historical remarks; 2. Liouville theorem and action-angle variables, with examples (harmonic oscillator, Kepler problem); 3. Algebraic tools: Lax pairs, monodromy and transfer matrices, classical r-matrices and exchange relations, non-ultralocal Poisson brackets, with examples (non-linear Schrödinger model, principal chiral field); 4. Features of classical r-matrices: Belavin-Drinfeld theorems, analyticity properties, and lift of the classical structures to quantum groups; 5. Classical inverse scattering method to solve integrable differential equations: soliton solutions, spectral properties and the Gel’fand-Levitan-Marchenko equation, with examples (KdV equation, Sine-Gordon model). Prepared for the Durham Young Researchers Integrability School, organised by the GATIS network. This is part of a collection of lecture notes.

  11. Mathematical Pattern Hunters

    ERIC Educational Resources Information Center

    Whitin, Phyllis; Whitin, David J.

    2011-01-01

    The habit of looking for patterns, the skills to find them, and the expectation that patterns have explanations is an essential mathematical habit of mind for young children (Goldenberg, Shteingold, & Feurzeig 2003, 23). Work with patterns leads to the ability to form generalizations, the bedrock of algebraic thinking, and teachers must nurture…

  12. Mathematical Pattern Hunters

    ERIC Educational Resources Information Center

    Whitin, Phyllis; Whitin, David J.

    2011-01-01

    The habit of looking for patterns, the skills to find them, and the expectation that patterns have explanations is an essential mathematical habit of mind for young children (Goldenberg, Shteingold, & Feurzeig 2003, 23). Work with patterns leads to the ability to form generalizations, the bedrock of algebraic thinking, and teachers must nurture…

  13. The Integrated Hazard Analysis Integrator

    NASA Technical Reports Server (NTRS)

    Morris, A. Terry; Massie, Michael J.

    2009-01-01

    Hazard analysis addresses hazards that arise in the design, development, manufacturing, construction, facilities, transportation, operations and disposal activities associated with hardware, software, maintenance, operations and environments. An integrated hazard is an event or condition that is caused by or controlled by multiple systems, elements, or subsystems. Integrated hazard analysis (IHA) is especially daunting and ambitious for large, complex systems such as NASA s Constellation program which incorporates program, systems and element components that impact others (International Space Station, public, International Partners, etc.). An appropriate IHA should identify all hazards, causes, controls and verifications used to mitigate the risk of catastrophic loss of crew, vehicle and/or mission. Unfortunately, in the current age of increased technology dependence, there is the tendency to sometimes overlook the necessary and sufficient qualifications of the integrator, that is, the person/team that identifies the parts, analyzes the architectural structure, aligns the analysis with the program plan and then communicates/coordinates with large and small components, each contributing necessary hardware, software and/or information to prevent catastrophic loss. As viewed from both Challenger and Columbia accidents, lack of appropriate communication, management errors and lack of resources dedicated to safety were cited as major contributors to these fatalities. From the accident reports, it would appear that the organizational impact of managers, integrators and safety personnel contributes more significantly to mission success and mission failure than purely technological components. If this is so, then organizations who sincerely desire mission success must put as much effort in selecting managers and integrators as they do when designing the hardware, writing the software code and analyzing competitive proposals. This paper will discuss the necessary and

  14. Numerical Integration

    ERIC Educational Resources Information Center

    Sozio, Gerry

    2009-01-01

    Senior secondary students cover numerical integration techniques in their mathematics courses. In particular, students would be familiar with the "midpoint rule," the elementary "trapezoidal rule" and "Simpson's rule." This article derives these techniques by methods which secondary students may not be familiar with and an approach that…

  15. Information Integrity

    ERIC Educational Resources Information Center

    Graves, Eric

    2013-01-01

    This dissertation introduces the concept of Information Integrity, which is the detection and possible correction of information manipulation by any intermediary node in a communication system. As networks continue to grow in complexity, information theoretic security has failed to keep pace. As a result many parties whom want to communicate,…

  16. Information Integrity

    ERIC Educational Resources Information Center

    Graves, Eric

    2013-01-01

    This dissertation introduces the concept of Information Integrity, which is the detection and possible correction of information manipulation by any intermediary node in a communication system. As networks continue to grow in complexity, information theoretic security has failed to keep pace. As a result many parties whom want to communicate,…

  17. Patterning via optical saturable transitions

    NASA Astrophysics Data System (ADS)

    Cantu, Precious

    For the past 40 years, optical lithography has been the patterning workhorse for the semiconductor industry. However, as integrated circuits have become more and more complex, and as device geometries shrink, more innovative methods are required to meet these needs. In the far-field, the smallest feature that can be generated with light is limited to approximately half the wavelength. This, so called far-field diffraction limit or the Abbe limit (after Prof. Ernst Abbe who first recognized this), effectively prevents the use of long-wavelength photons >300nm from patterning nanostructures <100nm. Even with a 193nm laser source and extremely complicated processing, patterns below ˜20nm are incredibly challenging to create. Sources with even shorter wavelengths can potentially be used. However, these tend be much more expensive and of much lower brightness, which in turn limits their patterning speed. Multi-photon reactions have been proposed to overcome the diffraction limit. However, these require very large intensities for modest gain in resolution. Moreover, the large intensities make it difficult to parallelize, thus limiting the patterning speed. In this dissertation, a novel nanopatterning technique using wavelength-selective small molecules that undergo single-photon reactions, enabling rapid top-down nanopatterning over large areas at low-light intensities, thereby allowing for the circumvention of the far-field diffraction barrier is developed and experimentally verified. This approach, which I refer to as Patterning via Optical Saturable Transitions (POST) has the potential for massive parallelism, enabling the creation of nanostructures and devices at a speed far surpassing what is currently possible with conventional optical lithographic techniques. The fundamental understanding of this technique goes beyond optical lithography in the semiconductor industry and is applicable to any area that requires the rapid patterning of large-area two or three

  18. Block Copolymer Thin Films: Patterns and Patterning

    NASA Astrophysics Data System (ADS)

    Register, Richard A.

    2001-03-01

    The nanostructures ("microdomains") in thin block copolymer films make excellent contact masks for surface patterning on the nanoscale. Using these thin films as templates, we have developed techniques based on reactive ion etching to uniformly and completely pattern the underlying substrate with a dense periodic pattern of dots, holes, or lines, with widths of order 20 nm. In addition, we have fabricated arrays of metal dots by backfilling these holes, and GaAs quantum dots by regrowth onto patterned GaAs substrates. A key issue in this nanopatterning approach is controlling the pattern which forms within the mask. While the local structure of the pattern (e.g., spheres vs. cylinders) is easily controlled through block copolymer composition, the long-range order ("grain size") is more difficult to manipulate. For cylinder-forming diblocks, we find that the correlation length of the microdomains grows as a weak power of annealing time, approximately 1/4. The principal types of defects which destroy the long-range order of the microdomains are disclinations. Sequential AFM images taken on the same region of the film after varying annealing times can be strung together into "movies" (to be shown at the talk) which directly show that the principal mode of defect annihilation (and hence grain growth) is the annihilation of disclination quadrupoles (pairs of +1/2 and -1/2 disclinations). We propose a model for quadrupole annihilation which reproduces the 1/4 exponent. Preliminary results for sphere-forming systems suggest that the exponent there is even lower than 1/4, making it difficult to achieve a significant degree of coarsening by extending the annealing time. * in collaboration with D.H. Adamson, P.M. Chaikin, Z. Cheng, P.D. Dapkus (USC), C.K. Harrison, D.A. Huse, R.R. Li (USC), and M. Park.

  19. Integrated nanocatalysts.

    PubMed

    Zeng, Hua Chun

    2013-02-19

    Despite significant advancements in catalysis research, the prevailing catalyst technology remains largely an art rather than a science. Rapid development in the fields of nanotechnology and materials chemistry in the past few decades, however, provides us with a new capacity to re-examine existing catalyst design and processing methods. In recent years, "nanocatalysts" has become a term often used by the materials chemistry and catalysis community. It refers to heterogeneous catalysts at nanoscale dimensions. Similar to homogeneous catalysts, freestanding (unsupported) nanocatalysts are difficult to separate after use. Because of their small sizes, they are also likely to be cytotoxic and pose a threat to the environment and therefore may not be practical for industrial use. On the other hand, if they are supported on ordinary catalyst carriers, the nanocatalysts would then revert to act as conventional heterogeneous catalysts, since chemists have known active metal clusters or oxide particles in the nanoscale regime long before the nanotechnology era. To resolve this problem, we need new research directions and synthetic strategies. Important advancements in catalysis research now allow chemists to prepare catalytic materials with greater precision. By controlling particle composition, structure, shape, and dimension, researchers can move into the next phase of catalyst development if they can bridge these old and new technologies. In this regard, one way seems to be to integrate active nanostructured catalysts with boundary-defined catalyst supports that are "not-so-nano" in dimension. However, these supports still have available hierarchical pores and cavity spaces. In principle, these devices keep the essence of traditional "catalyst-plus-support" type systems. They also have the advantages of nanoscale engineering, which involves both high level design and integration processes in their fabrication. Besides this, the active components in these devices are

  20. Ramadan Major Dietary Patterns

    PubMed Central

    Shadman, Zhaleh; Poorsoltan, Nooshin; Akhoundan, Mahdieh; Larijani, Bagher; Soleymanzadeh, Mozhdeh; Akhgar Zhand, Camelia; Seyed Rohani, Zahra Alsadat; Khoshniat Nikoo, Mohsen

    2014-01-01

    Background: There has been no data on population based dietary patterns during the Ramadan fasting month. Objectives: The purpose of this study was to detect Ramadan major dietary patterns among those who fast in Tehran. Materials and Methods: This cross-sectional study included 600 subjects, aged 18-65 with body mass index (BMI) of 18.5-40, who had decided to fast during Ramadan. Anthropometric measurements, usual physical activity level and educational status were collected two weeks before Ramadan. Information on Ramadan dietary intakes was obtained using a food frequency questionnaire and factor analysis was used to identify major dietary patterns. Results: We identified four major dietary patterns: 1) Western-like pattern; high in fast foods, salty snacks, nuts, potato, fish, poultry, chocolates, juices; 2) high cholesterol and high sweet junk food pattern; high in pickles, sweets and condiments, butter and cream, canned fish, visceral meats and eggs; 3) Mediterranean-like pattern; high in vegetables, olive oil, dates, dairy, dried fruits, fruits, red meats, tea and coffee and 4) Ramadan-style pattern; large consumption of Halim, soups, porridges, legumes and whole grains, soft drinks, Zoolbia and Bamieh. Age was positively and inversely associated with Mediterranean-like (P = 0.003; r = 0.17) and Ramadan style (P = 0.1; r = -0.13) dietary pattern, respectively. Pre-Ramadan physical activity level was associated with a Mediterranean-like dietary pattern (P < 0.0001; r = 0.20). Conclusions: This study showed a Ramadan-specific dietary pattern has unique characteristics, which has not yet been identified as a model of dietary pattern. Also, among identified dietary patterns, Mediterranean-like was the healthiest. PMID:25593728

  1. Ramadan major dietary patterns.

    PubMed

    Shadman, Zhaleh; Poorsoltan, Nooshin; Akhoundan, Mahdieh; Larijani, Bagher; Soleymanzadeh, Mozhdeh; Akhgar Zhand, Camelia; Seyed Rohani, Zahra Alsadat; Khoshniat Nikoo, Mohsen

    2014-09-01

    There has been no data on population based dietary patterns during the Ramadan fasting month. The purpose of this study was to detect Ramadan major dietary patterns among those who fast in Tehran. This cross-sectional study included 600 subjects, aged 18-65 with body mass index (BMI) of 18.5-40, who had decided to fast during Ramadan. Anthropometric measurements, usual physical activity level and educational status were collected two weeks before Ramadan. Information on Ramadan dietary intakes was obtained using a food frequency questionnaire and factor analysis was used to identify major dietary patterns. We identified four major dietary patterns: 1) Western-like pattern; high in fast foods, salty snacks, nuts, potato, fish, poultry, chocolates, juices; 2) high cholesterol and high sweet junk food pattern; high in pickles, sweets and condiments, butter and cream, canned fish, visceral meats and eggs; 3) Mediterranean-like pattern; high in vegetables, olive oil, dates, dairy, dried fruits, fruits, red meats, tea and coffee and 4) Ramadan-style pattern; large consumption of Halim, soups, porridges, legumes and whole grains, soft drinks, Zoolbia and Bamieh. Age was positively and inversely associated with Mediterranean-like (P = 0.003; r = 0.17) and Ramadan style (P = 0.1; r = -0.13) dietary pattern, respectively. Pre-Ramadan physical activity level was associated with a Mediterranean-like dietary pattern (P < 0.0001; r = 0.20). This study showed a Ramadan-specific dietary pattern has unique characteristics, which has not yet been identified as a model of dietary pattern. Also, among identified dietary patterns, Mediterranean-like was the healthiest.

  2. A symmetry relating certain processes in 2-and 4-dimensional space-times and the value {alpha}{sub 0} = 1/4{pi} of the bare fine structure constant

    SciTech Connect

    Ritus, V. I.

    2006-04-15

    The symmetry manifests itself in exact relations between the Bogoliubov coefficients for processes induced by an accelerated point mirror in 1 + 1 dimensional space and the current (charge) densities for the processes caused by an accelerated point charge in 3 + 1 dimensional space. The spectra of pairs of Bose (Fermi) massless quanta emitted by the mirror coincide with the spectra of photons (scalar quanta) emitted by the electric (scalar) charge up to the factor e{sup 2}/{Dirac_h}c. The integral relation between the propagator of a pair of oppositely directed massless particles in 1 + 1 dimensional space and the propagator of a single particle in 3 + 1 dimensional space leads to the equality of the vacuum-vacuum amplitudes for the charge and the mirror if the mean number of created particles is small and the charge e = {radical}{Dirac_h}c. Due to the symmetry, the mass shifts of electric and scalar charges (the sources of Bose fields with spin 1 and 0 in 3 + 1 dimensional space) for the trajectories with a subluminal relative velocity {beta}{sub 12} of the ends and the maximum proper acceleration w{sub 0} are expressed in terms of the heat capacity (or energy) spectral densities of Bose and Fermi gases of massless particles with the temperature w{sub 0}/2{pi} in 1 + 1 dimensional space. Thus, the acceleration excites 1-dimensional oscillation in the proper field of a charge, and the energy of oscillation is partly deexcited in the form of real quanta and partly remains in the field. As a result, the mass shift of an accelerated electric charge is nonzero and negative, while that of a scalar charge is zero. The symmetry is extended to the mirror and charge interactions with the fields carrying spacelike momenta and defining the Bogoliubov coefficients {alpha}{sup B,F}. The traces tr{alpha}{sup B,F}, which describe the vector and scalar interactions of the accelerated mirror with a uniformly moving detector, were found in analytic form for two mirror trajectories

  3. Integrating maps requires integrated data

    SciTech Connect

    Weissenbach, J.; Bentolila, S.

    1996-06-01

    The molecular genetics movement has proceeded admirably thanks to new technologies such as polymerase chain reaction (PCR) sequencing. However, the integration of mapping data has not yet been achieved. This article discussing several problem areas and serves as a reminder of the urgency of such concerns.

  4. 802GHz integrated horn antennas imaging array

    NASA Technical Reports Server (NTRS)

    Ali-Ahmad, Walid Y.; Rebeiz, Gabriel M.; Dave, Hemant; Chin, Gordon

    1991-01-01

    Pattern measurements at 802GHz of a single element in 256-element integrated horn imaging array are presented. The integrated-horn antenna consists of a dipole-antenna suspended on a 1-micron dielectric membrane inside a pyramidal cavity etched in silicon. The theoretical far-field patterns, calculated using reciprocity and Floquet-modes representation of the free-space field, agree well with the measured far-field patterns at 802GHz. The associated directivity for a 1.40 lambda horn aperture, calculated from the measured E and H-plane patterns is 12.3dB + or - 0.2dB. This work demonstrates that high-efficiency integrated-horn antennas are easily scalable to terahertz frequencies and could be used for radio-astronomical and plasma-diagnostic applications.

  5. Harnessing vocal patterns for social communication.

    PubMed

    Sweeney, Lora B; Kelley, Darcy B

    2014-10-01

    Work on vocal communication, influenced by a drive to understand the evolution of language, has focused on auditory processing and forebrain control of learned vocalizations. The actual hindbrain neural mechanisms used to create communication signals are understudied, in part because of the difficulty of experimental studies in species that rely on respiration for vocalization. In these experimental systems-including those that embody vocal learning-vocal behaviors have rhythmic qualities. Recent studies using molecular markers and 'fictive' patterns produced by isolated brains are beginning to reveal how hindbrain circuits generate vocal patterns. Insights from central pattern generators for respiration and locomotion are illuminating common neural and developmental mechanisms. Choice of vocal patterns is responsive to socially salient input. Studies of the vertebrate social brain network suggest mechanisms used to integrate socially salient information and produce an appropriate vocal response.

  6. RADIATION INTEGRATOR

    DOEpatents

    Glass, F.M.; Wilson, H.N.

    1959-02-17

    Radiation detecting and measuring systems, particularly a compact, integrating, background monitor, are discussed. One of the principal features of the system is the use of an electrometer tube where the input of the tube is directly connected to an electrode of the radiation detector and a capacitor is coupled to the tube input. When a predetermined quantity of radiation has been integrated, a trigger signal is fed to a recorder and a charge is delivered to the capacitor to render the tube inoperative. The capacitor is then recharged for the next period of operation. With this arrangement there is a substantial reduction in lead lengths and the principal components may be enclosed and hermetically sealed to insure low leakage.

  7. Integrated Optics.

    DTIC Science & Technology

    1974-10-01

    the attractive option of varying the bandgap F.S well as the refractive index. The crystal growth equipment was modified to grow epitaxial layers...loss .or1 us6 in optical integrated circuits. The limited melt slidebar method is most useful for growing double layers of Gan xiAlyAs...limited melt graphite slide bar, and infinite melt. We were able to grow GaAs layers on (GaADAs substrates using the vapor growth method and

  8. Integrated Fluorescence

    NASA Technical Reports Server (NTRS)

    Tuma, Margaret (Inventor); Gruhlke, Russell W. (Inventor)

    1998-01-01

    A detection method is integrated with a filtering method and an enhancement method to create a fluorescence sensor that can be miniaturized. The fluorescence sensor comprises a thin film geometry including a waveguide layer, a metal film layer and sensor layer. The thin film geometry of the fluorescence sensor allows the detection of fluorescent radiation over a narrow wavelength interval. This enables wavelength discrimination and eliminates the detection of unwanted light from unknown or spurious sources.

  9. Pattern randomness aftereffect

    PubMed Central

    Yamada, Yuki; Kawabe, Takahiro; Miyazaki, Makoto

    2013-01-01

    Humans can easily discriminate a randomly spaced from a regularly spaced visual pattern. Here, we demonstrate that observers can adapt to pattern randomness. Following their adaption to prolonged exposure to two-dimensional patterns with varying levels of physical randomness, observers judged the randomness of the pattern. Perceived randomness decreased (increased) following adaptation to high (low) physical randomness (Experiment 1). Adaptation to 22.5°-rotated adaptor stimuli did not cause a randomness aftereffect (Experiment 2), suggesting that positional variation is unlikely to be responsible for the pattern randomness perception. Moreover, the aftereffect was not selective to contrast polarity (Experiment 3) and was not affected by spatial jitter (Experiment 4). Last, the aftereffect was not affected by adaptor configuration (Experiment 5). Our data were consistent with a model assuming filter-rectify-filter processing for orientation inputs. Thus, we infer that neural processing for orientation grouping/segregation underlies the perception of pattern randomness. PMID:24113916

  10. Soil moisture and vegetation patterns in northern California forests

    Treesearch

    James R. Griffin

    1967-01-01

    Twenty-nine soil-vegetation plots were studied in a broad transect across the southern Cascade Range. Variations in soil moisture patterns during the growing season and in soil moisture tension values are discussed. Plot soil moisture values for 40- and 80-cm. depths in August and September are integrated into a soil drought index. Vegetation patterns are described in...

  11. Individual Differences in Consumer Buying Patterns: A Behavioral Economic Analysis

    ERIC Educational Resources Information Center

    Cavalcanti, Paulo R.; Oliveira-Castro, Jorge M.; Foxall, Gordon R.

    2013-01-01

    Although previous studies have identified several regularities in buying behavior, no integrated view of individual differences related to such patterns has been yet proposed. The present research examined individual differences in patterns of buying behavior of fast-moving consumer goods, using panel data with information concerning purchases of…

  12. Individual Differences in Consumer Buying Patterns: A Behavioral Economic Analysis

    ERIC Educational Resources Information Center

    Cavalcanti, Paulo R.; Oliveira-Castro, Jorge M.; Foxall, Gordon R.

    2013-01-01

    Although previous studies have identified several regularities in buying behavior, no integrated view of individual differences related to such patterns has been yet proposed. The present research examined individual differences in patterns of buying behavior of fast-moving consumer goods, using panel data with information concerning purchases of…

  13. Making patterns on graphene.

    PubMed

    Zhou, Yong; Loh, Kian Ping

    2010-08-24

    Graphene-based nanostructures are considered as promising alternatives to silicon-based mesostructures in future electronic nanodevices. The lithographical patterning of graphene, which are essential steps in any form of microelectronic processing, present interesting challenges because of the atomic layer thickness of graphene. Mesoscopic devices based on graphene require high spatial resolution patterning that will induce as little damage as possible. This research news highlights and evaluates recent developments in the nanostructuring and patterning of graphene.

  14. Hierarchical Pattern Classifier

    NASA Technical Reports Server (NTRS)

    Yates, Gigi L.; Eberlein, Susan J.

    1992-01-01

    Hierarchical pattern classifier reduces number of comparisons between input and memory vectors without reducing detail of final classification by dividing classification process into coarse-to-fine hierarchy that comprises first "grouping" step and second classification step. Three-layer neural network reduces computation further by reducing number of vector dimensions in processing. Concept applicable to pattern-classification problems with need to reduce amount of computation necessary to classify, identify, or match patterns to desired degree of resolution.

  15. [The central pattern generators].

    PubMed

    Balaban, P M; Vorontsov, D D; Dyakonova, V E; Dyakonova, T L; Zakharov, I S; Korshunova, T A; Orlov, O Yu; Pavlova, G A; Panchin, Yi V; Sakharov, D A; Falikman, M V

    2013-01-01

    The central pattern generator (CPG) is defined as a set of neurons involved in joint production of patterned motor output. The roundtable discussion on the CPG was a part of the 5th All-Russian Conference on Animal Behavior (Moscow, Nov. 21, 2012). The discussion centred on three core themes: 1) the mechanisms of the organization and reconfiguration of pattern generating neuronal ensembles, 2) extrapolations that extend the CPG concept beyond the motor systems, and 3) evolutionary and developmental aspects of CPG.

  16. Integrated structural health monitoring.

    SciTech Connect

    Farrar, C. R.

    2001-01-01

    Structural health monitoring is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. The goal of the research effort reported herein is to develop a robust and cost-effective structural health monitoring solution by integrating and extending technologies from various engineering and information technology disciplines. It is the authors opinion that all structural health monitoring systems must be application specific. Therefore, a specific application, monitoring welded moment resisting steel frame connections in structures subjected to seismic excitation, is described along with the motivation for choosing this application. The structural health monitoring solution for this application will integrate structural dynamics, wireless data acquisition, local actuation, micro-electromechanical systems (MEMS) technology, and statistical pattern recognition algorithms. The proposed system is based on an assessment of the deficiencies associated with many current structural health monitoring technologies including past efforts by the authors. This paper provides an example of the integrated approach to structural health monitoring being undertaken at Los Alamos National Laboratory and summarizes progress to date on various aspects of the technology development.

  17. Integrated structural health monitoring

    NASA Astrophysics Data System (ADS)

    Farrar, Charles R.; Sohn, Hoon; Fugate, Michael L.; Czarnecki, Jerry J.

    2001-07-01

    Structural health monitoring is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. The goal of the research effort reported herein is to develop a robust and cost-effective structural health monitoring solution by integrating and extending technologies from various engineering and information technology disciplines. It is the author's opinion that all structural health monitoring systems must be application specific. Therefore, a specific application, monitoring welded moment resisting steel frame connections in structures subjected to seismic excitation, is described along with the motivation for choosing this application. The structural health monitoring solution for this application will integrate structural dynamics, wireless data acquisition, local actuation, micro-electromechanical systems (MEMS) technology, and statistical pattern recognition algorithms. The proposed system is based on an assessment of the deficiencies associated with many current structural health monitoring technologies including past efforts by the authors. This paper provides an example of the integrated approach to structural health monitoring being undertaken at Los Alamos National Laboratory and summarizes progress to date on various aspects of the technology development.

  18. Optical Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Yu, Francis T. S.; Jutamulia, Suganda

    2008-10-01

    Contributors; Preface; 1. Pattern recognition with optics Francis T. S. Yu and Don A. Gregory; 2. Hybrid neural networks for nonlinear pattern recognition Taiwei Lu; 3. Wavelets, optics, and pattern recognition Yao Li and Yunglong Sheng; 4. Applications of the fractional Fourier transform to optical pattern recognition David Mendlovic, Zeev Zalesky and Haldum M. Oxaktas; 5. Optical implementation of mathematical morphology Tien-Hsin Chao; 6. Nonlinear optical correlators with improved discrimination capability for object location and recognition Leonid P. Yaroslavsky; 7. Distortion-invariant quadratic filters Gregory Gheen; 8. Composite filter synthesis as applied to pattern recognition Shizhou Yin and Guowen Lu; 9. Iterative procedures in electro-optical pattern recognition Joseph Shamir; 10. Optoelectronic hybrid system for three-dimensional object pattern recognition Guoguang Mu, Mingzhe Lu and Ying Sun; 11. Applications of photrefractive devices in optical pattern recognition Ziangyang Yang; 12. Optical pattern recognition with microlasers Eung-Gi Paek; 13. Optical properties and applications of bacteriorhodopsin Q. Wang Song and Yu-He Zhang; 14. Liquid-crystal spatial light modulators Aris Tanone and Suganda Jutamulia; 15. Representations of fully complex functions on real-time spatial light modulators Robert W. Cohn and Laurence G. Hassbrook; Index.

  19. Characterizations of natural patterns

    NASA Astrophysics Data System (ADS)

    Gunaratne, Gemunu H.; Hoffman, David K.; Kouri, Donald J.

    1998-05-01

    Labyrinthine patterns are observed in systems as diverse as animal coats, slime mold colonies, fish scales, and cloud streets. However, even under well-controlled conditions, repetition of an experiment gives structures with vastly different details. A theoretical analysis of ``universal'' aspects of patterns requires a quantitative description that gives similar values for distinct configurations. We introduce a function to characterize the ``disorder'' of labyrinthine patterns that is the same for structures generated under identical control parameters. Furthermore, patterns with different visual characteristics are described by distinct functions.

  20. Airborne antenna pattern calculations

    NASA Technical Reports Server (NTRS)

    Knerr, T. J.; Mielke, R. R.

    1981-01-01

    Progress on the development of modeling software, testing software against caclulated data from program VPAP and measured patterns, and calculating roll plane patterns for general aviation aircraft is reported. Major objectives are the continued development of computer software for aircraft modeling and use of this software and program OSUVOL to calculate principal plane and volumetric radiation patterns. The determination of proper placement of antennas on aircraft to meet the requirements of the Microwave Landing System is discussed. An overview of the performed work, and an example of a roll plane model for the Piper PA-31T Cheyenne aircraft and the resulting calculated roll plane radiation pattern are included.

  1. Respiratory Patterns and Strategies during Feeding in Preterm Infants

    ERIC Educational Resources Information Center

    Vice, Frank L.; Gewolb, Ira H.

    2008-01-01

    Because patterns of integration of respiration into rhythmic suck-swallow efforts are highly variable, we examined the vagaries of respiratory efforts as they evolve from the first tentative attempts at integration through more complex rhythmic interactions, with a focus on several strategies in which breathing and suck-swallow are coordinated.…

  2. Respiratory Patterns and Strategies during Feeding in Preterm Infants

    ERIC Educational Resources Information Center

    Vice, Frank L.; Gewolb, Ira H.

    2008-01-01

    Because patterns of integration of respiration into rhythmic suck-swallow efforts are highly variable, we examined the vagaries of respiratory efforts as they evolve from the first tentative attempts at integration through more complex rhythmic interactions, with a focus on several strategies in which breathing and suck-swallow are coordinated.…

  3. Integration: an agenda for developmental research.

    PubMed

    Scholnick, E K

    2001-01-01

    In their magnum opus, Lakoff and Johnson (1999) argued for a philosophy in the flesh. The research presented in the Monograph describes psychology in the flesh. There are ways to measure the changing constellations of interacting systems that influence and transform one another during development and many models to conceptualize the resulting patterns (Flavell, 1972). Development may consist of changing patterns of transactions among internal and external systems (Oyama, 1999). As Bloom and Tinker note, "Development leads to a variety of different abilities.... However, another developmental task not ordinarily considered is the integration of these abilities ... in a seamless pattern of contingency in everyday events." Development consists of more than acquisition; it consists of changing patterns of integration, and changing patterns of use of multifaceted abilities.

  4. Adaptive pattern for autonomous UAV guidance

    NASA Astrophysics Data System (ADS)

    Sung, Chen-Ko; Segor, Florian

    2013-09-01

    The research done at the Fraunhofer IOSB in Karlsruhe within the AMFIS project is focusing on a mobile system to support rescue forces in accidents or disasters. The system consists of a ground control station which has the capability to communicate with a large number of heterogeneous sensors and sensor carriers and provides several open interfaces to allow easy integration of additional sensors into the system. Within this research we focus mainly on UAV such as VTOL (Vertical takeoff and Landing) systems because of their ease of use and their high maneuverability. To increase the positioning capability of the UAV, different onboard processing chains of image exploitation for real time detection of patterns on the ground and the interfacing technology for controlling the UAV from the payload during flight were examined. The earlier proposed static ground pattern was extended by an adaptive component which admits an additional visual communication channel to the aircraft. For this purpose different components were conceived to transfer additive information using changeable patterns on the ground. The adaptive ground pattern and their application suitability had to be tested under external influence. Beside the adaptive ground pattern, the onboard process chains and the adaptations to the demands of changing patterns are introduced in this paper. The tracking of the guiding points, the UAV navigation and the conversion of the guiding point positions from the images to real world co-ordinates in video sequences, as well as use limits and the possibilities of an adaptable pattern are examined.

  5. Parameter learning for alpha integration.

    PubMed

    Choi, Heeyoul; Choi, Seungjin; Choe, Yoonsuck

    2013-06-01

    In pattern recognition, data integration is an important issue, and when properly done, it can lead to improved performance. Also, data integration can be used to help model and understand multimodal processing in the brain. Amari proposed α-integration as a principled way of blending multiple positive measures (e.g., stochastic models in the form of probability distributions), enabling an optimal integration in the sense of minimizing the α-divergence. It also encompasses existing integration methods as its special case, for example, a weighted average and an exponential mixture. The parameter α determines integration characteristics, and the weight vector w assigns the degree of importance to each measure. In most work, however, α and w are given in advance rather than learned. In this letter, we present a parameter learning algorithm for learning α and ω from data when multiple integrated target values are available. Numerical experiments on synthetic as well as real-world data demonstrate the effectiveness of the proposed method.

  6. Pattern collapse mitigation strategies for EUV lithography

    NASA Astrophysics Data System (ADS)

    Goldfarb, Dario L.; Bruce, Robert L.; Bucchignano, James J.; Klaus, David P.; Guillorn, Michael A.; Wu, Chunghsi J.

    2012-03-01

    In this study, a comprehensive approach towards assessing pattern collapse challenges and solutions for Extreme Ultraviolet Lithography (EUV) resists beyond the 14nm node is undertaken. The fundamental forces that drive pattern deformation are reassessed in order to propose a generalized design criterion for EUV photoresists and aqueous surfactanated rinses. Furthermore, ultimate pattern collapse solutions such as solvent drying utilizing pressurized fluids (supercritical CO2) are exemplified for sub-60nm pitch EUV patterning. In parallel, alternative EUV integration schemes that use a metal-based hardmask (MHM) are studied using a specifically tailored self-assembled monolayer (SAM) to prevent delamination-driven pattern collapse due to resist-hardmask interfacial adhesion failure. Finally, the marginal image transfer of 40nm pitched L/S of ultrathin EUV resist into a SiARC-underlayer stack appears to be gated by the EUV resist resolution limit and the reduced film thickness budget. An alternative method for achieving improved postetch line width roughness (LWR) with an ultrathin MHM-based integration scheme is herein demonstrated.

  7. Female-pattern baldness (image)

    MedlinePlus

    Female-pattern baldness is a pattern of hair loss (alopecia) caused by hormones, aging and genetics. Unlike male-pattern baldness, female-pattern baldness is an over-all thinning which maintains the normal ...

  8. Engaging with Islamic Patterns

    ERIC Educational Resources Information Center

    Sugarman, Ian

    2012-01-01

    Islamic patterns were a regular feature in mathematics classrooms, and probably still feature in many wall displays. However, as part of the learning process, these ancient designs appear to have lost any significant contemporary appeal. Here, the power of software is engaged to bring the construction of Islamic type patterns up to date. Forget…

  9. Patterning roadmap: 2017 prospects

    NASA Astrophysics Data System (ADS)

    Neisser, Mark

    2017-06-01

    Road mapping of semiconductor chips has been underway for over 20 years, first with the International Technology Roadmap for Semiconductors (ITRS) roadmap and now with the International Roadmap for Devices and Systems (IRDS) roadmap. The original roadmap was mostly driven bottom up and was developed to ensure that the large numbers of semiconductor producers and suppliers had good information to base their research and development on. The current roadmap is generated more top-down, where the customers of semiconductor chips anticipate what will be needed in the future and the roadmap projects what will be needed to fulfill that demand. The More Moore section of the roadmap projects that advanced logic will drive higher-resolution patterning, rather than memory chips. Potential solutions for patterning future logic nodes can be derived as extensions of `next-generation' patterning technologies currently under development. Advanced patterning has made great progress, and two `next-generation' patterning technologies, EUV and nanoimprint lithography, have potential to be in production as early as 2018. The potential adoption of two different next-generation patterning technologies suggests that patterning technology is becoming more specialized. This is good for the industry in that it lowers overall costs, but may lead to slower progress in extending any one patterning technology in the future.

  10. Biologic Patterns of Disability.

    ERIC Educational Resources Information Center

    Granger, Carl V.; Linn, Richard T.

    2000-01-01

    Describes the use of Rasch analysis to elucidate biological patterns of disability present in the functional ability of persons undergoing medical rehabilitation. Uses two measures, one for inpatients and one for outpatients, to illustrate the approach and provides examples of some biological patterns of disability associated with specific types…

  11. Is It a Pattern?

    ERIC Educational Resources Information Center

    McGarvey, Lynn M.

    2013-01-01

    This article describes how in early mathematics learning, young children are often asked to recognize and describe visual patterns in their environment--perhaps on their clothing, a toy, or the carpet; around a picture frame; or in the playground equipment. Exploring patterns in the early years is seen as an important introduction to algebraic…

  12. Patterned Personality Portraits

    ERIC Educational Resources Information Center

    Surrena, Michelle Flandera

    2008-01-01

    In this article, the author describes a self-portrait project she developed for her students. The project emphasizes personality and pattern as the main objectives through a series of steps that include drawing exercises, observation skills, stream-of-color, intense patterning and texturizing, and colored pencil techniques. By drawing down the…

  13. Airborne antenna pattern calculations

    NASA Technical Reports Server (NTRS)

    Bagherian, A. B.; Mielke, R. R.

    1983-01-01

    Use of calculation program START and modeling program P 3D to produce radiation patterns of antennas mounted on a space station is discussed. Basic components of two space stations in the early design stage are simulated and radiation patterns for antennas mounted on the modules are presented.

  14. Choreographing Patterns and Functions

    ERIC Educational Resources Information Center

    Hawes, Zachary; Moss, Joan; Finch, Heather; Katz, Jacques

    2012-01-01

    In this article, the authors begin with a description of an algebraic dance--the translation of composite linear growing patterns into choreographed movement--which was the last component of a research-based instructional unit that focused on fostering an understanding of linear functional rules through geometric growing patterns and…

  15. Is It a Pattern?

    ERIC Educational Resources Information Center

    McGarvey, Lynn M.

    2013-01-01

    This article describes how in early mathematics learning, young children are often asked to recognize and describe visual patterns in their environment--perhaps on their clothing, a toy, or the carpet; around a picture frame; or in the playground equipment. Exploring patterns in the early years is seen as an important introduction to algebraic…

  16. Interferometers without fringe patterns

    NASA Astrophysics Data System (ADS)

    Garcia-Marquez, Jorge L.; Malacara-Hernandez, Daniel; Malacara-Doblado, Daniel

    1995-08-01

    There are some optical arrangements closely resembling interferometric configurations. These, however, do not produce fringe patterns. An important characteristic of this device is that they do not have two different outputs with complementary patterns, but only one. Two of these configurations are described.

  17. Engaging with Islamic Patterns

    ERIC Educational Resources Information Center

    Sugarman, Ian

    2012-01-01

    Islamic patterns were a regular feature in mathematics classrooms, and probably still feature in many wall displays. However, as part of the learning process, these ancient designs appear to have lost any significant contemporary appeal. Here, the power of software is engaged to bring the construction of Islamic type patterns up to date. Forget…

  18. Patterns of Heart Attacks

    DTIC Science & Technology

    2010-06-01

    36 5.1 Pattern of gradually increasing occurrence of COPD .............................................. 37 5.2 Pattern of...deaths [1]. According to the Heart Disease and Stroke Statistics - 2010 Update from the American Heart Association, the estimated annual incidence of MI...7]. The study combined the insurance claims from the Medicare and the Manitoba Health Services Commission claims database with hospitalization

  19. How Neighborhood Poverty Structures Types and Levels of Social Integration.

    PubMed

    Marcus, Andrea Fleisch; Echeverria, Sandra E; Holland, Bart K; Abraido-Lanza, Ana F; Passannante, Marian R

    2015-09-01

    Social integration is fundamental to health and well-being. However, few studies have explored how neighborhood contexts pattern types and levels of social integration that individuals experience. We examined how neighborhood poverty structures two dimensions of social integration: integration with neighbors and social integration more generally. Using data from the United States Third National Health and Nutrition Examination Survey, we linked study participants to percent poverty in their neighborhood of residence (N = 16,040). Social integration was assessed using a modified Social Network Index and neighborhood integration based on yearly visits with neighbors. We fit multivariate logistic regression models that accounted for the complex survey design. Living in high poverty neighborhoods was associated with lower social integration but higher visits with neighbors. Neighborhood poverty distinctly patterns social integration, demonstrating that contexts shape the extent and quality of social relationships.

  20. Patterns in shrinking gels

    NASA Astrophysics Data System (ADS)

    Matsuo, Eriko Sato; Tanaka, Toyoichi

    1992-08-01

    POLYMER gels can undergo a volume phase transition (either continuous or discontinuous) when an external condition, such as temperature or solvent composition, is altered1-3. During this transition, the volume may change by a factor of several thousand, and various patterns develop in the gel. The patterns arising from swelling and shrinking differ in both their appearance and their physical mechanisms. The mechanism for the formation and evolution of patterns on swelling gels has been established as being due to a single kind of mechanical instability4-7 in contrast, the shrinking patterns seem to be sensitive to both the initial and final states of the transition. Here we classify the various shrinking patterns in the form of a phase diagram, and explain the poly-morphism in terms of macroscopic phase separation.

  1. Patterning of cells through patterning of biology.

    PubMed

    Kala, A; Jain, P K; Friedman, S H

    2014-07-01

    For the first time, cells have been patterned on surfaces through the spatial manipulation of native gene expression. By manipulating the inherent biology of the cell, as opposed to the chemical nature of the surfaces they are attached to, we have created a potentially more flexible way of creating patterns of cells that does not depend on the substrate. This was accomplished by bringing an siRNA that targets the expression of pten under the control of light, by modifying it with photocleavable groups. This pten-targeting siRNA has been previously demonstrated to induce dissociation of cells from surfaces. We modified this siRNA with dimethoxy nitro phenyl ethyl photocleavable groups (DMNPE) to allow the activity of the siRNA, and hence pten knockdown, to be toggled with light. Using this approach we demonstrated light dependent cell dissociation only with a DMNPE modified siRNA that targets pten and not with control siRNAs. In addition we demonstrated the ability to make simple patterns of cells through the application of masks during irradiation.

  2. Nurse attendee purchasing patterns.

    PubMed

    Weiss, M D; Savik, K; Kjervik, D K

    1993-01-01

    Retention of nursing professionals is crucial in responding to the increasing demand for and complexity of nursing care. Augmenting the decision-making role of nurses is one important retention-related strategy. Purchasing patterns reflect one aspect of nurses' decision-making role. National meetings provide nurses with an opportunity to investigate educational and employment options, as well as to preview technological advances in patient care products and supplies. Yet, the purchasing patterns of nurses related to the marketing of patient care supplies, or educational material at national meetings have rarely been acknowledged or researched. This study investigated the purchasing patterns of nurse attendees as revealed at a national meeting and how attendance influenced purchasing input following the meeting. The study addressed differences in purchasing patterns between specific groups of nurse attendees, as well as the relationship between meeting attendance motivators and purchasing patterns. A descriptive methodology utilizing participant observation at four national nursing meetings and mail survey in four phases was used to determine if there were: (1) identifiable purchasing patterns for nurses attending specific nursing-organization sponsored national meetings, (2) differences in purchasing patterns between nurse attendees from these meetings, (3) differences in self-reported post-meeting purchase input, and (4) relationships between meeting attendance motivators and purchasing patterns. The findings demonstrate that nurse attendee purchasing patterns can be identified and do vary among nursing groups. Nurse attendees at specialty meetings were more likely to act as specifiers, have a more dominant role in purchasing and were more likely to influence product purchases than were nurse attendees from generalist meetings. Self-reports of post-meeting purchasing input demonstrated that nurse attendees utilized information gained at national meetings in

  3. ACCELERATION INTEGRATOR

    DOEpatents

    Pope, K.E.

    1958-01-01

    This patent relates to an improved acceleration integrator and more particularly to apparatus of this nature which is gyrostabilized. The device may be used to sense the attainment by an airborne vehicle of a predetermined velocitv or distance along a given vector path. In its broad aspects, the acceleration integrator utilizes a magnetized element rotatable driven by a synchronous motor and having a cylin drical flux gap and a restrained eddy- current drag cap deposed to move into the gap. The angular velocity imparted to the rotatable cap shaft is transmitted in a positive manner to the magnetized element through a servo feedback loop. The resultant angular velocity of tae cap is proportional to the acceleration of the housing in this manner and means may be used to measure the velocity and operate switches at a pre-set magnitude. To make the above-described dcvice sensitive to acceleration in only one direction the magnetized element forms the spinning inertia element of a free gyroscope, and the outer housing functions as a gimbal of a gyroscope.

  4. Adaptive radiations, ecological specialization, and the evolutionary integration of complex morphological structures.

    PubMed

    Monteiro, Leandro R; Nogueira, Marcelo R

    2010-03-01

    The evolutionary integration of complex morphological structures is a macroevolutionary pattern in which morphogenetic components evolve in a coordinated fashion, which can result from the interplay among processes of developmental, genetic integration, and different types of selection. We tested hypotheses of ecological versus developmental factors underlying patterns of within-species and evolutionary integration in the mandible of phyllostomid bats, during the most impressive ecological and morphological radiation among mammals. Shape variation of mandibular morphogenetic components was associated with diet, and the transition of integration patterns from developmental to within-species to evolutionary was examined. Within-species (as a proxy to genetic) integration in different lineages resembled developmental integration regardless of diet specialization, however, evolutionary integration patterns reflected selection in different mandibular components. For dietary specializations requiring extensive functional changes in mastication patterns or biting, such as frugivores and sanguivores, the evolutionary integration pattern was not associated with expected within-species or developmental integration. On the other hand, specializations with lower mastication demands or without major functional reorganization (such as nectarivores and carnivores), presented evolutionary integration patterns similar to the expected developmental pattern. These results show that evolutionary integration patterns are largely a result of independent selection on specific components regardless of developmental modules.

  5. Pattern Formation in Hydrozoa

    NASA Astrophysics Data System (ADS)

    Berking, Stefan

    The fresh water polyp Hydra is famous for its ability to regenerate missing structures. Even aggregates of single cells transform eventually into normally shaped animals. This indicates a communication within the tissue and within the aggregates which determines the spatial pattern of gene expression. Such pattern-forming systems are thought to play a decisive role in the control of self-organization during embryogenesis. Marine and fresh water hydrozoa appear to allow an access to such a system. Although the molecular components are still mostly unknown, the regulatory properties of the pattern-forming system are increasingly well understood, and this may help eventually to identify the components involved.

  6. Parallel Algorithms and Patterns

    SciTech Connect

    Robey, Robert W.

    2016-06-16