Science.gov

Sample records for integrated 4-dimensional patterning

  1. Fringe patterns in integrated photoelasticity.

    PubMed

    Ainola, Leo; Aben, Hillar

    2009-07-01

    In integrated photoelasticity the measurement data may be strongly influenced by the rotation of the principal stress axes. By pointwise measurements, usually the characteristic directions and optical retardation are determined and on their basis conclusions about the stress distribution along the light beam are made. However, often the integrated fringe pattern, obtained in a circular polariscope, can be recorded. This fringe pattern is determined by the integrals of the principal stresses as well as by the rotation of the principal stress directions. We consider the effect of rotation of the principal stress axes in the general form. It is shown that the rotation diminishes the distance between interference fringes and the contrast of the fringe pattern is also diminished. PMID:19568308

  2. Pattern-integrated interference lithography instrumentation

    NASA Astrophysics Data System (ADS)

    Burrow, G. M.; Leibovici, M. C. R.; Kummer, J. W.; Gaylord, T. K.

    2012-06-01

    Multi-beam interference (MBI) provides the ability to form a wide range of sub-micron periodic optical-intensity distributions with applications to a variety of areas, including photonic crystals (PCs), nanoelectronics, biomedical structures, optical trapping, metamaterials, and numerous subwavelength structures. Recently, pattern-integrated interference lithography (PIIL) was presented as a new lithographic method that integrates superposed pattern imaging with interference lithography in a single-exposure step. In the present work, the basic design and systematic implementation of a pattern-integrated interference exposure system (PIIES) is presented to realize PIIL by incorporating a projection imaging capability in a novel three-beam interference configuration. A fundamental optimization methodology is presented to model the system and predict MBI-patterning performance. To demonstrate the PIIL method, a prototype PIIES experimental configuration is presented, including detailed alignment techniques and experimental procedures. Examples of well-defined PC structures, fabricated with a PIIES prototype, are presented to demonstrate the potential of PIIL for fabricating dense integrated optical circuits, as well as numerous other subwavelength structures.

  3. 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

  4. Investigation on navigation patterns of inertial/celestial integrated systems

    NASA Astrophysics Data System (ADS)

    Luo, Dacheng; Liu, Yan; Liu, Zhiguo; Jiao, Wei; Wang, Qiuyan

    2014-11-01

    It is known that Strapdown Inertial Navigation System (SINS), Global Navigation Satellite System (GNSS) and Celestial Navigation System (CNS) can complement each other's advantages. The SINS/CNS integrated system, which has the characteristics of strong autonomy, high accuracy and good anti-jamming, is widely used in military and civilian applications. Similar to SINS/GNSS integrated system, the SINS/CNS integrated system can also be divided into three kinds according to the difference of integrating depth, i.e., loosely coupled pattern, tightly coupled pattern and deeply coupled pattern. In this paper, the principle and characteristics of each pattern of SINS/CNS system are analyzed. Based on the comparison of these patterns, a novel deeply coupled SINS/CNS integrated navigation scheme is proposed. The innovation of this scheme is that a new star pattern matching method aided by SINS information is put forward. Thus the complementary features of these two subsystems are reflected.

  5. Gain calibration of a horn antenna using pattern integration

    NASA Technical Reports Server (NTRS)

    Ludwig, A. C.; Hardy, J.; Norman, R.

    1972-01-01

    Gain measurement of a horn antenna using three different techniques is discussed. The methods include a two-antenna insertion loss measurement, a pattern integration method, and a near-field measurement method. The application of the pattern integration method is considered, as well as the evaluation of the near-field gain correction factors for the horn, which are determined by a method based directly on measured data. This method involves a spherical wave expansion of the experimental radiation pattern of the specific antenna being tested, rather than evaluation of an assumed analytical model. The spherical wave expansion is also compared to experimental near-field pattern data.

  6. 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.

  7. Progress in multidisciplinary sensing of the 4-dimensional ocean

    NASA Astrophysics Data System (ADS)

    Dickey, Tommy

    2009-05-01

    Many luminaries of oceanography have articulated the problem of adequately sampling a multiplicity of interdisciplinary ocean processes. Progress has accelerated within the past two decades as societal and naval interests in monitoring and predicting the state of the ocean environment has heightened. Oceanographers are capitalizing on a host of new platform and sensing technologies. Some recent programs contributing to improved 4-dimensional open and coastal ocean multi-disciplinary observations are used to highlight the development of new integrated optical, chemical, and physical measurement systems that can be deployed from stationary and mobile platforms to telemeter data in near real-time or real-time. For example, the NOPP O-SCOPE and MOSEAN projects have developed and tested several optical and chemical sensors in deep waters off Bermuda and Hawaii, at OWS 'P' in the North Pacific Ocean, and in coastal waters off Santa Barbara and Monterey, California. Most of the testing for these projects has been conducted using moorings; however, NOPP instrumentation is also being used on mobile platforms including AUVs, profiling floats, and gliders. Progress in adequately sampling the temporal and spatial variability of selected ocean 'sampling volumes' using multi-platform, multi-disciplinary sampling is described using examples from selected recent programs.

  8. 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.

  9. A New Concept of Vertically Integrated Pattern Recognition Associative Memory

    NASA Astrophysics Data System (ADS)

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

    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&D proposal [1] 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&D project will be reported in the future. Here we will only focus on the concept of this new approach.

  10. Photomask design method for pattern-integrated interference lithography

    NASA Astrophysics Data System (ADS)

    Leibovici, Matthieu C. R.; Gaylord, Thomas K.

    2016-01-01

    Pattern-integrated interference lithography (PIIL) combines multibeam interference lithography and projection lithography simultaneously to produce two-dimensional (2-D) and three-dimensional (3-D) periodic-lattice-based microstructures in a rapid, single-exposure step. Using a comprehensive PIIL vector model and realistic photolithographic conditions, PIIL exposures for a representative photonic-crystal (PhC) 90 deg bend waveguide are simulated in the volume of the photoresist film. The etched structures in the underlying substrate are estimated as well. Due to the imperfect integration of the photomask within the interference pattern, the interference pattern is locally distorted, thereby impacting the PhC periodic lattice and potentially the device performance. To mitigate these distortions, a photomask optimization method for PIIL is presented in this work. With an improved photomask, pillar-area and pillar-displacement errors in the vicinity of the waveguide are reduced by factors of 3.3 and 2.7, respectively. Furthermore, calculated transmission spectra show that the performance of the PIIL-produced PhC device is as good as that of its idealized equivalent.

  11. 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

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

    PubMed

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

    2010-05-01

    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

  13. Dynamic time warp pattern matching using an integrated multiprocessing array

    SciTech Connect

    Weste, N.; Burr, D.J.; Ackland, B.D.

    1983-08-01

    Dynamic time warping is a well-established technique for time alignment and comparison of speech and image patterns. This paper describes the architecture, algorithms and design of a CMOS integrated processing array used for computing the dynamic time warp algorithm. Emphasis is placed on speech recognition applications because of the real-time constraints imposed by isolated and continuous speech recognition. High throughput is obtained through the use of extensive pipelining, parallel computation and simultaneous matching of multiple patterns. A realistic speech recognition application based on 40 nine-component linear predictor coefficient (LPC) vectors per word permits 20000 isolated word comparisons per second or, equivalently, real time recognition of a 20000 word vocabulary. The paper also illustrates a trend in IC design in which the architecture of the system leads to an embodiment which far outperforms solutions based on current design methodologies. 27 references.

  14. 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.

  15. 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.

  16. Spontaneous symmetry breaking in 4-dimensional heterotic string

    SciTech Connect

    Maharana, J.

    1989-07-01

    The evolution of a 4-dimensional heterotic string is considered in the background of its massless excitations such as graviton, antisymmetric tensor, gauge fields and scalar bosons. The compactified bosonic coordinates are fermionized. The world-sheet supersymmetry requirement enforces Thirring-like four fermion coupling to the background scalar fields. The non-abelian gauge symmetry is exhibited through the Ward identities of the S-matrix elements. The spontaneous symmetry breaking mechanism is exhibited through the broken Ward identities. An effective 4-dimensional action is constructed and the consequence of spontaneous symmetry breaking is envisaged for the effective action. 19 refs.

  17. 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. PMID:24867543

  18. Brane compactifications and 4-dimensional geometry in the IKKT model

    NASA Astrophysics Data System (ADS)

    Polychronakos, Alexios P.; Steinacker, Harold; Zahn, Jochen

    2013-10-01

    We study in detail certain brane solutions with compact extra dimensions M4×K in the IKKT matrix model, with K being a two-dimensional rotating torus embedded in R6. We focus on the compactification moduli and the fluctuations of K⊂R6 and their physical significance. Mediated by the Poisson tensor, they contribute to the effective 4-dimensional metric on the brane, and thereby become gravitational degrees of freedom. We show that the zero modes corresponding to the global symmetries of the model lead to Ricci-flat 4-dimensional metric perturbations, wherever the energy-momentum tensor vanishes. Their coupling to the energy-momentum tensor depends on the extrinsic curvature of the brane.

  19. 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.

  20. 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.

  1. 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

  2. Longitudinal Patterns of Religious Perspective and Civic Integration

    ERIC Educational Resources Information Center

    Kerestes, Michael; Youniss, James; Metz, Edward

    2004-01-01

    This study examined the association between adolescents' religious development, social integration, and risk-taking behaviors. Religious development was tracked along 4 trajectories from sophomore to senior year in high school: low religiosity (sophomore)-low religiosity (senior), low-high, high-low, and high-high. Civic integration was measured…

  3. 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)

  4. 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.

  5. RESOLUTION OF COMPLEX INTEGRATION PATTERNS TO OBTAIN SINGLE COPY TRANSGENES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The present invention provides methods for producing a transgenic cell having a stably integrated, single copy of an exogenous polynucleotide sequence. The method, which resolves repeated insertions of the introduced polynucleotide sequence into a single copy, involves introducing into a genetic loc...

  6. 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.

  7. 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.

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

    PubMed

    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

  9. 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. PMID:27250997

  10. 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.

  11. 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.

  12. 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. PMID:25403786

  13. 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.

  14. Analyzing unsaturated flow patterns in fractured rock using an integrated modeling approach

    NASA Astrophysics Data System (ADS)

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

    2007-05-01

    Characterizing percolation patterns in unsaturated fractured rock has posed a greater challenge to modeling investigations than comparable saturated zone studies due to the heterogeneous nature of unsaturated media and the great number of variables impacting unsaturated flow. An integrated modeling methodology has been developed for quantitatively characterizing percolation patterns in the unsaturated zone of Yucca Mountain, Nevada (USA), a proposed underground repository site for storing high-level radioactive waste. The approach integrates moisture, pneumatic, thermal, and isotopic geochemical field data into a comprehensive three-dimensional numerical model for 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 through analyzing flow patterns in the unsaturated zone. In particular, this model provides 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.

  15. 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.

  16. 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.

  17. Three-Dimensional Object Reconstruction and Recognition Using Computational Integral Imaging and Statistical Pattern Analysis

    NASA Astrophysics Data System (ADS)

    Yeom, Seokwon; Lee, Dongsu; Son, Jung-Young; Kim, Shin-Hwan

    2009-09-01

    In this paper, we discuss computational reconstruction and statistical pattern classification using integral imaging. Three-dimensional object information is numerically reconstructed at arbitrary depth-levels by averaging the corresponding pixels. The longitudinal distance and object boundary are estimated where the standard deviation of the intensity is minimized. Fisher linear discriminant analysis combined with principal component analysis is adopted for the classification of out-of-plane rotated objects. The Fisher linear discriminant analysis maximizes the class-discrimination while the principal component analysis minimizes the error between the original and the restored images. The presented method provides promising results for the distortion-tolerant pattern classification.

  18. Spike Train Dynamics Underlying Pattern Formation in Integrate-and-Fire Oscillator Networks

    NASA Astrophysics Data System (ADS)

    Bressloff, P. C.; Coombes, S.

    1998-09-01

    A dynamical mechanism underlying pattern formation in a spatially extended network of integrate-and-fire oscillators with synaptic interactions is identified. It is shown how in the strong coupling regime the network undergoes a discrete Turing-Hopf bifurcation of the firing times from a synchronous state to a state with periodic or quasiperiodic variations of the interspike intervals on closed orbits. The separation of these orbits in phase space results in a spatially periodic pattern of mean firing rate across the network that is modulated by deterministic fluctuations of the instantaneous firing rate.

  19. Neurobiology of vocal communication: mechanisms for sensorimotor integration and vocal patterning

    PubMed Central

    Kelley, Darcy B.; Bass, Andrew H.

    2010-01-01

    Summary This review will focus on recent developments in the sensorimotor integration of vocal communication. Two broad themes are emphasized: the evolution of vocal production and perception, and the role of social context. Advances include: a proposal for the emergence of vocal patterning during vertebrate evolution, the role of sensory mechanisms such as categorical perception in decoding communication signals, contributions of sensorimotor integration phenomena including mirror neurons and vocal learning, and mechanisms of hormone-dependent plasticity in both auditory and vocal systems. Transcriptional networks activated in humans but not in chimps by the FoxP2 gene suggest molecular mechanisms underlying vocal gestures and the emergence of human language. PMID:20829032

  20. 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. PMID:24791467

  1. Recovery of amplitude integrated electroencephalographic background patterns within 24 hours of perinatal asphyxia

    PubMed Central

    van Rooij, L G M; Toet, M; Osredkar, D; van Huffelen, A C; Groenendaal, F; de Vries, L S

    2005-01-01

    Objective: To assess the time course of recovery of severely abnormal initial amplitude integrated electroencephalographic (aEEG) patterns (flat trace (FT), continuous low voltage (CLV), or burst suppression (BS)) in full term asphyxiated neonates, in relation to other neurophysiological and neuroimaging findings and neurodevelopmental outcome. Methods: A total of 190 aEEGs of full term infants were reviewed. The neonates were admitted within 6 hours of birth to the neonatal intensive care unit because of perinatal asphyxia, and aEEG recording was started immediately. In all, 160 infants were included; 65 of these had an initial FT or CLV pattern and 25 an initial BS pattern. Neurodevelopmental outcome was assessed using a full neurological examination and the Griffiths' mental developmental scale. Results: In the FT/CLV group, the background pattern recovered to continuous normal voltage within 24 hours in six of the 65 infants (9%). All six infants survived the neonatal period; one had a severe disability, and five were normal at follow up. In the BS group, the background pattern improved to normal voltage in 12 of the 25 infants (48%) within 24 hours. Of these infants, one died, five survived with moderate to severe disability, two with mild disability, and four were normal. The patients who did not recover within 24 hours either died in the neonatal period or survived with a severe disability. Conclusion: In this study there was a small group of infants who presented with a severely abnormal aEEG background pattern within six hours of birth, but who achieved recovery to a continuous normal background pattern within the first 24 hours. Sixty one percent of these infants survived without, or with a mild, disability. PMID:15846017

  2. Toward sub-20nm pitch Fin patterning and integration with DSA

    NASA Astrophysics Data System (ADS)

    Sayan, Safak; Marzook, Taisir; Chan, BT; Vandenbroeck, Nadia; Singh, Arjun; Laidler, David; Sanchez, Efrain A.; Leray, Philippe; R. Delgadillo, Paulina; Gronheid, Roel; Vandenberghe, Geert; Clark, William; Juncker, Aurelie

    2016-03-01

    Directed Self Assembly (DSA) has gained increased momentum in recent years as a cost-effective means for extending lithography to sub-30nm pitch, primarily presenting itself as an alternative to mainstream 193i pitch division approaches such as SADP and SAQP. Towards these goals, IMEC has excelled at understanding and implementing directed self-assembly based on PS-b-PMMA block co-polymers (BCPs) using LiNe flow [1]. These efforts increase the understanding of how block copolymers might be implemented as part of HVM compatible DSA integration schemes. In recent contributions, we have proposed and successfully demonstrated two state-of-the-art CMOS process flows which employed DSA based on the PS-b-PMMA, LiNe flow at IMEC (pitch = 28 nm) to form FinFET arrays via both a `cut-last' and `cut-first' approach [2-4]. Therein, we described the relevant film stacks (hard mask and STI stacks) to achieve robust patterning and pattern transfer into IMEC's FEOL device film stacks. We also described some of the pattern placement and overlay challenges associated with these two strategies. In this contribution, we will present materials and processes for FinFET patterning and integration towards sub-20 nm pitch technology nodes. This presents a noteworthy challenge for DSA using BCPs as the ultimate resolution for PS-b-PMMA may not achieve such dimensions. The emphasis will continue to be towards patterning approaches, wafer alignment strategies, the effects of DSA processing on wafer alignment and overlay.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. A way to integrate multiple block layers for middle of line contact patterning

    NASA Astrophysics Data System (ADS)

    Kunnen, E.; Demuynck, S.; Brouri, M.; Boemmels, J.; Versluijs, J.; Ryckaert, J.

    2015-03-01

    It is clear today that further scaling towards smaller dimensions and pitches requires a multitude of additional process steps. Within this work we look for solutions to achieve a middle of line 193i based patterning scheme for N7 logic at a contacted poly pitch of 40-45 nm. At these pitches, trenches can still be printed by means of double patterning. However, they need to be blocked at certain positions because of a limited line end control below 90 nm pitch single print. Based on the 193i patterning abilities, the proposed SRAM (Static Random Access Memory) cell requires 5 blocking layers. Integrating 5 blocking layers is a new challenge since down to N10 one blocking layer was usually sufficient. The difficulty with multiple blocking layers is the removal of the masked parts, especially in cases of overlap. As a solution a novel patterning approach is proposed and tried out on relaxed dimensions (patent pending). The proposed solution is expected not to be sensitive to the number of blocking layers used, and tolerates their overlap. The stack is constructed to be compatible with N7 substrates such as SiGe or P:Si. Experimental results of the stack blocking performance on relaxed pitch will be presented and discussed.

  8. Tonic synaptic inhibition modulates neuronal output pattern and spatiotemporal synaptic integration.

    PubMed

    Häusser, M; Clark, B A

    1997-09-01

    Irregular firing patterns are observed in most central neurons in vivo, but their origin is controversial. Here, we show that two types of inhibitory neurons in the cerebellar cortex fire spontaneously and regularly in the absence of synaptic input but generate an irregular firing pattern in the presence of tonic synaptic inhibition. Paired recordings between synaptically connected neurons revealed that single action potentials in inhibitory interneurons cause highly variable delays in action potential firing in their postsynaptic cells. Activity in single and multiple inhibitory interneurons also significantly reduces postsynaptic membrane time constant and input resistance. These findings suggest that the time window for synaptic integration is a dynamic variable modulated by the level of tonic inhibition, and that rate coding and temporal coding strategies may be used in parallel in the same cell type. PMID:9331356

  9. 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

  10. New readout integrated circuit using continuous time fixed pattern noise correction

    NASA Astrophysics Data System (ADS)

    Dupont, Bertrand; Chammings, G.; Rapellin, G.; Mandier, C.; Tchagaspanian, M.; Dupont, Benoit; Peizerat, A.; Yon, J. J.

    2008-04-01

    LETI has been involved in IRFPA development since 1978; the design department (LETI/DCIS) has focused its work on new ROIC architecture since many years. The trend is to integrate advanced functions into the CMOS design to achieve cost efficient sensors production. Thermal imaging market is today more and more demanding of systems with instant ON capability and low power consumption. The purpose of this paper is to present the latest developments of fixed pattern noise continuous time correction. Several architectures are proposed, some are based on hardwired digital processing and some are purely analog. Both are using scene based algorithms. Moreover a new method is proposed for simultaneous correction of pixel offsets and sensitivities. In this scope, a new architecture of readout integrated circuit has been implemented; this architecture is developed with 0.18μm CMOS technology. The specification and the application of the ROIC are discussed in details.

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

    PubMed Central

    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. PMID:26390436

  12. 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.

  13. 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

    2011-01-01

    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

  14. 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.

  15. 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…

  16. 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

  17. 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.

  18. 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

  19. 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. PMID:26519373

  20. Admission policy, patterns of migration and integration: the German and French case compared.

    PubMed

    Seifert, W

    1997-10-01

    Germany and France differ in their concepts of citizenship and nationality. Those differences have led to different patterns of immigration to the two countries and to different policies on the integration of migrants. The French notion of equality has led to the development and implementation of a migration policy designed to assimilate migrants to mainstream French culture. Citizenship is therefore granted more on the principle of jus soli, with differences in status groups not held to exist. However, Germany's interpretation of citizenship has been based upon descent, and immigration policy has focused upon groups which have German ethnic backgrounds. During the period of economic demand for foreign labor, Germany did not plan to have permanent immigration and considered the employment of foreign labor to be a temporary measure. Yet even when the arrival of immigrants with no German ethnic background is accepted, there are still major differences in the integration of different ethnic groups. While ethnic Germans are privileged because they have the right to citizenship upon arrival to German, and are also entitled to various integration measures, other immigrant groups may often not be granted citizenship, even in the case of second or third generations. PMID:12179823

  1. A pilot point guided pattern matching approach to integrate dynamic data into geological modeling

    NASA Astrophysics Data System (ADS)

    Li, Liangping; Srinivasan, Sanjay; Zhou, Haiyan; Gómez-Hernández, J. J.

    2013-12-01

    Methods based on multiple-point statistics (MPS) have been routinely used to characterize complex geological formations in the last decade. These methods use the available static data (for example, measured conductivities) for conditioning. Integrating dynamic data (for example, measured transient piezometric head data) into the same framework is challenging because of the complex non-linear relationship between the dynamic response and geology. The Ensemble PATtern (EnPAT) search method was recently developed as a promising technique to handle this problem. In this approach, a pattern is postulated to be composed of both parameter and state variables, and then, parameter values are sequentially (point-wise) simulated by directly sampling the matched pattern from an ensemble of training images of both geologic parameters and state variables. As a consequence, the updated ensemble of realizations of the geological parameters preserve curvilinear structures (i.e., non-multiGaussanity) as well as the complex relationship between static and dynamic data. Moreover, the uncertainty of flow and transport predictions can be assessed using the updated ensemble of geological models. In this work, we further modify the EnPAT method by introducing the pilot-point concept into the algorithm. More specifically, the parameter values at a set of randomly selected pilot point locations are simulated by the pattern searching procedure, and then a faster MPS method is used to complete the simulation by conditioning to the previously simulated pilot point values. This pilot point guided MPS implementation results in lower computational cost and more accurate inference of the parameter field. In addition, in some situations where there is sparsity of measured geologic static data, the EnPAT algorithm is extended to work only with the dynamic data. We employed a synthetic example to demonstrate the effectiveness of pilot points in the implementation of EnPAT, and also the capability of

  2. Step and flash imprint process integration techniques for photonic crystal patterning: template replication through wafer patterning irrespective of tone

    NASA Astrophysics Data System (ADS)

    Miller, Mike; Brooks, Cindy; Lentz, David; Doyle, Gary; Resnick, Doug; LaBrake, Dwayne

    2008-02-01

    Photonic crystal structures in for example light emitting diodes (LED) have been demonstrated to improve performance by preferential mode coupling near the surface of the diode.1 Such demonstrations were limited by using direct write e-beam lithography due to long write times, a single tone and only small areas patterned for study. S-FIL technology provides a means to pattern entire wafers in a single imprint step using templates replicated by step and repeat (S&R) imprint2. Large area template replication by S-FIL/R has been described using S&R templates 3. Photonic crystal based LED manufacturers prefer holes in substrates requiring pillar tone templates for S-FIL patterning. Pillar tone templates are not easily derived from the preferred e-beam tone for sub-200 nm template fabrication. Therefore step and repeat and/or whole wafer template replication by the combination of S-FIL and/or S-FIL/R can be used to produce the desired working template tone. These processes further enable the desired tone and wafer die layout for fully patterning wafers to their edge with no missing die or edge fields. The advantages of using S-FIL processes for template and wafer patterning are clear in that there is no tone preference required by the original e-beam generated pattern, which allows the preferred positive tone to be used for e-beam patterning of templates. The present work will describe template replication processes for the fabrication of either pillar or hole tone templates and subsequent wafer pattern processes, through oxide hard mask, producing both pillar and hole tone patterns. In summary process flows exist so that any e-beam written template tone can be used to produce either tone in replicated templates and/or patterned wafers.

  3. Pattern of Social Interactions after Group Integration: A Possibility to Keep Stallions in Group

    PubMed Central

    Niederhäusern, Rudolf Von; 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

  4. 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.

  5. 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

  6. Individual classification of ADHD patients by integrating multiscale neuroimaging markers and advanced pattern recognition techniques.

    PubMed

    Cheng, Wei; Ji, Xiaoxi; Zhang, Jie; Feng, Jianfeng

    2012-01-01

    Accurate classification or prediction of the brain state across individual subject, i.e., healthy, or with brain disorders, is generally a more difficult task than merely finding group differences. The former must be approached with highly informative and sensitive biomarkers as well as effective pattern classification/feature selection approaches. In this paper, we propose a systematic methodology to discriminate attention deficit hyperactivity disorder (ADHD) patients from healthy controls on the individual level. Multiple neuroimaging markers that are proved to be sensitive features are identified, which include multiscale characteristics extracted from blood oxygenation level dependent (BOLD) signals, such as regional homogeneity (ReHo) and amplitude of low-frequency fluctuations. Functional connectivity derived from Pearson, partial, and spatial correlation is also utilized to reflect the abnormal patterns of functional integration, or, dysconnectivity syndromes in the brain. These neuroimaging markers are calculated on either voxel or regional level. Advanced feature selection approach is then designed, including a brain-wise association study (BWAS). Using identified features and proper feature integration, a support vector machine (SVM) classifier can achieve a cross-validated classification accuracy of 76.15% across individuals from a large dataset consisting of 141 healthy controls and 98 ADHD patients, with the sensitivity being 63.27% and the specificity being 85.11%. Our results show that the most discriminative features for classification are primarily associated with the frontal and cerebellar regions. The proposed methodology is expected to improve clinical diagnosis and evaluation of treatment for ADHD patient, and to have wider applications in diagnosis of general neuropsychiatric disorders. PMID:22888314

  7. Associative memory of phase-coded spatiotemporal patterns in leaky Integrate and Fire networks.

    PubMed

    Scarpetta, Silvia; Giacco, Ferdinando

    2013-04-01

    We study the collective dynamics of a Leaky Integrate and Fire network in which precise relative phase relationship of spikes among neurons are stored, as attractors of the dynamics, and selectively replayed at different time scales. Using an STDP-based learning process, we store in the connectivity several phase-coded spike patterns, and we find that, depending on the excitability of the network, different working regimes are possible, with transient or persistent replay activity induced by a brief signal. We introduce an order parameter to evaluate the similarity between stored and recalled phase-coded pattern, and measure the storage capacity. Modulation of spiking thresholds during replay changes the frequency of the collective oscillation or the number of spikes per cycle, keeping preserved the phases relationship. This allows a coding scheme in which phase, rate and frequency are dissociable. Robustness with respect to noise and heterogeneity of neurons parameters is studied, showing that, since dynamics is a retrieval process, neurons preserve stable precise phase relationship among units, keeping a unique frequency of oscillation, even in noisy conditions and with heterogeneity of internal parameters of the units. PMID:23053861

  8. 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

  9. Application of pattern recognition tools for classifying acute coronary syndrome: an integrated medical modeling

    PubMed Central

    2013-01-01

    Objective The classification of Acute Coronary Syndrome (ACS), using artificial intelligence (AI), has recently drawn the attention of the medical researchers. Using this approach, patients with myocardial infarction can be differentiated from those with unstable angina. The present study aims to develop an integrated model, based on the feature selection and classification, for the automatic classification of ACS. Methods A dataset containing medical records of 809 patients suspected to suffer from ACS was used. For each subject, 266 clinical factors were collected. At first, a feature selection was performed based on interviews with 20 cardiologists; thereby 40 seminal features for classifying ACS were selected. Next, a feature selection algorithm was also applied to detect a subset of the features with the best classification accuracy. As a result, the feature numbers considerably reduced to only seven. Lastly, based on the seven selected features, eight various common pattern recognition tools for classification of ACS were used. Results The performance of the aforementioned classifiers was compared based on their accuracy computed from their confusion matrices. Among these methods, the multi-layer perceptron showed the best performance with the 83.2% accuracy. Conclusion The results reveal that an integrated AI-based feature selection and classification approach is an effective method for the early and accurate classification of ACS and ultimately a timely diagnosis and treatment of this disease. PMID:24044669

  10. 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

  11. Inference for Size Demography from Point Pattern Data using Integral Projection Models

    PubMed Central

    Ghosh, Souparno; Gelfand, Alan E.; Clark, James S.

    2013-01-01

    Population dynamics with regard to evolution of traits has typically been studied using matrix projection models (MPMs). Recently, to work with continuous traits, integral projection models (IPMs) have been proposed. Imitating the path with MPMs, IPMs are handled first with a fitting stage, then with a projection stage. Fitting these models has so far been done only with individual-level transition data. These data are used to estimate the demographic functions (survival, growth, fecundity) that comprise the kernel of the IPM specification. Then, the estimated kernel is iterated from an initial trait distribution to project steady state population behavior under this kernel. When trait distributions are observed over time, such an approach does not align projected distributions with these observed temporal benchmarks. The contribution here, focusing on size distributions, is to address this issue. Our concern is that the above approach introduces an inherent mismatch in scales. The redistribution kernel in the IPM proposes a mechanistic description of population level redistribution. A kernel of the same functional form, fitted to data at the individual level, would provide a mechanistic model for individual-level processes. Resulting parameter estimates and the associated estimated kernel are at the wrong scale and do not allow population-level interpretation. Our approach views the observed size distribution at a given time as a point pattern over a bounded interval. We build a three-stage hierarchical model to infer about the dynamic intensities used to explain the observed point patterns. This model is driven by a latent deterministic IPM and we introduce uncertainty by having the operating IPM vary around this deterministic specification. Further uncertainty arises in the realization of the point pattern given the operating IPM. Fitted within a Bayesian framework, such modeling enables full inference about all features of the model. Such dynamic modeling

  12. Podoplanin and CLEC-2 drive cerebrovascular patterning and integrity during development

    PubMed Central

    Lowe, Kate L.; Finney, Brenda A.; Deppermann, Carsten; Hägerling, René; Gazit, Salomé L.; Frampton, Jon; Buckley, Christopher; Camerer, Eric; Nieswandt, Bernhard; Kiefer, Friedemann

    2015-01-01

    Mice with a constitutive or platelet-specific deletion of the C-type-lectin-like receptor (CLEC-2) exhibit hemorrhaging in the brain at mid-gestation. We sought to investigate the basis of this defect, hypothesizing that it is mediated by the loss of CLEC-2 activation by its endogenous ligand, podoplanin, which is expressed on the developing neural tube. To induce deletion of podoplanin at the 2-cell stage, we generated a podoplaninfl/fl mouse crossed to a PGK-Cre mouse. Using 3-dimensional light-sheet microscopy, we observed cerebral vessels were tortuous and aberrantly patterned at embryonic (E) day 10.5 in podoplanin- and CLEC-2-deficient mice, preceding the formation of large hemorrhages throughout the fore-, mid-, and hindbrain by E11.5. Immunofluorescence and electron microscopy revealed defective pericyte recruitment and misconnections between the endothelium of developing blood vessels and surrounding pericytes and neuro-epithelial cells. Nestin-Cre-driven deletion of podoplanin on neural progenitors also caused widespread cerebral hemorrhaging. Hemorrhaging was also seen in the ventricles of embryos deficient in the platelet integrin subunit glycoprotein IIb or in embryos in which platelet α-granule and dense granule secretion is abolished. We propose a novel role for podoplanin on the neuro-epithelium, which interacts with CLEC-2 on platelets, mediating platelet adhesion, aggregation, and secretion to guide the maturation and integrity of the developing vasculature and prevent hemorrhage. PMID:25908104

  13. Podoplanin and CLEC-2 drive cerebrovascular patterning and integrity during development.

    PubMed

    Lowe, Kate L; Finney, Brenda A; Deppermann, Carsten; Hägerling, René; Gazit, Salomé L; Frampton, Jon; Buckley, Christopher; Camerer, Eric; Nieswandt, Bernhard; Kiefer, Friedemann; Watson, Steve P

    2015-06-11

    Mice with a constitutive or platelet-specific deletion of the C-type-lectin-like receptor (CLEC-2) exhibit hemorrhaging in the brain at mid-gestation. We sought to investigate the basis of this defect, hypothesizing that it is mediated by the loss of CLEC-2 activation by its endogenous ligand, podoplanin, which is expressed on the developing neural tube. To induce deletion of podoplanin at the 2-cell stage, we generated a podoplanin(fl/fl) mouse crossed to a PGK-Cre mouse. Using 3-dimensional light-sheet microscopy, we observed cerebral vessels were tortuous and aberrantly patterned at embryonic (E) day 10.5 in podoplanin- and CLEC-2-deficient mice, preceding the formation of large hemorrhages throughout the fore-, mid-, and hindbrain by E11.5. Immunofluorescence and electron microscopy revealed defective pericyte recruitment and misconnections between the endothelium of developing blood vessels and surrounding pericytes and neuro-epithelial cells. Nestin-Cre-driven deletion of podoplanin on neural progenitors also caused widespread cerebral hemorrhaging. Hemorrhaging was also seen in the ventricles of embryos deficient in the platelet integrin subunit glycoprotein IIb or in embryos in which platelet α-granule and dense granule secretion is abolished. We propose a novel role for podoplanin on the neuro-epithelium, which interacts with CLEC-2 on platelets, mediating platelet adhesion, aggregation, and secretion to guide the maturation and integrity of the developing vasculature and prevent hemorrhage. PMID:25908104

  14. Uncharted ground: patterns of professional interaction among complementary/alternative and biomedical practitioners in integrative health care settings.

    PubMed

    Hollenberg, Daniel

    2006-02-01

    The development of "integrative health care" (IHC) settings combining various aspects of Western biomedicine and complementary/alternative medicine (CAM) is a relatively recent phenomenon among biomedical and CAM professions. While IHC is recognised internationally and occurs in many different contexts (e.g. clinic or hospital), patterns of interaction between biomedical and CAM practitioners, and the nature of IHC settings, are largely unknown. This paper presents findings from a research study of two newly established IHC settings in Canada. The main research question was: how are biomedical and CAM practitioners integrating or not integrating with each other at the level of professional interaction in IHC settings? Using a case study design, in-depth interviews were conducted with 13 biomedical and eight CAM practitioners during 2002-2003, and ethnographic observation and document analysis was conducted at each site. Drawing from closure theory of the professions, comparative analysis of the sites revealed that biomedical practitioners enact patterns of exclusionary and demarcationary closure, in addition to the use of "esoteric knowledge", by: (a) dominating patient charting, referrals and diagnostic tests; (b) regulating CAM practitioners to a specific "sphere of competence"; (c) appropriating certain CAM techniques from less powerful CAM professions; and (d) using biomedical language as the primary mode of communication. CAM practitioners, in turn, perform usurpationary closure strategies, by: (a) employing their own "esoteric knowledge" in relation to biomedicine and other CAM professions; (b) appropriating biomedical language and terminology; (c) increasing their professional status by working with biomedicine; and (d) referring among CAM practitioners to increase patient flow. The findings suggest that when attempts are made to integrate biomedicine and CAM, dominant biomedical patterns of professional interaction continue to exist. Despite continued

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  16. 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

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

    PubMed

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

    2011-07-01

    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

  18. Scaling Limits and Critical Behaviour of the 4 -Dimensional n -Component |\\varphi |^4 Spin Model

    NASA Astrophysics Data System (ADS)

    Bauerschmidt, Roland; Brydges, David C.; Slade, Gordon

    2014-08-01

    We consider the n -component |\\varphi |^4 spin model on {mathbb {Z}}^4 , for all n ge 1 , with small coupling constant. We prove that the susceptibility has a logarithmic correction to mean field scaling, with exponent n+2/n+8 for the logarithm. We also analyse the asymptotic behaviour of the pressure as the critical point is approached, and prove that the specific heat has fractional logarithmic scaling for n =1,2,3 ; double logarithmic scaling for n=4 ; and is bounded when n>4 . In addition, for the model defined on the 4 -dimensional discrete torus, we prove that the scaling limit as the critical point is approached is a multiple of a Gaussian free field on the continuum torus, whereas, in the subcritical regime, the scaling limit is Gaussian white noise with intensity given by the susceptibility. The proofs are based on a rigorous renormalisation group method in the spirit of Wilson, developed in a companion series of papers to study the 4-dimensional weakly self-avoiding walk, and adapted here to the |\\varphi |^4 model.

  19. Efficient water collection on integrative bioinspired surfaces with star-shaped wettability patterns.

    PubMed

    Bai, Hao; Wang, Lin; Ju, Jie; Sun, Ruize; Zheng, Yongmei; Jiang, Lei

    2014-08-01

    Inspired by the water-collecting strategies of desert beetles and spider silk, a novel kind of surface with star-shaped wettablity patterns has been developed. By combining both wettability and shape gradients, the as-prepared surface has gained higher efficiency in water collection compared to circle-shaped wettability patterns and uniformly superhydrophilic or superhydrophobic surfaces. PMID:24847736

  20. Integration of Color and Local Derivative Pattern Features for Content-Based Image Indexing and Retrieval

    NASA Astrophysics Data System (ADS)

    Vipparthi, Santosh Kumar; Nagar, Shyam Krishna

    2014-09-01

    This paper presents two new feature descriptors for content based image retrieval (CBIR) application. The proposed two descriptors are named as color local derivative patterns (CLDP) and inter color local derivative pattern (ICLDP). In order to reduce the computational complexity the uniform patterns are applied to both CLDP and ICLDP. Further, uniform CLDP (CLDPu2) and uniform ICLDP (ICLDPu2) are generated respectively. The proposed descriptors are able to exploit individual (R, G and B) spectral channel information and co-relating pair (RG, GB, BR, etc.) of spectral channel information. The retrieval performances of the proposed descriptors (CLDP and ICLDP) are tested by conducting two experiments on Corel-5000 and Corel-10000 benchmark databases. The results after investigation show a significant improvement in terms of precision, average retrieval precision (ARP), recall and average retrieval rate (ARR) as compared to local binary patterns (LBP), local derivative patterns (LDP) and other state-of-the-art techniques for image retrieval.

  1. Integration of Color and Local Derivative Pattern Features for Content-Based Image Indexing and Retrieval

    NASA Astrophysics Data System (ADS)

    Vipparthi, Santosh Kumar; Nagar, Shyam Krishna

    2015-09-01

    This paper presents two new feature descriptors for content based image retrieval (CBIR) application. The proposed two descriptors are named as color local derivative patterns (CLDP) and inter color local derivative pattern (ICLDP). In order to reduce the computational complexity the uniform patterns are applied to both CLDP and ICLDP. Further, uniform CLDP (CLDPu2) and uniform ICLDP (ICLDPu2) are generated respectively. The proposed descriptors are able to exploit individual (R, G and B) spectral channel information and co-relating pair (RG, GB, BR, etc.) of spectral channel information. The retrieval performances of the proposed descriptors (CLDP and ICLDP) are tested by conducting two experiments on Corel-5000 and Corel-10000 benchmark databases. The results after investigation show a significant improvement in terms of precision, average retrieval precision (ARP), recall and average retrieval rate (ARR) as compared to local binary patterns (LBP), local derivative patterns (LDP) and other state-of-the-art techniques for image retrieval.

  2. Patterning and integration of polyfluorene polymers on micro-pixellated UV AlInGaN light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Guilhabert, B.; Gong, Z.; Zhang, H.; Belton, C.; Mack Intosh, A.; Gu, E.; Campoy-Quiles, M.; Stavrinou, P. N.; Bradley, D. D. C.; Pethrick, R. A.; Dawson, M. D.

    2008-05-01

    We report the integration of micro-patterned polyfluorene conjugated polymers onto GaN-based ultraviolet (UV) micro-pixellated light-emitting diode arrays (micro-LEDs). The 64 × 64 element matrix-addressable AlInGaN devices have a pixel size of 20 µm diameter on a 50 µm pitch, emitting at 368 nm. Each array is covered with a 2.5 µm thick photo-curable deep-UV-transparent polymer and a 30 nm thick polyfluorene film. This polymer bi-layer is subsequently patterned into an array of 28 µm diameter discs aligned with the pixels of the micro-LED array. Polymer down-converted visible emission from these pattern-programmable organic/inorganic electroluminescent micro-arrays is achieved.

  3. 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

  4. 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.

  5. 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

  6. Integrated reactive ion etching to pattern cross-linked hydrophilic polymer structures for protein immobilization

    NASA Astrophysics Data System (ADS)

    Bhatnagar, Parijat; Strickland, Aaron D.; Kim, Il; Malliaras, George G.; Batt, Carl A.

    2007-04-01

    Patterning of cross-linked hydrophilic polymer features using reactive ion etching (RIE) capable of covalently immobilizing proteins has been achieved. Projection photolithography was used to pattern photoresist to create micromolds. Vapor phase molecular self-assembly of polymerizable monolayer in molds allowed covalent binding of hydrogel on surface during free-radical polymerization. Excess hydrogel blanket film was consumed with oxygen RIE resulting into hydrogel pattern of 1μm size aligned to prefabricated silicon oxide structures. Proteins were finally coupled through their primary amine groups selectively to acid functionalized hydrogel features through stable amide linkages using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride and N-hydroxysulfosuccinimide.

  7. 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...

  8. Temperature and Energy of 4-Dimensional Axisymmetric Black Holes from Entropic Force

    NASA Astrophysics Data System (ADS)

    Zhao, Ren; Zhang, Li-Chun; Wu, Yue-Qin; Li, Huai-Fan

    2011-01-01

    We investigate the temperature and energy on holographic screens for 4-dimensional axisymmetric black holes with the entropic force idea proposed by Verlinde. According to the principle of thermal equilibrium, the location of holographic screen outside the axisymmetric black hole horizon is not a equivalent radius surface. The location of isothermal holographic screen outside the axisymmetric black hole horizon is obtained. Using the equipartition rule, we derive the correction expression of energy of isothermal holographic screen. When holographic screens are far away the black hole horizon, the entropic force of charged rotating particles can be expressed as Newton's law of gravity. When the screen crosses the event horizon, the temperature of the screen agrees with the Hawking temperature and the entropic force gives rise to the surface gravity for both of the black holes.

  9. 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. PMID:26177535

  10. 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

  11. 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

    2014-08-01

    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. PMID:25104393

  12. 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.

  13. In-situ device integration of large-area patterned organic nanowire arrays for high-performance optical sensors

    PubMed Central

    Wu, Yiming; Zhang, Xiujuan; Pan, Huanhuan; Deng, Wei; Zhang, Xiaohong; Zhang, Xiwei; Jie, Jiansheng

    2013-01-01

    Single-crystalline organic nanowires (NWs) are important building blocks for future low-cost and efficient nano-optoelectronic devices due to their extraordinary properties. However, it remains a critical challenge to achieve large-scale organic NW array assembly and device integration. Herein, we demonstrate a feasible one-step method for large-area patterned growth of cross-aligned single-crystalline organic NW arrays and their in-situ device integration for optical image sensors. The integrated image sensor circuitry contained a 10 × 10 pixel array in an area of 1.3 × 1.3 mm2, showing high spatial resolution, excellent stability and reproducibility. More importantly, 100% of the pixels successfully operated at a high response speed and relatively small pixel-to-pixel variation. The high yield and high spatial resolution of the operational pixels, along with the high integration level of the device, clearly demonstrate the great potential of the one-step organic NW array growth and device construction approach for large-scale optoelectronic device integration. PMID:24287887

  14. Prestimulus oscillatory alpha power and connectivity patterns predispose perceptual integration of an audio and a tactile stimulus.

    PubMed

    Leonardelli, Elisa; Braun, Christoph; Weisz, Nathan; Lithari, Chrysa; Occelli, Valeria; Zampini, Massimiliano

    2015-09-01

    To efficiently perceive and respond to the external environment, our brain has to perceptually integrate or segregate stimuli of different modalities. The temporal relationship between the different sensory modalities is therefore essential for the formation of different multisensory percepts. In this magnetoencephalography study, we created a paradigm where an audio and a tactile stimulus were presented by an ambiguous temporal relationship so that perception of physically identical audiotactile stimuli could vary between integrated (emanating from the same source) and segregated. This bistable paradigm allowed us to compare identical bimodal stimuli that elicited different percepts, providing a possibility to directly infer multisensory interaction effects. Local differences in alpha power over bilateral inferior parietal lobules (IPLs) and superior parietal lobules (SPLs) preceded integrated versus segregated percepts of the two stimuli (audio and tactile). Furthermore, differences in long-range cortical functional connectivity seeded in rIPL (region of maximum difference) revealed differential patterns that predisposed integrated or segregated percepts encompassing secondary areas of all different modalities and prefrontal cortex. We showed that the prestimulus brain states predispose the perception of the audiotactile stimulus both in a global and a local manner. Our findings are in line with a recent consistent body of findings on the importance of prestimulus brain states for perception of an upcoming stimulus. This new perspective on how stimuli originating from different modalities are integrated suggests a non-modality specific network predisposing multisensory perception. PMID:26109518

  15. In-situ device integration of large-area patterned organic nanowire arrays for high-performance optical sensors.

    PubMed

    Wu, Yiming; Zhang, Xiujuan; Pan, Huanhuan; Deng, Wei; Zhang, Xiaohong; Zhang, Xiwei; Jie, Jiansheng

    2013-01-01

    Single-crystalline organic nanowires (NWs) are important building blocks for future low-cost and efficient nano-optoelectronic devices due to their extraordinary properties. However, it remains a critical challenge to achieve large-scale organic NW array assembly and device integration. Herein, we demonstrate a feasible one-step method for large-area patterned growth of cross-aligned single-crystalline organic NW arrays and their in-situ device integration for optical image sensors. The integrated image sensor circuitry contained a 10 × 10 pixel array in an area of 1.3 × 1.3 mm(2), showing high spatial resolution, excellent stability and reproducibility. More importantly, 100% of the pixels successfully operated at a high response speed and relatively small pixel-to-pixel variation. The high yield and high spatial resolution of the operational pixels, along with the high integration level of the device, clearly demonstrate the great potential of the one-step organic NW array growth and device construction approach for large-scale optoelectronic device integration. PMID:24287887

  16. Profiling the substitution pattern of xyloglucan derivatives by integrated enzymatic hydrolysis, hydrophilic-interaction liquid chromatography and mass spectrometry.

    PubMed

    Liu, Jun; Kisonen, Victor; Willför, Stefan; Xu, Chunlin; Vilaplana, Francisco

    2016-09-01

    Plant polysaccharides constitute arguably the most complex family of biomacromolecules in terms of the stereochemistry and regiochemistry of their intramolecular linkages. The chemical modification of such polysaccharides introduces an additional level of complexity for structural determinations. We have developed an integrated analytical procedure combining selective enzymatic hydrolysis, hydrophilic interaction liquid chromatography (HILIC), and mass spectrometry (MS) to describe the substitution pattern of xyloglucan (XyG) and its chemo-enzymatic derivatives (cationic, anionic, and benzyl aminated). Enzymatic hydrolysis of XyG derivatives by a xyloglucan-specific endoglucanase (XEG) generates oligosaccharides amenable for mass spectrometric identification with distinct structures, based on enzymatic substrate recognition and hydrolytic pattern. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) and electrospray ionisation mass spectrometry (ESI-MS) offer qualitative mass profiling of the chemical derivatives. Separation and identification of the complex oligosaccharide profiles released by enzymatic hydrolysis is achieved by hyphenation of hydrophilic interaction liquid chromatography with mass spectrometry (HILIC-ESI-MS). Further fragmentation by tandem mass spectrometry (ESI-MS/MS) in positive mode enables the structural sequencing of modified XyG oligosaccharides and the identification of the substituent position without further derivatisation. This integrated approach can be used to obtain semi-quantitative information of the substitution pattern of hemicellulose derivatives, with fundamental implications for their modification mechanisms and performance. PMID:27524300

  17. [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. PMID:27320150

  18. 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

  19. Pattern discovery and cancer gene identification in integrated cancer genomic data

    PubMed Central

    Mo, Qianxing; Wang, Sijian; Seshan, Venkatraman E.; Olshen, Adam B.; Schultz, Nikolaus; Sander, Chris; Powers, R. Scott; Ladanyi, Marc; Shen, Ronglai

    2013-01-01

    Large-scale integrated cancer genome characterization efforts including the cancer genome atlas and the cancer cell line encyclopedia have created unprecedented opportunities to study cancer biology in the context of knowing the entire catalog of genetic alterations. A clinically important challenge is to discover cancer subtypes and their molecular drivers in a comprehensive genetic context. Curtis et al. [Nature (2012) 486(7403):346–352] has recently shown that integrative clustering of copy number and gene expression in 2,000 breast tumors reveals novel subgroups beyond the classic expression subtypes that show distinct clinical outcomes. To extend the scope of integrative analysis for the inclusion of somatic mutation data by massively parallel sequencing, we propose a framework for joint modeling of discrete and continuous variables that arise from integrated genomic, epigenomic, and transcriptomic profiling. The core idea is motivated by the hypothesis that diverse molecular phenotypes can be predicted by a set of orthogonal latent variables that represent distinct molecular drivers, and thus can reveal tumor subgroups of biological and clinical importance. Using the cancer cell line encyclopedia dataset, we demonstrate our method can accurately group cell lines by their cell-of-origin for several cancer types, and precisely pinpoint their known and potential cancer driver genes. Our integrative analysis also demonstrates the power for revealing subgroups that are not lineage-dependent, but consist of different cancer types driven by a common genetic alteration. Application of the cancer genome atlas colorectal cancer data reveals distinct integrated tumor subtypes, suggesting different genetic pathways in colon cancer progression. PMID:23431203

  20. 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. PMID:25243640

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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.

  2. 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. PMID:27138863

  3. 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…

  4. 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. PMID:22272380

  5. 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.

  6. 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.

  7. Composite vortex patterns formed by component light beams with non-integral topological charge

    NASA Astrophysics Data System (ADS)

    Galvez, E. J.; Baumann, S. M.

    2007-01-01

    We present a study of composite vortices in light beams using component beams with no integral topological charge. We observed the same general features that are seen in when the component beams have an integral topological charge [E.J. Galvez, N. Smiley, and N. Fernandes, "Composite optical vortices formed by collinear Laguerre-Gauss beams," Proc. SPIE 6131, pp. 19-26, 2006.]. These are: (1) that new vortices appear at distances from the beam that depend on the ratio of the intensity of the component beams, and (2) that the angular location of the vortices depends on the phase difference between them. We also observed that some of the vortices associated with fractional charge that did not follow the same dynamics.

  8. 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.

  9. Exploring the Genetic Patterns of Complex Diseases via the Integrative Genome-Wide Approach.

    PubMed

    Teng, Ben; Yang, Can; Liu, Jiming; Cai, Zhipeng; Wan, Xiang

    2016-01-01

    Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However, most of the variants that have been identified contribute relatively small increments of risk and only explain a small portion of the genetic variation in complex diseases. This is the so-called missing heritability problem. Evidence has indicated that many complex diseases are genetically related, meaning these diseases share common genetic risk variants. Therefore, exploring the genetic correlations across multiple related studies could be a promising strategy for removing spurious associations and identifying underlying genetic risk variants, and thereby uncovering the mystery of missing heritability in complex diseases. We present a general and robust method to identify genetic patterns from multiple large-scale genomic datasets. We treat the summary statistics as a matrix and demonstrate that genetic patterns will form a low-rank matrix plus a sparse component. Hence, we formulate the problem as a matrix recovering problem, where we aim to discover risk variants shared by multiple diseases/traits and those for each individual disease/trait. We propose a convex formulation for matrix recovery and an efficient algorithm to solve the problem. We demonstrate the advantages of our method using both synthesized datasets and real datasets. The experimental results show that our method can successfully reconstruct both the shared and the individual genetic patterns from summary statistics and achieve comparable performances compared with alternative methods under a wide range of scenarios. The MATLAB code is available at: http://www.comp.hkbu.edu.hk/~xwan/iga.zip. PMID:27295639

  10. 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

    2016-01-01

    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

  11. Blood microcirculation monitoring by use of spatial filtering of time-integrated speckle patterns: potentialities to improve the depth resolution

    NASA Astrophysics Data System (ADS)

    Zimnyakov, Dmitry A.; Misnin, Alexander B.

    2001-06-01

    Statistical analysis of images of time-integrated dynamic speckle patterns is considered as the tool for diagnostics and imaging of in vivo tissue dynamics such as blood microcirculation in superficial layers of human tissues and organs. Basic approach for blood microcirculation monitoring using the contrast analysis of time-averaged speckle images is known as LASCA (Laser Speckle Contrast Analysis) technique. This paper presents the modified version of LASCA, which is based on application of the localized probe light source and the spatial filtration of analyzed speckle pattern in the object plane. Being compared with classical LASCA technique, this method has the certain disadvantage as the necessity of scanning procedure to provide the reconstruction of maps of blood microcirculation parameters, but it gives the additional possibilities for the analysis of depth distributions of these parameters. Theoretical background for the depth-resolved analysis of blood microcirculation parameters on the basis of the concept of effective optical path distributions for multiply scattered probe light is considered. The effect of non-zero residual contrast even in the case of large integration times is also discussed.

  12. Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis

    PubMed Central

    Ramaswamy, Vijay; Remke, Marc; Bouffet, Eric; Faria, Claudia C.; Perreault, Sebastien; Cho, Yoon-Jae; Shih, David J.; Luu, Betty; Dubuc, Adrian M.; Northcott, Paul A.; Schüller, Ulrich; Gururangan, Sridharan; McLendon, Roger; Bigner, Darell; Fouladi, Maryam; Ligon, Keith L.; Pomeroy, Scott L.; Dunn, Sandra; Triscott, Joanna; Jabado, Nada; Fontebasso, Adam; Jones, David T. W.; Kool, Marcel; Karajannis, Matthias A.; Gardner, Sharon L.; Zagzag, David; Nunes, Sofia; Pimentel, José; Mora, Jaume; Lipp, Eric; Walter, Andrew W.; Ryzhova, Marina; Zheludkova, Olga; Kumirova, Ella; Alshami, Jad; Croul, Sidney E.; Rutka, James T.; Hawkins, Cynthia; Tabori, Uri; Codispoti, Kari-Elise T.; Packer, Roger J.; Pfister, Stefan M.; Korshunov, Andrey; Taylor, Michael D.

    2014-01-01

    Background Recurrent medulloblastoma is a daunting therapeutic challenge as it is almost universally fatal. Recent studies confirmed that medulloblastoma comprises four distinct subgroups. We sought to delineate subgroup specific differences in medulloblastoma recurrence patterns. Methods We retrospectively identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children between 1994-2012, and performed molecular subgrouping on FFPE tissues using a nanoString-based assay. The anatomical site of recurrence (local tumour bed or leptomeningeal metastasis), time to recurrence and survival post-recurrence were determined in a subgroup specific fashion. Subgroup specific recurrence patterns were confirmed in two independent, non-overlapping FFPE validation cohorts. Where possible molecular subgrouping was performed on tissue obtained from both the initial surgery and at recurrence. Results A screening cohort of 30 recurrent medulloblastomas was assembled; nine with local recurrences, and 21 metastatic. When re-analysed in a subgroup specific manner, local recurrences were more frequent in SHH tumours (8/9, 88%) and metastatic recurrences were more common in Group 3 and 4 (17/20 [85%] with one WNT, p=0.0014, local vs metastatic recurrence, SHH vs Group 3 vs Group 4). The subgroup specific location of recurrence was confirmed in a multicenter validation cohort (p=0·0013 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=77), and a second independent validation cohort comprising 96 recurrences (p<0·0001 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=96). Treatment with craniospinal irradiation at diagnosis was not significantly associated with the anatomical pattern of recurrence. Survival post recurrence was significantly longer in Group 4 patients (p=0·013) as confirmed in a multicenter validation cohort (p=0·0075). Strikingly, subgroup affiliation remained stable at recurrence in all 34 cases with

  13. 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

  14. 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.

  15. 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

    2016-01-01

    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

  16. Integration of nanoimprint lithography with block copolymer directed self-assembly for fabrication of a sub-20 nm template for bit-patterned media.

    PubMed

    Yang, XiaoMin; Xiao, Shuaigang; Hu, Wei; Hwu, Justin; van de Veerdonk, René; Wago, Koichi; Lee, Kim; Kuo, David

    2014-10-01

    We propose a novel strategy to integrate the nanoimprint lithography (NIL) technique with directed self-assembly (DSA) of block copolymer (BCP) for providing a robust, high-yield, and low-defect-density path to sub-20 nm dense patterning. Through this new NIL-DSA method, UV nanoimprint resist is used as the DSA copolymer pre-pattern to expedite the DSA process. This method was successfully used to fabricate a 1.0 Td in(-2) servo-integrated nanoimprint template for bit-patterned media (BPM) application. The fabricated template was used for UV-cure NIL on a 2.5-inch disk. The imprint resist patterns were further transferred into the underlying CoCrPt magnetic layer through a carbon hard mask using ion beam etching. The successful integration of the NIL technique with the DSA process provides us with a new route to BPM nanofabrication, which includes the following three major advantages: (1) a simpler and faster way to implement DSA for high-density BPM patterning; (2) a novel method for fabricating a high-quality dot pattern template through an iterative imprint-DSA-template procedure; and (3) an uncomplicated integration scheme for implementing non-periodic servo features with BCP patterns, thus accelerating the transition of moving the DSA technique from laboratory research to the BPM manufacturing environment. PMID:25189432

  17. 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. PMID:26473062

  18. 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

  19. Laser trapping and patterning of protein microcrystals: Toward highly integrated protein microarrays

    NASA Astrophysics Data System (ADS)

    Hosokawa, Yoichiroh; Matsumura, Satoshi; Masuhara, Hiroshi; Ikeda, Keiko; Shimo-oka, Ai; Mori, Hajime

    2004-09-01

    Some insect virus infections occlude into a crystalline matrix consisting of a protein named polyhedrin. The shape of the matrix is a cubic polyhedron of the size of a few micrometers. Recently it was shown that these polyhedra could immobilize various functional proteins within them. Therefore, the polyhedron is interesting as an element in a protein chip. In this work, individual polyhedra were arrayed and bonded under a microscope by focused laser beams, with the aim of fabricating a highly integrated protein chip. The polyhedron was trapped and transferred to a suitable position on a polymer substrate by optical trapping with a 1064nmNd3+:YAG (YAG, yttrium aluminum garnet) laser. To bond the polyhedron on the substrate, the polymer surface was mechanically and chemically modified by multiphoton absorption of a 120fs, 800nm femtosecond Ti: sapphire laser, which results in strong adhesion of the polyhedron to the substrate. The arraying and bonding of polyhedra were successful, to a precision of about 1μm, with this procedure. The biological activity of polyhedra after these laser irradiations was confirmed by the fluorescence of green fluorescent protein occluded in the polyhedrin matrix.

  20. GeoGML - a Mark-up Language for 4-dimensional geomorphic objects and processes

    NASA Astrophysics Data System (ADS)

    Löwner, M.-O.

    2009-04-01

    We developed an use-oriented GML3 based data model that enables researchers to share 4-dimensional information about landforms and their process related interaction. Using the Unified Modelling Language it is implemented as a GML3-based application schema available on the Internet. As the science of the land's surface Geomorphology investigates landforms, their change, and the processes causing this change. The main problem of comparing research results in geomorphology is that the objects under investigation are composed of 3-dimensional geometries that change in time due to processes of material fluxes, e. g. soil erosion or mass movements. They have internal properties, e. g. soil texture or bulk density, that determine the effectiveness of these processes but are under change as well. Worldwide geographical data can be shared over the Internet using Web Feature Services. The precondition is the development of a semantic model or ontology based on international standards like GML3 as an implementation of the ISO 109107 and others. Here we present a GML3-based Mark-up Language or application schema for geomorphic purposes that fulfils the following requirements: First, an object-oriented view of landforms with a true 3-dimensional geometric data format was established. Second, the internal structure and attributes of landforms can be stored. Third, the interaction of processes and landforms is represented. Fourth, the change of all these mentioned attributes over time was considered. The presented application schema is available on the Internet and therefore a first step to enable researchers to share information using an OGC's Web feature service. In this vein comparing modelling results of landscape evolution with results of other scientist's observations is possible. Compared to prevalent data concepts the model presented makes it possible to store information about landforms, their geometry and the characteristics in more detail. It allows to represent the 3D

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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. PMID:26214548

  8. Cryptic Speciation Patterns in Iranian Rock Lizards Uncovered by Integrative Taxonomy

    PubMed Central

    Ahmadzadeh, Faraham; Flecks, Morris; Carretero, Miguel A.; Mozaffari, Omid; Böhme, Wolfgang; Harris, D. James; Freitas, Susana; Rödder, Dennis

    2013-01-01

    While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results

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

    PubMed Central

    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

    2016-01-01

    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. PMID:27527159

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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 a 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-analogue 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.

  11. 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

  12. Fabrication of servo-integrated template for 1.5 Teradot/inch2 bit patterned media with block copolymer directed assembly

    NASA Astrophysics Data System (ADS)

    Yang, XiaoMin; Xiao, Shuaigang; Hsu, Yautzong; Wang, HongYing; Hwu, Justin; Steiner, Philip; Wago, Koichi; Lee, Kim; Kuo, David

    2014-07-01

    Directed self-assembly (DSA) of block copolymers (BCPs) proves to be a viable solution for the ultrahigh density bit-patterned media (BPM) application. However, servo design integration is still extremely challenging since the servo layouts require more complex patterns than the simple arrays naturally achieved by the DSA process. We present an integration scheme to create BPM servo patterns by utilizing the BCP dot-array patterns. This proposed method is based on an imprint guided two-step DSA process, combined with conventional optical lithography to define two separate zones. Both the data zone and servo zone consist of self-assembled hexagonal dot arrays: a regular pattern in the data zone and an arbitrary pattern in the servo zone. This method was successfully used to fabricate a servo-integrated BPM template with an areal density of 1.5 Teradot/inch2 (Td/in.2) (Lo=22.3 nm). Using the fabricated quartz template, CoCrPt BPM media has been successfully patterned by nanoimprint lithography and subsequent ion-beam etching process on a 2.5 in. disk. Further, using patterned-in servo wedges on 1.5 Td/in.2 patterned CoCrPt media, we are able to close the servo control loop for track-following on a spin-stand test. The standard deviation of repeatable run-out over the full revolution is calculated to be about 4% of the 38.6 nm track pitch. This method is currently being used to fabricate a template at a much higher density of 3.2 Td/in.2 (Lo=15.2 nm).

  13. Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage

    PubMed Central

    2014-01-01

    Background Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which particular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing 'agretopes'. Here we set out a new means of evaluating the TCR faces of viral peptides in addition to their agretopes, integrating evaluations of both sides of the ternary complex in a single analysis. Methods This paper develops what we call the Janus Immunogenicity Score (JIS), bringing together a well-established method for predicting MHC binding, with a novel assessment of the potential for TCR binding based on similarity with self. Intuitively, both good MHC binding and poor self-similarity are required for high immunogenicity (i.e., a robust T effector response). Results Focusing on the class II antigen-processing pathway, we show that the JIS of T effector epitopes and null or regulatory epitopes deposited in a large database of epitopes (Immune Epitope Database) are significantly different. We then show that different types of viruses display significantly different patterns of scores over their constituent peptides, with viruses causing chronic infection (Epstein-Barr and cytomegalovirus) strongly shifted to lower scores relative to those causing acute infection (Ebola and Marburg). Similarly we find distinct patterns among influenza proteins in H1N1 (a strain against which human populations rapidly developed immunity) and H5N1 and H7N9 (highly pathogenic avian flu strains, with significantly greater case mortality rates). Conclusion The Janus Immunogenicity Score

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

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

    PubMed

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

    2012-06-01

    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

  1. 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

  2. 4-Dimensional Insights into Silicic Magma Reservoir Assembly from Late Miocene Southern Andean Plutons

    NASA Astrophysics Data System (ADS)

    Schaen, A. J.; Garibaldi, N.; Singer, B. S.; Schoene, B.; Cottle, J. M.; Tikoff, B.; Gutiérrez, F. J.; Jicha, B. R.; Payacán, I. J.

    2015-12-01

    Linking the development of magmatic flow fabrics to the T-X-t history of intraplutonic domains using modern structural and petrochronologic methods offers a frontier along which to explore for eruptability in plutonic rocks and better understand how shallow magma systems are assembled. The ~6.2 Ma Risco Bayo and Huemul plutons in the Chilean Andes (~36°S) exhibit a similar compositional spectrum and footprint to the active Laguna del Maule rhyolitic volcanic field nearby. The plutons comprise distinct lithological domains-each on the order of a few km3: gabbro to granite in Risco Bayo and granodiorite to leucogranite in Huemul. Whole rock variations and 87Sr/86Sr ratios highlight the importance of AFC processes during pluton assembly. Mixing and mingling of magma batches is observed geochemically and in the field as abundant mafic enclaves. U-Pb CA-ID-TIMS zircon ages of 6.36 to 6.18 Ma in Risco Bayo granodiorite and Huemul miarolitic leucogranite overlap with their 40Ar/39Ar biotite ages of ~6.24 Ma, suggesting coeval zircon saturation, emplacement, and rapid cooling of two compositionally and structurally distinct domains. A granodiorite domain within Huemul has a more protracted crystallization history and zircons with lower REE than in the adjacent miarolitic leucogranite, suggesting pluton construction by pulses on 10 to 100 kyr timescales. Al-in-hornblende barometry constrains emplacement to 3-4 km depth. Observations from Laguna del Maule (extrusion/intrusion rates, spatio-temporal pattern of mafic/rhyolitic volcanism, etc.) provide volcanic parallels with which to help interpret pluton assembly. AMS fabrics suggest possible upward migration of magma associated with decompression. Late Miocene silicic ignimbrites nearby are also being investigated to determine if they represent erupted products from the Risco Bayo-Huemul plutonic system.

  3. On the interpretation of integrated water vapor patterns in midlatitude cyclones derived from the Nimbus 7 scanning multichannel microwave radiometer

    NASA Technical Reports Server (NTRS)

    Mcmurdie, Lynn A.; Katsaros, Kristina B.

    1988-01-01

    The present exploration of methods for the interpretation of the Nimbus 7 satellite's Scanning Multichannel Microwave Radiometer (SMMR) vapor patterns and the ways in which they relate to the dynamical structure of individual midlatitude storms employs gridded meteorological data from the First GARP Global Experiment special observing period in order to calculate diagnostic quantities. SMMR patterns for a storm at a weak stage determined from the diagnostic quantities are compared with SMMR patterns for the storm at a stronger stage. A more complete interpretation of the SMMR patterns emerges from these considerations.

  4. 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. PMID:19335013

  5. 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.

  6. 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)

  7. 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

  8. 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

    2015-01-01

    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

  9. 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

  10. 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.

  11. 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. PMID:23683316

  12. 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

  13. Integrating a hive triangle pattern with subpixel analysis for noncontact measurement of structural dynamic response by using a novel image processing scheme.

    PubMed

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

    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

  14. Critical Correlation Functions for the 4-Dimensional Weakly Self-Avoiding Walk and n-Component {|\\varphi|^4} Model

    NASA Astrophysics Data System (ADS)

    Slade, Gordon; Tomberg, Alexandre

    2016-03-01

    We extend and apply a rigorous renormalisation group method to study critical correlation functions, on the 4-dimensional lattice Z4, for the weakly coupled n-component {|\\varphi|4} spin model for all {n ≥ 1}, and for the continuous-time weakly self-avoiding walk. For the {|\\varphi|4} model, we prove that the critical two-point function has | x|-2 (Gaussian) decay asymptotically, for {n ≥ 1}. We also determine the asymptotic decay of the critical correlations of the squares of components of {\\varphi}, including the logarithmic corrections to Gaussian scaling, for {n ≥ 1}. The above extends previously known results for n = 1 to all {n ≥ 1}, and also observes new phenomena for n > 1, all with a new method of proof. For the continuous-time weakly self-avoiding walk, we determine the decay of the critical generating function for the "watermelon" network consisting of p weakly mutually- and self-avoiding walks, for all {p ≥ 1}, including the logarithmic corrections. This extends a previously known result for p = 1, for which there is no logarithmic correction, to a much more general setting. In addition, for both models, we study the approach to the critical point and prove the existence of logarithmic corrections to scaling for certain correlation functions. Our method gives a rigorous analysis of the weakly self-avoiding walk as the n = 0 case of the {|\\varphi|4} model, and provides a unified treatment of both models, and of all the above results.

  15. Foam patterns

    SciTech Connect

    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.

  16. 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,…

  17. Strain Accommodation Along an Oblique Subduction Zone: Integrating Paleomagnetic Data and Stress Patterns in the Central Aleutian Forearc

    NASA Astrophysics Data System (ADS)

    Krutikov, L.; Reynolds, J. R.; Stone, D. B.

    2005-12-01

    Present day motion of the Pacific plate relative to the North American plate shifts along the Aleutian arc from normal convergence in the east to transform motion in the west. Oblique subduction, partitioned into an arc-normal component and an arc-parallel component, creates a spatially complex pattern of deformation in the overriding plate. Strain partitioning results in tectonic segmentation of the forearc region, caused by increasing obliquity of plate convergence and apparently characterized by clockwise rotation and westward translation of discrete blocks in the central and western Aleutian arc [e.g., Geist et al., Tectonics 7, 327-341, 1988]. Archived cores collected from islands in the central Aleutian arc for previous paleomagnetic studies are being remeasured and reanalyzed using modern thermal demagnetization techniques that were not available at the time of collection. These new measurements indicate counterclockwise rotation or less significant clockwise rotations than those predicted by the block rotation model. Paleomagnetic results are presented for Tertiary and Quaternary volcanic rocks from Adak and Amchitka Islands in the central Aleutians. Results range from no statistically significant rotation in young intrusives, to a number of paleomagnetic vectors in the Finger Bay volcanics (~55 Ma) that suggest clockwise rotation since the time of original magnetization. Paleomagnetic results are combined with analyses of seafloor lineations in high-resolution multibeam sonar data collected in 2003 and 2004 of representative sites between 173W and 179E along the central Aleutian arc. Major fault lineations and joint patterns observed in the bathymetry data are analyzed to estimate the direction of maximum horizontal stress. Lineations in rocks of different stratigraphic ages and paleomagnetic results are being compared with 0-5Ma regional stress patterns [Scholl et al., 1989] to constrain the style and timing of deformation.

  18. 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

  19. 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.

  20. 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.

  1. 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. PMID:16222462

  2. 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

  3. 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

  4. 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. PMID:26718988

  5. 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

  6. 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

  7. 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.

  8. The Regional Ocean Modeling System (ROMS) 4-dimensional variational data assimilation systems . Part I - System overview and formulation

    NASA Astrophysics Data System (ADS)

    Moore, Andrew M.; Arango, Hernan G.; Broquet, Gregoire; Powell, Brian S.; Weaver, Anthony T.; Zavala-Garay, Javier

    2011-10-01

    The Regional Ocean Modeling System (ROMS) is one of the few community ocean general circulation models for which a 4-dimensional variational data assimilation (4D-Var) capability has been developed. The ROMS 4D-Var capability is unique in that three variants of 4D-Var are supported: a primal formulation of incremental strong constraint 4D-Var (I4D-Var), a dual formulation based on a physical-space statistical analysis system (4D-PSAS), and a dual formulation representer-based variant of 4D-Var (R4D-Var). In each case, ROMS is used in conjunction with available observations to identify a best estimate of the ocean circulation based on a set of a priori hypotheses about errors in the initial conditions, boundary conditions, surface forcing, and errors in the model in the case of 4D-PSAS and R4D-Var. In the primal formulation of I4D-Var the search for the best circulation estimate is performed in the full space of the model control vector, while for the dual formulations of 4D-PSAS and R4D-Var only the sub-space of linear functions of the model state vector spanned by the observations (i.e. the dual space) is searched. In oceanographic applications, the number of observations is typically much less than the dimension of the model control vector, so there are clear advantages to limiting the search to the space spanned by the observations. In the case of 4D-PSAS and R4D-Var, the strong constraint assumption (i.e. that the model is error free) can be relaxed leading to the so-called weak constraint formulation. This paper describes the three aforementioned variants of 4D-Var as they are implemented in ROMS. Critical components that are common to each approach are conjugate gradient descent, preconditioning, and error covariance models, which are also described. Finally, several powerful 4D-Var diagnostic tools are discussed, namely computation of posterior errors, eigenvector analysis of the posterior error covariance, observation impact, and observation sensitivity.

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

    PubMed Central

    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. PMID:25598507

  10. 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

  11. 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

  12. 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.

  13. Extraction of bistable-percept-related features from local field potential by integration of local regression and common spatial patterns.

    PubMed

    Wang, Zhisong; Maier, Alexander; Logothetis, Nikos K; Liang, Hualou

    2009-08-01

    Bistable perception arises when an ambiguous stimulus under continuous view is perceived as an alternation of two mutually exclusive states. Such a stimulus provides a unique opportunity for understanding the neural basis of visual perception because it dissociates the perception from the visual input. In this paper, we focus on extracting the percept-related features from the local field potential (LFP) in monkey visual cortex for decoding its bistable structure-from-motion (SFM) perception. Our proposed feature extraction approach consists of two stages. First, we estimate and remove from each LFP trial the nonpercept-related stimulus-evoked activity via a local regression method called the locally weighted scatterplot smoothing because of the dissociation between the perception and the stimulus in our experimental paradigm. Second, we use the common spatial patterns approach to design spatial filters based on the residue signals of multiple channels to extract the percept-related features. We exploit a support vector machine (SVM) classifier on the extracted features to decode the reported perception on a single-trial basis. We apply the proposed approach to the multichannel intracortical LFP data collected from the middle temporal (MT) visual cortex in a macaque monkey performing an SFM task. We demonstrate that our approach is effective in extracting the discriminative features of the percept-related activity from LFP and achieves excellent decoding performance. We also find that the enhanced gamma band synchronization and reduced alpha and beta band desynchronization may be the underpinnings of the percept-related activity. PMID:19362902

  14. 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

  15. Patterns of integration of DNA microinjected into cultured mammalian cells: evidence for homologous recombination between injected plasmid DNA molecules.

    PubMed Central

    Folger, K R; Wong, E A; Wahl, G; Capecchi, M R

    1982-01-01

    We examined the fate of DNA microinjected into nuclei of cultured mammalian cells. The sequence composition and the physical form of the vector carrying the selectable gene affected the efficiency of DNA-mediated transformation. Introduction of sequences near the simian virus 40 origin of DNA replication or in the long terminal repeat of avian sarcoma provirus into a recombinant plasmid containing the herpes simplex virus thymidine kinase gene. (pBR322/HSV-tk) enhanced the frequency of transformation of LMtk- and RAT-2tk- cells to the TK+ phenotype 20- to 40-fold. In cells receiving injections of only a few plasmid DNA molecules, the transformation frequency was 40-fold higher after injection of linear molecules than after injection of supercoiled molecules. By controlling the number of gene copies injected into a recipient cell, we could obtain transformants containing a single copy or as many as 50 to 100 copies of the selectable gene. Multiple copies of the transforming gene were not scattered throughout the host genome but were integrated as a concatemer at one or a very few sites in the host chromosome. Independent transformants contained the donated genes in different chromosomes. The orientation of the gene copies within the concatemer was not random; rather, the copies were organized as tandem head-to-tail arrays. By analyzing transformants obtained by coinjecting two vectors which were identical except that in one a portion of the vector was inverted, we were able to conclude that the head-to-tail concatemers were generated predominantly by homologous recombination. Surprisingly, these head-to-tail concatemers were found in transformants obtained by injecting either supercoiled or linear plasmid DNA. Even though we demonstrated that cultured mammalian cells contain the enzymes for ligating two DNA molecules very efficiently irrespective of the sequences or topology at their ends, we found that even linear plasmid DNA was recruited into the concatemer by

  16. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra)

    PubMed Central

    2010-01-01

    the subspecies ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly divergent lineages in the central area of distribution. Our study points to the importance of reticulate evolution, with periods of isolation and reduction of population size followed by expansions and hybridizations, in the diversification at the level of close species or subspecies. PMID:20649956

  17. 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. PMID:27322873

  18. 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. PMID:23248816

  19. 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

  20. Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research.

    PubMed

    Camerlengo, Terry; Ozer, Hatice Gulcin; Yan, Pearlly; Parvin, Jeffrey; Huang, Tim; Huang, Kun; Perez, Francisco; Teng, Mingxiang; Li, Lang; Liu, Yunlong; Kurc, Tahsin

    2009-11-01

    Enabling data analysis in large data depositories for high throughput experimental data such as gene microarrays and ChIP-seq is challenging. In this paper, we discuss three methods for integrating QUEST, a data depository for epigenetic experiments, with a web-based data analysis platform GenePattern. These methods are universal and can serve as an exemplary implementation resolving the dilemma facing many similar database systems in integrating data analysis tools. PMID:21151835

  1. Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform – A Case Study on Integrating QUEST with GenePattern in Epigenetics Research

    PubMed Central

    Camerlengo, Terry; Ozer, Hatice Gulcin; Yan, Pearlly; Parvin, Jeffrey; Huang, Tim; Huang, Kun; Perez, Francisco; Teng, Mingxiang; Li, Lang; Liu, Yunlong; Kurc, Tahsin

    2010-01-01

    Enabling data analysis in large data depositories for high throughput experimental data such as gene microarrays and ChIP-seq is challenging. In this paper, we discuss three methods for integrating QUEST, a data depository for epigenetic experiments, with a web-based data analysis platform GenePattern. These methods are universal and can serve as an exemplary implementation resolving the dilemma facing many similar database systems in integrating data analysis tools. PMID:21151835

  2. Analysis of space-time non-stationary patterns of rainfall-groundwater interactions by integrating empirical orthogonal function and cross wavelet transform methods

    NASA Astrophysics Data System (ADS)

    Yu, Hwa-Lung; Lin, Yuan-Chien

    2015-06-01

    Rainfall-groundwater interactions are complex and can depend upon a variety of hydro-geological and geographical conditions and can commonly present high nonlinearity. This study proposed an integration of cross wavelet transform and empirical orthogonal function (EOF) analysis to analyze the space-time nonlinear relationships between the precipitation and groundwater changes. The proposed method was applied to investigating the non-stationary and nonlinear precipitation-groundwater relationships in Pingtung Plain aquifer during 2005-2010. We analyzed daily groundwater and rainfall observations at 47 wells and 27 stations across the study area operated by Taiwan Water Resources Agency and Central Weather Bureau respectively. Results show that EOF method revealed three major space-time patterns of the groundwater levels. The cross wavelet transform further identified the lagged effects between precipitation and groundwater changes. The temporal lags can vary not only with respect to the temporal scales of groundwater processes, but also the different identified groundwater regions, which can associate with distinct physical mechanisms. In general, the lagged periods between high frequency signals of precipitation and groundwater can range from 0 to 18 days, showing how rainfall events perturbed the groundwater levels across space. The long-term lags for the three identified underlying groundwater processes were 3.71, 56.6, and 72.07 days, respectively, showing seasonal recharge patterns can depend upon the geographical and geological conditions. Our results distinguished the space-time recharge processes in different frequencies, which present nonlinear and non-stationary rainfall-recharge interactions of a groundwater system, which can be spatially and frequency dependent.

  3. 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

  4. 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…

  5. 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

  6. Non-linear spatio-temporal filtering of dynamic PET data using a 4-dimensional Gaussian filter and expectation-maximization deconvolution

    PubMed Central

    Holden, J E

    2013-01-01

    We introduce a method for denoising dynamic PET data, spatio-temporal expectation-maximization (STEM) filtering, that combines 4-dimensional Gaussian filtering with EM deconvolution. The initial Gaussian filter suppresses noise at a broad range of spatial and temporal frequencies and EM deconvolution quickly restores the frequencies most important to the signal. We aim to demonstrate that STEM filtering can improve variance in both individual time frames and in parametric images without introducing significant bias. We evaluate STEM filtering with a dynamic phantom study, and with simulated and human dynamic PET studies of a tracer with reversible binding behaviour, [C-11]raclopride, and a tracer with irreversible binding behaviour, [F-18]FDOPA. STEM filtering is compared to a number of established 3 and 4-dimensional denoising methods. STEM filtering provides substantial improvements in variance in both individual time frames and in parametric images generated with a number of kinetic analysis techniques while introducing little bias. STEM filtering does bias early frames, but this does not affect quantitative parameter estimates. STEM filtering is shown to be superior to the other simple denoising methods studied. STEM filtering is a simple and effective denoising method that could be valuable for a wide range of dynamic PET applications. PMID:23370699

  7. 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

  8. Translating Response During Therapy into Ultimate Treatment Outcome: A Personalized 4-Dimensional MRI Tumor Volumetric Regression Approach in Cervical Cancer

    SciTech Connect

    Mayr, Nina A.; Wang, Jian Z.; Lo, Simon S.; Zhang Dongqing; Grecula, John C.; Lu Lanchun; Montebello, Joseph F.; Fowler, Jeffrey M.; Yuh, William T.C.

    2010-03-01

    Purpose: To assess individual volumetric tumor regression pattern in cervical cancer during therapy using serial four-dimensional MRI and to define the regression parameters' prognostic value validated with local control and survival correlation. Methods and Materials: One hundred and fifteen patients with Stage IB{sub 2}-IVA cervical cancer treated with radiation therapy (RT) underwent serial MRI before (MRI 1) and during RT, at 2-2.5 weeks (MRI 2, at 20-25 Gy), and at 4-5 weeks (MRI 3, at 40-50 Gy). Eighty patients had a fourth MRI 1-2 months post-RT. Mean follow-up was 5.3 years. Tumor volume was measured by MRI-based three-dimensional volumetry, and plotted as dose(time)/volume regression curves. Volume regression parameters were correlated with local control, disease-specific, and overall survival. Results: Residual tumor volume, slope, and area under the regression curve correlated significantly with local control and survival. Residual volumes >=20% at 40-50 Gy were independently associated with inferior 5-year local control (53% vs. 97%, p <0.001) and disease-specific survival rates (50% vs. 72%, p = 0.009) than smaller volumes. Patients with post-RT residual volumes >=10% had 0% local control and 17% disease-specific survival, compared with 91% and 72% for <10% volume (p <0.001). Conclusion: Using more accurate four-dimensional volumetric regression analysis, tumor response can now be directly translated into individual patients' outcome for clinical application. Our results define two temporal thresholds critically influencing local control and survival. In patients with >=20% residual volume at 40-50 Gy and >=10% post-RT, the risk for local failure and death are so high that aggressive intervention may be warranted.

  9. 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

  10. 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. PMID:25981294

  11. 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!

  12. Comparison of 4-Dimensional Computed Tomography Ventilation With Nuclear Medicine Ventilation-Perfusion Imaging: A Clinical Validation Study

    PubMed Central

    Vinogradskiy, Yevgeniy; Koo, Phillip J.; Castillo, Richard; Castillo, Edward; Guerrero, Thomas; Gaspar, Laurie E.; Miften, Moyed; Kavanagh, Brian D.

    2014-01-01

    on a regional level. Our study presents an important step for the integration of 4DCT-ventilation into thoracic clinical practice. PMID:24725702

  13. 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.

  14. Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 heterologou...

  15. 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.

  16. RUPTURED POLLEN GRAIN1, a Member of the MtN3/saliva Gene Family, Is Crucial for Exine Pattern Formation and Cell Integrity of Microspores in Arabidopsis1[C][W][OA

    PubMed Central

    Guan, Yue-Feng; Huang, Xue-Yong; Zhu, Jun; Gao, Ju-Fang; Zhang, Hong-Xia; Yang, Zhong-Nan

    2008-01-01

    During microsporogenesis, the microsporocyte (or microspore) plasma membrane plays multiple roles in pollen wall development, including callose secretion, primexine deposition, and exine pattern determination. However, plasma membrane proteins that participate in these processes are still not well known. Here, we report that a new gene, RUPTURED POLLEN GRAIN1 (RPG1), encodes a plasma membrane protein and is required for exine pattern formation of microspores in Arabidopsis (Arabidopsis thaliana). The rpg1 mutant exhibits severely reduced male fertility with an otherwise normal phenotype, which is largely due to the postmeiotic abortion of microspores. Scanning electron microscopy examination showed that exine pattern formation in the mutant is impaired, as sporopollenin is randomly deposited on the pollen surface. Transmission electron microscopy examination further revealed that the primexine formation of mutant microspores is aberrant at the tetrad stage, which leads to defective sporopollenin deposition on microspores and the locule wall. In addition, microspore rupture and cytoplasmic leakage were evident in the rpg1 mutant, which indicates impaired cell integrity of the mutant microspores. RPG1 encodes an MtN3/saliva family protein that is integral to the plasma membrane. In situ hybridization analysis revealed that RPG1 is strongly expressed in microsporocyte (or microspores) and tapetum during male meiosis. The possible role of RPG1 in microsporogenesis is discussed. PMID:18434608

  17. 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…

  18. Is it important to characterize complex patterns of riverbed hydraulic conductivities for assessing river-aquifer exchange fluxes? An evaluation with an integrated fully coupled hydrological model.

    NASA Astrophysics Data System (ADS)

    Tang, Qi; Kurtz, Wolfgang; Schilling, Oliver; Brunner, Philip; Vereecken, Harry; Hendricks Franssen, Harrie-Jan

    2016-04-01

    Riverbed hydraulic conductivity is a critical parameter for the prediction of exchange fluxes between groundwater and surface water bodies. It was found in previous studies that it is important to characterize heterogeneity of riverbed hydraulic conductivity. In this context, we also investigated in the past whether the heterogeneity pattern of riverbed hydraulic conductivities (i.e., multiGaussian, different types of non-multiGaussian patterns) plays an important role. It was found that the heterogeneity pattern does not matter so much. However, these past studies were conducted with the subsurface hydrological model SPRING which only considers one way coupling and only vertical fluxes through the river-aquifer interface. In this study, the role of patterns was further explored using the fully coupled hydrological model HydroGeoSphere. A synthetic 3-D river-aquifer model was set up with a heterogeneous riverbed showing non-multiGaussian patterns in the form of meandering channels as the reference field. Data assimilation experiments were carried out with help of the Ensemble Kalman Filter to characterize the heterogeneous riverbed. The data assimilation experiments were conducted for four types of riverbed hydraulic conductivity (K) fields: (i) spatially homogeneous, (ii) heterogeneous with multiGaussian distribution, (iii) heterogeneous with non-multiGaussian distribution (channelized structures) and (iv) heterogeneous with non-multiGaussian distribution (elliptic structures). For all the data assimilation scenarios, state variables and riverbed K were updated by assimilating piezometric heads. The experiments were repeated for ten reference fields. Results show that for all prior geostatistical models data assimilation was able to reduce the difference between simulated and measured hydraulic heads, and to improve the characterization of riverbed hydraulic conductivities and river-aquifer exchange fluxes. Results were slightly better for non-multiGaussian fields

  19. Integration of hydrologic and water allocation models in basin-scale water resources management considering crop pattern and climate change: Karkheh River Basin in Iran

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  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. 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.

  2. CMOS image sensor integrated with micro-LED and multielectrode arrays for the patterned photostimulation and multichannel recording of neuronal tissue.

    PubMed

    Nakajima, Arata; Kimura, Hiroshi; Sawadsaringkarn, Yosmongkol; Maezawa, Yasuyo; Kobayashi, Takuma; Noda, Toshihiko; Sasagawa, Kiyotaka; Tokuda, Takashi; Ishikawa, Yasuyuki; Shiosaka, Sadao; Ohta, Jun

    2012-03-12

    We developed a complementary metal oxide semiconductor (CMOS) integrated device for optogenetic applications. This device can interface via neuronal tissue with three functional modalities: imaging, optical stimulation and electrical recording. The CMOS image sensor was fabricated on 0.35 μm standard CMOS process with built-in control circuits for an on-chip blue light-emitting diode (LED) array. The effective imaging area was 2.0 × 1.8 mm². The pixel array was composed of 7.5 × 7.5 μm² 3-transistor active pixel sensors (APSs). The LED array had 10 × 8 micro-LEDs measuring 192 × 225 μm². We integrated the device with a commercial multichannel recording system to make electrical recordings. PMID:22418489

  3. 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. PMID:27565868

  4. Different Patterns of Correlation between Grey and White Matter Integrity Account for Behavioral and Psychological Symptoms in Alzheimer's Disease.

    PubMed

    Makovac, Elena; Serra, Laura; Spanò, Barbara; Giulietti, Giovanni; Torso, Mario; Cercignani, Mara; Caltagirone, Carlo; Bozzali, Marco

    2016-06-21

    Behavioral disorders and psychological symptoms (BPSD) in Alzheimer's disease (AD) are known to correlate with grey matter (GM) atrophy and, as shown recently, also with white matter (WM) damage. WM damage and its relationship with GM atrophy are reported in AD, reinforcing the interpretation of the AD pathology in light of a disconnection syndrome. It remains uncertain whether this disconnection might account also for different BPSD observable in AD. Here, we tested the hypothesis of different patterns of association between WM damage of the corpus callosum (CC) and GM atrophy in AD patients exhibiting one of the following BPSD clusters: Mood (i.e., anxiety and depression; ADmood), Frontal (i.e., dishinibition and elation; ADfrontal), and Psychotic (delusions and hallucinations; ADpsychotic) related symptoms, as well as AD patients without BPSD. Overall, this study brings to light the strict relationship between WM alterations in different parts of the CC and GM atrophy in AD patients exhibiting BPSD, supporting the hypothesis that such symptoms are likely to be caused by characteristic patterns of neurodegeneration of WM and GM, rather than being a reactive response to accumulation of cognitive disabilities, and should therefore be regarded as potential markers of diagnostic and prognostic value in AD. PMID:26836635

  5. 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.

    2012-10-01

    Carbon use efficiency (CUE) is a functional parameter that could possibly link the current increasingly accurate global estimates of gross primary production 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, net primary production (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 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 fruits: 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 ± 0.09, was higher than the previously suggested

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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%.

  12. Integrative Analysis Reveals an Outcome-associated and Targetable Pattern of p53 and Cell Cycle Deregulation in Diffuse Large B-cell Lymphoma

    PubMed Central

    Monti, Stefano; Chapuy, Bjoern; Takeyama, Kunihiko; Rodig, Scott J; Hao, Yangsheng; Yeda, Kelly T.; Inguilizian, Haig; Mermel, Craig; Curie, Treeve; Dogan, Ahmed; Kutok, Jeffery L; Beroukim, Rameen; Neuberg, Donna; Habermann, Thomas; Getz, Gad; Kung, Andrew L; Golub, Todd R; Shipp, Margaret A

    2013-01-01

    Summary Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease with a high proliferation rate. By integrating copy number data with transcriptional profiles and performing pathway analysis in primary DLBCLs, we identified a comprehensive set of copy number alterations (CNAs) that decreased p53 activity and perturbed cell cycle regulation. Primary tumors either had multiple complementary alterations of p53 and cell cycle components or largely lacked these lesions. DLBCLs with p53 and cell cycle pathway CNAs had decreased abundance of p53 target transcripts and increased expression of E2F target genes and the Ki67 proliferation marker. CNAs of the CDKN2A-TP53-RB-E2F axis provide a structural basis for increased proliferation in DLBCL, predict outcome with current therapy and suggest targeted treatment approaches. PMID:22975378

  13. Summation of spatiotemporal input patterns in leaky integrate-and-fire neurons: application to neurons in the cochlear nucleus receiving converging auditory nerve fiber input.

    PubMed

    Kuhlmann, Levin; Burkitt, Anthony N; Paolini, Antonio; Clark, Graeme M

    2002-01-01

    The response of leaky integrate-and-fire neurons is analyzed for periodic inputs whose phases vary with their spatial location. The model gives the relationship between the spatial summation distance and the degree of phase locking of the output spikes (i.e., locking to the periodic stochastic inputs, measured by the synchronization index). The synaptic inputs are modeled as an inhomogeneous Poisson process, and the analysis is carried out in the Gaussian approximation. The model has been applied to globular bushy cells of the cochlear nucleus, which receive converging inputs from auditory nerve fibers that originate at neighboring sites in the cochlea. The model elucidates the roles played by spatial summation and coincidence detection, showing how synchronization decreases with an increase in both frequency and spatial spread of inputs. It also shows under what conditions an enhancement of synchronization of the output relative to the input takes place. PMID:11932560

  14. 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

  15. 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

    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

  16. Changes in Characteristics and Treatment Patterns of Patients with Newly Diagnosed Type 2 Diabetes in a Large United States Integrated Health System between 2008 and 2013

    PubMed Central

    Pantalone, Kevin M.; Hobbs, Todd M.; Wells, Brian J.; Kong, Sheldon X.; Kattan, Michael W.; Bouchard, Jonathan; Chagin, Kevin M.; Yu, Changhong; Sakurada, Brian; Milinovich, Alex; Weng, Wayne; Bauman, Janine M.; Zimmerman, Robert S.

    2016-01-01

    To assess changes in the clinical characteristics and treatment patterns of patients with newly diagnosed type 2 diabetes (T2D), the electronic health record system at Cleveland Clinic was used to create cross-sectional summaries of all patients with new-onset T2D in 2008 and 2013. Differences between the 2008 and 2013 data sets were assessed after adjusting for age, gender, race, and income. Approximately one-third of patients with newly diagnosed T2D in 2008 and 2013 had an A1C ≥8%, suggesting the continued presence of a delayed recognition of the disease. Patients with newly diagnosed T2D in 2008 were older than those in 2013. Hypertension, cardiovascular disease, and neuropathy were highly prevalent among patients diagnosed with T2D. The prevalence of neuropathy, cerebrovascular disease, and peripheral vascular disease increased from 2008 to 2013. Metformin was the most commonly prescribed antidiabetic medication. Sulfonylurea usage remained unchanged, while use of thiazolidinediones decreased considerably. PMID:27398040

  17. Electrical relaxation induced by magnetostriction in a MEMS device. Architecture integrating a Co submillimetric pattern of submicrometric holes and a polymeric amplifying layer

    NASA Astrophysics Data System (ADS)

    Chiolerio, A.; Allia, P.

    2010-08-01

    Electrical resistance relaxation measurements were performed on a regular array of Co magnetic antidots submitted to a magnetic field, using a thin Cu film with bone-like shape positioned across the pattern; the introduction of a thin resist layer spin-coated on the Cu bridge before the deposition of the external leads introduced a hopping-dominated path for injected currents, controlled by the barrier thickness. The in-plane magnetic field generated by an electromagnet was switched between 0 and 3.5 kOe (fully saturated Co) and kept constant while the resistance was continuously monitored under steady current injection. A strong, unsaturating resistance variation with time after field switching was measured, corresponding to a resistance decrease greater than 20% after tents of ks. When the field was switched from 3.5 kOe back to zero the measured resistance displayed a corresponding positive variation. The two effects were repeatedly observed by subsequently cycling the magnetic field. Electron microscopy analysis showed that a peculiar dendritic structure had developed in the polymeric resist, consisting of mass density oscillations whose principal arms were oriented roughly at 45° with respect to the current density vector, possibly because of the mechanical stress induced by magnetostriction of Co antidots. A detailed analysis showed that mass density fluctuations within dendritic structures may be correlated with specific perturbation events observed in the electrical resistance relaxation during the measurements.

  18. 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).

  19. 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

  20. Pattern formation today

    PubMed Central

    Chuong, Cheng-Ming; Richardson, Michael K.

    2010-01-01

    Patterns are orders embedded in randomness. They may appear as spatial arrangements or temporal series, and the elements may appear identical or with variations. Patterns exist in the physical world as well as in living systems. In the biological world, patterns can range from simple to complex, forming the basic building blocks of life. The process which generates this ordering in the biological world was termed pattern formation. Since Wolpert promoted this concept four decades ago, scientists from molecular biology, developmental biology, stem cell biology, tissue engineering, theoretical modeling and other disciplines have made remarkable progress towards understanding its mechanisms. It is time to review and re-integrate our understanding. Here, we explore the origin of pattern formation, how the genetic code is translated into biological form, and how complex phenotypes are selected over evolutionary time. We present four topics: Principles, Evolution, Development, and Stem Cells and Regeneration. We have interviewed several leaders in the field to gain insight into how their research and the field of pattern formation have shaped each other. We have learned that both molecular process and physico-chemical principles are important for biological pattern formation. New understanding will emerge through integration of the analytical approach of molecular-genetic manipulation and the systemic approach of model simulation. We regret that we could not include every major investigator in the field, but hope that this Special Issue of the Int. J. Dev. Biol. represents a sample of our knowledge of pattern formation today, which will help to stimulate more research on this fundamental process. PMID:19557673

  1. 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

  2. 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. PMID:21718004

  3. 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

  4. 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

  5. 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…

  6. 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

  7. 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.

  8. Patterns and Intelligent Systems

    SciTech Connect

    Cordes, Gail A.

    2003-01-15

    The recognition and analysis of evolving patterns provides a unifying concept for studying and implementing intelligent information processing for open feedback control systems within the nuclear industry. Control is considered as influence of a large system to achieve the goals of the human (who might or might not be part of an open feedback loop) and is not limited to operation of a component within a nuclear power plant. The intelligent control system includes open logic and can automatically react to new data in an unprogrammed way. This application of evolving patterns integrates current research developments in human cognition and scientific semiotics with traditional feedback control. A preliminary implementation of such a system using existing computational techniques is postulated, and tools that are lacking at this time are identified. Proof-of-concept applications for the nuclear industry are referenced.

  9. 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…

  10. Integration and Integrity.

    ERIC Educational Resources Information Center

    Cassano, Paul; Antol, Rayna A.

    2001-01-01

    Explains two middle school teachers' cooperation with integrating regular and gifted students with disabled students. Focuses on disabled students' collaboration with their peers and their social skill development rather than their academic development. (YDS)

  11. Experimental investigation of 4-dimensional superspace crystals

    SciTech Connect

    Rasing, T.; Janner, A.

    1983-09-01

    The symmetry of incommensurate crystals can be described by higher dimensional space groups in the so called superspace approach. The basic ideas are explained and used for showing that superspace groups provide an adequate frame for analyzing experimental results on incommensurate crystals.

  12. 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…

  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. Glass strengthening and patterning methods

    DOEpatents

    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.

  15. 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

  16. 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…

  17. 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.

  18. 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.

  19. Capacitance enhancement via electrode patterning.

    PubMed

    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. PMID:24289370

  20. 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.

  1. 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

  2. Regular patterns stabilize auditory streams.

    PubMed

    Bendixen, Alexandra; Denham, Susan L; Gyimesi, Kinga; Winkler, István

    2010-12-01

    The auditory system continuously parses the acoustic environment into auditory objects, usually representing separate sound sources. Sound sources typically show characteristic emission patterns. These regular temporal sound patterns are possible cues for distinguishing sound sources. The present study was designed to test whether regular patterns are used as cues for source distinction and to specify the role that detecting these regularities may play in the process of auditory stream segregation. Participants were presented with tone sequences, and they were asked to continuously indicate whether they perceived the tones in terms of a single coherent sequence of sounds (integrated) or as two concurrent sound streams (segregated). Unknown to the participant, in some stimulus conditions, regular patterns were present in one or both putative streams. In all stimulus conditions, participants' perception switched back and forth between the two sound organizations. Importantly, regular patterns occurring in either one or both streams prolonged the mean duration of two-stream percepts, whereas the duration of one-stream percepts was unaffected. These results suggest that temporal regularities are utilized in auditory scene analysis. It appears that the role of this cue lies in stabilizing streams once they have been formed on the basis of simpler acoustic cues. PMID:21218898

  3. 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. PMID:289292

  4. Frizzled6 controls hair patterning in mice.

    PubMed

    Guo, Nini; Hawkins, Charles; Nathans, Jeremy

    2004-06-22

    Hair whorls and other macroscopic hair patterns are found in a variety of mammalian species, including humans. We show here that Frizzled6 (Fz6), one member of a large family of integral membrane Wnt receptors, controls macroscopic hair patterning in the mouse. Fz6 is expressed in the skin and hair follicles, and targeted deletion of the Fz6 gene produces stereotyped whorls on the hind feet, variable whorls and tufts on the head, and misorientation of hairs on the torso. Embryo chimera experiments imply that Fz6 acts locally to control or propagate the macroscopic hair pattern and that epithelial cells rather than melanocytes are the source of Fz6-dependent signaling. The Fz6 phenotype strongly resembles the wing-hair and bristle patterning defects observed in Drosophila frizzled mutants. These data imply that hair patterning in mammals uses a Fz-dependent tissue polarity system similar to the one that patterns the Drosophila cuticle. PMID:15169958

  5. Integrative taxonomy of a new species of planarian from the Lake Ohrid basin, including an analysis of biogeographical patterns in freshwater triclads from the Ohrid region (Platyhelminthes, Tricladida, Dugesiidae)

    PubMed Central

    Stocchino, Giacinta Angela; Sluys, Ronald; Deri, Paolo; Manconi, Renata

    2013-01-01

    Abstract A new species of the genus Dugesia is described from the Lake Ohrid region in the western part of the Balkan Peninsula, forming the first fully documented species description for this genus in the Ohrid area. The morphological species delimitation is supported by complementary molecular, karyological, and cytogenetic data available from the literature. Therefore, species delineation is based on a truly integrative approach. Further, a short account on the degree of freshwater planarian endemicity in the Ohrid region is provided. PMID:23840163

  6. Integrative taxonomy of a new species of planarian from the Lake Ohrid basin, including an analysis of biogeographical patterns in freshwater triclads from the Ohrid region (Platyhelminthes, Tricladida, Dugesiidae).

    PubMed

    Stocchino, Giacinta Angela; Sluys, Ronald; Deri, Paolo; Manconi, Renata

    2013-01-01

    A new species of the genus Dugesia is described from the Lake Ohrid region in the western part of the Balkan Peninsula, forming the first fully documented species description for this genus in the Ohrid area. The morphological species delimitation is supported by complementary molecular, karyological, and cytogenetic data available from the literature. Therefore, species delineation is based on a truly integrative approach. Further, a short account on the degree of freshwater planarian endemicity in the Ohrid region is provided. PMID:23840163

  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. 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.

  9. From Local Patterns to Classification Models

    NASA Astrophysics Data System (ADS)

    Bringmann, Björn; Nijssen, Siegfried; Zimmermann, Albrecht

    Using pattern mining techniques for building a predictive model is currently a popular topic of research. The aim of these techniques is to obtain classifiers of better predictive performance as compared to greedily constructed models, as well as to allow the construction of predictive models for data not represented in attribute-value vectors. In this chapter we provide an overview of recent techniques we developed for integrating pattern mining and classification tasks. The range of techniques spans the entire range from approaches that select relevant patterns from a previously mined set for propositionalization of the data, over inducing patternbased rule sets, to algorithms that integrate pattern mining and model construction. We provide an overview of the algorithms which are most closely related to our approaches in order to put our techniques in a context.

  10. Patterned when wet: environment-dependent multifunctional patterns within amphiphilic colloidal crystals.

    PubMed

    Brozell, Adrian M; Muha, Michelle A; Abed-Amoli, Arian; Bricarello, Daniel; Parikh, Atul N

    2007-12-01

    A simple integration of molecular and colloidal self-assembly approaches with photopatterning is shown to produce multifunctional patterns of amphiphilic colloidal crystals. These crystals display binary spatial patterns of wettability by water and a single photonic stop-band in air. Upon exposure to water, the uniform stop-band is replaced by a pattern of coexisting stop-bands that reflect the underlying pattern of surface wetting. These hydration-dependent photonic patterns within single colloidal crystals form because of near-complete water rejection from the three-dimensionally disposed nanoscale interstices in hydrophobic regions and its exclusive permeation within the hydrophilic regions. This water permeation pattern is further structured by the three-dimensional (3D) distribution and contiguity of the nanoscale interstices between individual colloids, allowing 3D patterned organization of functional units in secondary self-assembly processes, as illustrated using quantum dots, metal nanoparticles, and fluorescent probes. PMID:17994784