A Simple and Scalable Fabrication Method for Organic Electronic Devices on Textiles.

PubMed

Ismailov, Usein; Ismailova, Esma; Takamatsu, Seiichi

2017-03-13

Today, wearable electronics devices combine a large variety of functional, stretchable, and flexible technologies. However, in many cases, these devices cannot be worn under everyday conditions. Therefore, textiles are commonly considered the best substrate to accommodate electronic devices in wearable use. In this paper, we describe how to selectively pattern organic electroactive materials on textiles from a solution in an easy and scalable manner. This versatile deposition technique enables the fabrication of wearable organic electronic devices on clothes.

Biogeography of Iberian freshwater fishes revisited: The roles of historical versus contemporary constraints

USGS Publications Warehouse

Filipe, Ana F.; Araújo, Miguel B.; Doadrio, Ignacio; Angermeier, Paul L.; Collares-Pereira, Maria J.

2009-01-01

Main conclusions The results support the hypothesis that historical factors exert greater constraints on native freshwater fish assemblages in the Iberian Peninsula than do current environmental factors. After examining patterns of assemblage variation across space, as evidenced by the biogeographical provinces, we discuss the likely dispersal and speciation events that underlie these patterns. 

A Computational Method to Quantify Fly Circadian Activity.

PubMed

Lazopulo, Andrey; Syed, Sheyum

2017-10-28

In most animals and plants, circadian clocks orchestrate behavioral and molecular processes and synchronize them to the daily light-dark cycle. Fundamental mechanisms that underlie this temporal control are widely studied using the fruit fly Drosophila melanogaster as a model organism. In flies, the clock is typically studied by analyzing multiday locomotor recording. Such a recording shows a complex bimodal pattern with two peaks of activity: a morning peak that happens around dawn, and an evening peak that happens around dusk. These two peaks together form a waveform that is very different from sinusoidal oscillations observed in clock genes, suggesting that mechanisms in addition to the clock have profound effects in producing the observed patterns in behavioral data. Here we provide instructions on using a recently developed computational method that mathematically describes temporal patterns in fly activity. The method fits activity data with a model waveform that consists of four exponential terms and nine independent parameters that fully describe the shape and size of the morning and evening peaks of activity. The extracted parameters can help elucidate the kinetic mechanisms of substrates that underlie the commonly observed bimodal activity patterns in fly locomotor rhythms.

The landscape ecology and microbiota of the human nose, mouth and throat

PubMed Central

Proctor, Diana M.; Relman, David A.

2017-01-01

Landscape ecology examines the relationships between the spatial arrangement of different landforms and the processes that give rise to spatial and temporal patterns in local community structure. These relationships that underlie the patterns of the microbial communities that inhabit the human body, and in particular, those of the nose, mouth and throat, deserve greater attention. Important questions include what defines the size of a population (i.e., ‘patch’) in a given body site; what defines the boundaries of distinct patches within a single body site, and where and over what spatial scales within a body site are gradients detected. This review looks at the landscape ecology in the upper respiratory tract and mouth, and seeks greater clarity about the physiological factors, whether immunological, chemical or physical, that govern microbial community composition and function, and the ecological traits that underlie health and disease. PMID:28407480

FPGA implementation of a configurable neuromorphic CPG-based locomotion controller.

PubMed

Barron-Zambrano, Jose Hugo; Torres-Huitzil, Cesar

2013-09-01

Neuromorphic engineering is a discipline devoted to the design and development of computational hardware that mimics the characteristics and capabilities of neuro-biological systems. In recent years, neuromorphic hardware systems have been implemented using a hybrid approach incorporating digital hardware so as to provide flexibility and scalability at the cost of power efficiency and some biological realism. This paper proposes an FPGA-based neuromorphic-like embedded system on a chip to generate locomotion patterns of periodic rhythmic movements inspired by Central Pattern Generators (CPGs). The proposed implementation follows a top-down approach where modularity and hierarchy are two desirable features. The locomotion controller is based on CPG models to produce rhythmic locomotion patterns or gaits for legged robots such as quadrupeds and hexapods. The architecture is configurable and scalable for robots with either different morphologies or different degrees of freedom (DOFs). Experiments performed on a real robot are presented and discussed. The obtained results demonstrate that the CPG-based controller provides the necessary flexibility to generate different rhythmic patterns at run-time suitable for adaptable locomotion. Copyright © 2013 Elsevier Ltd. All rights reserved.

AEGIS: a robust and scalable real-time public health surveillance system.

PubMed

Reis, Ben Y; Kirby, Chaim; Hadden, Lucy E; Olson, Karen; McMurry, Andrew J; Daniel, James B; Mandl, Kenneth D

2007-01-01

In this report, we describe the Automated Epidemiological Geotemporal Integrated Surveillance system (AEGIS), developed for real-time population health monitoring in the state of Massachusetts. AEGIS provides public health personnel with automated near-real-time situational awareness of utilization patterns at participating healthcare institutions, supporting surveillance of bioterrorism and naturally occurring outbreaks. As real-time public health surveillance systems become integrated into regional and national surveillance initiatives, the challenges of scalability, robustness, and data security become increasingly prominent. A modular and fault tolerant design helps AEGIS achieve scalability and robustness, while a distributed storage model with local autonomy helps to minimize risk of unauthorized disclosure. The report includes a description of the evolution of the design over time in response to the challenges of a regional and national integration environment.

Laboratory Instrumentation Design Research for Scalable Next Generation Epitaxy: Non-Equilibrium Wide Application Epitaxial Patterning by Intelligent Control (NEW-EPIC). Volume 1. 3D Composition/Doping Control via Micromiror Patterned Deep UV Photodesorption: Revolutionary in situ Characterization/Control

DTIC Science & Technology

2009-02-19

magnesium dopant concentration. A digital micromirror device is introduced to pattern incident UV radiation during InGaN growth, demonstrating that the...magnesium dopant concentration. A digital micromirror device is introduced to pattern incident UV radiation during InGaN growth, demonstrating that the...successful compositional patterning of InGaN using in situ digital micromirror device (DMD) patterning of ultraviolet (UV

Scalable metadata environments (MDE): artistically impelled immersive environments for large-scale data exploration

NASA Astrophysics Data System (ADS)

West, Ruth G.; Margolis, Todd; Prudhomme, Andrew; Schulze, Jürgen P.; Mostafavi, Iman; Lewis, J. P.; Gossmann, Joachim; Singh, Rajvikram

2014-02-01

Scalable Metadata Environments (MDEs) are an artistic approach for designing immersive environments for large scale data exploration in which users interact with data by forming multiscale patterns that they alternatively disrupt and reform. Developed and prototyped as part of an art-science research collaboration, we define an MDE as a 4D virtual environment structured by quantitative and qualitative metadata describing multidimensional data collections. Entire data sets (e.g.10s of millions of records) can be visualized and sonified at multiple scales and at different levels of detail so they can be explored interactively in real-time within MDEs. They are designed to reflect similarities and differences in the underlying data or metadata such that patterns can be visually/aurally sorted in an exploratory fashion by an observer who is not familiar with the details of the mapping from data to visual, auditory or dynamic attributes. While many approaches for visual and auditory data mining exist, MDEs are distinct in that they utilize qualitative and quantitative data and metadata to construct multiple interrelated conceptual coordinate systems. These "regions" function as conceptual lattices for scalable auditory and visual representations within virtual environments computationally driven by multi-GPU CUDA-enabled fluid dyamics systems.

Light refocusing with up-scalable resonant waveguide gratings in confocal prolate spheroid arrangements

NASA Astrophysics Data System (ADS)

Quaranta, Giorgio; Basset, Guillaume; Benes, Zdenek; Martin, Olivier J. F.; Gallinet, Benjamin

2018-01-01

Resonant waveguide gratings (RWGs) are thin-film structures, where coupled modes interfere with the diffracted incoming wave and produce strong angular and spectral filtering. The combination of two finite-length and impedance matched RWGs allows the creation of a passive beam steering element, which is compatible with up-scalable fabrication processes. Here, we propose a design method to create large patterns of such elements able to filter, steer, and focus the light from one point source to another. The method is based on ellipsoidal mirrors to choose a system of confocal prolate spheroids where the two focal points are the source point and observation point, respectively. It allows finding the proper orientation and position of each RWG element of the pattern, such that the phase is constructively preserved at the observation point. The design techniques presented here could be implemented in a variety of systems, where large-scale patterns are needed, such as optical security, multifocal or monochromatic lenses, biosensors, and see-through optical combiners for near-eye displays.

pcircle - A Suite of Scalable Parallel File System Tools

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

WANG, FEIYI

2015-10-01

Most of the software related to file system are written for conventional local file system, they are serialized and can't take advantage of the benefit of a large scale parallel file system. "pcircle" software builds on top of ubiquitous MPI in cluster computing environment and "work-stealing" pattern to provide a scalable, high-performance suite of file system tools. In particular - it implemented parallel data copy and parallel data checksumming, with advanced features such as async progress report, checkpoint and restart, as well as integrity checking.

Scalable printed electronics: an organic decoder addressing ferroelectric non-volatile memory.

PubMed

Ng, Tse Nga; Schwartz, David E; Lavery, Leah L; Whiting, Gregory L; Russo, Beverly; Krusor, Brent; Veres, Janos; Bröms, Per; Herlogsson, Lars; Alam, Naveed; Hagel, Olle; Nilsson, Jakob; Karlsson, Christer

2012-01-01

Scalable circuits of organic logic and memory are realized using all-additive printing processes. A 3-bit organic complementary decoder is fabricated and used to read and write non-volatile, rewritable ferroelectric memory. The decoder-memory array is patterned by inkjet and gravure printing on flexible plastics. Simulation models for the organic transistors are developed, enabling circuit designs tolerant of the variations in printed devices. We explain the key design rules in fabrication of complex printed circuits and elucidate the performance requirements of materials and devices for reliable organic digital logic.

Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invicta.

PubMed

Bowsher, Julia H; Wray, Gregory A; Abouheif, Ehab

2007-12-15

Over the last decade, it has become clear that organismal form is largely determined by developmental and evolutionary changes in the growth and pattern formation of tissues. Yet, there is little known about how these two integrated processes respond to environmental cues or how they evolve relative to one another. Here, we present the discovery of vestigial wing imaginal discs in worker larvae of the red imported fire ant, Solenopsis invicta. These vestigial wing discs are present in all worker larvae, which is uncommon for a species with a large worker size distribution. Furthermore, the growth trajectory of these vestigial discs is distinct from all of the ant species examined to date because they grow at a rate slower than the leg discs. We predicted that the growth trajectory of the vestigial wing discs would be mirrored by evolutionary changes in their patterning. We tested this prediction by examining the expression of three patterning genes, extradenticle, ultrabithorax, and engrailed, known to underlie the wing polyphenism in ants. Surprisingly, the expression patterns of these three genes in the vestigial wing discs was the same as those found in ant species with different worker size distributions and wing disc growth than fire ants. We conclude that growth and patterning are evolutionarily dissociated in the vestigial wing discs of S. invicta because patterning in these discs is conserved, whereas their growth trajectories are not. The evolutionary dissociation of growth and patterning may be an important feature of gene networks that underlie polyphenic traits. 2007 Wiley-Liss, Inc

UPMC Prescription for Wellness: A Quality Improvement Case Study for Supporting Patient Engagement and Health Behavior Change.

PubMed

Maners, Rebecca J; Bakow, Eric; Parkinson, Michael D; Fischer, Gary S; Camp, Geoffrey R

Addressing patient health and care behaviors that underlie much of chronic disease continues to challenge providers, medical practices, health systems, and insurers. Improving health and care as described by the Quadruple Aim requires innovation at the front lines of clinical care: the doctor-patient interaction and office practice. This article describes the use of Lean Six Sigma in a quality improvement (QI) effort to design an effective and scalable method for physicians to prescribe health coaching for healthy behaviors in a primary care medical home within a large integrated delivery and financing system. Building on the national Agency for Healthcare Research and Quality and Robert Wood Johnson Foundation-funded Prescription for Health multisite demonstration, this QI case study provides important lessons for transforming patient-physician-practice support systems to better address lifestyle and care management challenges critical to producing better outcomes.

NPTool: Towards Scalability and Reliability of Business Process Management

NASA Astrophysics Data System (ADS)

Braghetto, Kelly Rosa; Ferreira, João Eduardo; Pu, Calton

Currently one important challenge in business process management is provide at the same time scalability and reliability of business process executions. This difficulty becomes more accentuated when the execution control assumes complex countless business processes. This work presents NavigationPlanTool (NPTool), a tool to control the execution of business processes. NPTool is supported by Navigation Plan Definition Language (NPDL), a language for business processes specification that uses process algebra as formal foundation. NPTool implements the NPDL language as a SQL extension. The main contribution of this paper is a description of the NPTool showing how the process algebra features combined with a relational database model can be used to provide a scalable and reliable control in the execution of business processes. The next steps of NPTool include reuse of control-flow patterns and support to data flow management.

An investigation into scalability and compliance for triple patterning with stitches for metal 1 at the 14nm node

NASA Astrophysics Data System (ADS)

Cork, Christopher; Miloslavsky, Alexander; Friedberg, Paul; Luk-Pat, Gerry

2013-04-01

Lithographers had hoped that single patterning would be enabled at the 20nm node by way of EUV lithography. However, due to delays in EUV readiness, double patterning with 193i lithography is currently relied upon for volume production for the 20nm node's metal 1 layer. At the 14nm and likely at the 10nm node, LE-LE-LE triple patterning technology (TPT) is one of the favored options [1,2] for patterning local interconnect and Metal 1 layers. While previous research has focused on TPT for contact mask, metal layers offer new challenges and opportunities, in particular the ability to decompose design polygons across more than one mask. The extra flexibility offered by the third mask and ability to leverage polygon stitching both serve to improve compliance. However, ensuring TPT compliance - the task of finding a 3-color mask decomposition for a design - is still a difficult task. Moreover, scalability concerns multiply the difficulty of triple patterning decomposition which is an NP-complete problem. Indeed previous work shows that network sizes above a few thousand nodes or polygons start to take significantly longer times to compute [3], making full chip decomposition for arbitrary layouts impractical. In practice Metal 1 layouts can be considered as two separate problem domains, namely: decomposition of standard cells and decomposition of IP blocks. Standard cells typically include only a few 10's of polygons and should be amenable to fast decomposition. Successive design iterations should resolve compliance issues and improve packing density. Density improvements are multiplied repeatedly as standard cells are placed multiple times. IP blocks, on the other hand, may involve very large networks. This paper evaluates multiple approaches to triple patterning decomposition for the Metal 1 layer. The benefits of polygon stitching, in particular, the ability to resolve commonly encountered non-compliant layout configurations and improve packing density, are weighed against the increased difficulty in finding an optimized, legal decomposition and coping with the increased scalability challenges.

Scalable Inference and Learning in Very Large Graphical Models Patterned after the Primate Visual Cortex

DTIC Science & Technology

2008-04-07

Chbelazzi. Atteni onal modulation of visial po e,- Iig . .Anmial R/evictr of Neltroscience, 27:611 617, 2004. [26] \\M. Ri(,seiiiihear and T. Popoio. ierar...cortex-like mechanisms. IEEE Transactions on Pattern Analysis and aloinc Intc/byocc.e 2)9(3)AI :A126. 2007. 130] Erik B. Sudderth. Antonio B. Torralba

Evaluation of MPEG-7-Based Audio Descriptors for Animal Voice Recognition over Wireless Acoustic Sensor Networks.

PubMed

Luque, Joaquín; Larios, Diego F; Personal, Enrique; Barbancho, Julio; León, Carlos

2016-05-18

Environmental audio monitoring is a huge area of interest for biologists all over the world. This is why some audio monitoring system have been proposed in the literature, which can be classified into two different approaches: acquirement and compression of all audio patterns in order to send them as raw data to a main server; or specific recognition systems based on audio patterns. The first approach presents the drawback of a high amount of information to be stored in a main server. Moreover, this information requires a considerable amount of effort to be analyzed. The second approach has the drawback of its lack of scalability when new patterns need to be detected. To overcome these limitations, this paper proposes an environmental Wireless Acoustic Sensor Network architecture focused on use of generic descriptors based on an MPEG-7 standard. These descriptors demonstrate it to be suitable to be used in the recognition of different patterns, allowing a high scalability. The proposed parameters have been tested to recognize different behaviors of two anuran species that live in Spanish natural parks; the Epidalea calamita and the Alytes obstetricans toads, demonstrating to have a high classification performance.

Evaluation of MPEG-7-Based Audio Descriptors for Animal Voice Recognition over Wireless Acoustic Sensor Networks

PubMed Central

Luque, Joaquín; Larios, Diego F.; Personal, Enrique; Barbancho, Julio; León, Carlos

2016-01-01

Environmental audio monitoring is a huge area of interest for biologists all over the world. This is why some audio monitoring system have been proposed in the literature, which can be classified into two different approaches: acquirement and compression of all audio patterns in order to send them as raw data to a main server; or specific recognition systems based on audio patterns. The first approach presents the drawback of a high amount of information to be stored in a main server. Moreover, this information requires a considerable amount of effort to be analyzed. The second approach has the drawback of its lack of scalability when new patterns need to be detected. To overcome these limitations, this paper proposes an environmental Wireless Acoustic Sensor Network architecture focused on use of generic descriptors based on an MPEG-7 standard. These descriptors demonstrate it to be suitable to be used in the recognition of different patterns, allowing a high scalability. The proposed parameters have been tested to recognize different behaviors of two anuran species that live in Spanish natural parks; the Epidalea calamita and the Alytes obstetricans toads, demonstrating to have a high classification performance. PMID:27213375

Association mapping across numerous traits reveals patterns of functional variation in maize

USDA-ARS?s Scientific Manuscript database

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie funct...

Odor-identity dependent motor programs underlie behavioral responses to odors

PubMed Central

Jung, Seung-Hye; Hueston, Catherine; Bhandawat, Vikas

2015-01-01

All animals use olfactory information to perform tasks essential to their survival. Odors typically activate multiple olfactory receptor neuron (ORN) classes and are therefore represented by the patterns of active ORNs. How the patterns of active ORN classes are decoded to drive behavior is under intense investigation. In this study, using Drosophila as a model system, we investigate the logic by which odors modulate locomotion. We designed a novel behavioral arena in which we could examine a fly’s locomotion under precisely controlled stimulus condition. In this arena, in response to similarly attractive odors, flies modulate their locomotion differently implying that odors have a more diverse effect on locomotion than was anticipated. Three features underlie odor-guided locomotion: First, in response to odors, flies modulate a surprisingly large number of motor parameters. Second, similarly attractive odors elicit changes in different motor programs. Third, different ORN classes modulate different subset of motor parameters. DOI: http://dx.doi.org/10.7554/eLife.11092.001 PMID:26439011

Scalable printed electronics: an organic decoder addressing ferroelectric non-volatile memory

PubMed Central

Ng, Tse Nga; Schwartz, David E.; Lavery, Leah L.; Whiting, Gregory L.; Russo, Beverly; Krusor, Brent; Veres, Janos; Bröms, Per; Herlogsson, Lars; Alam, Naveed; Hagel, Olle; Nilsson, Jakob; Karlsson, Christer

2012-01-01

Scalable circuits of organic logic and memory are realized using all-additive printing processes. A 3-bit organic complementary decoder is fabricated and used to read and write non-volatile, rewritable ferroelectric memory. The decoder-memory array is patterned by inkjet and gravure printing on flexible plastics. Simulation models for the organic transistors are developed, enabling circuit designs tolerant of the variations in printed devices. We explain the key design rules in fabrication of complex printed circuits and elucidate the performance requirements of materials and devices for reliable organic digital logic. PMID:22900143

Direct laser writing of micro-supercapacitors on hydrated graphite oxide films.

PubMed

Gao, Wei; Singh, Neelam; Song, Li; Liu, Zheng; Reddy, Arava Leela Mohana; Ci, Lijie; Vajtai, Robert; Zhang, Qing; Wei, Bingqing; Ajayan, Pulickel M

2011-07-31

Microscale supercapacitors provide an important complement to batteries in a variety of applications, including portable electronics. Although they can be manufactured using a number of printing and lithography techniques, continued improvements in cost, scalability and form factor are required to realize their full potential. Here, we demonstrate the scalable fabrication of a new type of all-carbon, monolithic supercapacitor by laser reduction and patterning of graphite oxide films. We pattern both in-plane and conventional electrodes consisting of reduced graphite oxide with micrometre resolution, between which graphite oxide serves as a solid electrolyte. The substantial amounts of trapped water in the graphite oxide makes it simultaneously a good ionic conductor and an electrical insulator, allowing it to serve as both an electrolyte and an electrode separator with ion transport characteristics similar to that observed for Nafion membranes. The resulting micro-supercapacitor devices show good cyclic stability, and energy storage capacities comparable to existing thin-film supercapacitors.

Direct laser writing of micro-supercapacitors on hydrated graphite oxide films

NASA Astrophysics Data System (ADS)

Gao, Wei; Singh, Neelam; Song, Li; Liu, Zheng; Reddy, Arava Leela Mohana; Ci, Lijie; Vajtai, Robert; Zhang, Qing; Wei, Bingqing; Ajayan, Pulickel M.

2011-08-01

Microscale supercapacitors provide an important complement to batteries in a variety of applications, including portable electronics. Although they can be manufactured using a number of printing and lithography techniques, continued improvements in cost, scalability and form factor are required to realize their full potential. Here, we demonstrate the scalable fabrication of a new type of all-carbon, monolithic supercapacitor by laser reduction and patterning of graphite oxide films. We pattern both in-plane and conventional electrodes consisting of reduced graphite oxide with micrometre resolution, between which graphite oxide serves as a solid electrolyte. The substantial amounts of trapped water in the graphite oxide makes it simultaneously a good ionic conductor and an electrical insulator, allowing it to serve as both an electrolyte and an electrode separator with ion transport characteristics similar to that observed for Nafion membranes. The resulting micro-supercapacitor devices show good cyclic stability, and energy storage capacities comparable to existing thin-film supercapacitors.

Scalable Sub-micron Patterning of Organic Materials Toward High Density Soft Electronics.

PubMed

Kim, Jaekyun; Kim, Myung-Gil; Kim, Jaehyun; Jo, Sangho; Kang, Jingu; Jo, Jeong-Wan; Lee, Woobin; Hwang, Chahwan; Moon, Juhyuk; Yang, Lin; Kim, Yun-Hi; Noh, Yong-Young; Jaung, Jae Yun; Kim, Yong-Hoon; Park, Sung Kyu

2015-09-28

The success of silicon based high density integrated circuits ignited explosive expansion of microelectronics. Although the inorganic semiconductors have shown superior carrier mobilities for conventional high speed switching devices, the emergence of unconventional applications, such as flexible electronics, highly sensitive photosensors, large area sensor array, and tailored optoelectronics, brought intensive research on next generation electronic materials. The rationally designed multifunctional soft electronic materials, organic and carbon-based semiconductors, are demonstrated with low-cost solution process, exceptional mechanical stability, and on-demand optoelectronic properties. Unfortunately, the industrial implementation of the soft electronic materials has been hindered due to lack of scalable fine-patterning methods. In this report, we demonstrated facile general route for high throughput sub-micron patterning of soft materials, using spatially selective deep-ultraviolet irradiation. For organic and carbon-based materials, the highly energetic photons (e.g. deep-ultraviolet rays) enable direct photo-conversion from conducting/semiconducting to insulating state through molecular dissociation and disordering with spatial resolution down to a sub-μm-scale. The successful demonstration of organic semiconductor circuitry promise our result proliferate industrial adoption of soft materials for next generation electronics.

Scalable Sub-micron Patterning of Organic Materials Toward High Density Soft Electronics

NASA Astrophysics Data System (ADS)

Kim, Jaekyun; Kim, Myung-Gil; Kim, Jaehyun; Jo, Sangho; Kang, Jingu; Jo, Jeong-Wan; Lee, Woobin; Hwang, Chahwan; Moon, Juhyuk; Yang, Lin; Kim, Yun-Hi; Noh, Yong-Young; Yun Jaung, Jae; Kim, Yong-Hoon; Kyu Park, Sung

2015-09-01

The success of silicon based high density integrated circuits ignited explosive expansion of microelectronics. Although the inorganic semiconductors have shown superior carrier mobilities for conventional high speed switching devices, the emergence of unconventional applications, such as flexible electronics, highly sensitive photosensors, large area sensor array, and tailored optoelectronics, brought intensive research on next generation electronic materials. The rationally designed multifunctional soft electronic materials, organic and carbon-based semiconductors, are demonstrated with low-cost solution process, exceptional mechanical stability, and on-demand optoelectronic properties. Unfortunately, the industrial implementation of the soft electronic materials has been hindered due to lack of scalable fine-patterning methods. In this report, we demonstrated facile general route for high throughput sub-micron patterning of soft materials, using spatially selective deep-ultraviolet irradiation. For organic and carbon-based materials, the highly energetic photons (e.g. deep-ultraviolet rays) enable direct photo-conversion from conducting/semiconducting to insulating state through molecular dissociation and disordering with spatial resolution down to a sub-μm-scale. The successful demonstration of organic semiconductor circuitry promise our result proliferate industrial adoption of soft materials for next generation electronics.

A Simulation Study of Mutations in the Genetic Regulatory Hierarchy for Butterfly Eyespot Focus Determination

PubMed Central

Marcus, Jeffrey M.; Evans, Travis M.

2008-01-01

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci (Evans and Marcus, 2006). The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci. PMID:18586070

Scalable Directed Assembly of Highly Crystalline 2,7-Dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) Films.

PubMed

Chai, Zhimin; Abbasi, Salman A; Busnaina, Ahmed A

2018-05-30

Assembly of organic semiconductors with ordered crystal structure has been actively pursued for electronics applications such as organic field-effect transistors (OFETs). Among various film deposition methods, solution-based film growth from small molecule semiconductors is preferable because of its low material and energy consumption, low cost, and scalability. Here, we show scalable and controllable directed assembly of highly crystalline 2,7-dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) films via a dip-coating process. Self-aligned stripe patterns with tunable thickness and morphology over a centimeter scale are obtained by adjusting two governing parameters: the pulling speed of a substrate and the solution concentration. OFETs are fabricated using the C8-BTBT films assembled at various conditions. A field-effect hole mobility up to 3.99 cm 2 V -1 s -1 is obtained. Owing to the highly scalable crystalline film formation, the dip-coating directed assembly process could be a great candidate for manufacturing next-generation electronics. Meanwhile, the film formation mechanism discussed in this paper could provide a general guideline to prepare other organic semiconducting films from small molecule solutions.

The Mechanism by which Neurofibromin Suppresses Tumorigenesis

DTIC Science & Technology

2013-02-01

et al., 2011; Taichman et al., 2002; Zeelenberg et al., 2003; Zhou et al., 2002), as well as non-Hodgkin’s lymphoma (Bertolini et al., 2002), and...underlie the unique pattern of optic glioma growth in neurofibromatosis type Cancer Res 67, 8588-8595. Zeelenberg , I.S., Ruuls-Van Stalle, L., and

Modeling Temporal Behavior in Large Networks: A Dynamic Mixed-Membership Model

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

Rossi, R; Gallagher, B; Neville, J

Given a large time-evolving network, how can we model and characterize the temporal behaviors of individual nodes (and network states)? How can we model the behavioral transition patterns of nodes? We propose a temporal behavior model that captures the 'roles' of nodes in the graph and how they evolve over time. The proposed dynamic behavioral mixed-membership model (DBMM) is scalable, fully automatic (no user-defined parameters), non-parametric/data-driven (no specific functional form or parameterization), interpretable (identifies explainable patterns), and flexible (applicable to dynamic and streaming networks). Moreover, the interpretable behavioral roles are generalizable, computationally efficient, and natively supports attributes. We applied ourmore » model for (a) identifying patterns and trends of nodes and network states based on the temporal behavior, (b) predicting future structural changes, and (c) detecting unusual temporal behavior transitions. We use eight large real-world datasets from different time-evolving settings (dynamic and streaming). In particular, we model the evolving mixed-memberships and the corresponding behavioral transitions of Twitter, Facebook, IP-Traces, Email (University), Internet AS, Enron, Reality, and IMDB. The experiments demonstrate the scalability, flexibility, and effectiveness of our model for identifying interesting patterns, detecting unusual structural transitions, and predicting the future structural changes of the network and individual nodes.« less

A novel approach to describing and detecting performance anti-patterns

NASA Astrophysics Data System (ADS)

Sheng, Jinfang; Wang, Yihan; Hu, Peipei; Wang, Bin

2017-08-01

Anti-pattern, as an extension to pattern, describes a widely used poor solution which can bring negative influence to application systems. Aiming at the shortcomings of the existing anti-pattern descriptions, an anti-pattern description method based on first order predicate is proposed. This method synthesizes anti-pattern forms and symptoms, which makes the description more accurate and has good scalability and versatility as well. In order to improve the accuracy of anti-pattern detection, a Bayesian classification method is applied in validation for detection results, which can reduce false negatives and false positives of anti-pattern detection. Finally, the proposed approach in this paper is applied to a small e-commerce system, the feasibility and effectiveness of the approach is demonstrated further through experiments.

Random or predictable?: Adoption patterns of chronic care management practices in physician organizations.

PubMed

Miake-Lye, Isomi M; Chuang, Emmeline; Rodriguez, Hector P; Kominski, Gerald F; Yano, Elizabeth M; Shortell, Stephen M

2017-08-24

Theories, models, and frameworks used by implementation science, including Diffusion of Innovations, tend to focus on the adoption of one innovation, when often organizations may be facing multiple simultaneous adoption decisions. For instance, despite evidence that care management practices (CMPs) are helpful in managing chronic illness, there is still uneven adoption by physician organizations. This exploratory paper leverages this natural variation in uptake to describe inter-organizational patterns in adoption of CMPs and to better understand how adoption choices may be related to one another. We assessed a cross section of national survey data from physician organizations reporting on the use of 20 CMPs (5 each for asthma, congestive heart failure, depression, and diabetes). Item response theory was used to explore patterns in adoption, first considering all 20 CMPs together and then by subsets according to disease focus or CMP type (e.g., registries, patient reminders). Mokken scale analysis explored whether adoption choices were linked by disease focus or CMP type and whether a consistent ordering of adoption choices was present. The Mokken scale for all 20 CMPs demonstrated medium scalability (H = 0.43), but no consistent ordering. Scales for subsets of CMPs sharing a disease focus had medium scalability (0.4 < H < 0.5), while subsets sharing a CMP type had strong scalability (H > 0.5). Scales for CMP type consistently ranked diabetes CMPs as most adoptable and depression CMPs as least adoptable. Within disease focus scales, patient reminders were ranked as the most adoptable CMP, while clinician feedback and patient education were ranked the least adoptable. Patterns of adoption indicate that innovation characteristics may influence adoption. CMP dissemination efforts may be strengthened by encouraging traditionally non-adopting organizations to focus on more adoptable practices first and then describing a pathway for the adoption of subsequent CMPs. Clarifying why certain CMPs are "less adoptable" may also provide insights into how to overcome CMP adoption constraints.

The Characteristics of, and Motivations for, Indigenous Student Mobility: Examples from Urban and Regional Queensland, Australia

ERIC Educational Resources Information Center

Navin, Fiona; Hill, Angela; Doyle, Tanya

2012-01-01

Using the notion that research should "enlighten" policy responses, this paper considers the complex locational factors that affect and underlie patterns of Indigenous student mobility in Queensland, Australia. The paper presents data, captured through an action research project, to explore mobility "in and through" two…

How Language Limits Our Understanding of Environmental Education.

ERIC Educational Resources Information Center

Bowers, Chet

2001-01-01

Develops a theory of metaphor that helps explain how environmental education contributes to the double bind of helping to address environmental problems while at the same time reinforcing the use of the language-thought patterns that underlie the digital phase of the Industrial Revolution that we are now entering on a global scale. (Author/SAH)

Executive Functions in Asperger's Syndrome: An Empirical Investigation of Verbal and Nonverbal Skills

ERIC Educational Resources Information Center

McCrimmon, Adam W.; Schwean, Vicki L.; Saklofske, Donald H.; Montgomery, Janine M.; Brady, Danielle I.

2012-01-01

Deficits in executive functioning (EF) have been proposed to underlie the behavioural patterns of individuals with an autism spectrum disorder. Researchers have shown that the Asperger's syndrome (AS) population performs more poorly than typically developing controls on many EF tasks. However, the research literature is inconsistent in identifying…

What Can Errors Tell Us about Differences between Monolingual and Bilingual Vocabulary Learning?

ERIC Educational Resources Information Center

Kaushanskaya, Margarita

2018-01-01

Error patterns in vocabulary learning data were used as a window into the mechanisms that underlie vocabulary learning performance in bilinguals vs. monolinguals. English--Spanish bilinguals (n = 18) and English-speaking monolinguals (n = 18) were taught novel vocabulary items in association with English translations. At testing, participants…

Conserved and divergent functions of Pax6 underlie species-specific neurogenic patterns in the developing amniote brain.

PubMed

Yamashita, Wataru; Takahashi, Masanori; Kikkawa, Takako; Gotoh, Hitoshi; Osumi, Noriko; Ono, Katsuhiko; Nomura, Tadashi

2018-04-16

The evolution of unique organ structures is associated with changes in conserved developmental programs. However, characterizing the functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics has remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that the neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, whereas stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, consistent with Pax6-dependent temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium is highly divergent in these species. Our results suggest that spatiotemporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie the morphological divergence of the amniote pallial architectures. © 2018. Published by The Company of Biologists Ltd.

A general design strategy for block copolymer directed self-assembly patterning of integrated circuits contact holes using an alphabet approach.

PubMed

Yi, He; Bao, Xin-Yu; Tiberio, Richard; Wong, H-S Philip

2015-02-11

Directed self-assembly (DSA) is a promising lithography candidate for technology nodes beyond 14 nm. Researchers have shown contact hole patterning for random logic circuits using DSA with small physical templates. This paper introduces an alphabet approach that uses a minimal set of small physical templates to pattern all contacts configurations on integrated circuits. We illustrate, through experiments, a general and scalable template design strategy that links the DSA material properties to the technology node requirements.

Scalable Sub-micron Patterning of Organic Materials Toward High Density Soft Electronics

PubMed Central

Kim, Jaekyun; Kim, Myung-Gil; Kim, Jaehyun; Jo, Sangho; Kang, Jingu; Jo, Jeong-Wan; Lee, Woobin; Hwang, Chahwan; Moon, Juhyuk; Yang, Lin; Kim, Yun-Hi; Noh, Yong-Young; Yun Jaung, Jae; Kim, Yong-Hoon; Kyu Park, Sung

2015-01-01

The success of silicon based high density integrated circuits ignited explosive expansion of microelectronics. Although the inorganic semiconductors have shown superior carrier mobilities for conventional high speed switching devices, the emergence of unconventional applications, such as flexible electronics, highly sensitive photosensors, large area sensor array, and tailored optoelectronics, brought intensive research on next generation electronic materials. The rationally designed multifunctional soft electronic materials, organic and carbon-based semiconductors, are demonstrated with low-cost solution process, exceptional mechanical stability, and on-demand optoelectronic properties. Unfortunately, the industrial implementation of the soft electronic materials has been hindered due to lack of scalable fine-patterning methods. In this report, we demonstrated facile general route for high throughput sub-micron patterning of soft materials, using spatially selective deep-ultraviolet irradiation. For organic and carbon-based materials, the highly energetic photons (e.g. deep-ultraviolet rays) enable direct photo-conversion from conducting/semiconducting to insulating state through molecular dissociation and disordering with spatial resolution down to a sub-μm-scale. The successful demonstration of organic semiconductor circuitry promise our result proliferate industrial adoption of soft materials for next generation electronics. PMID:26411932

Scalable sub-micron patterning of organic materials toward high density soft electronics

DOE PAGES

Kim, Jaekyun; Kim, Myung -Gil; Kim, Jaehyun; ...

2015-09-28

The success of silicon based high density integrated circuits ignited explosive expansion of microelectronics. Although the inorganic semiconductors have shown superior carrier mobilities for conventional high speed switching devices, the emergence of unconventional applications, such as flexible electronics, highly sensitive photosensors, large area sensor array, and tailored optoelectronics, brought intensive research on next generation electronic materials. The rationally designed multifunctional soft electronic materials, organic and carbon-based semiconductors, are demonstrated with low-cost solution process, exceptional mechanical stability, and on-demand optoelectronic properties. Unfortunately, the industrial implementation of the soft electronic materials has been hindered due to lack of scalable fine-patterning methods. Inmore » this report, we demonstrated facile general route for high throughput sub-micron patterning of soft materials, using spatially selective deep-ultraviolet irradiation. For organic and carbon-based materials, the highly energetic photons (e.g. deep-ultraviolet rays) enable direct photo-conversion from conducting/semiconducting to insulating state through molecular dissociation and disordering with spatial resolution down to a sub-μm-scale. As a result, the successful demonstration of organic semiconductor circuitry promise our result proliferate industrial adoption of soft materials for next generation electronics.« less

Large Scale Frequent Pattern Mining using MPI One-Sided Model

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

Vishnu, Abhinav; Agarwal, Khushbu

In this paper, we propose a work-stealing runtime --- Library for Work Stealing LibWS --- using MPI one-sided model for designing scalable FP-Growth --- {\\em de facto} frequent pattern mining algorithm --- on large scale systems. LibWS provides locality efficient and highly scalable work-stealing techniques for load balancing on a variety of data distributions. We also propose a novel communication algorithm for FP-growth data exchange phase, which reduces the communication complexity from state-of-the-art O(p) to O(f + p/f) for p processes and f frequent attributed-ids. FP-Growth is implemented using LibWS and evaluated on several work distributions and support counts. Anmore » experimental evaluation of the FP-Growth on LibWS using 4096 processes on an InfiniBand Cluster demonstrates excellent efficiency for several work distributions (87\\% efficiency for Power-law and 91% for Poisson). The proposed distributed FP-Tree merging algorithm provides 38x communication speedup on 4096 cores.« less

Enhanced Condensation Heat Transfer On Patterned Surfaces

NASA Astrophysics Data System (ADS)

Alizadeh-Birjandi, Elaheh; Kavehpour, H. Pirouz

2017-11-01

Transition from film to drop wise condensation can improve the efficiency of thermal management applications and result in considerable savings in investments and operating costs by millions of dollars every year. The current methods available are either hydrophobic coating or nanostructured surfaces. The former has little adhesion to the structure which tends to detach easily under working conditions, the fabrication techniques of the latter are neither cost-effective nor scalable, and both are made with low thermal conductivity materials that would negate the heat transfer enhancement by drop wise condensation. Therefore, the existing technologies have limitations in enhancing vapor-to-liquid condensation. This work focuses on development of surfaces with wettability contrast to boost drop wise condensation, which its overall heat transfer efficiency is 2-3 times film wise condensation, while maintaining high conduction rate through the surface at low manufacturing costs. The variation in interfacial energy is achieved through crafting hydrophobic patterns to the surface of the metal via scalable fabrication techniques. The results of experimental and surface optimization studies are also presented.

Highly sensitive MoS2 photodetectors with graphene contacts

NASA Astrophysics Data System (ADS)

Han, Peize; St. Marie, Luke; Wang, Qing X.; Quirk, Nicholas; El Fatimy, Abdel; Ishigami, Masahiro; Barbara, Paola

2018-05-01

Two-dimensional materials such as graphene and transition metal dichalcogenides (TMDs) are ideal candidates to create ultra-thin electronics suitable for flexible substrates. Although optoelectronic devices based on TMDs have demonstrated remarkable performance, scalability is still a significant issue. Most devices are created using techniques that are not suitable for mass production, such as mechanical exfoliation of monolayer flakes and patterning by electron-beam lithography. Here we show that large-area MoS2 grown by chemical vapor deposition and patterned by photolithography yields highly sensitive photodetectors, with record shot-noise-limited detectivities of 8.7 × 1014 Jones in ambient condition and even higher when sealed with a protective layer. These detectivity values are higher than the highest values reported for photodetectors based on exfoliated MoS2. We study MoS2 devices with gold electrodes and graphene electrodes. The devices with graphene electrodes have a tunable band alignment and are especially attractive for scalable ultra-thin flexible optoelectronics.

Highly sensitive MoS2 photodetectors with graphene contacts.

PubMed

Han, Peize; St Marie, Luke; Wang, Qing X; Quirk, Nicholas; El Fatimy, Abdel; Ishigami, Masahiro; Barbara, Paola

2018-05-18

Two-dimensional materials such as graphene and transition metal dichalcogenides (TMDs) are ideal candidates to create ultra-thin electronics suitable for flexible substrates. Although optoelectronic devices based on TMDs have demonstrated remarkable performance, scalability is still a significant issue. Most devices are created using techniques that are not suitable for mass production, such as mechanical exfoliation of monolayer flakes and patterning by electron-beam lithography. Here we show that large-area MoS 2 grown by chemical vapor deposition and patterned by photolithography yields highly sensitive photodetectors, with record shot-noise-limited detectivities of 8.7 × 10 14 Jones in ambient condition and even higher when sealed with a protective layer. These detectivity values are higher than the highest values reported for photodetectors based on exfoliated MoS 2 . We study MoS 2 devices with gold electrodes and graphene electrodes. The devices with graphene electrodes have a tunable band alignment and are especially attractive for scalable ultra-thin flexible optoelectronics.

Frequency-domain nonlinear optics in two-dimensionally patterned quasi-phase-matching media.

PubMed

Phillips, C R; Mayer, B W; Gallmann, L; Keller, U

2016-07-11

Advances in the amplification and manipulation of ultrashort laser pulses have led to revolutions in several areas. Examples include chirped pulse amplification for generating high peak-power lasers, power-scalable amplification techniques, pulse shaping via modulation of spatially-dispersed laser pulses, and efficient frequency-mixing in quasi-phase-matched nonlinear crystals to access new spectral regions. In this work, we introduce and demonstrate a new platform for nonlinear optics which has the potential to combine these separate functionalities (pulse amplification, frequency transfer, and pulse shaping) into a single monolithic device that is bandwidth- and power-scalable. The approach is based on two-dimensional (2D) patterning of quasi-phase-matching (QPM) gratings combined with optical parametric interactions involving spatially dispersed laser pulses. Our proof of principle experiment demonstrates this technique via mid-infrared optical parametric chirped pulse amplification of few-cycle pulses. Additionally, we present a detailed theoretical and numerical analysis of such 2D-QPM devices and how they can be designed.

Hierarchically structured lithium titanate for ultrafast charging in long-life high capacity batteries

NASA Astrophysics Data System (ADS)

Odziomek, Mateusz; Chaput, Frédéric; Rutkowska, Anna; Świerczek, Konrad; Olszewska, Danuta; Sitarz, Maciej; Lerouge, Frédéric; Parola, Stephane

2017-05-01

High-performance Li-ion batteries require materials with well-designed and controlled structures on nanometre and micrometre scales. Electrochemical properties can be enhanced by reducing crystallite size and by manipulating structure and morphology. Here we show a method for preparing hierarchically structured Li4Ti5O12 yielding nano- and microstructure well-suited for use in lithium-ion batteries. Scalable glycothermal synthesis yields well-crystallized primary 4-8 nm nanoparticles, assembled into porous secondary particles. X-ray photoelectron spectroscopy reveals presence of Ti+4 only; combined with chemical analysis showing lithium deficiency, this suggests oxygen non-stoichiometry. Electron microscopy confirms hierarchical morphology of the obtained material. Extended cycling tests in half cells demonstrates capacity of 170 mAh g-1 and no sign of capacity fading after 1,000 cycles at 50C rate (charging completed in 72 s). The particular combination of nanostructure, microstructure and non-stoichiometry for the prepared lithium titanate is believed to underlie the observed electrochemical performance of material.

A Comparative Study of Frequent and Maximal Periodic Pattern Mining Algorithms in Spatiotemporal Databases

NASA Astrophysics Data System (ADS)

Obulesu, O.; Rama Mohan Reddy, A., Dr; Mahendra, M.

2017-08-01

Detecting regular and efficient cyclic models is the demanding activity for data analysts due to unstructured, vigorous and enormous raw information produced from web. Many existing approaches generate large candidate patterns in the occurrence of huge and complex databases. In this work, two novel algorithms are proposed and a comparative examination is performed by considering scalability and performance parameters. The first algorithm is, EFPMA (Extended Regular Model Detection Algorithm) used to find frequent sequential patterns from the spatiotemporal dataset and the second one is, ETMA (Enhanced Tree-based Mining Algorithm) for detecting effective cyclic models with symbolic database representation. EFPMA is an algorithm grows models from both ends (prefixes and suffixes) of detected patterns, which results in faster pattern growth because of less levels of database projection compared to existing approaches such as Prefixspan and SPADE. ETMA uses distinct notions to store and manage transactions data horizontally such as segment, sequence and individual symbols. ETMA exploits a partition-and-conquer method to find maximal patterns by using symbolic notations. Using this algorithm, we can mine cyclic models in full-series sequential patterns including subsection series also. ETMA reduces the memory consumption and makes use of the efficient symbolic operation. Furthermore, ETMA only records time-series instances dynamically, in terms of character, series and section approaches respectively. The extent of the pattern and proving efficiency of the reducing and retrieval techniques from synthetic and actual datasets is a really open & challenging mining problem. These techniques are useful in data streams, traffic risk analysis, medical diagnosis, DNA sequence Mining, Earthquake prediction applications. Extensive investigational outcomes illustrates that the algorithms outperforms well towards efficiency and scalability than ECLAT, STNR and MAFIA approaches.

A simulation study of mutations in the genetic regulatory hierarchy for butterfly eyespot focus determination.

PubMed

Marcus, Jeffrey M; Evans, Travis M

2008-09-01

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci [Evans, T.M., Marcus, J.M., 2006. A simulation study of the genetic regulatory hierarchy for butterfly eyespot focus determination. Evol. Dev. 8, 273-283]. The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci.

Current versus future reproduction and longevity: a re-evaluation of predictions and mechanisms.

PubMed

Zhang, Yufeng; Hood, Wendy R

2016-10-15

Oxidative damage is predicted to be a mediator of trade-offs between current reproduction and future reproduction or survival, but most studies fail to support such predictions. We suggest that two factors underlie the equivocal nature of these findings: (1) investigators typically assume a negative linear relationship between current reproduction and future reproduction or survival, even though this is not consistently shown by empirical studies; and (2) studies often fail to target mechanisms that could link interactions between sequential life-history events. Here, we review common patterns of reproduction, focusing on the relationships between reproductive performance, survival and parity in females. Observations in a range of species show that performance between sequential reproductive events can decline, remain consistent or increase. We describe likely bioenergetic consequences of reproduction that could underlie these changes in fitness, including mechanisms that could be responsible for negative effects being ephemeral, persistent or delayed. Finally, we make recommendations for designing future studies. We encourage investigators to carefully consider additional or alternative measures of bioenergetic function in studies of life-history trade-offs. Such measures include reactive oxygen species production, oxidative repair, mitochondrial biogenesis, cell proliferation, mitochondrial DNA mutation and replication error and, importantly, a measure of the respiratory function to determine whether measured differences in bioenergetic state are associated with a change in the energetic capacity of tissues that could feasibly affect future reproduction or lifespan. More careful consideration of the life-history context and bioenergetic variables will improve our understanding of the mechanisms that underlie the life-history patterns of animals. © 2016. Published by The Company of Biologists Ltd.

Current versus future reproduction and longevity: a re-evaluation of predictions and mechanisms

PubMed Central

Zhang, Yufeng

2016-01-01

ABSTRACT Oxidative damage is predicted to be a mediator of trade-offs between current reproduction and future reproduction or survival, but most studies fail to support such predictions. We suggest that two factors underlie the equivocal nature of these findings: (1) investigators typically assume a negative linear relationship between current reproduction and future reproduction or survival, even though this is not consistently shown by empirical studies; and (2) studies often fail to target mechanisms that could link interactions between sequential life-history events. Here, we review common patterns of reproduction, focusing on the relationships between reproductive performance, survival and parity in females. Observations in a range of species show that performance between sequential reproductive events can decline, remain consistent or increase. We describe likely bioenergetic consequences of reproduction that could underlie these changes in fitness, including mechanisms that could be responsible for negative effects being ephemeral, persistent or delayed. Finally, we make recommendations for designing future studies. We encourage investigators to carefully consider additional or alternative measures of bioenergetic function in studies of life-history trade-offs. Such measures include reactive oxygen species production, oxidative repair, mitochondrial biogenesis, cell proliferation, mitochondrial DNA mutation and replication error and, importantly, a measure of the respiratory function to determine whether measured differences in bioenergetic state are associated with a change in the energetic capacity of tissues that could feasibly affect future reproduction or lifespan. More careful consideration of the life-history context and bioenergetic variables will improve our understanding of the mechanisms that underlie the life-history patterns of animals. PMID:27802148

3D structural patterns in scalable, elastomeric scaffolds guide engineered tissue architecture.

PubMed

Kolewe, Martin E; Park, Hyoungshin; Gray, Caprice; Ye, Xiaofeng; Langer, Robert; Freed, Lisa E

2013-08-27

Microfabricated elastomeric scaffolds with 3D structural patterns are created by semiautomated layer-by-layer assembly of planar polymer sheets with through-pores. The mesoscale interconnected pore architectures governed by the relative alignment of layers are shown to direct cell and muscle-like fiber orientation in both skeletal and cardiac muscle, enabling scale up of tissue constructs towards clinically relevant dimensions. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Testing the Item-Order Account of Design Effects Using the Production Effect

ERIC Educational Resources Information Center

Jonker, Tanya R.; Levene, Merrick; MacLeod, Colin M.

2014-01-01

A number of memory phenomena evident in recall in within-subject, mixed-lists designs are reduced or eliminated in between-subject, pure-list designs. The item-order account (McDaniel & Bugg, 2008) proposes that differential retention of order information might underlie this pattern. According to this account, order information may be encoded…

Big-leaf mahogany (Swietenia macrophylla) seedling survival and growth across a topographic gradient in southeast Pará, Brazil

Treesearch

James Grogana; Mark S. Ashtona; Galv& atilde; Jurandir oc

2003-01-01

Adult populations of big-leaf mahogany (Swietenia macrophylla) occur in aggregations along seasonal streams in transitional evergreen forests of southeast Pará, Brazil. To test whether variable seedling survival and growth across topography may underlie this observed distribution pattern, we planted nursery-grown seedlings in the...

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Treesearch

Samuel A. Cushman

2006-01-01

Habitat loss and fragmentation are among the largest threats to amphibian populations. However, most studies have not provided clear insights into their population-level implications. There is a critical need to investigate the mechanisms that underlie patterns of distribution and abundance. In order to understand the population- and species-level implications of...

Scalable Kernel Methods and Algorithms for General Sequence Analysis

ERIC Educational Resources Information Center

Kuksa, Pavel

2011-01-01

Analysis of large-scale sequential data has become an important task in machine learning and pattern recognition, inspired in part by numerous scientific and technological applications such as the document and text classification or the analysis of biological sequences. However, current computational methods for sequence comparison still lack…

Distinct Patterns of Cognitive Conflict Dynamics in Promise Keepers and Promise Breakers.

PubMed

Calluso, Cinzia; Saulin, Anne; Baumgartner, Thomas; Knoch, Daria

2018-01-01

On a daily basis, we see how different people can be in keeping or breaking a given promise. However, we know very little about the cognitive conflict dynamics that underlie the decision to keep or break a promise and whether this is shaped by inter-individual variability. In order to fill this gap, we applied an ecologically valid promise decision task with real monetary consequences for all involved interaction partners and used mouse tracking to identify the dynamic, on-line cognitive processes that underlie the decision to keep or break a promise. Our findings revealed that on average, the process of breaking a promise is associated with largely curved mouse trajectories, while the process of keeping a promise was not, indicating that breaking a promise is associated with a larger conflict. Interestingly, however, this conflict pattern was strongly shaped by individual differences. Individuals who always kept their promises did not show any signs of conflict (i.e., straight mouse trajectories), indicating that they were not tempted by the monetary benefits associated with breaking the promise. In contrast, individuals who did not always keep their promise exhibited a large conflict (i.e., curved mouse trajectories), irrespective of whether they broke or kept their promise. A possible interpretation of these findings is that these individuals were always tempted by the unchosen decision option - the desire to act in a fair manner when breaking the promise and the monetary benefits when keeping the promise. This study provides the first piece of evidence that there are substantial inter-individual differences in cognitive conflict dynamics that underlie the decision to keep or break promises and that mouse tracking is able to illuminate important insights into individual differences in complex human's decision processes.

Horizontal and vertical combination of multi-tenancy patterns in service-oriented applications

NASA Astrophysics Data System (ADS)

Mietzner, Ralph; Leymann, Frank; Unger, Tobias

2011-02-01

Software as a service (SaaS) providers exploit economies of scale by offering the same instance of an application to multiple customers typically in a single-instance multi-tenant architecture model. Therefore the applications must be scalable, multi-tenant aware and configurable. In this article, we show how the services in a service-oriented SaaS application can be deployed using different multi-tenancy patterns. We describe how services in different multi-tenancy patterns can be composed on the application level. In addition to that, we also describe how these multi-tenancy patterns can be applied to middleware and hardware components. We then show with some real world examples how the different multi-tenancy patterns can be combined.

Global Neural Pattern Similarity as a Common Basis for Categorization and Recognition Memory

PubMed Central

Xue, Gui; Love, Bradley C.; Preston, Alison R.; Poldrack, Russell A.

2014-01-01

Familiarity, or memory strength, is a central construct in models of cognition. In previous categorization and long-term memory research, correlations have been found between psychological measures of memory strength and activation in the medial temporal lobes (MTLs), which suggests a common neural locus for memory strength. However, activation alone is insufficient for determining whether the same mechanisms underlie neural function across domains. Guided by mathematical models of categorization and long-term memory, we develop a theory and a method to test whether memory strength arises from the global similarity among neural representations. In human subjects, we find significant correlations between global similarity among activation patterns in the MTLs and both subsequent memory confidence in a recognition memory task and model-based measures of memory strength in a category learning task. Our work bridges formal cognitive theories and neuroscientific models by illustrating that the same global similarity computations underlie processing in multiple cognitive domains. Moreover, by establishing a link between neural similarity and psychological memory strength, our findings suggest that there may be an isomorphism between psychological and neural representational spaces that can be exploited to test cognitive theories at both the neural and behavioral levels. PMID:24872552

A construct divided: prosocial behavior as helping, sharing, and comforting subtypes.

PubMed

Dunfield, Kristen A

2014-01-01

The development and maintenance of prosocial, other-oriented behaviors has been of considerable recent interest. Though it is clear that prosocial behaviors emerge early and play a uniquely important role in the social lives of humans, there is less consensus regarding the mechanisms that underlie and maintain these fundamental acts. The goal of this paper is to clarify inconsistencies in our understanding of the early emergence and development of prosocial behavior by proposing a taxonomy of prosocial behavior anchored in the social-cognitive constraints that underlie the ability to act on behalf of others. I will argue that within the general domain of prosocial behavior, other-oriented actions can be categorized into three distinct types (helping, sharing, and comforting) that reflect responses to three distinct negative states (instrumental need, unmet material desire, and emotional distress). In support of this proposal, I will demonstrate that the three varieties of prosocial behavior show unique ages of onset, uncorrelated patterns of production, and distinct patterns of individual differences. Importantly, by differentiating specific varieties of prosocial behavior within the general category, we can begin to explain inconsistencies in the past literature and provide a framework for directing future research into the ontogenetic origins of these essential social behaviors.

Neural basis for hand muscle synergies in the primate spinal cord.

PubMed

Takei, Tomohiko; Confais, Joachim; Tomatsu, Saeka; Oya, Tomomichi; Seki, Kazuhiko

2017-08-08

Grasping is a highly complex movement that requires the coordination of multiple hand joints and muscles. Muscle synergies have been proposed to be the functional building blocks that coordinate such complex motor behaviors, but little is known about how they are implemented in the central nervous system. Here we demonstrate that premotor interneurons (PreM-INs) in the primate cervical spinal cord underlie the spatiotemporal patterns of hand muscle synergies during a voluntary grasping task. Using spike-triggered averaging of hand muscle activity, we found that the muscle fields of PreM-INs were not uniformly distributed across hand muscles but rather distributed as clusters corresponding to muscle synergies. Moreover, although individual PreM-INs have divergent activation patterns, the population activity of PreM-INs reflects the temporal activation of muscle synergies. These findings demonstrate that spinal PreM-INs underlie the muscle coordination required for voluntary hand movements in primates. Given the evolution of neural control of primate hand functions, we suggest that spinal premotor circuits provide the fundamental coordination of multiple joints and muscles upon which more fractionated control is achieved by superimposed, phylogenetically newer, pathways.

Programming Pluralism: Using Learning Analytics to Detect Patterns in the Learning of Computer Programming

ERIC Educational Resources Information Center

Blikstein, Paulo; Worsley, Marcelo; Piech, Chris; Sahami, Mehran; Cooper, Steven; Koller, Daphne

2014-01-01

New high-frequency, automated data collection and analysis algorithms could offer new insights into complex learning processes, especially for tasks in which students have opportunities to generate unique open-ended artifacts such as computer programs. These approaches should be particularly useful because the need for scalable project-based and…

Improving the Scalability of an Exact Approach for Frequent Item Set Hiding

ERIC Educational Resources Information Center

LaMacchia, Carolyn

2013-01-01

Technological advances have led to the generation of large databases of organizational data recognized as an information-rich, strategic asset for internal analysis and sharing with trading partners. Data mining techniques can discover patterns in large databases including relationships considered strategically relevant to the owner of the data.…

Self-assembled large scale metal alloy grid patterns as flexible transparent conductive layers

NASA Astrophysics Data System (ADS)

Mohl, Melinda; Dombovari, Aron; Vajtai, Robert; Ajayan, Pulickel M.; Kordas, Krisztian

2015-09-01

The development of scalable synthesis techniques for optically transparent, electrically conductive coatings is in great demand due to the constantly increasing market price and limited resources of indium for indium tin oxide (ITO) materials currently applied in most of the optoelectronic devices. This work pioneers the scalable synthesis of transparent conductive films (TCFs) by exploiting the coffee-ring effect deposition coupled with reactive inkjet printing and subsequent chemical copper plating. Here we report two different promising alternatives to replace ITO, palladium-copper (PdCu) grid patterns and silver-copper (AgCu) fish scale like structures printed on flexible poly(ethylene terephthalate) (PET) substrates, achieving sheet resistance values as low as 8.1 and 4.9 Ω/sq, with corresponding optical transmittance of 79% and 65% at 500 nm, respectively. Both films show excellent adhesion and also preserve their structural integrity and good contact with the substrate for severe bending showing less than 4% decrease of conductivity even after 105 cycles. Transparent conductive films for capacitive touch screens and pixels of microscopic resistive electrodes are demonstrated.

Self-assembled large scale metal alloy grid patterns as flexible transparent conductive layers

PubMed Central

Mohl, Melinda; Dombovari, Aron; Vajtai, Robert; Ajayan, Pulickel M.; Kordas, Krisztian

2015-01-01

The development of scalable synthesis techniques for optically transparent, electrically conductive coatings is in great demand due to the constantly increasing market price and limited resources of indium for indium tin oxide (ITO) materials currently applied in most of the optoelectronic devices. This work pioneers the scalable synthesis of transparent conductive films (TCFs) by exploiting the coffee-ring effect deposition coupled with reactive inkjet printing and subsequent chemical copper plating. Here we report two different promising alternatives to replace ITO, palladium-copper (PdCu) grid patterns and silver-copper (AgCu) fish scale like structures printed on flexible poly(ethylene terephthalate) (PET) substrates, achieving sheet resistance values as low as 8.1 and 4.9 Ω/sq, with corresponding optical transmittance of 79% and 65% at 500 nm, respectively. Both films show excellent adhesion and also preserve their structural integrity and good contact with the substrate for severe bending showing less than 4% decrease of conductivity even after 105 cycles. Transparent conductive films for capacitive touch screens and pixels of microscopic resistive electrodes are demonstrated. PMID:26333520

Printable Fabrication of Nanocoral-Structured Electrodes for High-Performance Flexible and Planar Supercapacitor with Artistic Design.

PubMed

Lin, Yuanjing; Gao, Yuan; Fan, Zhiyong

2017-11-01

Planar supercapacitors with high flexibility, desirable operation safety, and high performance are considered as attractive candidates to serve as energy-storage devices for portable and wearable electronics. Here, a scalable and printable technique is adopted to construct novel and unique hierarchical nanocoral structures as the interdigitated electrodes on flexible substrates. The as-fabricated flexible all-solid-state planar supercapacitors with nanocoral structures achieve areal capacitance up to 52.9 mF cm -2 , which is 2.5 times that of devices without nanocoral structures, and this figure-of-merit is among the highest in the literature for the same category of devices. More interestingly, due to utilization of the inkjet-printing technique, excellent versatility on electrode-pattern artistic design is achieved. Particularly, working supercapacitors with artistically designed patterns are demonstrated. Meanwhile, the high scalability of such a printable method is also demonstrated by fabrication of large-sized artistic supercapacitors serving as energy-storage devices in a wearable self-powered system as a proof of concept. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development, Verification and Validation of Parallel, Scalable Volume of Fluid CFD Program for Propulsion Applications

NASA Technical Reports Server (NTRS)

West, Jeff; Yang, H. Q.

2014-01-01

There are many instances involving liquid/gas interfaces and their dynamics in the design of liquid engine powered rockets such as the Space Launch System (SLS). Some examples of these applications are: Propellant tank draining and slosh, subcritical condition injector analysis for gas generators, preburners and thrust chambers, water deluge mitigation for launch induced environments and even solid rocket motor liquid slag dynamics. Commercially available CFD programs simulating gas/liquid interfaces using the Volume of Fluid approach are currently limited in their parallel scalability. In 2010 for instance, an internal NASA/MSFC review of three commercial tools revealed that parallel scalability was seriously compromised at 8 cpus and no additional speedup was possible after 32 cpus. Other non-interface CFD applications at the time were demonstrating useful parallel scalability up to 4,096 processors or more. Based on this review, NASA/MSFC initiated an effort to implement a Volume of Fluid implementation within the unstructured mesh, pressure-based algorithm CFD program, Loci-STREAM. After verification was achieved by comparing results to the commercial CFD program CFD-Ace+, and validation by direct comparison with data, Loci-STREAM-VoF is now the production CFD tool for propellant slosh force and slosh damping rate simulations at NASA/MSFC. On these applications, good parallel scalability has been demonstrated for problems sizes of tens of millions of cells and thousands of cpu cores. Ongoing efforts are focused on the application of Loci-STREAM-VoF to predict the transient flow patterns of water on the SLS Mobile Launch Platform in order to support the phasing of water for launch environment mitigation so that vehicle determinantal effects are not realized.

The Heteroscedastic Graded Response Model with a Skewed Latent Trait: Testing Statistical and Substantive Hypotheses Related to Skewed Item Category Functions

ERIC Educational Resources Information Center

Molenaar, Dylan; Dolan, Conor V.; de Boeck, Paul

2012-01-01

The Graded Response Model (GRM; Samejima, "Estimation of ability using a response pattern of graded scores," Psychometric Monograph No. 17, Richmond, VA: The Psychometric Society, 1969) can be derived by assuming a linear regression of a continuous variable, Z, on the trait, [theta], to underlie the ordinal item scores (Takane & de Leeuw in…

Multivariate landscape trajectory analysis: An example using simulation modeling of American marten habitat change under four timber harvest scenarios

Treesearch

Samuel A. Cushman; Kevin McGarigal

2007-01-01

Integrating temporal variabilily into spatial analyses is one of the abiding challenges in landscape ecology. In this chapter we use landscape trajectory analysis to assess changes in landscape patterns over time. Landscape trajectory analysis is an approach to quantify changes in landscape structure over time. There are three key concepts which underlie the...

Biochemical acclimation, stomatal limitation and precipitation patterns underlie decreases in photosynthetic stimulation of Soybean (Glycine max) at elevated [CO2] and temperatures under fully open air field conditions

USDA-ARS?s Scientific Manuscript database

The net effect of elevated [CO2] and temperature on photosynthetic acclimation and plant productivity is poorly resolved. We assessed the effects of canopy warming and fully open air [CO2] enrichment on 1) the acclimation of two biochemical parameters that frequently limit photosynthesis (A), the ma...

Development of the GEM-TPC X-ray Polarimeter with the Scalable Readout System

NASA Astrophysics Data System (ADS)

Kitaguchi, Takao; Hayato, Asami; Iwakiri, Wataru; Takeuchi, Yoko; Kubota, Megu; Nishida, Kazuki; Enoto, Teruaki; Tamagawa, Toru

2018-02-01

We have developed a gaseous Time Projection Chamber (TPC) containing a single-layered foil of a gas electron multiplier (GEM) to open up a new window on cosmic X-ray polarimetry in the 2-10 keV band. The micro-pattern TPC polarimeter in combination with the Scalable Readout System produced by the RD51 collaboration has been built as an engineering model to optimize detector parameters and improve polarimeter sensitivity. The polarimeter was characterized with unpolarized X-rays from an X-ray generator in a laboratory and polarized X-rays on the BL32B2 beamline at the SPring-8 synchrotron radiation facility. Preliminary results show that the polarimeter has a comparable modulation factor to a prototype of the flight one.

Diagnostic, Predictive and Compositional Modeling with Data Mining in Integrated Learning Environments

ERIC Educational Resources Information Center

Lee, Chien-Sing

2007-01-01

Models represent a set of generic patterns to test hypotheses. This paper presents the CogMoLab student model in the context of an integrated learning environment. Three aspects are discussed: diagnostic and predictive modeling with respect to the issues of credit assignment and scalability and compositional modeling of the student profile in the…

Representing metarepresentations: is there theory of mind-specific cognition?

PubMed

Egeth, Marc; Kurzban, Robert

2009-03-01

What cognitive mechanisms underlie Theory of Mind? Some infer domain-specific Theory of Mind cognition based the pattern of children diagnosed with autism failing the False Belief test but passing the False Photograph test. However, we argue that the False Belief test entails various task demands the False Photograph task does not, including the necessity to represent a higher-order representation (a metarepresentation), thus confounding the inference of domain-specificity. Instead, a general difficulty that affects representations of metarepresentations might account for the seeming domain-specific failure. Here we find that False-Belief failing False-Photograph passing children fail the Meta Photograph test, a new photograph-domain test that requires subjects to represent a metarepresentation. We conclude that people who fail the False Belief test but pass the False Photograph test do not necessarily have a content-specific Theory of Mind deficit. Instead, the general ability to represent representations and metarepresentations might underlie Theory of Mind.

802GHz integrated horn antennas imaging array

NASA Technical Reports Server (NTRS)

Ali-Ahmad, Walid Y.; Rebeiz, Gabriel M.; Dave, Hemant; Chin, Gordon

1991-01-01

Pattern measurements at 802GHz of a single element in 256-element integrated horn imaging array are presented. The integrated-horn antenna consists of a dipole-antenna suspended on a 1-micron dielectric membrane inside a pyramidal cavity etched in silicon. The theoretical far-field patterns, calculated using reciprocity and Floquet-modes representation of the free-space field, agree well with the measured far-field patterns at 802GHz. The associated directivity for a 1.40 lambda horn aperture, calculated from the measured E and H-plane patterns is 12.3dB + or - 0.2dB. This work demonstrates that high-efficiency integrated-horn antennas are easily scalable to terahertz frequencies and could be used for radio-astronomical and plasma-diagnostic applications.

Functional patterned coatings by thin polymer film dewetting.

PubMed

Telford, Andrew M; Thickett, Stuart C; Neto, Chiara

2017-12-01

An approach for the fabrication of functional polymer surface coatings is introduced, where micro-scale structure and surface functionality are obtained by means of self-assembly mechanisms. We illustrate two main applications of micro-patterned polymer surfaces obtained through dewetting of bilayers of thin polymer films. By tuning the physical and chemical properties of the polymer bilayers, micro-patterned surface coatings could be produced that have applications both for the selective attachment and patterning of proteins and cells, with potential applications as biomaterials, and for the collection of water from the atmosphere. In all cases, the aim is to achieve functional coatings using approaches that are simple to realize, use low cost materials and are potentially scalable. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated Verification of Design Patterns with LePUS3

NASA Technical Reports Server (NTRS)

Nicholson, Jonathan; Gasparis, Epameinondas; Eden, Ammon H.; Kazman, Rick

2009-01-01

Specification and [visual] modelling languages are expected to combine strong abstraction mechanisms with rigour, scalability, and parsimony. LePUS3 is a visual, object-oriented design description language axiomatized in a decidable subset of the first-order predicate logic. We demonstrate how LePUS3 is used to formally specify a structural design pattern and prove ( verify ) whether any JavaTM 1.4 program satisfies that specification. We also show how LePUS3 specifications (charts) are composed and how they are verified fully automatically in the Two-Tier Programming Toolkit.

Situating emotional experience

PubMed Central

Wilson-Mendenhall, Christine D.; Barrett, Lisa Feldman; Barsalou, Lawrence W.

2013-01-01

Psychological construction approaches to emotion suggest that emotional experience is situated and dynamic. Fear, for example, is typically studied in a physical danger context (e.g., threatening snake), but in the real world, it often occurs in social contexts, especially those involving social evaluation (e.g., public speaking). Understanding situated emotional experience is critical because adaptive responding is guided by situational context (e.g., inferring the intention of another in a social evaluation situation vs. monitoring the environment in a physical danger situation). In an fMRI study, we assessed situated emotional experience using a newly developed paradigm in which participants vividly imagine different scenarios from a first-person perspective, in this case scenarios involving either social evaluation or physical danger. We hypothesized that distributed neural patterns would underlie immersion in social evaluation and physical danger situations, with shared activity patterns across both situations in multiple sensory modalities and in circuitry involved in integrating salient sensory information, and with unique activity patterns for each situation type in coordinated large-scale networks that reflect situated responding. More specifically, we predicted that networks underlying the social inference and mentalizing involved in responding to a social threat (in regions that make up the “default mode” network) would be reliably more active during social evaluation situations. In contrast, networks underlying the visuospatial attention and action planning involved in responding to a physical threat would be reliably more active during physical danger situations. The results supported these hypotheses. In line with emerging psychological construction approaches, the findings suggest that coordinated brain networks offer a systematic way to interpret the distributed patterns that underlie the diverse situational contexts characterizing emotional life. PMID:24324420

Perspectives and Open Problems in the Early Phases of Left-Right Patterning

PubMed Central

Vandenberg, Laura N.; Levin, Michael

2009-01-01

Summary Embryonic left-right (LR) patterning is a fascinating aspect of embryogenesis. The field currently faces important questions about the origin of LR asymmetry, the mechanisms by which consistent asymmetry is imposed on the scale of the whole embryo, and the degree of conservation of early phases of LR patterning among model systems. Recent progress on planar cell polarity and cellular asymmetry in a variety of tissues and species provides a new perspective on the early phases of LR patterning. Despite the huge diversity in body-plans over which consistent LR asymmetry is imposed, and the apparent divergence in molecular pathways that underlie laterality, the data reveal conservation of physiological modules among phyla and a basic scheme of cellular chirality amplified by a planar cell polarity-like pathway over large cell fields. PMID:19084609

Self-similar conductance patterns in graphene Cantor-like structures.

PubMed

García-Cervantes, H; Gaggero-Sager, L M; Díaz-Guerrero, D S; Sotolongo-Costa, O; Rodríguez-Vargas, I

2017-04-04

Graphene has proven to be an ideal system for exotic transport phenomena. In this work, we report another exotic characteristic of the electron transport in graphene. Namely, we show that the linear-regime conductance can present self-similar patterns with well-defined scaling rules, once the graphene sheet is subjected to Cantor-like nanostructuring. As far as we know the mentioned system is one of the few in which a self-similar structure produces self-similar patterns on a physical property. These patterns are analysed quantitatively, by obtaining the scaling rules that underlie them. It is worth noting that the transport properties are an average of the dispersion channels, which makes the existence of scale factors quite surprising. In addition, that self-similarity be manifested in the conductance opens an excellent opportunity to test this fundamental property experimentally.

Identifying DNA Methylation Features that Underlie Prostate Cancer Disparities

DTIC Science & Technology

2016-10-01

Report We will continue to recruit African American patients and bank their prostate tissue . We will continue dissecting tumor samples into tumor...in prostate tumors and adjacent normal tissue derived from both AA and EA individuals. We will determine if DNA methylation patterns in prostate... tissue (both cancerous and normal tissue ) differ between AA and EA individuals. We will also identify methylation features that differ between tumor

Testing the item-order account of design effects using the production effect.

PubMed

Jonker, Tanya R; Levene, Merrick; Macleod, Colin M

2014-03-01

A number of memory phenomena evident in recall in within-subject, mixed-lists designs are reduced or eliminated in between-subject, pure-list designs. The item-order account (McDaniel & Bugg, 2008) proposes that differential retention of order information might underlie this pattern. According to this account, order information may be encoded when a common form of processing is used alone in a list (e.g., reading), but not when an unusual form of processing is used (e.g., generation) or when a common form and an unusual form are mixed within a list. The production effect--better memory for words said aloud than for words read silently--shows this same design-contingent pattern. In 2 experiments, we investigated whether differential order retention might underlie the production effect. Consistent with the item-order account, we found that retention of order information was better in pure silent lists than in either pure aloud lists or mixed lists, as measured using an order reconstruction test. Moreover, in Experiment 2, order was better preserved in free recall of pure silent lists than of either pure aloud or mixed lists. Thus, production joins the set of tasks identified by McDaniel and Bugg (2008), and our findings suggest a role for order processing in explaining the production effect.

A construct divided: prosocial behavior as helping, sharing, and comforting subtypes

PubMed Central

Dunfield, Kristen A.

2014-01-01

The development and maintenance of prosocial, other-oriented behaviors has been of considerable recent interest. Though it is clear that prosocial behaviors emerge early and play a uniquely important role in the social lives of humans, there is less consensus regarding the mechanisms that underlie and maintain these fundamental acts. The goal of this paper is to clarify inconsistencies in our understanding of the early emergence and development of prosocial behavior by proposing a taxonomy of prosocial behavior anchored in the social-cognitive constraints that underlie the ability to act on behalf of others. I will argue that within the general domain of prosocial behavior, other-oriented actions can be categorized into three distinct types (helping, sharing, and comforting) that reflect responses to three distinct negative states (instrumental need, unmet material desire, and emotional distress). In support of this proposal, I will demonstrate that the three varieties of prosocial behavior show unique ages of onset, uncorrelated patterns of production, and distinct patterns of individual differences. Importantly, by differentiating specific varieties of prosocial behavior within the general category, we can begin to explain inconsistencies in the past literature and provide a framework for directing future research into the ontogenetic origins of these essential social behaviors. PMID:25228893

Global neural pattern similarity as a common basis for categorization and recognition memory.

PubMed

Davis, Tyler; Xue, Gui; Love, Bradley C; Preston, Alison R; Poldrack, Russell A

2014-05-28

Familiarity, or memory strength, is a central construct in models of cognition. In previous categorization and long-term memory research, correlations have been found between psychological measures of memory strength and activation in the medial temporal lobes (MTLs), which suggests a common neural locus for memory strength. However, activation alone is insufficient for determining whether the same mechanisms underlie neural function across domains. Guided by mathematical models of categorization and long-term memory, we develop a theory and a method to test whether memory strength arises from the global similarity among neural representations. In human subjects, we find significant correlations between global similarity among activation patterns in the MTLs and both subsequent memory confidence in a recognition memory task and model-based measures of memory strength in a category learning task. Our work bridges formal cognitive theories and neuroscientific models by illustrating that the same global similarity computations underlie processing in multiple cognitive domains. Moreover, by establishing a link between neural similarity and psychological memory strength, our findings suggest that there may be an isomorphism between psychological and neural representational spaces that can be exploited to test cognitive theories at both the neural and behavioral levels. Copyright © 2014 the authors 0270-6474/14/347472-13$15.00/0.

A scalable architecture for online anomaly detection of WLCG batch jobs

NASA Astrophysics Data System (ADS)

Kuehn, E.; Fischer, M.; Giffels, M.; Jung, C.; Petzold, A.

2016-10-01

For data centres it is increasingly important to monitor the network usage, and learn from network usage patterns. Especially configuration issues or misbehaving batch jobs preventing a smooth operation need to be detected as early as possible. At the GridKa data and computing centre we therefore operate a tool BPNetMon for monitoring traffic data and characteristics of WLCG batch jobs and pilots locally on different worker nodes. On the one hand local information itself are not sufficient to detect anomalies for several reasons, e.g. the underlying job distribution on a single worker node might change or there might be a local misconfiguration. On the other hand a centralised anomaly detection approach does not scale regarding network communication as well as computational costs. We therefore propose a scalable architecture based on concepts of a super-peer network.

The Characterization of Laser Ablation Patterns and a New Definition of Resolution in Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS).

PubMed

O'Rourke, Matthew B; Raymond, Benjamin B A; Padula, Matthew P

2017-05-01

Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) is a technique that has seen a sharp rise in both use and development. Despite this rapid adoption, there have been few thorough investigations into the actual physical mechanisms that underlie the acquisition of IMS images. We therefore set out to characterize the effect of IMS laser ablation patterns on the surface of a sample. We also concluded that the governing factors that control spatial resolution have not been correctly defined and therefore propose a new definition of resolution. Graphical Abstract ᅟ.

US Household Food Shopping Patterns: Dynamic Shifts since 2000 and Socioeconomic Predictors

PubMed Central

Stern, Dalia; Robinson, Whitney R; Ng, Shu Wen; Gordon-Larsen, Penny; Popkin, Barry M

2016-01-01

Under the assumption that differential food access might underlie nutritional disparities, programs and policies have focused on the need to build supermarkets in underserved areas, in an effort to improve dietary quality. However, there is limited evidence about which types of stores different income and race-ethnic households use. We used cross-sectional cluster analysis to derive shopping patterns from US households’ volume food purchases (Nielsen Homescan) by store from 2000–2012. Multinomial logistic regression identified household SES characteristics that were associated with shopping patterns in 2012. We found three shopping patterns: primary-grocery, primary-mass-merchandise, and combination cluster. In 2012, we found no income/race-ethnic differences for grocery cluster membership. However, low-income non-Hispanic blacks (vs. non-Hispanic whites) had a significantly lower probability of belonging to the mass-merchandise cluster. These varied shopping patterns must be considered in future policy initiatives. Further, it is important to continue studying the complex rationale for people’s food shopping patterns. PMID:26526241

Huygens-Fresnel Acoustic Interference and the Development of Robust Time-Averaged Patterns from Traveling Surface Acoustic Waves

NASA Astrophysics Data System (ADS)

Devendran, Citsabehsan; Collins, David J.; Ai, Ye; Neild, Adrian

2017-04-01

Periodic pattern generation using time-averaged acoustic forces conventionally requires the intersection of counterpropagating wave fields, where suspended micro-objects in a microfluidic system collect along force potential minimizing nodal or antinodal lines. Whereas this effect typically requires either multiple transducer elements or whole channel resonance, we report the generation of scalable periodic patterning positions without either of these conditions. A single propagating surface acoustic wave interacts with the proximal channel wall to produce a knife-edge effect according to the Huygens-Fresnel principle, where these cylindrically propagating waves interfere with classical wave fronts emanating from the substrate. We simulate these conditions and describe a model that accurately predicts the lateral spacing of these positions in a robust and novel approach to acoustic patterning.

Electrically pumped continuous wave quantum dot lasers epitaxially grown on patterned, on-axis (001) Si

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

Norman, Justin; Kennedy, M. J.; Selvidge, Jennifer

High performance III-V lasers at datacom and telecom wavelengths on on-axis (001) Si are needed for scalable datacenter interconnect technologies. We demonstrate electrically injected quantum dot lasers grown on on-axis (001) Si patterned with {111} v-grooves lying in the [110] direction. No additional Ge buffers or substrate miscut was used. The active region consists of five InAs/InGaAs dot-in-a-well layers. Here, we achieve continuous wave lasing with thresholds as low as 36 mA and operation up to 80°C.

Electrically pumped continuous wave quantum dot lasers epitaxially grown on patterned, on-axis (001) Si

DOE PAGES

Norman, Justin; Kennedy, M. J.; Selvidge, Jennifer; ...

2017-02-14

High performance III-V lasers at datacom and telecom wavelengths on on-axis (001) Si are needed for scalable datacenter interconnect technologies. We demonstrate electrically injected quantum dot lasers grown on on-axis (001) Si patterned with {111} v-grooves lying in the [110] direction. No additional Ge buffers or substrate miscut was used. The active region consists of five InAs/InGaAs dot-in-a-well layers. Here, we achieve continuous wave lasing with thresholds as low as 36 mA and operation up to 80°C.

Identifying DNA Methylation Features that Underlie Prostate Cancer Disparities

DTIC Science & Technology

2017-10-01

Army position, policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE Form Approved OMB No. 0704- 0188 Public...failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE...men are more likely to die from prostate cancer than EA men. We hypothesize that differences in DNA methylation patterns across ethnic groups may

Dynamic Patterns of Clonal Evolution in Tumor Vasculature Underlie Alterations in Lymphocyte-Endothelial Recognition to Foster Tumor Immune Escape.

PubMed

Corey, Daniel M; Rinkevich, Yuval; Weissman, Irving L

2016-03-15

Although tumor blood vessels have been a major therapeutic target for cancer chemotherapy, little is known regarding the stepwise development of the tumor microenvironment. Here, we use a multicolor Cre-dependent marker system to trace clonality within the tumor microenvironment to show that tumor blood vessels follow a pattern of dynamic clonal evolution. In an advanced melanoma tumor microenvironment, the vast majority of tumor vasculature clones are derived from a common precursor. Quantitative lineage analysis reveals founder clones diminish in frequency and are replaced by subclones as tumors evolve. These tumor-specific blood vessels are characterized by a developmental switch to a more invasive and immunologically silent phenotype. Gene expression profiling and pathway analysis reveals selection for traits promoting upregulation of alternative angiogenic programs such as unregulated HGF-MET signaling and enhanced autocrine signaling through VEGF and PDGF. Furthermore, we show a developmental switch in the expression of functionally significant primary lymphocyte adhesion molecules on tumor endothelium, such as the loss in expression of the mucosal addressin MAdCAM-1, whose counter receptor a4β7 on lymphocytes controls lymphocyte homing. Changes in adhesive properties on tumor endothelial subclones are accompanied by decreases in expression of lymphocyte chemokines CXCL16, CXCL13, CXCL12, CXCL9, CXCL10, and CCL19. These evolutionary patterns in the expressed genetic program within tumor endothelium will have both a quantitative and functional impact on lymphocyte distribution that may well influence tumor immune function and underlie escape mechanisms from current antiangiogenic pharmacotherapies. ©2015 American Association for Cancer Research.

Blood flow patterns underlie developmental heart defects

PubMed Central

Midgett, Madeline; Thornburg, Kent

2017-01-01

Although cardiac malformations at birth are typically associated with genetic anomalies, blood flow dynamics also play a crucial role in heart formation. However, the relationship between blood flow patterns in the early embryo and later cardiovascular malformation has not been determined. We used the chicken embryo model to quantify the extent to which anomalous blood flow patterns predict cardiac defects that resemble those in humans and found that restricting either the inflow to the heart or the outflow led to reproducible abnormalities with a dose-response type relationship between blood flow stimuli and the expression of cardiac phenotypes. Constricting the outflow tract by 10–35% led predominantly to ventricular septal defects, whereas constricting by 35–60% most often led to double outlet right ventricle. Ligation of the vitelline vein caused mostly pharyngeal arch artery malformations. We show that both cardiac inflow reduction and graded outflow constriction strongly influence the development of specific and persistent abnormal cardiac structure and function. Moreover, the hemodynamic-associated cardiac defects recapitulate those caused by genetic disorders. Thus our data demonstrate the importance of investigating embryonic blood flow conditions to understand the root causes of congenital heart disease as a prerequisite to future prevention and treatment. NEW & NOTEWORTHY Congenital heart defects result from genetic anomalies, teratogen exposure, and altered blood flow during embryonic development. We show here a novel “dose-response” type relationship between the level of blood flow alteration and manifestation of specific cardiac phenotypes. We speculate that abnormal blood flow may frequently underlie congenital heart defects. PMID:28062416

Data, data everywhere: detecting spatial patterns in fine-scale ecological information collected across a continent

Treesearch

Kevin M. Potter; Frank H. Koch; Christopher M. Oswalt; Basil V. Iannone

2016-01-01

Context Fine-scale ecological data collected across broad regions are becoming increasingly available. Appropriate geographic analyses of these data can help identify locations of ecological concern. Objectives We present one such approach, spatial association of scalable hexagons (SASH), whichidentifies locations where ecological phenomena occur at greater...

Fully Scalable Porous Metal Electrospray Propulsion

DTIC Science & Technology

2012-03-20

particular emphasis on the variation of specific impulse for multi-modal propulsion is currently carried out by MIT and the Busek Company under an...Beam profile distributions in the negative (left) and positive (center) modes as visualized directly thorough a multi-channel plate and phosphor...screen. These profiles are parabolic (right) indicating the non-thermal character of these type of ion beams. Microscopic Image of pattern imprinted on Si

Scalable Directed Self-Assembly Using Ultrasound Waves

DTIC Science & Technology

2015-09-04

SECURITY CLASSIFICATION OF: We aim to understand how ultrasound waves can be used to create organized patterns of nanoparticles in a host medium such...as a polymer matrix material. The critical difference between the ultrasound technology studied in this project, and other directed self-assembly...of nanoparticles dispersed in a host medium are assembled by means of standing ultrasound waves. Additionally, we have obtained experimental

Bayesian Aggregation of Evidence for Detection and Characterization of Patterns in Multiple Noisy Observations

DTIC Science & Technology

2015-07-01

undergraduate student coauthors Aashish Jindia, Parag Srivastava, and Jay Jin for help with the research. In addition, thank you to the numerous...103 A.1.1 Sacramento Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 A.1.2 RadMap and SUNS Data Sets...parameters in a joint hypothesis space. We develop scalable branch and bound and pruning mechanisms for searching (at multiple resolutions) over source

Dead simple OWL design patterns

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

Osumi-Sutherland, David; Courtot, Melanie; Balhoff, James P.

Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies. We describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating themore » system with examples from the Gene Ontology. In conclusion, the rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.« less

Dead simple OWL design patterns

DOE PAGES

Osumi-Sutherland, David; Courtot, Melanie; Balhoff, James P.; ...

2017-06-05

Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies. We describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating themore » system with examples from the Gene Ontology. In conclusion, the rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.« less

Scalable maskless patterning of nanostructures using high-speed scanning probe arrays

NASA Astrophysics Data System (ADS)

Chen, Chen; Akella, Meghana; Du, Zhidong; Pan, Liang

2017-08-01

Nanoscale patterning is the key process to manufacture important products such as semiconductor microprocessors and data storage devices. Many studies have shown that it has the potential to revolutionize the functions of a broad range of products for a wide variety of applications in energy, healthcare, civil, defense and security. However, tools for mass production of these devices usually cost tens of million dollars each and are only affordable to the established semiconductor industry. A new method, nominally known as "pattern-on-the- y", that involves scanning an array of optical or electrical probes at high speed to form nanostructures and offers a new low-cost approach for nanoscale additive patterning. In this paper, we report some progress on using this method to pattern self-assembled monolayers (SAMs) on silicon substrate. We also functionalize the substrate with gold nanoparticle based on the SAM to show the feasibility of preparing amphiphilic and multi-functional surfaces.

Scalable persistent identifier systems for dynamic datasets

NASA Astrophysics Data System (ADS)

Golodoniuc, P.; Cox, S. J. D.; Klump, J. F.

2016-12-01

Reliable and persistent identification of objects, whether tangible or not, is essential in information management. Many Internet-based systems have been developed to identify digital data objects, e.g., PURL, LSID, Handle, ARK. These were largely designed for identification of static digital objects. The amount of data made available online has grown exponentially over the last two decades and fine-grained identification of dynamically generated data objects within large datasets using conventional systems (e.g., PURL) has become impractical. We have compared capabilities of various technological solutions to enable resolvability of data objects in dynamic datasets, and developed a dataset-centric approach to resolution of identifiers. This is particularly important in Semantic Linked Data environments where dynamic frequently changing data is delivered live via web services, so registration of individual data objects to obtain identifiers is impractical. We use identifier patterns and pattern hierarchies for identification of data objects, which allows relationships between identifiers to be expressed, and also provides means for resolving a single identifier into multiple forms (i.e. views or representations of an object). The latter can be implemented through (a) HTTP content negotiation, or (b) use of URI querystring parameters. The pattern and hierarchy approach has been implemented in the Linked Data API supporting the United Nations Spatial Data Infrastructure (UNSDI) initiative and later in the implementation of geoscientific data delivery for the Capricorn Distal Footprints project using International Geo Sample Numbers (IGSN). This enables flexible resolution of multi-view persistent identifiers and provides a scalable solution for large heterogeneous datasets.

A Node Linkage Approach for Sequential Pattern Mining

PubMed Central

Navarro, Osvaldo; Cumplido, René; Villaseñor-Pineda, Luis; Feregrino-Uribe, Claudia; Carrasco-Ochoa, Jesús Ariel

2014-01-01

Sequential Pattern Mining is a widely addressed problem in data mining, with applications such as analyzing Web usage, examining purchase behavior, and text mining, among others. Nevertheless, with the dramatic increase in data volume, the current approaches prove inefficient when dealing with large input datasets, a large number of different symbols and low minimum supports. In this paper, we propose a new sequential pattern mining algorithm, which follows a pattern-growth scheme to discover sequential patterns. Unlike most pattern growth algorithms, our approach does not build a data structure to represent the input dataset, but instead accesses the required sequences through pseudo-projection databases, achieving better runtime and reducing memory requirements. Our algorithm traverses the search space in a depth-first fashion and only preserves in memory a pattern node linkage and the pseudo-projections required for the branch being explored at the time. Experimental results show that our new approach, the Node Linkage Depth-First Traversal algorithm (NLDFT), has better performance and scalability in comparison with state of the art algorithms. PMID:24933123

Embedded DCT and wavelet methods for fine granular scalable video: analysis and comparison

NASA Astrophysics Data System (ADS)

van der Schaar-Mitrea, Mihaela; Chen, Yingwei; Radha, Hayder

2000-04-01

Video transmission over bandwidth-varying networks is becoming increasingly important due to emerging applications such as streaming of video over the Internet. The fundamental obstacle in designing such systems resides in the varying characteristics of the Internet (i.e. bandwidth variations and packet-loss patterns). In MPEG-4, a new SNR scalability scheme, called Fine-Granular-Scalability (FGS), is currently under standardization, which is able to adapt in real-time (i.e. at transmission time) to Internet bandwidth variations. The FGS framework consists of a non-scalable motion-predicted base-layer and an intra-coded fine-granular scalable enhancement layer. For example, the base layer can be coded using a DCT-based MPEG-4 compliant, highly efficient video compression scheme. Subsequently, the difference between the original and decoded base-layer is computed, and the resulting FGS-residual signal is intra-frame coded with an embedded scalable coder. In order to achieve high coding efficiency when compressing the FGS enhancement layer, it is crucial to analyze the nature and characteristics of residual signals common to the SNR scalability framework (including FGS). In this paper, we present a thorough analysis of SNR residual signals by evaluating its statistical properties, compaction efficiency and frequency characteristics. The signal analysis revealed that the energy compaction of the DCT and wavelet transforms is limited and the frequency characteristic of SNR residual signals decay rather slowly. Moreover, the blockiness artifacts of the low bit-rate coded base-layer result in artificial high frequencies in the residual signal. Subsequently, a variety of wavelet and embedded DCT coding techniques applicable to the FGS framework are evaluated and their results are interpreted based on the identified signal properties. As expected from the theoretical signal analysis, the rate-distortion performances of the embedded wavelet and DCT-based coders are very similar. However, improved results can be obtained for the wavelet coder by deblocking the base- layer prior to the FGS residual computation. Based on the theoretical analysis and our measurements, we can conclude that for an optimal complexity versus coding-efficiency trade- off, only limited wavelet decomposition (e.g. 2 stages) needs to be performed for the FGS-residual signal. Also, it was observed that the good rate-distortion performance of a coding technique for a certain image type (e.g. natural still-images) does not necessarily translate into similarly good performance for signals with different visual characteristics and statistical properties.

Single-shot thermal ghost imaging using wavelength-division multiplexing

NASA Astrophysics Data System (ADS)

Deng, Chao; Suo, Jinli; Wang, Yuwang; Zhang, Zhili; Dai, Qionghai

2018-01-01

Ghost imaging (GI) is an emerging technique that reconstructs the target scene from its correlated measurements with a sequence of patterns. Restricted by the multi-shot principle, GI usually requires long acquisition time and is limited in observation of dynamic scenes. To handle this problem, this paper proposes a single-shot thermal ghost imaging scheme via a wavelength-division multiplexing technique. Specifically, we generate thousands of correlated patterns simultaneously by modulating a broadband light source with a wavelength dependent diffuser. These patterns carry the scene's spatial information and then the correlated photons are coupled into a spectrometer for the final reconstruction. This technique increases the speed of ghost imaging and promotes the applications in dynamic ghost imaging with high scalability and compatibility.

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

PubMed Central

Domyan, Eric T; Kronenberg, Zev; Infante, Carlos R; Vickrey, Anna I; Stringham, Sydney A; Bruders, Rebecca; Guernsey, Michael W; Park, Sungdae; Payne, Jason; Beckstead, Robert B; Kardon, Gabrielle; Menke, Douglas B; Yandell, Mark; Shapiro, Michael D

2016-01-01

Birds display remarkable diversity in the distribution and morphology of scales and feathers on their feet, yet the genetic and developmental mechanisms governing this diversity remain unknown. Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species. These results show how changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide viable molecular mechanisms for diversity in hindlimb scale and feather distribution. DOI: http://dx.doi.org/10.7554/eLife.12115.001 PMID:26977633

TCM Pattern Questionnaire for Lateral Elbow Pain: Development of an Instrument via a Delphi Process

PubMed Central

Bian, Zhao-Xiang

2016-01-01

Individualized acupuncture treatment has been practiced for pain therapy. This study used acupuncture treatment for lateral elbow pain (LEP) as an example to study the diagnostic practice of individualized acupuncture treatment. A provisional version of LEP pattern questionnaire was developed based on a recent systematic review on TCM pattern diagnosis for LEP. A Delphi panel of 33 clinical experts from seven different countries was formed, and the Delphi survey was conducted in Chinese and English language for two rounds. Consensus was achieved from all 26 panelists who responded to the second round on 243 items of the instrument, which included a 72-question-long questionnaire. The mean level of expert consensus on the items of the final questionnaire was 85%. Consensus was found on four TCM patterns that could underlie LEP, namely, the wind-cold-dampness pattern, the qi stagnation and blood stasis pattern, the dual deficiency of qi and blood pattern, and the retained dampness-heat pattern. A list of signs and symptoms indicating one of the four TCM patterns and a list of preferred treatment modalities for each pattern were also generated. Our instrument shows considerable content validity. Further validity and reliability studies are under way. PMID:27525024

Core regulatory network motif underlies the ocellar complex patterning in Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Aguilar-Hidalgo, D.; Lemos, M. C.; Córdoba, A.

2015-03-01

During organogenesis, developmental programs governed by Gene Regulatory Networks (GRN) define the functionality, size and shape of the different constituents of living organisms. Robustness, thus, is an essential characteristic that GRNs need to fulfill in order to maintain viability and reproducibility in a species. In the present work we analyze the robustness of the patterning for the ocellar complex formation in Drosophila melanogaster fly. We have systematically pruned the GRN that drives the development of this visual system to obtain the minimum pathway able to satisfy this pattern. We found that the mechanism underlying the patterning obeys to the dynamics of a 3-nodes network motif with a double negative feedback loop fed by a morphogenetic gradient that triggers the inhibition in a French flag problem fashion. A Boolean modeling of the GRN confirms robustness in the patterning mechanism showing the same result for different network complexity levels. Interestingly, the network provides a steady state solution in the interocellar part of the patterning and an oscillatory regime in the ocelli. This theoretical result predicts that the ocellar pattern may underlie oscillatory dynamics in its genetic regulation.

Molecular nanomagnets with switchable coupling for quantum simulation

DOE PAGES

Chiesa, Alessandro; Whitehead, George F. S.; Carretta, Stefano; ...

2014-12-11

Molecular nanomagnets are attractive candidate qubits because of their wide inter- and intra-molecular tunability. Uniform magnetic pulses could be exploited to implement one- and two-qubit gates in presence of a properly engineered pattern of interactions, but the synthesis of suitable and potentially scalable supramolecular complexes has proven a very hard task. Indeed, no quantum algorithms have ever been implemented, not even a proof-of-principle two-qubit gate. In this paper we show that the magnetic couplings in two supramolecular {Cr7Ni}-Ni-{Cr7Ni} assemblies can be chemically engineered to fit the above requisites for conditional gates with no need of local control. Microscopic parameters aremore » determined by a recently developed many-body ab-initio approach and used to simulate quantum gates. We find that these systems are optimal for proof-of-principle two-qubit experiments and can be exploited as building blocks of scalable architectures for quantum simulation.« less

Evaluation of the Huawei UDS cloud storage system for CERN specific data

NASA Astrophysics Data System (ADS)

Zotes Resines, M.; Heikkila, S. S.; Duellmann, D.; Adde, G.; Toebbicke, R.; Hughes, J.; Wang, L.

2014-06-01

Cloud storage is an emerging architecture aiming to provide increased scalability and access performance, compared to more traditional solutions. CERN is evaluating this promise using Huawei UDS and OpenStack SWIFT storage deployments, focusing on the needs of high-energy physics. Both deployed setups implement S3, one of the protocols that are emerging as a standard in the cloud storage market. A set of client machines is used to generate I/O load patterns to evaluate the storage system performance. The presented read and write test results indicate scalability both in metadata and data perspectives. Futher the Huawei UDS cloud storage is shown to be able to recover from a major failure of losing 16 disks. Both cloud storages are finally demonstrated to function as back-end storage systems to a filesystem, which is used to deliver high energy physics software.

High-frequency self-aligned graphene transistors with transferred gate stacks.

PubMed

Cheng, Rui; Bai, Jingwei; Liao, Lei; Zhou, Hailong; Chen, Yu; Liu, Lixin; Lin, Yung-Chen; Jiang, Shan; Huang, Yu; Duan, Xiangfeng

2012-07-17

Graphene has attracted enormous attention for radio-frequency transistor applications because of its exceptional high carrier mobility, high carrier saturation velocity, and large critical current density. Herein we report a new approach for the scalable fabrication of high-performance graphene transistors with transferred gate stacks. Specifically, arrays of gate stacks are first patterned on a sacrificial substrate, and then transferred onto arbitrary substrates with graphene on top. A self-aligned process, enabled by the unique structure of the transferred gate stacks, is then used to position precisely the source and drain electrodes with minimized access resistance or parasitic capacitance. This process has therefore enabled scalable fabrication of self-aligned graphene transistors with unprecedented performance including a record-high cutoff frequency up to 427 GHz. Our study defines a unique pathway to large-scale fabrication of high-performance graphene transistors, and holds significant potential for future application of graphene-based devices in ultra-high-frequency circuits.

ACS from development to operations

NASA Astrophysics Data System (ADS)

Caproni, Alessandro; Colomer, Pau; Jeram, Bogdan; Sommer, Heiko; Chiozzi, Gianluca; Mañas, Miguel M.

2016-08-01

The ALMA Common Software (ACS), provides the infrastructure of the distributed software system of ALMA and other projects. ACS, built on top of CORBA and Data Distribution Service (DDS) middleware, is based on a Component- Container paradigm and hides the complexity of the middleware allowing the developer to focus on domain specific issues. The transition of the ALMA observatory from construction to operations brings with it that ACS effort focuses primarily on scalability, stability and robustness rather than on new features. The transition came together with a shorter release cycle and a more extensive testing. For scalability, the most problematic area has been the CORBA notification service, used to implement the publisher subscriber pattern because of the asynchronous nature of the paradigm: a lot of effort has been spent to improve its stability and recovery from run time errors. The original bulk data mechanism, implemented using the CORBA Audio/Video Streaming Service, showed its limitations and has been replaced with a more performant and scalable DDS implementation. Operational needs showed soon the difference between releases cycles for Online software (i.e. used during observations) and Offline software, which requires much more frequent releases. This paper attempts to describe the impact the transition from construction to operations had on ACS, the solution adopted so far and a look into future evolution.

Method of fabricating a scalable nanoporous membrane filter

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

Tringe, Joseph W; Balhorn, Rodney L; Zaidi, Saleem

A method of fabricating a nanoporous membrane filter having a uniform array of nanopores etch-formed in a thin film structure (e.g. (100)-oriented single crystal silicon) having a predetermined thickness, by (a) using interferometric lithography to create an etch pattern comprising a plurality array of unit patterns having a predetermined width/diameter, (b) using the etch pattern to etch frustum-shaped cavities or pits in the thin film structure such that the dimension of the frustum floors of the cavities are substantially equal to a desired pore size based on the predetermined thickness of the thin film structure and the predetermined width/diameter ofmore » the unit patterns, and (c) removing the frustum floors at a boundary plane of the thin film structure to expose, open, and thereby create the nanopores substantially having the desired pore size.« less

Myosin Heads Are Displaced from Actin Filaments in the In Situ Beating Rat Heart in Early Diabetes

PubMed Central

Jenkins, Mathew J.; Pearson, James T.; Schwenke, Daryl O.; Edgley, Amanda J.; Sonobe, Takashi; Fujii, Yutaka; Ishibashi-Ueda, Hatsue; Kelly, Darren J.; Yagi, Naoto; Shirai, Mikiyasu

2013-01-01

Diabetes is independently associated with a specific cardiomyopathy, characterized by impaired cardiac muscle relaxation and force development. Using synchrotron radiation small-angle x-ray scattering, this study investigated in the in situ heart and in real-time whether changes in cross-bridge disposition and myosin interfilament spacing underlie the early development of diabetic cardiomyopathy. Experiments were conducted using anesthetized Sprague-Dawley rats 3 weeks after treatment with either vehicle (control) or streptozotocin (diabetic). Diffraction patterns were recorded during baseline and dobutamine infusions simultaneous with ventricular pressure-volumetry. From these diffraction patterns myosin mass transfer to actin filaments was assessed as the change in intensity ratio (I1,0/I1,1). In diabetic hearts cross-bridge disposition was most notably abnormal in the diastolic phase (p < 0.05) and to a lesser extent the systolic phase (p < 0.05). In diabetic rats only, there was a transmural gradient of contractile depression. Elevated diabetic end-diastolic intensity ratios were correlated with the suppression of diastolic function (p < 0.05). Furthermore, the expected increase in myosin head transfer by dobutamine was significantly blunted in diabetic animals (p < 0.05). Interfilament spacing did not differ between groups. We reveal that impaired cross-bridge disposition and radial transfer may thus underlie the early decline in ventricular function observed in diabetic cardiomyopathy. PMID:23473489

Dynamic full-scalability conversion in scalable video coding

NASA Astrophysics Data System (ADS)

Lee, Dong Su; Bae, Tae Meon; Thang, Truong Cong; Ro, Yong Man

2007-02-01

For outstanding coding efficiency with scalability functions, SVC (Scalable Video Coding) is being standardized. SVC can support spatial, temporal and SNR scalability and these scalabilities are useful to provide a smooth video streaming service even in a time varying network such as a mobile environment. But current SVC is insufficient to support dynamic video conversion with scalability, thereby the adaptation of bitrate to meet a fluctuating network condition is limited. In this paper, we propose dynamic full-scalability conversion methods for QoS adaptive video streaming in SVC. To accomplish full scalability dynamic conversion, we develop corresponding bitstream extraction, encoding and decoding schemes. At the encoder, we insert the IDR NAL periodically to solve the problems of spatial scalability conversion. At the extractor, we analyze the SVC bitstream to get the information which enable dynamic extraction. Real time extraction is achieved by using this information. Finally, we develop the decoder so that it can manage the changing scalability. Experimental results showed that dynamic full-scalability conversion was verified and it was necessary for time varying network condition.

Graphene Inks with Cellulosic Dispersants: Development and Applications for Printed Electronics

NASA Astrophysics Data System (ADS)

Secor, Ethan Benjamin

Graphene offers promising opportunities for applications in printed and flexible electronic devices due to its high electrical and thermal conductivity, mechanical flexibility and strength, and chemical and environmental stability. However, scalable production and processing of graphene presents a critical technological challenge preventing the application of graphene for flexible electronic interconnects, electrochemical energy storage, and chemically robust electrical contacts. In this thesis, a promising and versatile platform for the production, patterning, and application of graphene inks is presented based on cellulosic dispersants. Graphene is produced from flake graphite using scalable liquid-phase exfoliation methods, using the polymers ethyl cellulose and nitrocellulose as multifunctional dispersing agents. These cellulose derivatives offer high colloidal stability and broadly tunable rheology for graphene dispersions, providing an effective and tunable platform for graphene ink development. Thermal or photonic annealing decomposes the polymer dispersant to yield high conductivity, flexible graphene patterns for various electronics applications. In particular, the chemical stability of graphene enables robust electrical contacts for ceramic, metallic, organic and electrolytic materials, validating the diverse applicability of graphene in printed electronics. Overall, the strategy for graphene ink design presented here offers a simple, efficient, and versatile method for integrating graphene in a wide range of printed devices and systems, providing both fundamental insight for nanomaterial ink development and realistic opportunities for practical applications.

Understanding Graphics on a Scalable Latching Assistive Haptic Display Using a Shape Memory Polymer Membrane.

PubMed

Besse, Nadine; Rosset, Samuel; Zarate, Juan Jose; Ferrari, Elisabetta; Brayda, Luca; Shea, Herbert

2018-01-01

We present a fully latching and scalable 4 × 4 haptic display with 4 mm pitch, 5 s refresh time, 400 mN holding force, and 650 μm displacement per taxel. The display serves to convey dynamic graphical information to blind and visually impaired users. Combining significant holding force with high taxel density and large amplitude motion in a very compact overall form factor was made possible by exploiting the reversible, fast, hundred-fold change in the stiffness of a thin shape memory polymer (SMP) membrane when heated above its glass transition temperature. Local heating is produced using an addressable array of 3 mm in diameter stretchable microheaters patterned on the SMP. Each taxel is selectively and independently actuated by synchronizing the local Joule heating with a single pressure supply. Switching off the heating locks each taxel into its position (up or down), enabling holding any array configuration with zero power consumption. A 3D-printed pin array is mounted over the SMP membrane, providing the user with a smooth and room temperature array of movable pins to explore by touch. Perception tests were carried out with 24 blind users resulting in 70 percent correct pattern recognition over a 12-word tactile dictionary.

Scalable patterning using laser-induced shock waves

NASA Astrophysics Data System (ADS)

Ilhom, Saidjafarzoda; Kholikov, Khomidkhodza; Li, Peizhen; Ottman, Claire; Sanford, Dylan; Thomas, Zachary; San, Omer; Karaca, Haluk E.; Er, Ali O.

2018-04-01

An advanced direct imprinting method with low cost, quick, and minimal environmental impact to create a thermally controllable surface pattern using the laser pulses is reported. Patterned microindents were generated on Ni50Ti50 shape memory alloys and aluminum using an Nd: YAG laser operating at 1064 nm combined with a suitable transparent overlay, a sacrificial layer of graphite, and copper grid. Laser pulses at different energy densities, which generate pressure pulses up to a few GPa on the surface, were focused through the confinement medium, ablating the copper grid to create plasma and transferring the grid pattern onto the surface. Scanning electron microscope and optical microscope images show that various patterns were obtained on the surface with high fidelity. One-dimensional profile analysis indicates that the depth of the patterned sample initially increases with the laser energy and later levels off. Our simulations of laser irradiation process also confirm that high temperature and high pressure could be generated when the laser energy density of 2 J/cm2 is used.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

Sleep-disordered breathing after targeted ablation of preBötzinger complex neurons.

PubMed

McKay, Leanne C; Janczewski, Wiktor A; Feldman, Jack L

2005-09-01

Ablation of preBötzinger complex (preBötC) neurons, critical for respiratory rhythm generation, resulted in a progressive, increasingly severe disruption of respiratory pattern, initially during sleep and then also during wakefulness in adult rats. Sleep-disordered breathing is highly prevalent in elderly humans and in some patients with neurodegenerative disease. We propose that sleep-disordered breathing results from loss of preBötC neurons and could underlie death during sleep in these populations.

Sleep-disordered breathing after targeted ablation of preBötzinger complex neurons

PubMed Central

McKay, Leanne C; Janczewski, Wiktor A; Feldman, Jack L

2010-01-01

Ablation of preBötzinger complex (preBötC) neurons, critical for respiratory rhythm generation, resulted in a progressive, increasingly severe disruption of respiratory pattern, initially during sleep and then also during wakefulness in adult rats. Sleep-disordered breathing is highly prevalent in elderly humans and in some patients with neurodegenerative disease. We propose that sleep-disordered breathing results from loss of preBötC neurons and could underlie death during sleep in these populations. PMID:16116455

The DIAGNOSER project: combining assessment and learning.

PubMed

Thissen-Roe, Anne; Hunt, Earl; Minstrell, Jim

2004-05-01

DIAGNOSER is an Internet-based tool for classroom instruction. It delivers continuous formative assessment and feedback to high school physics students and their teachers about the correct and incorrect concepts and ideas the students may hold regarding physical situations. That is, it diagnoses misconceptions that underlie wrong answers of students, such as a confusion of velocity with acceleration. We use data about patterns of student responses, particularly consistency of errors from question to question, to improve the system's understanding of student concepts.

Epitaxial graphene growth on FIB patterned 3C-SiC nanostructures on Si (111): reducing milling damage.

PubMed

Amjadipour, Mojtaba; MacLeod, Jennifer; Lipton-Duffin, Josh; Iacopi, Francesca; Motta, Nunzio

2017-08-25

Epitaxial growth of graphene on SiC is a scalable procedure that does not require any further transfer step, making this an ideal platform for graphene nanostructure fabrication. Focused ion beam (FIB) is a very promising tool for exploring the reduction of the lateral dimension of graphene on SiC to the nanometre scale. However, exposure of graphene to the Ga + beam causes significant surface damage through amorphisation and contamination, preventing epitaxial graphene growth. In this paper we demonstrate that combining a protective silicon layer with FIB patterning implemented prior to graphene growth can significantly reduce the damage associated with FIB milling. Using this approach, we successfully achieved graphene growth over 3C-SiC/Si FIB patterned nanostructures.

Femtosecond laser patterning, synthesis, defect formation, and structural modification of atomic layered materials

DOE PAGES

Yoo, Jae-Hyuck; Kim, Eunpa; Hwang, David J.

2016-12-06

This article summarizes recent research on laser-based processing of twodimensional (2D) atomic layered materials, including graphene and transition metal dichalcogenides (TMDCs). Ultrafast lasers offer unique processing routes that take advantage of distinct interaction mechanisms with 2D materials to enable extremely localized energy deposition. Experiments have shown that ablative direct patterning of graphene by ultrafast lasers can achieve resolutions of tens of nanometers, as well as single-step pattern transfer. Ultrafast lasers also induce non-thermal excitation mechanisms that are useful for the thinning of TMDCs to tune the 2D material bandgap. Laser-assisted site-specific doping was recently demonstrated where ultrafast laser radiation undermore » ambient air environment could be used for the direct writing of high-quality graphene patterns on insulating substrates. This article concludes with an outlook towards developing further advanced laser processing with scalability, in situ monitoring strategies and potential applications.« less

Topological Patterns for Scalable Representation and Analysis of Dataflow Graphs

DTIC Science & Technology

2011-11-01

dimensional mesh structure. Such a structure is of particular use to model DSP architectures in which data flows across a network of processing elements...ACSSC.1998.751616 3. Andrews, J.G., Ghosh, A., Muhamed, R.: Fundamentals of WiMAX: understanding broad- band wireless networking . Prentice Hall (2007... SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 23 19a. NAME OF RESPONSIBLE PERSON a. REPORT

KOJAK: Scalable Semantic Link Discovery Via Integrated Knowledge-Based and Statistical Reasoning

DTIC Science & Technology

2006-11-01

program can find interesting connections in a network without having to learn the patterns of interestingness beforehand. The key advantage of our...Interesting Instances in Semantic Graphs Below we describe how the UNICORN framework can discover interesting instances in a multi-relational dataset...We can now describe how UNICORN solves the first problem of finding the top interesting nodes in a semantic net by ranking them according to

Linking dynamic patterns of neural activity in orbitofrontal cortex with decision making.

PubMed

Rich, Erin L; Stoll, Frederic M; Rudebeck, Peter H

2018-04-01

Humans and animals demonstrate extraordinary flexibility in choice behavior, particularly when deciding based on subjective preferences. We evaluate options on different scales, deliberate, and often change our minds. Little is known about the neural mechanisms that underlie these dynamic aspects of decision-making, although neural activity in orbitofrontal cortex (OFC) likely plays a central role. Recent evidence from studies in macaques shows that attention modulates value responses in OFC, and that ensembles of OFC neurons dynamically signal different options during choices. When contexts change, these ensembles flexibly remap to encode the new task. Determining how these dynamic patterns emerge and relate to choices will inform models of decision-making and OFC function. Copyright © 2017 Elsevier Ltd. All rights reserved.

The neurogenetic frontier--lessons from misbehaving zebrafish.

PubMed

Burgess, Harold A; Granato, Michael

2008-11-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish.

The neurogenetic frontier—lessons from misbehaving zebrafish

PubMed Central

Granato, Michael

2008-01-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish. PMID:18836206

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

Short winters threaten temperate fish populations

PubMed Central

Farmer, Troy M.; Marschall, Elizabeth A.; Dabrowski, Konrad; Ludsin, Stuart A.

2015-01-01

Although climate warming is expected to benefit temperate ectotherms by lengthening the summer growing season, declines in reproductive success following short, warm winters may counter such positive effects. Here we present long-term (1973–2010) field patterns for Lake Erie yellow perch, Perca flavescens, which show that failed annual recruitment events followed short, warm winters. Subsequent laboratory experimentation and field investigations revealed how reduced reproductive success following short, warm winters underlie these observed field patterns. Following short winters, females spawn at warmer temperatures and produce smaller eggs that both hatch at lower rates and produce smaller larvae than females exposed to long winters. Our research suggests that continued climate warming can lead to unanticipated, negative effects on temperate fish populations. PMID:26173734

The Contribution of Game Genre and other Use Patterns to Problem Video Game Play among Adult Video Gamers.

PubMed

Elliott, Luther; Ream, Geoffrey; McGinsky, Elizabeth; Dunlap, Eloise

2012-12-01

AIMS: To assess the contribution of patterns of video game play, including game genre, involvement, and time spent gaming, to problem use symptomatology. DESIGN: Nationally representative survey. SETTING: Online. PARTICIPANTS: Large sample (n=3,380) of adult video gamers in the US. MEASUREMENTS: Problem video game play (PVGP) scale, video game genre typology, use patterns (gaming days in the past month and hours on days used), enjoyment, consumer involvement, and background variables. FINDINGS: Study confirms game genre's contribution to problem use as well as demographic variation in play patterns that underlie problem video game play vulnerability. CONCLUSIONS: Identification of a small group of game types positively correlated with problem use suggests new directions for research into the specific design elements and reward mechanics of "addictive" video games. Unique vulnerabilities to problem use among certain groups demonstrate the need for ongoing investigation of health disparities related to contextual dimensions of video game play.

The Contribution of Game Genre and other Use Patterns to Problem Video Game Play among Adult Video Gamers

PubMed Central

Ream, Geoffrey; McGinsky, Elizabeth; Dunlap, Eloise

2012-01-01

Aims To assess the contribution of patterns of video game play, including game genre, involvement, and time spent gaming, to problem use symptomatology. Design Nationally representative survey. Setting Online. Participants Large sample (n=3,380) of adult video gamers in the US. Measurements Problem video game play (PVGP) scale, video game genre typology, use patterns (gaming days in the past month and hours on days used), enjoyment, consumer involvement, and background variables. Findings Study confirms game genre's contribution to problem use as well as demographic variation in play patterns that underlie problem video game play vulnerability. Conclusions Identification of a small group of game types positively correlated with problem use suggests new directions for research into the specific design elements and reward mechanics of “addictive” video games. Unique vulnerabilities to problem use among certain groups demonstrate the need for ongoing investigation of health disparities related to contextual dimensions of video game play. PMID:23284310

Distinct Mechanisms for Synchronization and Temporal Patterning of Odor-Encoding Neural Assemblies

NASA Astrophysics Data System (ADS)

MacLeod, Katrina; Laurent, Gilles

1996-11-01

Stimulus-evoked oscillatory synchronization of neural assemblies and temporal patterns of neuronal activity have been observed in many sensory systems, such as the visual and auditory cortices of mammals or the olfactory system of insects. In the locust olfactory system, single odor puffs cause the immediate formation of odor-specific neural assemblies, defined both by their transient synchronized firing and their progressive transformation over the course of a response. The application of an antagonist of ionotropic γ-aminobutyric acid (GABA) receptors to the first olfactory relay neuropil selectively blocked the fast inhibitory synapse between local and projection neurons. This manipulation abolished the synchronization of the odor-coding neural ensembles but did not affect each neuron's temporal response patterns to odors, even when these patterns contained periods of inhibition. Fast GABA-mediated inhibition, therefore, appears to underlie neuronal synchronization but not response tuning in this olfactory system. The selective desynchronization of stimulus-evoked oscillating neural assemblies in vivo is now possible, enabling direct functional tests of their significance for sensation and perception.

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

PubMed Central

2010-01-01

Background An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets. Methods This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model. Results A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center. Conclusion WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data. PMID:21210985

Global Characteristics of Childhood Acute Promyelocytic Leukemia

PubMed Central

Zhang, L; Samad, A; Pombo-de-Oliveira, MS; Scelo, G; Smith, MT; Feusner, J; Wiemels, JL; Metayer, C

2014-01-01

Acute promyelocytic leukemia (APL) comprises approximately 5–10% of childhood acute myeloid leukemia (AML) cases in the US. While variation in this percentage among other populations was noted previously, global patterns of childhood APL have not been thoroughly characterized. In this comprehensive review of childhood APL, we examined its geographic pattern and the potential contribution of environmental factors to observed variation. In 142 studies (spanning >60 countries) identified, variation was apparent—de novo APL represented from 2% (Switzerland) to >50% (Nicaragua) of childhood AML in different geographic regions. Because a limited number of previous studies addressed specific environmental exposures that potentially underlie childhood APL development, we gathered 28 childhood cases of therapy-related APL, which exemplified associations between prior exposures to chemotherapeutic drugs/radiation and APL diagnosis. Future population-based studies examining childhood APL patterns and the potential association with specific environmental exposures and other risk factors are needed. PMID:25445717

Human connectome module pattern detection using a new multi-graph MinMax cut model.

PubMed

De, Wang; Wang, Yang; Nie, Feiping; Yan, Jingwen; Cai, Weidong; Saykin, Andrew J; Shen, Li; Huang, Heng

2014-01-01

Many recent scientific efforts have been devoted to constructing the human connectome using Diffusion Tensor Imaging (DTI) data for understanding the large-scale brain networks that underlie higher-level cognition in human. However, suitable computational network analysis tools are still lacking in human connectome research. To address this problem, we propose a novel multi-graph min-max cut model to detect the consistent network modules from the brain connectivity networks of all studied subjects. A new multi-graph MinMax cut model is introduced to solve this challenging computational neuroscience problem and the efficient optimization algorithm is derived. In the identified connectome module patterns, each network module shows similar connectivity patterns in all subjects, which potentially associate to specific brain functions shared by all subjects. We validate our method by analyzing the weighted fiber connectivity networks. The promising empirical results demonstrate the effectiveness of our method.

Learning multiple variable-speed sequences in striatum via cortical tutoring.

PubMed

Murray, James M; Escola, G Sean

2017-05-08

Sparse, sequential patterns of neural activity have been observed in numerous brain areas during timekeeping and motor sequence tasks. Inspired by such observations, we construct a model of the striatum, an all-inhibitory circuit where sequential activity patterns are prominent, addressing the following key challenges: (i) obtaining control over temporal rescaling of the sequence speed, with the ability to generalize to new speeds; (ii) facilitating flexible expression of distinct sequences via selective activation, concatenation, and recycling of specific subsequences; and (iii) enabling the biologically plausible learning of sequences, consistent with the decoupling of learning and execution suggested by lesion studies showing that cortical circuits are necessary for learning, but that subcortical circuits are sufficient to drive learned behaviors. The same mechanisms that we describe can also be applied to circuits with both excitatory and inhibitory populations, and hence may underlie general features of sequential neural activity pattern generation in the brain.

Handling Dynamic Weights in Weighted Frequent Pattern Mining

NASA Astrophysics Data System (ADS)

Ahmed, Chowdhury Farhan; Tanbeer, Syed Khairuzzaman; Jeong, Byeong-Soo; Lee, Young-Koo

Even though weighted frequent pattern (WFP) mining is more effective than traditional frequent pattern mining because it can consider different semantic significances (weights) of items, existing WFP algorithms assume that each item has a fixed weight. But in real world scenarios, the weight (price or significance) of an item can vary with time. Reflecting these changes in item weight is necessary in several mining applications, such as retail market data analysis and web click stream analysis. In this paper, we introduce the concept of a dynamic weight for each item, and propose an algorithm, DWFPM (dynamic weighted frequent pattern mining), that makes use of this concept. Our algorithm can address situations where the weight (price or significance) of an item varies dynamically. It exploits a pattern growth mining technique to avoid the level-wise candidate set generation-and-test methodology. Furthermore, it requires only one database scan, so it is eligible for use in stream data mining. An extensive performance analysis shows that our algorithm is efficient and scalable for WFP mining using dynamic weights.

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

PubMed Central

Morgani, Sophie M; Metzger, Jakob J; Nichols, Jennifer

2018-01-01

During gastrulation epiblast cells exit pluripotency as they specify and spatially arrange the three germ layers of the embryo. Similarly, human pluripotent stem cells (PSCs) undergo spatially organized fate specification on micropatterned surfaces. Since in vivo validation is not possible for the human, we developed a mouse PSC micropattern system and, with direct comparisons to mouse embryos, reveal the robust specification of distinct regional identities. BMP, WNT, ACTIVIN and FGF directed mouse epiblast-like cells to undergo an epithelial-to-mesenchymal transition and radially pattern posterior mesoderm fates. Conversely, WNT, ACTIVIN and FGF patterned anterior identities, including definitive endoderm. By contrast, epiblast stem cells, a developmentally advanced state, only specified anterior identities, but without patterning. The mouse micropattern system offers a robust scalable method to generate regionalized cell types present in vivo, resolve how signals promote distinct identities and generate patterns, and compare mechanisms operating in vivo and in vitro and across species. PMID:29412136

Roll-to-Roll Laser-Printed Graphene-Graphitic Carbon Electrodes for High-Performance Supercapacitors.

PubMed

Kang, Sangmin; Lim, Kyungmi; Park, Hyeokjun; Park, Jong Bo; Park, Seong Chae; Cho, Sung-Pyo; Kang, Kisuk; Hong, Byung Hee

2018-01-10

Carbon electrodes including graphene and thin graphite films have been utilized for various energy and sensor applications, where the patterning of electrodes is essentially included. Laser scribing in a DVD writer and inkjet printing were used to pattern the graphene-like materials, but the size and speed of fabrication has been limited for practical applications. In this work, we devise a simple strategy to use conventional laser-printer toner materials as precursors for graphitic carbon electrodes. The toner was laser-printed on metal foils, followed by thermal annealing in hydrogen environment, finally resulting in the patterned thin graphitic carbon or graphene electrodes for supercapacitors. The electrochemical cells made of the graphene-graphitic carbon electrodes show remarkably higher energy and power performance compared to conventional supercapacitors. Furthermore, considering the simplicity and scalability of roll-to-roll (R2R) electrode patterning processes, the proposed method would enable cheaper and larger-scale synthesis and patterning of graphene-graphitic carbon electrodes for various energy applications in the future.

Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps

PubMed Central

Antolík, Ján

2017-01-01

Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added. PMID:28408869

Beneath the Surface: Understanding Patterns of Intra-Domain Orientational Order

NASA Astrophysics Data System (ADS)

Prasad, Ishan; Seo, Youngmi; Hall, Lisa; Grason, Gregory

Block copolymers (BCP) self assemble into a rich spectrum of ordered phases due to asymmetry in copolymer architecture. Despite extensive study of spatially-ordered composition patterns of BCP, knowledge of orientational order of chain segments that underlie these spatial patterns is evidently missing. We show using self consistent field (SCF) theory and coarse-grained molecular dynamics (MD) simulations that, even without explicit orientational interactions between segments, BCP exhibit generic patterns of intra-domain segment orientation, which vary both within a given morphology and from morphology to morphology. We find that segment alignment is usually both normal and parallel to the interface within different local regions of a BCP sub-domain. We describe principles that control relative strength and directionality of alignment in different morphologies and report a surprising yet generic emergence of biaxial segment order in morphologies with anisotropic curved interfaces, such as cylinders and gyroid phases. Finally, we focus our study on cholesteric textures that pervade mesochiral BCP morphologies, specifically alternating double gyroid (aDG) and helical cylinder (H*) phases, and analyze patterns of twisted (nematic and polar) segment order within these domains.

Evapotranspiration partitioning, stomatal conductance, and components of the water balance: A special case of a desert ecosystem in China

NASA Astrophysics Data System (ADS)

Zhao, Wenzhi; Liu, Bing; Chang, Xuexiang; Yang, Qiyue; Yang, Yuting; Liu, Zhiling; Cleverly, James; Eamus, Derek

2016-07-01

Partitioning evapotranspiration (ET) into its components reveals details of the processes that underlie ecosystem hydrologic budgets and their feedback to the water cycle. We measured rates of actual evapotranspiration (ETa), canopy transpiration (Tc), soil evaporation (Eg), canopy-intercepted precipitation (EI), and patterns of stomatal conductance of the desert shrub Calligonum mongolicum in northern China to determine the water balance of this ecosystem. The ETa was 251 ± 8 mm during the growing period, while EI, Tc, and Eg accounted for 3.2%, 63.9%, and 31.3%, respectively, of total water use (256 ± 4 mm) during the growing period. In this unique ecosystem, groundwater was the main water source for plant transpiration and soil evaporation, Tc and exceeded 60% of the total annual water used by desert plants. ET was not sensitive to air temperature in this unique desert ecosystem. Partitioning ET into its components improves our understanding of the mechanisms that underlie adaptation of desert shrubs, especially the role of stomatal regulation of Tc as a determinant of ecosystem water balance.

An Approach to Self-Assembling Swarm Robots Using Multitree Genetic Programming

PubMed Central

An, Jinung

2013-01-01

In recent days, self-assembling swarm robots have been studied by a number of researchers due to their advantages such as high efficiency, stability, and scalability. However, there are still critical issues in applying them to practical problems in the real world. The main objective of this study is to develop a novel self-assembling swarm robot algorithm that overcomes the limitations of existing approaches. To this end, multitree genetic programming is newly designed to efficiently discover a set of patterns necessary to carry out the mission of the self-assembling swarm robots. The obtained patterns are then incorporated into their corresponding robot modules. The computational experiments prove the effectiveness of the proposed approach. PMID:23861655

An approach to self-assembling swarm robots using multitree genetic programming.

PubMed

Lee, Jong-Hyun; Ahn, Chang Wook; An, Jinung

2013-01-01

In recent days, self-assembling swarm robots have been studied by a number of researchers due to their advantages such as high efficiency, stability, and scalability. However, there are still critical issues in applying them to practical problems in the real world. The main objective of this study is to develop a novel self-assembling swarm robot algorithm that overcomes the limitations of existing approaches. To this end, multitree genetic programming is newly designed to efficiently discover a set of patterns necessary to carry out the mission of the self-assembling swarm robots. The obtained patterns are then incorporated into their corresponding robot modules. The computational experiments prove the effectiveness of the proposed approach.

Strong photon antibunching in weakly nonlinear two-dimensional exciton-polaritons

NASA Astrophysics Data System (ADS)

Ryou, Albert; Rosser, David; Saxena, Abhi; Fryett, Taylor; Majumdar, Arka

2018-06-01

A deterministic and scalable array of single photon nonlinearities in the solid state holds great potential for both fundamental physics and technological applications, but its realization has proved extremely challenging. Despite significant advances, leading candidates such as quantum dots and group III-V quantum wells have yet to overcome their respective bottlenecks in random positioning and weak nonlinearity. Here we consider a hybrid light-matter platform, marrying an atomically thin two-dimensional material to a photonic crystal cavity, and analyze its second-order coherence function. We identify several mechanisms for photon antibunching under different system parameters, including one characterized by large dissipation and weak nonlinearity. Finally, we show that by patterning the two-dimensional material into different sizes, we can drive our system dynamics from a coherent state into a regime of strong antibunching with second-order coherence function g(2 )(0 ) ˜10-3 , opening a possible route to scalable, on-chip quantum simulations with correlated photons.

Using S3 cloud storage with ROOT and CvmFS

NASA Astrophysics Data System (ADS)

Arsuaga-Ríos, María; Heikkilä, Seppo S.; Duellmann, Dirk; Meusel, René; Blomer, Jakob; Couturier, Ben

2015-12-01

Amazon S3 is a widely adopted web API for scalable cloud storage that could also fulfill storage requirements of the high-energy physics community. CERN has been evaluating this option using some key HEP applications such as ROOT and the CernVM filesystem (CvmFS) with S3 back-ends. In this contribution we present an evaluation of two versions of the Huawei UDS storage system stressed with a large number of clients executing HEP software applications. The performance of concurrently storing individual objects is presented alongside with more complex data access patterns as produced by the ROOT data analysis framework. Both Huawei UDS generations show a successful scalability by supporting multiple byte-range requests in contrast with Amazon S3 or Ceph which do not support these commonly used HEP operations. We further report the S3 integration with recent CvmFS versions and summarize the experience with CvmFS/S3 for publishing daily releases of the full LHCb experiment software stack.

Scalable quantum computer architecture with coupled donor-quantum dot qubits

DOEpatents

Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph; Lyon, Stephen; Tyryshkin, Alexei; Bokor, Jeffrey

2014-08-26

A quantum bit computing architecture includes a plurality of single spin memory donor atoms embedded in a semiconductor layer, a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, wherein a first voltage applied across at least one pair of the aligned quantum dot and donor atom controls a donor-quantum dot coupling. A method of performing quantum computing in a scalable architecture quantum computing apparatus includes arranging a pattern of single spin memory donor atoms in a semiconductor layer, forming a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, applying a first voltage across at least one aligned pair of a quantum dot and donor atom to control a donor-quantum dot coupling, and applying a second voltage between one or more quantum dots to control a Heisenberg exchange J coupling between quantum dots and to cause transport of a single spin polarized electron between quantum dots.

Screening of lipid composition for scalable fabrication of solvent free lipid microarrays

NASA Astrophysics Data System (ADS)

Ghazanfari, Lida; Lenhert, Steven

2016-12-01

Liquid microdroplet arrays on surfaces are a promising approach to the miniaturization of laboratory processes such as high throughput screening. The fluid nature of these droplets poses unique challenges and opportunities in their fabrication and application, particularly for the scalable integration of multiple materials over large areas and immersion into cell culture solution. Here we use pin spotting and nanointaglio printing to screen a library of lipids and their mixtures for their compatibility with these fabrication processes, as well as stability upon immersion into aqueous solution. More than 200 combinations of natural and synthetic oils composed of fatty acids, triglycerides, and hydrocarbons were tested for their pin-spotting and nanointaglio print quality and their ability to contain the fluorescent compound TRITC upon immersion in water. A combination of castor oil and hexanoic acid at the ratio of 1:1 (w/w) was found optimal for producing reproducible patterns that are stable upon immersion into water. This method is capable of large scale nano-materials integration.

Validating Quantitative Measurement Using Qualitative Data: Combining Rasch Scaling and Latent Semantic Analysis in Psychiatry

NASA Astrophysics Data System (ADS)

Lange, Rense

2015-02-01

An extension of concurrent validity is proposed that uses qualitative data for the purpose of validating quantitative measures. The approach relies on Latent Semantic Analysis (LSA) which places verbal (written) statements in a high dimensional semantic space. Using data from a medical / psychiatric domain as a case study - Near Death Experiences, or NDE - we established concurrent validity by connecting NDErs qualitative (written) experiential accounts with their locations on a Rasch scalable measure of NDE intensity. Concurrent validity received strong empirical support since the variance in the Rasch measures could be predicted reliably from the coordinates of their accounts in the LSA derived semantic space (R2 = 0.33). These coordinates also predicted NDErs age with considerable precision (R2 = 0.25). Both estimates are probably artificially low due to the small available data samples (n = 588). It appears that Rasch scalability of NDE intensity is a prerequisite for these findings, as each intensity level is associated (at least probabilistically) with a well- defined pattern of item endorsements.

High-frequency self-aligned graphene transistors with transferred gate stacks

PubMed Central

Cheng, Rui; Bai, Jingwei; Liao, Lei; Zhou, Hailong; Chen, Yu; Liu, Lixin; Lin, Yung-Chen; Jiang, Shan; Huang, Yu; Duan, Xiangfeng

2012-01-01

Graphene has attracted enormous attention for radio-frequency transistor applications because of its exceptional high carrier mobility, high carrier saturation velocity, and large critical current density. Herein we report a new approach for the scalable fabrication of high-performance graphene transistors with transferred gate stacks. Specifically, arrays of gate stacks are first patterned on a sacrificial substrate, and then transferred onto arbitrary substrates with graphene on top. A self-aligned process, enabled by the unique structure of the transferred gate stacks, is then used to position precisely the source and drain electrodes with minimized access resistance or parasitic capacitance. This process has therefore enabled scalable fabrication of self-aligned graphene transistors with unprecedented performance including a record-high cutoff frequency up to 427 GHz. Our study defines a unique pathway to large-scale fabrication of high-performance graphene transistors, and holds significant potential for future application of graphene-based devices in ultra–high-frequency circuits. PMID:22753503

Automated Performance Prediction of Message-Passing Parallel Programs

NASA Technical Reports Server (NTRS)

Block, Robert J.; Sarukkai, Sekhar; Mehra, Pankaj; Woodrow, Thomas S. (Technical Monitor)

1995-01-01

The increasing use of massively parallel supercomputers to solve large-scale scientific problems has generated a need for tools that can predict scalability trends of applications written for these machines. Much work has been done to create simple models that represent important characteristics of parallel programs, such as latency, network contention, and communication volume. But many of these methods still require substantial manual effort to represent an application in the model's format. The NIK toolkit described in this paper is the result of an on-going effort to automate the formation of analytic expressions of program execution time, with a minimum of programmer assistance. In this paper we demonstrate the feasibility of our approach, by extending previous work to detect and model communication patterns automatically, with and without overlapped computations. The predictions derived from these models agree, within reasonable limits, with execution times of programs measured on the Intel iPSC/860 and Paragon. Further, we demonstrate the use of MK in selecting optimal computational grain size and studying various scalability metrics.

Scalable and balanced dynamic hybrid data assimilation

NASA Astrophysics Data System (ADS)

Kauranne, Tuomo; Amour, Idrissa; Gunia, Martin; Kallio, Kari; Lepistö, Ahti; Koponen, Sampsa

2017-04-01

Scalability of complex weather forecasting suites is dependent on the technical tools available for implementing highly parallel computational kernels, but to an equally large extent also on the dependence patterns between various components of the suite, such as observation processing, data assimilation and the forecast model. Scalability is a particular challenge for 4D variational assimilation methods that necessarily couple the forecast model into the assimilation process and subject this combination to an inherently serial quasi-Newton minimization process. Ensemble based assimilation methods are naturally more parallel, but large models force ensemble sizes to be small and that results in poor assimilation accuracy, somewhat akin to shooting with a shotgun in a million-dimensional space. The Variational Ensemble Kalman Filter (VEnKF) is an ensemble method that can attain the accuracy of 4D variational data assimilation with a small ensemble size. It achieves this by processing a Gaussian approximation of the current error covariance distribution, instead of a set of ensemble members, analogously to the Extended Kalman Filter EKF. Ensemble members are re-sampled every time a new set of observations is processed from a new approximation of that Gaussian distribution which makes VEnKF a dynamic assimilation method. After this a smoothing step is applied that turns VEnKF into a dynamic Variational Ensemble Kalman Smoother VEnKS. In this smoothing step, the same process is iterated with frequent re-sampling of the ensemble but now using past iterations as surrogate observations until the end result is a smooth and balanced model trajectory. In principle, VEnKF could suffer from similar scalability issues as 4D-Var. However, this can be avoided by isolating the forecast model completely from the minimization process by implementing the latter as a wrapper code whose only link to the model is calling for many parallel and totally independent model runs, all of them implemented as parallel model runs themselves. The only bottleneck in the process is the gathering and scattering of initial and final model state snapshots before and after the parallel runs which requires a very efficient and low-latency communication network. However, the volume of data communicated is small and the intervening minimization steps are only 3D-Var, which means their computational load is negligible compared with the fully parallel model runs. We present example results of scalable VEnKF with the 4D lake and shallow sea model COHERENS, assimilating simultaneously continuous in situ measurements in a single point and infrequent satellite images that cover a whole lake, with the fully scalable VEnKF.

Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns

DOE PAGES

Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M.; ...

2016-08-16

Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyreneblock-poly(methyl methacrylate). Faster assembly kinetics aremore » observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. Lastly, the rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces.« less

Gene expression underlying adaptive variation in Heliconius wing patterns: non-modular regulation of overlapping cinnabar and vermilion prepatterns.

PubMed

Reed, Robert D; McMillan, W Owen; Nagy, Lisa M

2008-01-07

Geographical variation in the mimetic wing patterns of the butterfly Heliconius erato is a textbook example of adaptive polymorphism; however, little is known about how this variation is controlled developmentally. Using microarrays and qPCR, we identified and compared expression of candidate genes potentially involved with a red/yellow forewing band polymorphism in H. erato. We found that transcripts encoding the pigment synthesis enzymes cinnabar and vermilion showed pattern- and polymorphism-related expression patterns, respectively. cinnabar expression was associated with the forewing band regardless of pigment colour, providing the first gene expression pattern known to be correlated with a major Heliconius colour pattern. In contrast, vermilion expression changed spatially over time in red-banded butterflies, but was not expressed at detectable levels in yellow-banded butterflies, suggesting that regulation of this gene may be involved with the red/yellow polymorphism. Furthermore, we found that the yellow pigment, 3-hydroxykynurenine, is incorporated into wing scales from the haemolymph rather than being synthesized in situ. We propose that some aspects of Heliconius colour patterns are determined by spatio-temporal overlap of pigment gene transcription prepatterns and speculate that evolutionary changes in vermilion regulation may in part underlie an adaptive colour pattern polymorphism.

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

PubMed Central

2017-01-01

Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the “pair-rule” genes, are still not well understood at the system level. Building on established genetic interactions, I construct a logical model of the Drosophila pair-rule system that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic “gap” inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries and explains the aetiology of the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggests that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods. PMID:28953896

Underdevelopment and the political economy of malnutrition and ill health.

PubMed

Chossudovsky, M

1983-01-01

This article applies Marx's abstract subdivision of social consumption to the prevailing patterns of capital accumulation in the Third World. Built-in scarcities in the availability of necessary consumer goods, alongside patterns of overconsumption and social waste by the upper-income groups, are conducive to conditions of mass poverty, malnutrition, and disease that coexist with small pockets of social privilege and affluence. Malnutrition and ill health must be understood and analyzed in relation to the dual and divided structure of social consumption: necessities of life as opposed to luxury and semi-luxury goods. The relationship between capital accumulation, the distribution of money income, and patterns of malnutrition and ill health is analyzed. It is shown that patterns of malnutrition and ill health are socially differentiated, and the core disease pattern in Third World social formations is discussed in relation to the material and social conditions of life which generate ill health and which underlie particular patterns of peripheral capital accumulation. The study focuses on empirical procedures for analyzing the relationship between levels of money income and levels of calorie and protein intake. An appendix outlines a methodology for estimating undernourishment in urban areas from household budget surveys.

Sparse network-based models for patient classification using fMRI

PubMed Central

Rosa, Maria J.; Portugal, Liana; Hahn, Tim; Fallgatter, Andreas J.; Garrido, Marta I.; Shawe-Taylor, John; Mourao-Miranda, Janaina

2015-01-01

Pattern recognition applied to whole-brain neuroimaging data, such as functional Magnetic Resonance Imaging (fMRI), has proved successful at discriminating psychiatric patients from healthy participants. However, predictive patterns obtained from whole-brain voxel-based features are difficult to interpret in terms of the underlying neurobiology. Many psychiatric disorders, such as depression and schizophrenia, are thought to be brain connectivity disorders. Therefore, pattern recognition based on network models might provide deeper insights and potentially more powerful predictions than whole-brain voxel-based approaches. Here, we build a novel sparse network-based discriminative modeling framework, based on Gaussian graphical models and L1-norm regularized linear Support Vector Machines (SVM). In addition, the proposed framework is optimized in terms of both predictive power and reproducibility/stability of the patterns. Our approach aims to provide better pattern interpretation than voxel-based whole-brain approaches by yielding stable brain connectivity patterns that underlie discriminative changes in brain function between the groups. We illustrate our technique by classifying patients with major depressive disorder (MDD) and healthy participants, in two (event- and block-related) fMRI datasets acquired while participants performed a gender discrimination and emotional task, respectively, during the visualization of emotional valent faces. PMID:25463459

Neuroscience, evolution and the sapient paradox: the factuality of value and of the sacred.

PubMed

Renfrew, Colin

2008-06-12

The human genome, and hence the human brain at birth, may not have changed greatly over the past 60000 years. Yet many of the major behavioural changes that we associate with most human societies are very much more recent, some appearing with the sedentary revolution of some 10000 years ago. Among these are activities implying the emergence of powerful concepts of value and of the sacred. What then are the neuronal mechanisms that may underlie these consistent, significant (and emergent) patterns of behaviour?

Learning to play Go using recursive neural networks.

PubMed

Wu, Lin; Baldi, Pierre

2008-11-01

Go is an ancient board game that poses unique opportunities and challenges for artificial intelligence. Currently, there are no computer Go programs that can play at the level of a good human player. However, the emergence of large repositories of games is opening the door for new machine learning approaches to address this challenge. Here we develop a machine learning approach to Go, and related board games, focusing primarily on the problem of learning a good evaluation function in a scalable way. Scalability is essential at multiple levels, from the library of local tactical patterns, to the integration of patterns across the board, to the size of the board itself. The system we propose is capable of automatically learning the propensity of local patterns from a library of games. Propensity and other local tactical information are fed into recursive neural networks, derived from a probabilistic Bayesian network architecture. The recursive neural networks in turn integrate local information across the board in all four cardinal directions and produce local outputs that represent local territory ownership probabilities. The aggregation of these probabilities provides an effective strategic evaluation function that is an estimate of the expected area at the end, or at various other stages, of the game. Local area targets for training can be derived from datasets of games played by human players. In this approach, while requiring a learning time proportional to N(4), skills learned on a board of size N(2) can easily be transferred to boards of other sizes. A system trained using only 9 x 9 amateur game data performs surprisingly well on a test set derived from 19 x 19 professional game data. Possible directions for further improvements are briefly discussed.

Higher predation risk for insect prey at low latitudes and elevations.

PubMed

Roslin, Tomas; Hardwick, Bess; Novotny, Vojtech; Petry, William K; Andrew, Nigel R; Asmus, Ashley; Barrio, Isabel C; Basset, Yves; Boesing, Andrea Larissa; Bonebrake, Timothy C; Cameron, Erin K; Dáttilo, Wesley; Donoso, David A; Drozd, Pavel; Gray, Claudia L; Hik, David S; Hill, Sarah J; Hopkins, Tapani; Huang, Shuyin; Koane, Bonny; Laird-Hopkins, Benita; Laukkanen, Liisa; Lewis, Owen T; Milne, Sol; Mwesige, Isaiah; Nakamura, Akihiro; Nell, Colleen S; Nichols, Elizabeth; Prokurat, Alena; Sam, Katerina; Schmidt, Niels M; Slade, Alison; Slade, Victor; Suchanková, Alžběta; Teder, Tiit; van Nouhuys, Saskya; Vandvik, Vigdis; Weissflog, Anita; Zhukovich, Vital; Slade, Eleanor M

2017-05-19

Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic trend in attack rates by birds or mammals. These matching gradients at global and regional scales suggest consistent drivers of biotic interaction strength, a finding that needs to be integrated into general theories of herbivory, community organization, and life-history evolution. Copyright © 2017, American Association for the Advancement of Science.

Structural synaptic plasticity in the hippocampus induced by spatial experience and its implications in information processing.

PubMed

Carasatorre, M; Ramírez-Amaya, V; Díaz Cintra, S

2016-10-01

Long-lasting memory formation requires that groups of neurons processing new information develop the ability to reproduce the patterns of neural activity acquired by experience. Changes in synaptic efficiency let neurons organise to form ensembles that repeat certain activity patterns again and again. Among other changes in synaptic plasticity, structural modifications tend to be long-lasting which suggests that they underlie long-term memory. There is a large body of evidence supporting that experience promotes changes in the synaptic structure, particularly in the hippocampus. Structural changes to the hippocampus may be functionally implicated in stabilising acquired memories and encoding new information. Copyright © 2012 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Kant, cognitive psychotherapy, and the hardening of the categories.

PubMed

Nevid, Jeffrey S

2007-12-01

Contemporary models of psychotherapy owe a considerable intellectual debt to philosophy, even though the contributions of philosophers to contemporary practice in the field often go unrecognized. A case in point is Kant's epistemology, which is foundational to cognitive approaches to psychotherapy. Here, it is argued that the rigid use of certain judgments represented in Kant's conceptual scheme underlies patterns of distorted or dysfunctional thinking associated with emotional disorders. Kantian judgments of necessity, disjunction, particularity and universality have counterpoints in contemporary conceptions of cognitive distortions. Moreover, Kantian epistemology has important therapeutic implications with respect to helping people with emotional disorders recognize and challenge rigidly held judgments or categories of understanding. The Kantian perspective also leads us to consider the cognitive frameworks or thought structures that underlie dysfunctional thinking patterns.

Bodily maps of emotions across child development.

PubMed

Hietanen, Jari K; Glerean, Enrico; Hari, Riitta; Nummenmaa, Lauri

2016-11-01

Different basic emotions (anger, fear, disgust, happiness, sadness, and surprise) are consistently associated with distinct bodily sensation maps, which may underlie subjectively felt emotions. Here we investigated the development of bodily sensations associated with basic emotions in 6- to 17-year-old children and adolescents (n = 331). Children as young as 6 years of age associated statistically discernible, discrete patterns of bodily sensations with happiness, fear, and surprise, as well as with emotional neutrality. The bodily sensation maps changed from less to more specific, adult-like patterns as a function of age. We conclude that emotion-related bodily sensations become increasingly discrete over child development. Developing awareness of their emotion-related bodily sensations may shape the way children perceive, label, and interpret emotions. © 2016 John Wiley & Sons Ltd.

Hotspot detection using image pattern recognition based on higher-order local auto-correlation

NASA Astrophysics Data System (ADS)

Maeda, Shimon; Matsunawa, Tetsuaki; Ogawa, Ryuji; Ichikawa, Hirotaka; Takahata, Kazuhiro; Miyairi, Masahiro; Kotani, Toshiya; Nojima, Shigeki; Tanaka, Satoshi; Nakagawa, Kei; Saito, Tamaki; Mimotogi, Shoji; Inoue, Soichi; Nosato, Hirokazu; Sakanashi, Hidenori; Kobayashi, Takumi; Murakawa, Masahiro; Higuchi, Tetsuya; Takahashi, Eiichi; Otsu, Nobuyuki

2011-04-01

Below 40nm design node, systematic variation due to lithography must be taken into consideration during the early stage of design. So far, litho-aware design using lithography simulation models has been widely applied to assure that designs are printed on silicon without any error. However, the lithography simulation approach is very time consuming, and under time-to-market pressure, repetitive redesign by this approach may result in the missing of the market window. This paper proposes a fast hotspot detection support method by flexible and intelligent vision system image pattern recognition based on Higher-Order Local Autocorrelation. Our method learns the geometrical properties of the given design data without any defects as normal patterns, and automatically detects the design patterns with hotspots from the test data as abnormal patterns. The Higher-Order Local Autocorrelation method can extract features from the graphic image of design pattern, and computational cost of the extraction is constant regardless of the number of design pattern polygons. This approach can reduce turnaround time (TAT) dramatically only on 1CPU, compared with the conventional simulation-based approach, and by distributed processing, this has proven to deliver linear scalability with each additional CPU.

A probabilistic approach to randomness in geometric configuration of scalable origami structures

NASA Astrophysics Data System (ADS)

Liu, Ke; Paulino, Glaucio; Gardoni, Paolo

2015-03-01

Origami, an ancient paper folding art, has inspired many solutions to modern engineering challenges. The demand for actual engineering applications motivates further investigation in this field. Although rooted from the historic art form, many applications of origami are based on newly designed origami patterns to match the specific requirenments of an engineering problem. The application of origami to structural design problems ranges from micro-structure of materials to large scale deployable shells. For instance, some origami-inspired designs have unique properties such as negative Poisson ratio and flat foldability. However, origami structures are typically constrained by strict mathematical geometric relationships, which in reality, can be easily violated, due to, for example, random imperfections introduced during manufacturing, or non-uniform deformations under working conditions (e.g. due to non-uniform thermal effects). Therefore, the effects of uncertainties in origami-like structures need to be studied in further detail in order to provide a practical guide for scalable origami-inspired engineering designs. Through reliability and probabilistic analysis, we investigate the effect of randomness in origami structures on their mechanical properties. Dislocations of vertices of an origami structure have different impacts on different mechanical properties, and different origami designs could have different sensitivities to imperfections. Thus we aim to provide a preliminary understanding of the structural behavior of some common scalable origami structures subject to randomness in their geometric configurations in order to help transition the technology toward practical applications of origami engineering.

Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

PubMed Central

Islam, Tanveer ul; Gandhi, Prasanna S.

2016-01-01

Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use. PMID:27849003

Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

NASA Astrophysics Data System (ADS)

Islam, Tanveer Ul; Gandhi, Prasanna S.

2016-11-01

Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use.

Childhood pneumonia diagnostics: community health workers' and national stakeholders' differing perspectives of new and existing aids.

PubMed

Spence, Hollie; Baker, Kevin; Wharton-Smith, Alexandra; Mucunguzi, Akasiima; Matata, Lena; Habte, Tedila; Nanyumba, Diana; Sebsibe, Anteneh; Thany, Thol; Källander, Karin

2017-01-01

Pneumonia heavily contributes to global under-five mortality. Many countries use community case management to detect and treat childhood pneumonia. Community health workers (CHWs) have limited tools to help them assess signs of pneumonia. New respiratory rate (RR) counting devices and pulse oximeters are being considered for this purpose. To explore perspectives of CHWs and national stakeholders regarding the potential usability and scalability of seven devices to aid community assessment of pneumonia signs. Pile sorting was conducted to rate the usability and scalability of 7 different RR counting aids and pulse oximeters amongst 16 groups of participants. Following each pile-sorting session, a focus group discussion (FGD) explored participants' sorting rationale. Purposive sampling was used to select CHWs and national stakeholders with experience in childhood pneumonia and integrated community case management (iCCM) in Cambodia, Ethiopia, Uganda and South Sudan. Pile-sorting data were aggregated for countries and participant groups. FGDs were audio recorded and transcribed verbatim. Translated FGDs transcripts were coded in NVivo 10 and analysed using thematic content analysis. Comparative analysis was performed between countries and groups to identify thematic patterns. CHWs and national stakeholders across the four countries perceived the acute respiratory infection (ARI) timer and fingertip pulse oximeter as highly scalable and easy for CHWs to use. National stakeholders were less receptive to new technologies. CHWs placed greater priority on device acceptability to caregivers and children. Both groups felt that heavy reliance on electricity reduced potential scalability and usability in rural areas. Device simplicity, affordability and sustainability were universally valued. CHWs and national stakeholders prioritise different device characteristics according to their specific focus of work. The views of all relevant stakeholders, including health workers, policy makers, children and parents, should be considered in future policy decisions, research and development regarding suitable pneumonia diagnostic aids for community use.

An exploratory statistical approach to depression pattern identification

NASA Astrophysics Data System (ADS)

Feng, Qing Yi; Griffiths, Frances; Parsons, Nick; Gunn, Jane

2013-02-01

Depression is a complex phenomenon thought to be due to the interaction of biological, psychological and social factors. Currently depression assessment uses self-reported depressive symptoms but this is limited in the degree to which it can characterise the different expressions of depression emerging from the complex causal pathways that are thought to underlie depression. In this study, we aimed to represent the different patterns of depression with pattern values unique to each individual, where each value combines all the available information about an individual’s depression. We considered the depressed individual as a subsystem of an open complex system, proposed Generalized Information Entropy (GIE) to represent the general characteristics of information entropy of the system, and then implemented Maximum Entropy Estimates to derive equations for depression patterns. We also introduced a numerical simulation method to process the depression related data obtained by the Diamond Cohort Study which has been underway in Australia since 2005 involving 789 people. Unlike traditional assessment, we obtained a unique value for each depressed individual which gives an overall assessment of the depression pattern. Our work provides a novel way to visualise and quantitatively measure the depression pattern of the depressed individual which could be used for pattern categorisation. This may have potential for tailoring health interventions to depressed individuals to maximize health benefit.

Concurrent design of quasi-random photonic nanostructures

PubMed Central

Lee, Won-Kyu; Yu, Shuangcheng; Engel, Clifford J.; Reese, Thaddeus; Rhee, Dongjoon; Chen, Wei

2017-01-01

Nanostructured surfaces with quasi-random geometries can manipulate light over broadband wavelengths and wide ranges of angles. Optimization and realization of stochastic patterns have typically relied on serial, direct-write fabrication methods combined with real-space design. However, this approach is not suitable for customizable features or scalable nanomanufacturing. Moreover, trial-and-error processing cannot guarantee fabrication feasibility because processing–structure relations are not included in conventional designs. Here, we report wrinkle lithography integrated with concurrent design to produce quasi-random nanostructures in amorphous silicon at wafer scales that achieved over 160% light absorption enhancement from 800 to 1,200 nm. The quasi-periodicity of patterns, materials filling ratio, and feature depths could be independently controlled. We statistically represented the quasi-random patterns by Fourier spectral density functions (SDFs) that could bridge the processing–structure and structure–performance relations. Iterative search of the optimal structure via the SDF representation enabled concurrent design of nanostructures and processing. PMID:28760975

Biopatterning of Silk Proteins for Soft Micro-optics.

PubMed

Pal, Ramendra K; Kurland, Nicholas E; Wang, Congzhou; Kundu, Subhas C; Yadavalli, Vamsi K

2015-04-29

Silk proteins from spiders and silkworms have been proposed as outstanding candidates for soft micro-optic and photonic applications because of their optical transparency, unique biological properties, and mechanical robustness. Here, we present a method to form microstructures of the two constituent silk proteins, fibroin and sericin for use as an optical biomaterial. Using photolithography, chemically modified silk protein photoresists are patterned in 2D arrays of periodic patterns and Fresnel zone plates. Angle-dependent iridescent colors are produced in these periodic micropatterns because of the Bragg diffraction. Silk protein photolithography can used to form patterns on different substrates including flexible sheets with features of any shape with high fidelity and resolution over large areas. Finally, we show that these mechanically stable and transparent iridescent architectures are also completely biodegradable. This versatile and scalable technique can therefore be used to develop biocompatible, soft micro-optic devices that can be degraded in a controlled manner.

Reversible patterning of spherical shells through constrained buckling

NASA Astrophysics Data System (ADS)

Marthelot, J.; Brun, P.-T.; Jiménez, F. López; Reis, P. M.

2017-07-01

Recent advances in active soft structures envision the large deformations resulting from mechanical instabilities as routes for functional shape morphing. Numerous such examples exist for filamentary and plate systems. However, examples with double-curved shells are rarer, with progress hampered by challenges in fabrication and the complexities involved in analyzing their underlying geometrical nonlinearities. We show that on-demand patterning of hemispherical shells can be achieved through constrained buckling. Their postbuckling response is stabilized by an inner rigid mandrel. Through a combination of experiments, simulations, and scaling analyses, our investigation focuses on the nucleation and evolution of the buckling patterns into a reticulated network of sharp ridges. The geometry of the system, namely, the shell radius and the gap between the shell and the mandrel, is found to be the primary ingredient to set the surface morphology. This prominence of geometry suggests a robust, scalable, and tunable mechanism for reversible shape morphing of elastic shells.

Segmentation and classification of cell cycle phases in fluorescence imaging.

PubMed

Ersoy, Ilker; Bunyak, Filiz; Chagin, Vadim; Cardoso, M Christina; Palaniappan, Kannappan

2009-01-01

Current chemical biology methods for studying spatiotemporal correlation between biochemical networks and cell cycle phase progression in live-cells typically use fluorescence-based imaging of fusion proteins. Stable cell lines expressing fluorescently tagged protein GFP-PCNA produce rich, dynamically varying sub-cellular foci patterns characterizing the cell cycle phases, including the progress during the S-phase. Variable fluorescence patterns, drastic changes in SNR, shape and position changes and abundance of touching cells require sophisticated algorithms for reliable automatic segmentation and cell cycle classification. We extend the recently proposed graph partitioning active contours (GPAC) for fluorescence-based nucleus segmentation using regional density functions and dramatically improve its efficiency, making it scalable for high content microscopy imaging. We utilize surface shape properties of GFP-PCNA intensity field to obtain descriptors of foci patterns and perform automated cell cycle phase classification, and give quantitative performance by comparing our results to manually labeled data.

Cell segmentation in time-lapse fluorescence microscopy with temporally varying sub-cellular fusion protein patterns.

PubMed

Bunyak, Filiz; Palaniappan, Kannappan; Chagin, Vadim; Cardoso, M

2009-01-01

Fluorescently tagged proteins such as GFP-PCNA produce rich dynamically varying textural patterns of foci distributed in the nucleus. This enables the behavioral study of sub-cellular structures during different phases of the cell cycle. The varying punctuate patterns of fluorescence, drastic changes in SNR, shape and position during mitosis and abundance of touching cells, however, require more sophisticated algorithms for reliable automatic cell segmentation and lineage analysis. Since the cell nuclei are non-uniform in appearance, a distribution-based modeling of foreground classes is essential. The recently proposed graph partitioning active contours (GPAC) algorithm supports region descriptors and flexible distance metrics. We extend GPAC for fluorescence-based cell segmentation using regional density functions and dramatically improve its efficiency for segmentation from O(N(4)) to O(N(2)), for an image with N(2) pixels, making it practical and scalable for high throughput microscopy imaging studies.

Silk protein nanowires patterned using electron beam lithography.

PubMed

Pal, Ramendra K; Yadavalli, Vamsi K

2018-08-17

Nanofabrication approaches to pattern proteins at the nanoscale are useful in applications ranging from organic bioelectronics to cellular engineering. Specifically, functional materials based on natural polymers offer sustainable and environment-friendly substitutes to synthetic polymers. Silk proteins (fibroin and sericin) have emerged as an important class of biomaterials for next generation applications owing to excellent optical and mechanical properties, inherent biocompatibility, and biodegradability. However, the ability to precisely control their spatial positioning at the nanoscale via high throughput tools continues to remain a challenge. In this study electron beam lithography (EBL) is used to provide nanoscale patterning using methacrylate conjugated silk proteins that are photoreactive 'photoresists' materials. Very low energy electron beam radiation can be used to pattern silk proteins at the nanoscale and over large areas, whereby such nanostructure fabrication can be performed without specialized EBL tools. Significantly, using conducting polymers in conjunction with these silk proteins, the formation of protein nanowires down to 100 nm is shown. These wires can be easily degraded using enzymatic degradation. Thus, proteins can be precisely and scalably patterned and doped with conducting polymers and enzymes to form degradable, organic bioelectronic devices.

Complex auditory behaviour emerges from simple reactive steering

NASA Astrophysics Data System (ADS)

Hedwig, Berthold; Poulet, James F. A.

2004-08-01

The recognition and localization of sound signals is fundamental to acoustic communication. Complex neural mechanisms are thought to underlie the processing of species-specific sound patterns even in animals with simple auditory pathways. In female crickets, which orient towards the male's calling song, current models propose pattern recognition mechanisms based on the temporal structure of the song. Furthermore, it is thought that localization is achieved by comparing the output of the left and right recognition networks, which then directs the female to the pattern that most closely resembles the species-specific song. Here we show, using a highly sensitive method for measuring the movements of female crickets, that when walking and flying each sound pulse of the communication signal releases a rapid steering response. Thus auditory orientation emerges from reactive motor responses to individual sound pulses. Although the reactive motor responses are not based on the song structure, a pattern recognition process may modulate the gain of the responses on a longer timescale. These findings are relevant to concepts of insect auditory behaviour and to the development of biologically inspired robots performing cricket-like auditory orientation.

Irregular behavior in an excitatory-inhibitory neuronal network

NASA Astrophysics Data System (ADS)

Park, Choongseok; Terman, David

2010-06-01

Excitatory-inhibitory networks arise in many regions throughout the central nervous system and display complex spatiotemporal firing patterns. These neuronal activity patterns (of individual neurons and/or the whole network) are closely related to the functional status of the system and differ between normal and pathological states. For example, neurons within the basal ganglia, a group of subcortical nuclei that are responsible for the generation of movement, display a variety of dynamic behaviors such as correlated oscillatory activity and irregular, uncorrelated spiking. Neither the origins of these firing patterns nor the mechanisms that underlie the patterns are well understood. We consider a biophysical model of an excitatory-inhibitory network in the basal ganglia and explore how specific biophysical properties of the network contribute to the generation of irregular spiking. We use geometric dynamical systems and singular perturbation methods to systematically reduce the model to a simpler set of equations, which is suitable for analysis. The results specify the dependence on the strengths of synaptic connections and the intrinsic firing properties of the cells in the irregular regime when applied to the subthalamopallidal network of the basal ganglia.

Perovskite Technology is Scalable, But Questions Remain about the Best

Science.gov Websites

Methods | News | NREL Perovskite Technology is Scalable, But Questions Remain about the Best Methods News Release: Perovskite Technology is Scalable, But Questions Remain about the Best Methods NREL be used on a larger surface. The NREL researchers examined potential scalable deposition methods

Quality Scalability Aware Watermarking for Visual Content.

PubMed

Bhowmik, Deepayan; Abhayaratne, Charith

2016-11-01

Scalable coding-based content adaptation poses serious challenges to traditional watermarking algorithms, which do not consider the scalable coding structure and hence cannot guarantee correct watermark extraction in media consumption chain. In this paper, we propose a novel concept of scalable blind watermarking that ensures more robust watermark extraction at various compression ratios while not effecting the visual quality of host media. The proposed algorithm generates scalable and robust watermarked image code-stream that allows the user to constrain embedding distortion for target content adaptations. The watermarked image code-stream consists of hierarchically nested joint distortion-robustness coding atoms. The code-stream is generated by proposing a new wavelet domain blind watermarking algorithm guided by a quantization based binary tree. The code-stream can be truncated at any distortion-robustness atom to generate the watermarked image with the desired distortion-robustness requirements. A blind extractor is capable of extracting watermark data from the watermarked images. The algorithm is further extended to incorporate a bit-plane discarding-based quantization model used in scalable coding-based content adaptation, e.g., JPEG2000. This improves the robustness against quality scalability of JPEG2000 compression. The simulation results verify the feasibility of the proposed concept, its applications, and its improved robustness against quality scalable content adaptation. Our proposed algorithm also outperforms existing methods showing 35% improvement. In terms of robustness to quality scalable video content adaptation using Motion JPEG2000 and wavelet-based scalable video coding, the proposed method shows major improvement for video watermarking.

Model of polar auxin transport coupled to mechanical forces retrieves robust morphogenesis along the Arabidopsis root

NASA Astrophysics Data System (ADS)

Romero-Arias, J. Roberto; Hernández-Hernández, Valeria; Benítez, Mariana; Alvarez-Buylla, Elena R.; Barrio, Rafael A.

2017-03-01

Stem cells are identical in many scales, they share the same molecular composition, DNA, genes, and genetic networks, yet they should acquire different properties to form a functional tissue. Therefore, they must interact and get some external information from their environment, either spatial (dynamical fields) or temporal (lineage). In this paper we test to what extent coupled chemical and physical fields can underlie the cell's positional information during development. We choose the root apical meristem of Arabidopsis thaliana to model the emergence of cellular patterns. We built a model to study the dynamics and interactions between the cell divisions, the local auxin concentration, and physical elastic fields. Our model recovers important aspects of the self-organized and resilient behavior of the observed cellular patterns in the Arabidopsis root, in particular, the reverse fountain pattern observed in the auxin transport, the PIN-FORMED (protein family of auxin transporters) polarization pattern and the accumulation of auxin near the region of maximum curvature in a bent root. Our model may be extended to predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions.

Neural Substrates of Spontaneous Musical Performance: An fMRI Study of Jazz Improvisation

PubMed Central

Limb, Charles J.; Braun, Allen R.

2008-01-01

To investigate the neural substrates that underlie spontaneous musical performance, we examined improvisation in professional jazz pianists using functional MRI. By employing two paradigms that differed widely in musical complexity, we found that improvisation (compared to production of over-learned musical sequences) was consistently characterized by a dissociated pattern of activity in the prefrontal cortex: extensive deactivation of dorsolateral prefrontal and lateral orbital regions with focal activation of the medial prefrontal (frontal polar) cortex. Such a pattern may reflect a combination of psychological processes required for spontaneous improvisation, in which internally motivated, stimulus-independent behaviors unfold in the absence of central processes that typically mediate self-monitoring and conscious volitional control of ongoing performance. Changes in prefrontal activity during improvisation were accompanied by widespread activation of neocortical sensorimotor areas (that mediate the organization and execution of musical performance) as well as deactivation of limbic structures (that regulate motivation and emotional tone). This distributed neural pattern may provide a cognitive context that enables the emergence of spontaneous creative activity. PMID:18301756

Neural substrates of spontaneous musical performance: an FMRI study of jazz improvisation.

PubMed

Limb, Charles J; Braun, Allen R

2008-02-27

To investigate the neural substrates that underlie spontaneous musical performance, we examined improvisation in professional jazz pianists using functional MRI. By employing two paradigms that differed widely in musical complexity, we found that improvisation (compared to production of over-learned musical sequences) was consistently characterized by a dissociated pattern of activity in the prefrontal cortex: extensive deactivation of dorsolateral prefrontal and lateral orbital regions with focal activation of the medial prefrontal (frontal polar) cortex. Such a pattern may reflect a combination of psychological processes required for spontaneous improvisation, in which internally motivated, stimulus-independent behaviors unfold in the absence of central processes that typically mediate self-monitoring and conscious volitional control of ongoing performance. Changes in prefrontal activity during improvisation were accompanied by widespread activation of neocortical sensorimotor areas (that mediate the organization and execution of musical performance) as well as deactivation of limbic structures (that regulate motivation and emotional tone). This distributed neural pattern may provide a cognitive context that enables the emergence of spontaneous creative activity.

Activation and regulation of the pattern recognition receptors in obesity-induced adipose tissue inflammation and insulin resistance.

PubMed

Watanabe, Yasuharu; Nagai, Yoshinori; Takatsu, Kiyoshi

2013-09-23

Obesity-associated chronic tissue inflammation is a key contributing factor to type 2 diabetes mellitus, and a number of studies have clearly demonstrated that the immune system and metabolism are highly integrated. Recent advances in deciphering the various immune cells and signaling networks that link the immune and metabolic systems have contributed to our understanding of the pathogenesis of obesity-associated inflammation. Other recent studies have suggested that pattern recognition receptors in the innate immune system recognize various kinds of endogenous and exogenous ligands, and have a crucial role in initiating or promoting obesity-associated chronic inflammation. Importantly, these mediators act on insulin target cells or on insulin-producing cells impairing insulin sensitivity and its secretion. Here, we discuss how various pattern recognition receptors in the immune system underlie the etiology of obesity-associated inflammation and insulin resistance, with a particular focus on the TLR (Toll-like receptor) family protein Radioprotective 105 (RP105)/myeloid differentiation protein-1 (MD-1).

Laterality patterns of brain functional connectivity: gender effects.

PubMed

Tomasi, Dardo; Volkow, Nora D

2012-06-01

Lateralization of brain connectivity may be essential for normal brain function and may be sexually dimorphic. Here, we study the laterality patterns of short-range (implicated in functional specialization) and long-range (implicated in functional integration) connectivity and the gender effects on these laterality patterns. Parallel computing was used to quantify short- and long-range functional connectivity densities in 913 healthy subjects. Short-range connectivity was rightward lateralized and most asymmetrical in areas around the lateral sulcus, whereas long-range connectivity was rightward lateralized in lateral sulcus and leftward lateralizated in inferior prefrontal cortex and angular gyrus. The posterior inferior occipital cortex was leftward lateralized (short- and long-range connectivity). Males had greater rightward lateralization of brain connectivity in superior temporal (short- and long-range), inferior frontal, and inferior occipital cortices (short-range), whereas females had greater leftward lateralization of long-range connectivity in the inferior frontal cortex. The greater lateralization of the male's brain (rightward and predominantly short-range) may underlie their greater vulnerability to disorders with disrupted brain asymmetries (schizophrenia, autism).

Laterality Patterns of Brain Functional Connectivity: Gender Effects

PubMed Central

Tomasi, Dardo; Volkow, Nora D.

2012-01-01

Lateralization of brain connectivity may be essential for normal brain function and may be sexually dimorphic. Here, we study the laterality patterns of short-range (implicated in functional specialization) and long-range (implicated in functional integration) connectivity and the gender effects on these laterality patterns. Parallel computing was used to quantify short- and long-range functional connectivity densities in 913 healthy subjects. Short-range connectivity was rightward lateralized and most asymmetrical in areas around the lateral sulcus, whereas long-range connectivity was rightward lateralized in lateral sulcus and leftward lateralizated in inferior prefrontal cortex and angular gyrus. The posterior inferior occipital cortex was leftward lateralized (short- and long-range connectivity). Males had greater rightward lateralization of brain connectivity in superior temporal (short- and long-range), inferior frontal, and inferior occipital cortices (short-range), whereas females had greater leftward lateralization of long-range connectivity in the inferior frontal cortex. The greater lateralization of the male's brain (rightward and predominantly short-range) may underlie their greater vulnerability to disorders with disrupted brain asymmetries (schizophrenia, autism). PMID:21878483

Microbial pattern of pressure ulcer in pediatric patients

NASA Astrophysics Data System (ADS)

Paramita, D. A.; Khairina; Lubis, N. Z.

2018-03-01

Pressure ulcer (PU) is a localized trauma to the skin and or tissue beneath which lies in bony prominence due to pressure or pressure that combines with a sharp surface. Several studies have found that PU is a common problem in pediatrics population. Infection at the site of a PU is the most common complication in which the PU may host a resistant microorganism and may turn into a local infection that will be the source of bacteremia in hospitalized patients. To reveal which is the most common microbial species that underlie in pressure ulcer of pediatrics patients.A cross-sectional study was conducted in July-September 2017, involving 18 PU pediatric patients in Haji Adam Malik Hospital. To each subject, swab culture from the ulcer was madein microbial laboratory in Haji Adam Malik Hospital to determine the microbial pattern. This study found that the most common microbial pattern in pressure ulcers of pediatrics patient in Haji Adam Malik Hospital is Acinetobacter baumannii (22.2%).

Long-distance communication by specialized cellular projections during pigment pattern development and evolution

PubMed Central

Eom, Dae Seok; Bain, Emily J; Patterson, Larissa B; Grout, Megan E; Parichy, David M

2015-01-01

Changes in gene activity are essential for evolutionary diversification. Yet, elucidating the cellular behaviors that underlie modifications to adult form remains a profound challenge. We use neural crest-derived adult pigmentation of zebrafish and pearl danio to uncover cellular bases for alternative pattern states. We show that stripes in zebrafish require a novel class of thin, fast cellular projection to promote Delta-Notch signaling over long distances from cells of the xanthophore lineage to melanophores. Projections depended on microfilaments and microtubules, exhibited meandering trajectories, and stabilized on target cells to which they delivered membraneous vesicles. By contrast, the uniformly patterned pearl danio lacked such projections, concomitant with Colony stimulating factor 1-dependent changes in xanthophore differentiation that likely curtail signaling available to melanophores. Our study reveals a novel mechanism of cellular communication, roles for differentiation state heterogeneity in pigment cell interactions, and an unanticipated morphogenetic behavior contributing to a striking difference in adult form. DOI: http://dx.doi.org/10.7554/eLife.12401.001 PMID:26701906

Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation.

PubMed

Lin, Yi G; Weadick, Cameron J; Santini, Francesco; Chang, Belinda S W

2013-12-01

Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the rod and cone photoreceptor cells of the vertebrate retina. Rods, highly sensitive cells that recover from photoactivation slowly, underlie dim-light vision, whereas cones are less sensitive, recover more quickly, and underlie bright-light vision. Transducin deactivation is a critical step in photoreceptor recovery and may underlie the functional distinction between rods and cones. Rods and cones possess distinct transducin α subunits, yet they share a common deactivation mechanism, the GTPase activating protein (GAP) complex. Here, we used codon models to examine patterns of sequence evolution in rod (GNAT1) and cone (GNAT2) α subunits. Our results indicate that purifying selection is the dominant force shaping GNAT1 and GNAT2 evolution, but that GNAT2 has additionally been subject to positive selection operating at multiple phylogenetic scales; phylogeny-wide analysis identified several sites in the GNAT2 helical domain as having substantially elevated dN/dS estimates, and branch-site analysis identified several nearby sites as targets of strong positive selection during early vertebrate history. Examination of aligned GNAT and GAP complex crystal structures revealed steric clashes between several positively selected sites and the deactivating GAP complex. This suggests that GNAT2 sequence variation could play an important role in adaptive evolution of the vertebrate visual system via effects on photoreceptor deactivation kinetics and provides an alternative perspective to previous work that focused instead on the effect of GAP complex concentration. Our findings thus further the understanding of the molecular biology, physiology, and evolution of vertebrate visual systems.

Selective attrition and intraindividual variability in response time moderate cognitive change.

PubMed

Yao, Christie; Stawski, Robert S; Hultsch, David F; MacDonald, Stuart W S

2016-01-01

Selection of a developmental time metric is useful for understanding causal processes that underlie aging-related cognitive change and for the identification of potential moderators of cognitive decline. Building on research suggesting that time to attrition is a metric sensitive to non-normative influences of aging (e.g., subclinical health conditions), we examined reason for attrition and intraindividual variability (IIV) in reaction time as predictors of cognitive performance. Three hundred and four community dwelling older adults (64-92 years) completed annual assessments in a longitudinal study. IIV was calculated from baseline performance on reaction time tasks. Multilevel models were fit to examine patterns and predictors of cognitive change. We show that time to attrition was associated with cognitive decline. Greater IIV was associated with declines on executive functioning and episodic memory measures. Attrition due to personal health reasons was also associated with decreased executive functioning compared to that of individuals who remained in the study. These findings suggest that time to attrition is a useful metric for representing cognitive change, and reason for attrition and IIV are predictive of non-normative influences that may underlie instances of cognitive loss in older adults.

Selective Attrition and Intraindividual Variability in Response Time Moderate Cognitive Change

PubMed Central

Yao, Christie; Stawski, Robert S.; Hultsch, David F.; MacDonald, Stuart W.S.

2016-01-01

Objectives Selection of a developmental time metric is useful for understanding causal processes that underlie aging-related cognitive change, and for the identification of potential moderators of cognitive decline. Building on research suggesting that time to attrition is a metric sensitive to non-normative influences of aging (e.g., subclinical health conditions), we examined reason for attrition and intraindividual variability (IIV) in reaction time as predictors of cognitive performance. Method Three-hundred and four community dwelling older adults (64-92 years) completed annual assessments in a longitudinal study. IIV was calculated from baseline performance on reaction time tasks. Multilevel models were fit to examine patterns and predictors of cognitive change. Results We show that time to attrition was associated with cognitive decline. Greater IIV was associated with declines on executive functioning and episodic memory measures. Attrition due to personal health reasons was also associated with decreased executive functioning compared to individuals who remained in study. Discussion These findings suggest that time to attrition is a useful metric for representing cognitive change, and reason for attrition and IIV are predictive of non-normative influences that may underlie instances of cognitive loss in older adults. PMID:26647008

Evolutionary Trade-Off between Secondary Sexual Traits and Ejaculates.

PubMed

Simmons, Leigh W; Lüpold, Stefan; Fitzpatrick, John L

2017-12-01

Recent theoretical models predict that the evolutionary diversification of the weapons and ornaments of pre-mating sexual selection should be influenced by trade-offs with male expenditure on ejaculates. However, the patterns of association between secondary sexual traits and ejaculate expenditure are frequently inconsistent in their support of this prediction. We show why consideration of additional life-history, ecological, and mating-system variables is crucial for the interpretation of associations between secondary sexual traits and ejaculate production. Incorporation of these 'missing variables' provides evidence that interactions between pre- and post-mating sexual selection can underlie broad patterns of diversification in male weapons and ornaments. We call for more experimental and genetic approaches to uncover trade-offs, as well as for studies that consider the costs of mate-searching. Copyright © 2017 Elsevier Ltd. All rights reserved.

The fabrication of vertically aligned and periodically distributed carbon nanotube bundles and periodically porous carbon nanotube films through a combination of laser interference ablation and metal-catalyzed chemical vapor deposition.

PubMed

Yuan, Dajun; Lin, Wei; Guo, Rui; Wong, C P; Das, Suman

2012-06-01

Scalable fabrication of carbon nanotube (CNT) bundles is essential to future advances in several applications. Here, we report on the development of a simple, two-step method for fabricating vertically aligned and periodically distributed CNT bundles and periodically porous CNT films at the sub-micron scale. The method involves laser interference ablation (LIA) of an iron film followed by CNT growth via iron-catalyzed chemical vapor deposition. CNT bundles with square widths ranging from 0.5 to 1.5 µm in width, and 50-200 µm in length, are grown atop the patterned catalyst over areas spanning 8 cm(2). The CNT bundles exhibit a high degree of control over square width, orientation, uniformity, and periodicity. This simple scalable method of producing well-placed and oriented CNT bundles demonstrates a high application potential for wafer-scale integration of CNT structures into various device applications, including IC interconnects, field emitters, sensors, batteries, and optoelectronics, etc.

Template-Assisted Scalable Nanowire Networks

NASA Astrophysics Data System (ADS)

Friedl, Martin; Cerveny, Kris; Weigele, Pirmin; Tütüncüoglu, Gozde; Martí-Sánchez, Sara; Huang, Chunyi; Patlatiuk, Taras; Potts, Heidi; Sun, Zhiyuan; Hill, Megan O.; Güniat, Lucas; Kim, Wonjong; Zamani, Mahdi; Dubrovskii, Vladimir G.; Arbiol, Jordi; Lauhon, Lincoln J.; Zumbühl, Dominik M.; Fontcuberta i Morral, Anna

2018-04-01

Topological qubits based on Majorana fermions have the potential to revolutionize the emerging field of quantum computing by making information processing significantly more robust to decoherence. Nanowires (NWs) are a promising medium for hosting these kinds of qubits, though branched NWs are needed to perform qubit manipulations. Here we report gold-free templated growth of III-V NWs by molecular beam epitaxy using an approach that enables patternable and highly regular branched NW arrays on a far greater scale than what has been reported thus far. Our approach relies on the lattice-mismatched growth of InAs on top of defect-free GaAs nanomembranes (NMs) yielding laterally-oriented, low-defect InAs and InGaAs NWs whose shapes are determined by surface and strain energy minimization. By controlling NM width and growth time, we demonstrate the formation of compositionally graded NWs with cross-sections less than 50 nm. Scaling the NWs below 20 nm leads to the formation of homogenous InGaAs NWs which exhibit phase-coherent, quasi-1D quantum transport as shown by magnetoconductance measurements. These results are an important advance towards scalable topological quantum computing.

Gigwa-Genotype investigator for genome-wide analyses.

PubMed

Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre

2016-06-06

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

Bioinspired Multifunctional Superhydrophobic Surfaces with Carbon-Nanotube-Based Conducting Pastes by Facile and Scalable Printing.

PubMed

Han, Joong Tark; Kim, Byung Kuk; Woo, Jong Seok; Jang, Jeong In; Cho, Joon Young; Jeong, Hee Jin; Jeong, Seung Yol; Seo, Seon Hee; Lee, Geon-Woong

2017-03-01

Directly printed superhydrophobic surfaces containing conducting nanomaterials can be used for a wide range of applications in terms of nonwetting, anisotropic wetting, and electrical conductivity. Here, we demonstrated that direct-printable and flexible superhydrophobic surfaces were fabricated on flexible substrates via with an ultrafacile and scalable screen printing with carbon nanotube (CNT)-based conducting pastes. A polydimethylsiloxane (PDMS)-polyethylene glycol (PEG) copolymer was used as an additive for conducting pastes to realize the printability of the conducting paste as well as the hydrophobicity of the printed surface. The screen-printed conducting surfaces showed a high water contact angle (WCA) (>150°) and low contact angle hysteresis (WCA < 5°) at 25 wt % PDMS-PEG copolymer in the paste, and they have an electrical conductivity of over 1000 S m -1 . Patterned superhydrophobic surfaces also showed sticky superhydrophobic characteristics and were used to transport water droplets. Moreover, fabricated films on metal meshes were used for an oil/water separation filter, and liquid evaporation behavior was investigated on the superhydrophobic and conductive thin-film heaters by applying direct current voltage to the film.

Template-Assisted Scalable Nanowire Networks.

PubMed

Friedl, Martin; Cerveny, Kris; Weigele, Pirmin; Tütüncüoglu, Gozde; Martí-Sánchez, Sara; Huang, Chunyi; Patlatiuk, Taras; Potts, Heidi; Sun, Zhiyuan; Hill, Megan O; Güniat, Lucas; Kim, Wonjong; Zamani, Mahdi; Dubrovskii, Vladimir G; Arbiol, Jordi; Lauhon, Lincoln J; Zumbühl, Dominik M; Fontcuberta I Morral, Anna

2018-04-11

Topological qubits based on Majorana Fermions have the potential to revolutionize the emerging field of quantum computing by making information processing significantly more robust to decoherence. Nanowires are a promising medium for hosting these kinds of qubits, though branched nanowires are needed to perform qubit manipulations. Here we report a gold-free templated growth of III-V nanowires by molecular beam epitaxy using an approach that enables patternable and highly regular branched nanowire arrays on a far greater scale than what has been reported thus far. Our approach relies on the lattice-mismatched growth of InAs on top of defect-free GaAs nanomembranes yielding laterally oriented, low-defect InAs and InGaAs nanowires whose shapes are determined by surface and strain energy minimization. By controlling nanomembrane width and growth time, we demonstrate the formation of compositionally graded nanowires with cross-sections less than 50 nm. Scaling the nanowires below 20 nm leads to the formation of homogeneous InGaAs nanowires, which exhibit phase-coherent, quasi-1D quantum transport as shown by magnetoconductance measurements. These results are an important advance toward scalable topological quantum computing.

Design and Evaluation of a Scalable and Reconfigurable Multi-Platform System for Acoustic Imaging

PubMed Central

Izquierdo, Alberto; Villacorta, Juan José; del Val Puente, Lara; Suárez, Luis

2016-01-01

This paper proposes a scalable and multi-platform framework for signal acquisition and processing, which allows for the generation of acoustic images using planar arrays of MEMS (Micro-Electro-Mechanical Systems) microphones with low development and deployment costs. Acoustic characterization of MEMS sensors was performed, and the beam pattern of a module, based on an 8 × 8 planar array and of several clusters of modules, was obtained. A flexible framework, formed by an FPGA, an embedded processor, a computer desktop, and a graphic processing unit, was defined. The processing times of the algorithms used to obtain the acoustic images, including signal processing and wideband beamforming via FFT, were evaluated in each subsystem of the framework. Based on this analysis, three frameworks are proposed, defined by the specific subsystems used and the algorithms shared. Finally, a set of acoustic images obtained from sound reflected from a person are presented as a case study in the field of biometric identification. These results reveal the feasibility of the proposed system. PMID:27727174

A scalable population code for time in the striatum.

PubMed

Mello, Gustavo B M; Soares, Sofia; Paton, Joseph J

2015-05-04

To guide behavior and learn from its consequences, the brain must represent time over many scales. Yet, the neural signals used to encode time in the seconds-to-minute range are not known. The striatum is a major input area of the basal ganglia associated with learning and motor function. Previous studies have also shown that the striatum is necessary for normal timing behavior. To address how striatal signals might be involved in timing, we recorded from striatal neurons in rats performing an interval timing task. We found that neurons fired at delays spanning tens of seconds and that this pattern of responding reflected the interaction between time and the animals' ongoing sensorimotor state. Surprisingly, cells rescaled responses in time when intervals changed, indicating that striatal populations encoded relative time. Moreover, time estimates decoded from activity predicted timing behavior as animals adjusted to new intervals, and disrupting striatal function led to a decrease in timing performance. These results suggest that striatal activity forms a scalable population code for time, providing timing signals that animals use to guide their actions. Copyright © 2015 Elsevier Ltd. All rights reserved.

DSPCP: A Data Scalable Approach for Identifying Relationships in Parallel Coordinates.

PubMed

Nguyen, Hoa; Rosen, Paul

2018-03-01

Parallel coordinates plots (PCPs) are a well-studied technique for exploring multi-attribute datasets. In many situations, users find them a flexible method to analyze and interact with data. Unfortunately, using PCPs becomes challenging as the number of data items grows large or multiple trends within the data mix in the visualization. The resulting overdraw can obscure important features. A number of modifications to PCPs have been proposed, including using color, opacity, smooth curves, frequency, density, and animation to mitigate this problem. However, these modified PCPs tend to have their own limitations in the kinds of relationships they emphasize. We propose a new data scalable design for representing and exploring data relationships in PCPs. The approach exploits the point/line duality property of PCPs and a local linear assumption of data to extract and represent relationship summarizations. This approach simultaneously shows relationships in the data and the consistency of those relationships. Our approach supports various visualization tasks, including mixed linear and nonlinear pattern identification, noise detection, and outlier detection, all in large data. We demonstrate these tasks on multiple synthetic and real-world datasets.

US Household Food Shopping Patterns: Dynamic Shifts Since 2000 And Socioeconomic Predictors.

PubMed

Stern, Dalia; Robinson, Whitney R; Ng, Shu Wen; Gordon-Larsen, Penny; Popkin, Barry M

2015-11-01

Under the assumption that differential food access might underlie nutritional disparities, programs and policies have focused on the need to build supermarkets in underserved areas, in an effort to improve dietary quality. However, there is limited evidence about which types of stores are used by households of different income levels and differing races/ethnicities. We used cross-sectional cluster analysis to derive shopping patterns from US households' volume food purchases by store from 2000 to 2012. Multinomial logistic regression identified household socioeconomic characteristics that were associated with shopping patterns in 2012. We found three food shopping patterns or clusters: households that primarily shopped at grocery stores, households that primarily shopped at mass merchandisers, and a combination cluster in which households split their purchases among multiple store types. In 2012 we found no income or race/ethnicity differences for the cluster of households that primarily shopped at grocery stores. However, low-income non-Hispanic blacks (versus non-Hispanic whites) had a significantly lower probability of belonging to the mass merchandise cluster. These varied shopping patterns must be considered in future policy initiatives. Furthermore, it is important to continue studying the complex rationales for people's food shopping patterns. Project HOPE—The People-to-People Health Foundation, Inc.

Adaptive format conversion for scalable video coding

NASA Astrophysics Data System (ADS)

Wan, Wade K.; Lim, Jae S.

2001-12-01

The enhancement layer in many scalable coding algorithms is composed of residual coding information. There is another type of information that can be transmitted instead of (or in addition to) residual coding. Since the encoder has access to the original sequence, it can utilize adaptive format conversion (AFC) to generate the enhancement layer and transmit the different format conversion methods as enhancement data. This paper investigates the use of adaptive format conversion information as enhancement data in scalable video coding. Experimental results are shown for a wide range of base layer qualities and enhancement bitrates to determine when AFC can improve video scalability. Since the parameters needed for AFC are small compared to residual coding, AFC can provide video scalability at low enhancement layer bitrates that are not possible with residual coding. In addition, AFC can also be used in addition to residual coding to improve video scalability at higher enhancement layer bitrates. Adaptive format conversion has not been studied in detail, but many scalable applications may benefit from it. An example of an application that AFC is well-suited for is the migration path for digital television where AFC can provide immediate video scalability as well as assist future migrations.

Brain activity across the development of automatic categorization: A comparison of categorization tasks using multi-voxel pattern analysis

PubMed Central

Soto, Fabian A.; Waldschmidt, Jennifer G.; Helie, Sebastien; Ashby, F. Gregory

2013-01-01

Previous evidence suggests that relatively separate neural networks underlie initial learning of rule-based and information-integration categorization tasks. With the development of automaticity, categorization behavior in both tasks becomes increasingly similar and exclusively related to activity in cortical regions. The present study uses multi-voxel pattern analysis to directly compare the development of automaticity in different categorization tasks. Each of three groups of participants received extensive training in a different categorization task: either an information-integration task, or one of two rule-based tasks. Four training sessions were performed inside an MRI scanner. Three different analyses were performed on the imaging data from a number of regions of interest (ROIs). The common patterns analysis had the goal of revealing ROIs with similar patterns of activation across tasks. The unique patterns analysis had the goal of revealing ROIs with dissimilar patterns of activation across tasks. The representational similarity analysis aimed at exploring (1) the similarity of category representations across ROIs and (2) how those patterns of similarities compared across tasks. The results showed that common patterns of activation were present in motor areas and basal ganglia early in training, but only in the former later on. Unique patterns were found in a variety of cortical and subcortical areas early in training, but they were dramatically reduced with training. Finally, patterns of representational similarity between brain regions became increasingly similar across tasks with the development of automaticity. PMID:23333700

Ontology and modeling patterns for state-based behavior representation

NASA Technical Reports Server (NTRS)

Castet, Jean-Francois; Rozek, Matthew L.; Ingham, Michel D.; Rouquette, Nicolas F.; Chung, Seung H.; Kerzhner, Aleksandr A.; Donahue, Kenneth M.; Jenkins, J. Steven; Wagner, David A.; Dvorak, Daniel L.;

A Framework for Mining Actionable Navigation Patterns from In-Store RFID Datasets via Indoor Mapping

PubMed Central

Shen, Bin; Zheng, Qiuhua; Li, Xingsen; Xu, Libo

2015-01-01

With the quick development of RFID technology and the decreasing prices of RFID devices, RFID is becoming widely used in various intelligent services. Especially in the retail application domain, RFID is increasingly adopted to capture the shopping tracks and behavior of in-store customers. To further enhance the potential of this promising application, in this paper, we propose a unified framework for RFID-based path analytics, which uses both in-store shopping paths and RFID-based purchasing data to mine actionable navigation patterns. Four modules of this framework are discussed, which are: (1) mapping from the physical space to the cyber space, (2) data preprocessing, (3) pattern mining and (4) knowledge understanding and utilization. In the data preprocessing module, the critical problem of how to capture the mainstream shopping path sequences while wiping out unnecessary redundant and repeated details is addressed in detail. To solve this problem, two types of redundant patterns, i.e., loop repeat pattern and palindrome-contained pattern are recognized and the corresponding processing algorithms are proposed. The experimental results show that the redundant pattern filtering functions are effective and scalable. Overall, this work builds a bridge between indoor positioning and advanced data mining technologies, and provides a feasible way to study customers’ shopping behaviors via multi-source RFID data. PMID:25751076

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging.

PubMed

Tokuhisa, Atsushi; Arai, Junya; Joti, Yasumasa; Ohno, Yoshiyuki; Kameyama, Toyohisa; Yamamoto, Keiji; Hatanaka, Masayuki; Gerofi, Balazs; Shimada, Akio; Kurokawa, Motoyoshi; Shoji, Fumiyoshi; Okada, Kensuke; Sugimoto, Takashi; Yamaga, Mitsuhiro; Tanaka, Ryotaro; Yokokawa, Mitsuo; Hori, Atsushi; Ishikawa, Yutaka; Hatsui, Takaki; Go, Nobuhiro

2013-11-01

Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 10(6) noisy X-ray diffraction patterns, each for an unknown random target orientation. To cope with the severe quantum noise, patterns need to be classified according to their similarities and average similar patterns to improve the signal-to-noise ratio. A high-speed scalable scheme has been developed to carry out classification on the K computer, a 10PFLOPS supercomputer at RIKEN Advanced Institute for Computational Science. It is designed to work on the real-time basis with the experimental diffraction pattern collection at the X-ray free-electron laser facility SACLA so that the result of classification can be feedback for optimizing experimental parameters during the experiment. The present status of our effort developing the system and also a result of application to a set of simulated diffraction patterns is reported. About 1 × 10(6) diffraction patterns were successfully classificatied by running 255 separate 1 h jobs in 385-node mode.

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

PubMed Central

Tokuhisa, Atsushi; Arai, Junya; Joti, Yasumasa; Ohno, Yoshiyuki; Kameyama, Toyohisa; Yamamoto, Keiji; Hatanaka, Masayuki; Gerofi, Balazs; Shimada, Akio; Kurokawa, Motoyoshi; Shoji, Fumiyoshi; Okada, Kensuke; Sugimoto, Takashi; Yamaga, Mitsuhiro; Tanaka, Ryotaro; Yokokawa, Mitsuo; Hori, Atsushi; Ishikawa, Yutaka; Hatsui, Takaki; Go, Nobuhiro

2013-01-01

Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 106 noisy X-ray diffraction patterns, each for an unknown random target orientation. To cope with the severe quantum noise, patterns need to be classified according to their similarities and average similar patterns to improve the signal-to-noise ratio. A high-speed scalable scheme has been developed to carry out classification on the K computer, a 10PFLOPS supercomputer at RIKEN Advanced Institute for Computational Science. It is designed to work on the real-time basis with the experimental diffraction pattern collection at the X-ray free-electron laser facility SACLA so that the result of classification can be feedback for optimizing experimental parameters during the experiment. The present status of our effort developing the system and also a result of application to a set of simulated diffraction patterns is reported. About 1 × 106 diffraction patterns were successfully classificatied by running 255 separate 1 h jobs in 385-node mode. PMID:24121336

Turing mechanism underlying a branching model for lung morphogenesis.

PubMed

Xu, Hui; Sun, Mingzhu; Zhao, Xin

2017-01-01

The mammalian lung develops through branching morphogenesis. Two primary forms of branching, which occur in order, in the lung have been identified: tip bifurcation and side branching. However, the mechanisms of lung branching morphogenesis remain to be explored. In our previous study, a biological mechanism was presented for lung branching pattern formation through a branching model. Here, we provide a mathematical mechanism underlying the branching patterns. By decoupling the branching model, we demonstrated the existence of Turing instability. We performed Turing instability analysis to reveal the mathematical mechanism of the branching patterns. Our simulation results show that the Turing patterns underlying the branching patterns are spot patterns that exhibit high local morphogen concentration. The high local morphogen concentration induces the growth of branching. Furthermore, we found that the sparse spot patterns underlie the tip bifurcation patterns, while the dense spot patterns underlies the side branching patterns. The dispersion relation analysis shows that the Turing wavelength affects the branching structure. As the wavelength decreases, the spot patterns change from sparse to dense, the rate of tip bifurcation decreases and side branching eventually occurs instead. In the process of transformation, there may exists hybrid branching that mixes tip bifurcation and side branching. Since experimental studies have reported that branching mode switching from side branching to tip bifurcation in the lung is under genetic control, our simulation results suggest that genes control the switch of the branching mode by regulating the Turing wavelength. Our results provide a novel insight into and understanding of the formation of branching patterns in the lung and other biological systems.

Imbalanced pattern completion vs. separation in cognitive disease: network simulations of synaptic pathologies predict a personalized therapeutics strategy.

PubMed

Hanson, Jesse E; Madison, Daniel V

2010-08-13

Diverse Mouse genetic models of neurodevelopmental, neuropsychiatric, and neurodegenerative causes of impaired cognition exhibit at least four convergent points of synaptic malfunction: 1) Strength of long-term potentiation (LTP), 2) Strength of long-term depression (LTD), 3) Relative inhibition levels (Inhibition), and 4) Excitatory connectivity levels (Connectivity). To test the hypothesis that pathological increases or decreases in these synaptic properties could underlie imbalances at the level of basic neural network function, we explored each type of malfunction in a simulation of autoassociative memory. These network simulations revealed that one impact of impairments or excesses in each of these synaptic properties is to shift the trade-off between pattern separation and pattern completion performance during memory storage and recall. Each type of synaptic pathology either pushed the network balance towards intolerable error in pattern separation or intolerable error in pattern completion. Imbalances caused by pathological impairments or excesses in LTP, LTD, inhibition, or connectivity, could all be exacerbated, or rescued, by the simultaneous modulation of any of the other three synaptic properties. Because appropriate modulation of any of the synaptic properties could help re-balance network function, regardless of the origins of the imbalance, we propose a new strategy of personalized cognitive therapeutics guided by assay of pattern completion vs. pattern separation function. Simulated examples and testable predictions of this theorized approach to cognitive therapeutics are presented.

An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.

PubMed

Ye, Kai; Kosters, Walter A; Ijzerman, Adriaan P

2007-03-15

Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets. In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets. The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/.

A scalable healthcare information system based on a service-oriented architecture.

PubMed

Yang, Tzu-Hsiang; Sun, Yeali S; Lai, Feipei

2011-06-01

Many existing healthcare information systems are composed of a number of heterogeneous systems and face the important issue of system scalability. This paper first describes the comprehensive healthcare information systems used in National Taiwan University Hospital (NTUH) and then presents a service-oriented architecture (SOA)-based healthcare information system (HIS) based on the service standard HL7. The proposed architecture focuses on system scalability, in terms of both hardware and software. Moreover, we describe how scalability is implemented in rightsizing, service groups, databases, and hardware scalability. Although SOA-based systems sometimes display poor performance, through a performance evaluation of our HIS based on SOA, the average response time for outpatient, inpatient, and emergency HL7Central systems are 0.035, 0.04, and 0.036 s, respectively. The outpatient, inpatient, and emergency WebUI average response times are 0.79, 1.25, and 0.82 s. The scalability of the rightsizing project and our evaluation results show that the SOA HIS we propose provides evidence that SOA can provide system scalability and sustainability in a highly demanding healthcare information system.

Cued Memory Reactivation During SWS Abolishes the Beneficial Effect of Sleep on Abstraction.

PubMed

Hennies, Nora; Lambon Ralph, Matthew A; Durrant, Simon J; Cousins, James N; Lewis, Penelope A

2017-08-01

Extracting regularities from stimuli in our environment and generalizing these to new situations are fundamental processes in human cognition. Sleep has been shown to enhance these processes, possibly by facilitating reactivation-triggered memory reorganization. Here, we assessed whether cued reactivation during slow wave sleep (SWS) promotes the beneficial effect of sleep on abstraction of statistical regularities. We used an auditory statistical learning task, in which the benefit of sleep has been firmly established. Participants were exposed to a probabilistically determined sequence of tones and subsequently tested for recognition of novel short sequences adhering to this same statistical pattern in both immediate and delayed recall sessions. In different groups, the exposure stream was replayed during SWS in the night between the recall sessions (SWS-replay group), in wake just before sleep (presleep replay group), or not at all (control group). Surprisingly, participants who received replay in sleep performed worse in the delayed recall session than the control and the presleep replay group. They also failed to show the association between SWS and task performance that has been observed in previous studies and was present in the controls. Importantly, sleep structure and sleep quality did not differ between groups, suggesting that replay during SWS did not impair sleep but rather disrupted or interfered with sleep-dependent mechanisms that underlie the extraction of the statistical pattern. These findings raise important questions about the scope of cued memory reactivation and the mechanisms that underlie sleep-related generalization. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Tailoring plasmonic nanoparticles and fractal patterns

NASA Astrophysics Data System (ADS)

Rosa, Lorenzo; Juodkazis, Saulius

2011-12-01

We studied new three-dimensional tailoring of nano-particles by ion-beam and electron-beam lithographies, aiming for features and nano-gaps down to 10 nm size. Electron-beam patterning is demonstrated for 2D fabrication in combination with plasmonic metal deposition and lift-off, with full control of spectral features of plasmonic nano-particles and patterns on dielectric substrates. We present wide-angle bow-tie rounded nano-antennas whose plasmonic resonances achieve strong field enhancement at engineered wavelength range, and show how the addition of fractal patterns defined by standard electron beam lithography achieve light field enhancement from visible to far-IR spectral range and scalable up towards THz band. Field enhancement is evaluated by FDTD modeling on full-3D simulation domains using complex material models, showing the modeling method capabilities and the effect of staircase approximations on field enhancement and resonance conditions, especially at metal corners, where a minimum rounding radius of 2 nm is resolved and a five-fold reduction of spurious ringing at sharp corners is obtained by the use of conformal meshing.

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

DOE PAGES

Carter Edwards, H.; Trott, Christian R.; Sunderland, Daniel

2014-07-22

The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. We found that a major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diversemore » manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos’ abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. Furthermore, the Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries.« less

PM2006: a highly scalable urban planning management information system--Case study: Suzhou Urban Planning Bureau

NASA Astrophysics Data System (ADS)

Jing, Changfeng; Liang, Song; Ruan, Yong; Huang, Jie

2008-10-01

During the urbanization process, when facing complex requirements of city development, ever-growing urban data, rapid development of planning business and increasing planning complexity, a scalable, extensible urban planning management information system is needed urgently. PM2006 is such a system that can deal with these problems. In response to the status and problems in urban planning, the scalability and extensibility of PM2006 are introduced which can be seen as business-oriented workflow extensibility, scalability of DLL-based architecture, flexibility on platforms of GIS and database, scalability of data updating and maintenance and so on. It is verified that PM2006 system has good extensibility and scalability which can meet the requirements of all levels of administrative divisions and can adapt to ever-growing changes in urban planning business. At the end of this paper, the application of PM2006 in Urban Planning Bureau of Suzhou city is described.

Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea

PubMed Central

Fukushima, Kenji; Fujita, Hironori; Yamaguchi, Takahiro; Kawaguchi, Masayoshi; Tsukaya, Hirokazu; Hasebe, Mitsuyasu

2015-01-01

Complex morphology is an evolutionary outcome of phenotypic diversification. In some carnivorous plants, the ancestral planar leaf has been modified to form a pitcher shape. However, how leaf development was altered during evolution remains unknown. Here we show that the pitcher leaves of Sarracenia purpurea develop through cell division patterns of adaxial tissues that are distinct from those in bifacial and peltate leaves, subsequent to standard expression of adaxial and abaxial marker genes. Differences in the orientation of cell divisions in the adaxial domain cause bifacial growth in the distal region and adaxial ridge protrusion in the middle region. These different growth patterns establish pitcher morphology. A computer simulation suggests that the cell division plane is critical for the pitcher morphogenesis. Our results imply that tissue-specific changes in the orientation of cell division underlie the development of a morphologically complex leaf. PMID:25774486

Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea.

PubMed

Fukushima, Kenji; Fujita, Hironori; Yamaguchi, Takahiro; Kawaguchi, Masayoshi; Tsukaya, Hirokazu; Hasebe, Mitsuyasu

2015-03-16

Complex morphology is an evolutionary outcome of phenotypic diversification. In some carnivorous plants, the ancestral planar leaf has been modified to form a pitcher shape. However, how leaf development was altered during evolution remains unknown. Here we show that the pitcher leaves of Sarracenia purpurea develop through cell division patterns of adaxial tissues that are distinct from those in bifacial and peltate leaves, subsequent to standard expression of adaxial and abaxial marker genes. Differences in the orientation of cell divisions in the adaxial domain cause bifacial growth in the distal region and adaxial ridge protrusion in the middle region. These different growth patterns establish pitcher morphology. A computer simulation suggests that the cell division plane is critical for the pitcher morphogenesis. Our results imply that tissue-specific changes in the orientation of cell division underlie the development of a morphologically complex leaf.

Biodiversity and biogeography of the atmosphere

PubMed Central

Womack, Ann M.; Bohannan, Brendan J. M.; Green, Jessica L.

2010-01-01

The variation of life has predominantly been studied on land and in water, but this focus is changing. There is a resurging interest in the distribution of life in the atmosphere and the processes that underlie patterns in this distribution. Here, we review our current state of knowledge about the biodiversity and biogeography of the atmosphere, with an emphasis on micro-organisms, the numerically dominant forms of aerial life. We present evidence to suggest that the atmosphere is a habitat for micro-organisms, and not purely a conduit for terrestrial and aquatic life. Building on a rich history of research in terrestrial and aquatic systems, we explore biodiversity patterns that are likely to play an important role in the emerging field of air biogeography. We discuss the possibility of a more unified understanding of the biosphere, one that links knowledge about biodiversity and biogeography in the lithosphere, hydrosphere and atmosphere. PMID:20980313

Food nanotechnology in the news. Coverage patterns and thematic emphases during the last decade.

PubMed

Dudo, Anthony; Choi, Doo-Hun; Scheufele, Dietram A

2011-02-01

For novel issues like food nanotechnology, media can play an important role in shaping the awareness and mental associations that underlie public opinion. Seeking to complement recent research exploring public opinion formation about food nanotechnology, this study tracks the evolution of U.S. newspaper coverage of food nanotechnology, identifying the descriptive and thematic traits that have characterized this coverage over time. We use a rigorous methodology to examine the levels of coverage, authorship patterns, and thematic emphases exhibited in the American journalistic narrative about this burgeoning application of nanoscience. Our findings indicate that U.S. newspaper coverage of food nanotechnology is relatively modest in terms of how often it has been covered, its thematic diversity, and the level of journalistic expertise from which it was produced. To our knowledge, this is the first study to empirically assess journalistic coverage of food nanotechnology. Copyright © 2010 Elsevier Ltd. All rights reserved.

Unfolding large-scale online collaborative human dynamics

PubMed Central

Zha, Yilong; Zhou, Tao; Zhou, Changsong

2016-01-01

Large-scale interacting human activities underlie all social and economic phenomena, but quantitative understanding of regular patterns and mechanism is very challenging and still rare. Self-organized online collaborative activities with a precise record of event timing provide unprecedented opportunity. Our empirical analysis of the history of millions of updates in Wikipedia shows a universal double–power-law distribution of time intervals between consecutive updates of an article. We then propose a generic model to unfold collaborative human activities into three modules: (i) individual behavior characterized by Poissonian initiation of an action, (ii) human interaction captured by a cascading response to previous actions with a power-law waiting time, and (iii) population growth due to the increasing number of interacting individuals. This unfolding allows us to obtain an analytical formula that is fully supported by the universal patterns in empirical data. Our modeling approaches reveal “simplicity” beyond complex interacting human activities. PMID:27911766

Delay and probability discounting among payday and title loan recipients.

PubMed

Mahoney, Colin T; Lawyer, Steven R

2016-04-01

Payday and title loans are short-term loans associated with significant economic impact. Behavioral theories of impulsive choice may provide insight into behavioral processes that underlie the propensity to take out payday and title loans. Adults between the ages of 18 and 30 recruited from the community completed delay and probability discounting tasks for hypothetical money as well as measures of substance use. Patterns of discounting were characterized using a hyperbolic decay model and area under the curve. Participants who took out a payday and/or title loan in the past (n=41) exhibited more impulsive choice patterns on the delay discounting task than did those who did not (n=255). Substance use mediated this relationship between payday and title loan retention and delay discounting. These findings suggest potentially important relationships between payday/title loan borrowing, substance use, and delay discounting. Copyright © 2016 Elsevier B.V. All rights reserved.

Attenuated Auditory Event-Related Potentials and Associations with Atypical Sensory Response Patterns in Children with Autism

PubMed Central

Donkers, Franc C.L.; Schipul, Sarah E.; Baranek, Grace T.; Cleary, Katherine M.; Willoughby, Michael T.; Evans, Anna M.; Bulluck, John C.; Lovmo, Jeanne E.; Belger, Aysenil

2015-01-01

Neurobiological underpinnings of unusual sensory features in individuals with autism are unknown. Event-related potentials (ERPs) elicited by task-irrelevant sounds were used to elucidate neural correlates of auditory processing and associations with three common sensory response patterns (hyperresponsiveness; hyporesponsiveness; sensory seeking). Twenty-eight children with autism and 39 typically developing children (4–12 year-olds) completed an auditory oddball paradigm. Results revealed marginally attenuated P1 and N2 to standard tones and attenuated P3a to novel sounds in autism versus controls. Exploratory analyses suggested that within the autism group, attenuated N2 and P3a amplitudes were associated with greater sensory seeking behaviors for specific ranges of P1 responses. Findings suggest that attenuated early sensory as well as later attention-orienting neural responses to stimuli may underlie selective sensory features via complex mechanisms. PMID:24072639

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

PubMed Central

De La Vega, Francisco M.; Isaac, Hadar; Collins, Andrew; Scafe, Charles R.; Halldórsson, Bjarni V.; Su, Xiaoping; Lippert, Ross A.; Wang, Yu; Laig-Webster, Marion; Koehler, Ryan T.; Ziegle, Janet S.; Wogan, Lewis T.; Stevens, Junko F.; Leinen, Kyle M.; Olson, Sheri J.; Guegler, Karl J.; You, Xiaoqing; Xu, Lily H.; Hemken, Heinz G.; Kalush, Francis; Itakura, Mitsuo; Zheng, Yi; de Thé, Guy; O'Brien, Stephen J.; Clark, Andrew G.; Istrail, Sorin; Hunkapiller, Michael W.; Spier, Eugene G.; Gilbert, Dennis A.

2005-01-01

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies. PMID:15781572

Prosodic domain-initial effects on the acoustic structure of vowels

NASA Astrophysics Data System (ADS)

Fox, Robert Allen; Jacewicz, Ewa; Salmons, Joseph

2003-10-01

In the process of language change, vowels tend to shift in ``chains,'' leading to reorganizations of entire vowel systems over time. A long research tradition has described such patterns, but little is understood about what factors motivate such shifts. Drawing data from changes in progress in American English dialects, the broad hypothesis is tested that changes in vowel systems are related to prosodic organization and stress patterns. Changes in vowels under greater prosodic prominence correlate directly with, and likely underlie, historical patterns of shift. This study examines acoustic characteristics of vowels at initial edges of prosodic domains [Fougeron and Keating, J. Acoust. Soc. Am. 101, 3728-3740 (1997)]. The investigation is restricted to three distinct prosodic levels: utterance (sentence-initial), phonological phrase (strong branch of a foot), and syllable (weak branch of a foot). The predicted changes in vowels /e/ and /ɛ/ in two American English dialects (from Ohio and Wisconsin) are examined along a set of acoustic parameters: duration, formant frequencies (including dynamic changes over time), and fundamental frequency (F0). In addition to traditional methodology which elicits list-like intonation, a design is adapted to examine prosodic patterns in more typical sentence intonations. [Work partially supported by NIDCD R03 DC005560-01.

Multi-layered fabrication of large area PDMS flexible optical light guide sheets

NASA Astrophysics Data System (ADS)

Green, Robert; Knopf, George K.; Bordatchev, Evgueni V.

2017-02-01

Large area polydimethylsiloxane (PDMS) flexible optical light guide sheets can be used to create a variety of passive light harvesting and illumination systems for wearable technology, advanced indoor lighting, non-planar solar light collectors, customized signature lighting, and enhanced safety illumination for motorized vehicles. These thin optically transparent micro-patterned polymer sheets can be draped over a flat or arbitrarily curved surface. The light guiding behavior of the optical light guides depends on the geometry and spatial distribution of micro-optical structures, thickness and shape of the flexible sheet, refractive indices of the constituent layers, and the wavelength of the incident light. A scalable fabrication method that combines soft-lithography, closed thin cavity molding, partial curing, and centrifugal casting is described in this paper for building thin large area multi-layered PDMS optical light guide sheets. The proposed fabrication methodology enables the of internal micro-optical structures (MOSs) in the monolithic PDMS light guide by building the optical system layer-by-layer. Each PDMS layer in the optical light guide can have the similar, or a slightly different, indices of refraction that permit total internal reflection within the optical sheet. The individual molded layers may also be defect free or micro-patterned with microlens or reflecting micro-features. In addition, the bond between adjacent layers is ensured because each layer is only partially cured before the next functional layer is added. To illustrate the scalable build-by-layers fabrication method a three-layer mechanically flexible illuminator with an embedded LED strip is constructed and demonstrated.

Unusual X-chromosome inactivation pattern in patients with Xp11.23-p11.22 duplication: Report and review.

PubMed

Di-Battista, Adriana; Meloni, Vera Ayres; da Silva, Magnus Dias; Moysés-Oliveira, Mariana; Melaragno, Maria Isabel

2016-12-01

In females carrying structural rearrangements of an X-chromosome, cells with the best dosage balance are preferentially selected, frequently resulting in a skewed inactivation pattern and amelioration of the phenotype. The Xp11.23-p11.22 region is involved in a recently described microduplication syndrome associated with severe clinical consequences in males and females, causing intellectual disability, behavior problems, epilepsy with electroencephalogram anomalies, minor facial anomalies, and early onset of puberty. Female carriers usually present an unusual X-chromosome inactivation pattern in favor of the aberrant chromosome, resulting in functional disomy of the duplicated segment. Here, we describe a girl carrying a de novo ∼9.7 Mb Xp11.3-p11.22 duplication of paternal origin and skewed X-chromosome inactivation pattern of the normal X-chromosome. We reviewed other cases previously reported and determined the minimal critical region possibly responsible for this unusual inactivation pattern. The critical region encompasses 36 RefSeq genes, including at least 10 oncogenes and/or genes related to the cell cycle control. We discuss the molecular mechanisms that underlie the positive selection of the cells with the active duplicated chromosome. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Laser-induced porous graphene films from commercial polymers

NASA Astrophysics Data System (ADS)

Lin, Jian; Peng, Zhiwei; Liu, Yuanyue; Ruiz-Zepeda, Francisco; Ye, Ruquan; Samuel, Errol L. G.; Yacaman, Miguel Jose; Yakobson, Boris I.; Tour, James M.

2014-12-01

The cost effective synthesis and patterning of carbon nanomaterials is a challenge in electronic and energy storage devices. Here we report a one-step, scalable approach for producing and patterning porous graphene films with three-dimensional networks from commercial polymer films using a CO2 infrared laser. The sp3-carbon atoms are photothermally converted to sp2-carbon atoms by pulsed laser irradiation. The resulting laser-induced graphene (LIG) exhibits high electrical conductivity. The LIG can be readily patterned to interdigitated electrodes for in-plane microsupercapacitors with specific capacitances of >4 mF cm-2 and power densities of ~9 mW cm-2. Theoretical calculations partially suggest that enhanced capacitance may result from LIG’s unusual ultra-polycrystalline lattice of pentagon-heptagon structures. Combined with the advantage of one-step processing of LIG in air from commercial polymer sheets, which would allow the employment of a roll-to-roll manufacturing process, this technique provides a rapid route to polymer-written electronic and energy storage devices.

Emergent 1d Ising Behavior in AN Elementary Cellular Automaton Model

NASA Astrophysics Data System (ADS)

Kassebaum, Paul G.; Iannacchione, Germano S.

The fundamental nature of an evolving one-dimensional (1D) Ising model is investigated with an elementary cellular automaton (CA) simulation. The emergent CA simulation employs an ensemble of cells in one spatial dimension, each cell capable of two microstates interacting with simple nearest-neighbor rules and incorporating an external field. The behavior of the CA model provides insight into the dynamics of coupled two-state systems not expressible by exact analytical solutions. For instance, state progression graphs show the causal dynamics of a system through time in relation to the system's entropy. Unique graphical analysis techniques are introduced through difference patterns, diffusion patterns, and state progression graphs of the 1D ensemble visualizing the evolution. All analyses are consistent with the known behavior of the 1D Ising system. The CA simulation and new pattern recognition techniques are scalable (in both dimension, complexity, and size) and have many potential applications such as complex design of materials, control of agent systems, and evolutionary mechanism design.

Laser-induced porous graphene films from commercial polymers

PubMed Central

Lin, Jian; Peng, Zhiwei; Liu, Yuanyue; Ruiz-Zepeda, Francisco; Ye, Ruquan; Samuel, Errol L. G.; Yacaman, Miguel Jose; Yakobson, Boris I.; Tour, James M.

2014-01-01

Synthesis and patterning of carbon nanomaterials cost effectively is a challenge in electronic and energy storage devices. Here report a one-step, scalable approach for producing and patterning porous graphene films with 3-dimensional networks from commercial polymer films using a CO2 infrared laser. The sp3-carbon atoms are photothermally converted to sp2-carbon atoms by pulsed laser irradiation. The resulting laser-induced graphene (LIG) exhibits high electrical conductivity. The LIG can be readily patterned to interdigitated electrodes for in-plane microsupercapacitors with specific capacitances of >4 mF·cm−2 and power densities of ~9 mW·cm−2. Theoretical calculations partially suggest that enhanced capacitance may result from LIG’s unusual ultra-polycrystalline lattice of pentagon-heptagon structures. Combined with the advantage of one-step processing of LIG in air from commercial polymer sheets, which would allow the employment of a roll-to-roll manufacturing process, this technique provides a rapid route to polymer-written electronic and energy storage devices. PMID:25493446

Equalizer: a scalable parallel rendering framework.

PubMed

Eilemann, Stefan; Makhinya, Maxim; Pajarola, Renato

2009-01-01

Continuing improvements in CPU and GPU performances as well as increasing multi-core processor and cluster-based parallelism demand for flexible and scalable parallel rendering solutions that can exploit multipipe hardware accelerated graphics. In fact, to achieve interactive visualization, scalable rendering systems are essential to cope with the rapid growth of data sets. However, parallel rendering systems are non-trivial to develop and often only application specific implementations have been proposed. The task of developing a scalable parallel rendering framework is even more difficult if it should be generic to support various types of data and visualization applications, and at the same time work efficiently on a cluster with distributed graphics cards. In this paper we introduce a novel system called Equalizer, a toolkit for scalable parallel rendering based on OpenGL which provides an application programming interface (API) to develop scalable graphics applications for a wide range of systems ranging from large distributed visualization clusters and multi-processor multipipe graphics systems to single-processor single-pipe desktop machines. We describe the system architecture, the basic API, discuss its advantages over previous approaches, present example configurations and usage scenarios as well as scalability results.

Gene Profiling in Experimental Models of Eye Growth: Clues to Myopia Pathogenesis

PubMed Central

Stone, Richard A.; Khurana, Tejvir S.

2010-01-01

To understand the complex regulatory pathways that underlie the development of refractive errors, expression profiling has evaluated gene expression in ocular tissues of well-characterized experimental models that alter postnatal eye growth and induce refractive errors. Derived from a variety of platforms (e.g. differential display, spotted microarrays or Affymetrix GeneChips), gene expression patterns are now being identified in species that include chicken, mouse and primate. Reconciling available results is hindered by varied experimental designs and analytical/statistical features. Continued application of these methods offers promise to provide the much-needed mechanistic framework to develop therapies to normalize refractive development in children. PMID:20363242

Global Mapping of the Yeast Genetic Interaction Network

NASA Astrophysics Data System (ADS)

Tong, Amy Hin Yan; Lesage, Guillaume; Bader, Gary D.; Ding, Huiming; Xu, Hong; Xin, Xiaofeng; Young, James; Berriz, Gabriel F.; Brost, Renee L.; Chang, Michael; Chen, YiQun; Cheng, Xin; Chua, Gordon; Friesen, Helena; Goldberg, Debra S.; Haynes, Jennifer; Humphries, Christine; He, Grace; Hussein, Shamiza; Ke, Lizhu; Krogan, Nevan; Li, Zhijian; Levinson, Joshua N.; Lu, Hong; Ménard, Patrice; Munyana, Christella; Parsons, Ainslie B.; Ryan, Owen; Tonikian, Raffi; Roberts, Tania; Sdicu, Anne-Marie; Shapiro, Jesse; Sheikh, Bilal; Suter, Bernhard; Wong, Sharyl L.; Zhang, Lan V.; Zhu, Hongwei; Burd, Christopher G.; Munro, Sean; Sander, Chris; Rine, Jasper; Greenblatt, Jack; Peter, Matthias; Bretscher, Anthony; Bell, Graham; Roth, Frederick P.; Brown, Grant W.; Andrews, Brenda; Bussey, Howard; Boone, Charles

2004-02-01

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

Applying knowledge-anchored hypothesis discovery methods to advance clinical and translational research: the OAMiner project

PubMed Central

Jackson, Rebecca D; Best, Thomas M; Borlawsky, Tara B; Lai, Albert M; James, Stephen; Gurcan, Metin N

2012-01-01

The conduct of clinical and translational research regularly involves the use of a variety of heterogeneous and large-scale data resources. Scalable methods for the integrative analysis of such resources, particularly when attempting to leverage computable domain knowledge in order to generate actionable hypotheses in a high-throughput manner, remain an open area of research. In this report, we describe both a generalizable design pattern for such integrative knowledge-anchored hypothesis discovery operations and our experience in applying that design pattern in the experimental context of a set of driving research questions related to the publicly available Osteoarthritis Initiative data repository. We believe that this ‘test bed’ project and the lessons learned during its execution are both generalizable and representative of common clinical and translational research paradigms. PMID:22647689

Direct Prototyping of Patterned Nanoporous Carbon: A Route from Materials to On-chip Devices

PubMed Central

Shen, Caiwei; Wang, Xiaohong; Zhang, Wenfeng; Kang, Feiyu

2013-01-01

Prototyping of nanoporous carbon membranes with three-dimensional microscale patterns is significant for integration of such multifunctional materials into various miniaturized systems. Incorporating nano material synthesis into microelectronics technology, we present a novel approach to direct prototyping of carbon membranes with highly nanoporous structures inside. Membranes with significant thicknesses (1 ~ 40 μm) are rapidly prototyped at wafer level by combining nano templating method with readily available microfabrication techniques, which include photolithography, high-temperature annealing and etching. In particular, the high-surface-area membranes are specified as three-dimensional electrodes for micro supercapacitors and show high performance compared to reported ones. Improvements in scalability, compatibility and cost make the general strategy promising for batch fabrication of operational on-chip devices or full integration of three-dimensional nanoporous membranes with existing micro systems. PMID:23887486

Pattern search in multi-structure data: a framework for the next-generation evidence-based medicine

NASA Astrophysics Data System (ADS)

Sukumar, Sreenivas R.; Ainsworth, Keela C.

2014-03-01

With the impetus towards personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledgebase, etc.) to predict diagnostic risks is fast emerging. Addressing this need, we pose and answer the following questions: (i) How can we jointly analyze and explore measurement data in context with qualitative domain knowledge? (ii) How can we search and hypothesize patterns (not known apriori) from such multi-structure data? (iii) How can we build predictive models by integrating weakly-associated multi-relational multi-structure data? We propose a framework towards answering these questions. We describe a software solution that leverages hardware for scalable in-memory analytics and applies next-generation semantic query tools on medical data.

Dysfunctions in brain networks supporting empathy: An fMRI study in adults with autism spectrum disorders

PubMed Central

Schulte-Rüther, Martin; Greimel, Ellen; Markowitsch, Hans J.; Kamp-Becker, Inge; Remschmidt, Helmut; Fink, Gereon R.; Piefke, Martina

2010-01-01

The present study aimed at identifying dysfunctions in brain networks that may underlie disturbed empathic behavior in autism spectrum disorders (ASD). During functional magnetic resonance imaging, subjects were asked to identify the emotional state observed in a facial stimulus (other-task) or to evaluate their own emotional response (self-task). Behaviorally, ASD subjects performed equally to the control group during the other-task, but showed less emotionally congruent responses in the self-task. Activations in brain regions related to theory of mind were observed in both groups. Activations of the medial prefrontal cortex (MPFC) were located in dorsal subregions in ASD subjects and in ventral areas in control subjects. During the self-task, ASD subjects activated an additional network of frontal and inferior temporal areas. Frontal areas previously associated with the human mirror system were activated in both tasks in control subjects, while ASD subjects recruited these areas during the self-task only. Activations in the ventral MPFC may provide the basis for one's “emotional bond” with other persons’ emotions. Such atypical patterns of activation may underlie disturbed empathy in individuals with ASD. Subjects with ASD may use an atypical cognitive strategy to gain access to their own emotional state in response to other people's emotions. PMID:20945256

Fair lineups are better than biased lineups and showups, but not because they increase underlying discriminability.

PubMed

Smith, Andrew M; Wells, Gary L; Lindsay, R C L; Penrod, Steven D

2017-04-01

Receiver Operating Characteristic (ROC) analysis has recently come in vogue for assessing the underlying discriminability and the applied utility of lineup procedures. Two primary assumptions underlie recommendations that ROC analysis be used to assess the applied utility of lineup procedures: (a) ROC analysis of lineups measures underlying discriminability, and (b) the procedure that produces superior underlying discriminability produces superior applied utility. These same assumptions underlie a recently derived diagnostic-feature detection theory, a theory of discriminability, intended to explain recent patterns observed in ROC comparisons of lineups. We demonstrate, however, that these assumptions are incorrect when ROC analysis is applied to lineups. We also demonstrate that a structural phenomenon of lineups, differential filler siphoning, and not the psychological phenomenon of diagnostic-feature detection, explains why lineups are superior to showups and why fair lineups are superior to biased lineups. In the process of our proofs, we show that computational simulations have assumed, unrealistically, that all witnesses share exactly the same decision criteria. When criterial variance is included in computational models, differential filler siphoning emerges. The result proves dissociation between ROC curves and underlying discriminability: Higher ROC curves for lineups than for showups and for fair than for biased lineups despite no increase in underlying discriminability. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Dysfunctions in brain networks supporting empathy: an fMRI study in adults with autism spectrum disorders.

PubMed

Schulte-Rüther, Martin; Greimel, Ellen; Markowitsch, Hans J; Kamp-Becker, Inge; Remschmidt, Helmut; Fink, Gereon R; Piefke, Martina

2011-01-01

The present study aimed at identifying dysfunctions in brain networks that may underlie disturbed empathic behavior in autism spectrum disorders (ASD). During functional magnetic resonance imaging, subjects were asked to identify the emotional state observed in a facial stimulus (other-task) or to evaluate their own emotional response (self-task). Behaviorally, ASD subjects performed equally to the control group during the other-task, but showed less emotionally congruent responses in the self-task. Activations in brain regions related to theory of mind were observed in both groups. Activations of the medial prefrontal cortex (MPFC) were located in dorsal subregions in ASD subjects and in ventral areas in control subjects. During the self-task, ASD subjects activated an additional network of frontal and inferior temporal areas. Frontal areas previously associated with the human mirror system were activated in both tasks in control subjects, while ASD subjects recruited these areas during the self-task only. Activations in the ventral MPFC may provide the basis for one's "emotional bond" with other persons' emotions. Such atypical patterns of activation may underlie disturbed empathy in individuals with ASD. Subjects with ASD may use an atypical cognitive strategy to gain access to their own emotional state in response to other people's emotions.

Scalability problems of simple genetic algorithms.

PubMed

Thierens, D

1999-01-01

Scalable evolutionary computation has become an intensively studied research topic in recent years. The issue of scalability is predominant in any field of algorithmic design, but it became particularly relevant for the design of competent genetic algorithms once the scalability problems of simple genetic algorithms were understood. Here we present some of the work that has aided in getting a clear insight in the scalability problems of simple genetic algorithms. Particularly, we discuss the important issue of building block mixing. We show how the need for mixing places a boundary in the GA parameter space that, together with the boundary from the schema theorem, delimits the region where the GA converges reliably to the optimum in problems of bounded difficulty. This region shrinks rapidly with increasing problem size unless the building blocks are tightly linked in the problem coding structure. In addition, we look at how straightforward extensions of the simple genetic algorithm-namely elitism, niching, and restricted mating are not significantly improving the scalability problems.

Low-complexity transcoding algorithm from H.264/AVC to SVC using data mining

NASA Astrophysics Data System (ADS)

Garrido-Cantos, Rosario; De Cock, Jan; Martínez, Jose Luis; Van Leuven, Sebastian; Cuenca, Pedro; Garrido, Antonio

2013-12-01

Nowadays, networks and terminals with diverse characteristics of bandwidth and capabilities coexist. To ensure a good quality of experience, this diverse environment demands adaptability of the video stream. In general, video contents are compressed to save storage capacity and to reduce the bandwidth required for its transmission. Therefore, if these compressed video streams were compressed using scalable video coding schemes, they would be able to adapt to those heterogeneous networks and a wide range of terminals. Since the majority of the multimedia contents are compressed using H.264/AVC, they cannot benefit from that scalability. This paper proposes a low-complexity algorithm to convert an H.264/AVC bitstream without scalability to scalable bitstreams with temporal scalability in baseline and main profiles by accelerating the mode decision task of the scalable video coding encoding stage using machine learning tools. The results show that when our technique is applied, the complexity is reduced by 87% while maintaining coding efficiency.

The spectro-contextual encoding and retrieval theory of episodic memory.

PubMed

Watrous, Andrew J; Ekstrom, Arne D

2014-01-01

The spectral fingerprint hypothesis, which posits that different frequencies of oscillations underlie different cognitive operations, provides one account for how interactions between brain regions support perceptual and attentive processes (Siegel etal., 2012). Here, we explore and extend this idea to the domain of human episodic memory encoding and retrieval. Incorporating findings from the synaptic to cognitive levels of organization, we argue that spectrally precise cross-frequency coupling and phase-synchronization promote the formation of hippocampal-neocortical cell assemblies that form the basis for episodic memory. We suggest that both cell assembly firing patterns as well as the global pattern of brain oscillatory activity within hippocampal-neocortical networks represents the contents of a particular memory. Drawing upon the ideas of context reinstatement and multiple trace theory, we argue that memory retrieval is driven by internal and/or external factors which recreate these frequency-specific oscillatory patterns which occur during episodic encoding. These ideas are synthesized into a novel model of episodic memory (the spectro-contextual encoding and retrieval theory, or "SCERT") that provides several testable predictions for future research.

Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition.

PubMed

Cannon, Jonathan; Kopell, Nancy; Gardner, Timothy; Markowitz, Jeffrey

2015-11-01

Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement. One of the most prominent theoretical models of neural sequence generation is the synfire chain, in which pulses of synchronized spiking activity propagate robustly along a chain of cells connected by highly redundant feedforward excitation. But recent experimental observations in the avian song production pathway during song generation have shown excitatory activity interacting strongly with the firing patterns of inhibitory neurons, suggesting a process of sequence generation more complex than feedforward excitation. Here we propose a model of sequence generation inspired by these observations in which a pulse travels along a spatially recurrent excitatory chain, passing repeatedly through zones of local feedback inhibition. In this model, synchrony and robust timing are maintained not through redundant excitatory connections, but rather through the interaction between the pulse and the spatiotemporal pattern of inhibition that it creates as it circulates the network. These results suggest that spatially and temporally structured inhibition may play a key role in sequence generation.

The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

PubMed

Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2016-06-01

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors

PubMed Central

Rey-Villamizar, Nicolas; Merouane, Amine; Lu, Yanbin; Mukherjee, Amit; Trett, Kristen; Chong, Peter; Harris, Carolyn; Shain, William; Roysam, Badrinath

2015-01-01

Motivation: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. Results: Thick rat brain sections (100–300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni’s L-measure. Coifman’s harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. Availability and implementation: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors Contact: broysam@central.uh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701570

Scalable asynchronous execution of cellular automata

NASA Astrophysics Data System (ADS)

Folino, Gianluigi; Giordano, Andrea; Mastroianni, Carlo

2016-10-01

The performance and scalability of cellular automata, when executed on parallel/distributed machines, are limited by the necessity of synchronizing all the nodes at each time step, i.e., a node can execute only after the execution of the previous step at all the other nodes. However, these synchronization requirements can be relaxed: a node can execute one step after synchronizing only with the adjacent nodes. In this fashion, different nodes can execute different time steps. This can be a notable advantageous in many novel and increasingly popular applications of cellular automata, such as smart city applications, simulation of natural phenomena, etc., in which the execution times can be different and variable, due to the heterogeneity of machines and/or data and/or executed functions. Indeed, a longer execution time at a node does not slow down the execution at all the other nodes but only at the neighboring nodes. This is particularly advantageous when the nodes that act as bottlenecks vary during the application execution. The goal of the paper is to analyze the benefits that can be achieved with the described asynchronous implementation of cellular automata, when compared to the classical all-to-all synchronization pattern. The performance and scalability have been evaluated through a Petri net model, as this model is very useful to represent the synchronization barrier among nodes. We examined the usual case in which the territory is partitioned into a number of regions, and the computation associated with a region is assigned to a computing node. We considered both the cases of mono-dimensional and two-dimensional partitioning. The results show that the advantage obtained through the asynchronous execution, when compared to the all-to-all synchronous approach is notable, and it can be as large as 90% in terms of speedup.

Scalable PGAS Metadata Management on Extreme Scale Systems

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

Chavarría-Miranda, Daniel; Agarwal, Khushbu; Straatsma, TP

Programming models intended to run on exascale systems have a number of challenges to overcome, specially the sheer size of the system as measured by the number of concurrent software entities created and managed by the underlying runtime. It is clear from the size of these systems that any state maintained by the programming model has to be strictly sub-linear in size, in order not to overwhelm memory usage with pure overhead. A principal feature of Partitioned Global Address Space (PGAS) models is providing easy access to global-view distributed data structures. In order to provide efficient access to these distributedmore » data structures, PGAS models must keep track of metadata such as where array sections are located with respect to processes/threads running on the HPC system. As PGAS models and applications become ubiquitous on very large transpetascale systems, a key component to their performance and scalability will be efficient and judicious use of memory for model overhead (metadata) compared to application data. We present an evaluation of several strategies to manage PGAS metadata that exhibit different space/time tradeoffs. We use two real-world PGAS applications to capture metadata usage patterns and gain insight into their communication behavior.« less

Machine learning patterns for neuroimaging-genetic studies in the cloud.

PubMed

Da Mota, Benoit; Tudoran, Radu; Costan, Alexandru; Varoquaux, Gaël; Brasche, Goetz; Conrod, Patricia; Lemaitre, Herve; Paus, Tomas; Rietschel, Marcella; Frouin, Vincent; Poline, Jean-Baptiste; Antoniu, Gabriel; Thirion, Bertrand

2014-01-01

Brain imaging is a natural intermediate phenotype to understand the link between genetic information and behavior or brain pathologies risk factors. Massive efforts have been made in the last few years to acquire high-dimensional neuroimaging and genetic data on large cohorts of subjects. The statistical analysis of such data is carried out with increasingly sophisticated techniques and represents a great computational challenge. Fortunately, increasing computational power in distributed architectures can be harnessed, if new neuroinformatics infrastructures are designed and training to use these new tools is provided. Combining a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library), we design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data. End-users describe the statistical procedure to perform and can then test the model on their own computers before running the very same code in the cloud at a larger scale. We illustrate the potential of our approach on real data with an experiment showing how the functional signal in subcortical brain regions can be significantly fit with genome-wide genotypes. This experiment demonstrates the scalability and the reliability of our framework in the cloud with a 2 weeks deployment on hundreds of virtual machines.

Diameter and Geometry Control of Vertically Aligned SWNTs through Catalyst Manipulation

NASA Astrophysics Data System (ADS)

Xiang, Rong; Einarsson, Erik; Okawa, Jun; Murakami, Yoichi; Maruyama, Shigeo

2009-03-01

We present our recent progress on manipulating our liquid-based catalyst loading process, which possesses greater potential than conventional deposition in terms of cost and scalability, to control the diameter and morphology of single-walled carbon nanotubes (SWNTs). We demonstrate that the diameter of aligned SWNTs synthesized by alcohol catalytic CVD can be tailored over a wide range by modifying the catalyst recipe. SWNT arrays with an average diameter as small as 1.2 nm were obtained by this method. Additionally, owing to the alignment of the array, the continuous change of the SWNT diameter during a single CVD process can be clearly observed and quantitatively characterized. We have also developed a versatile wet chemistry method to localize the growth of SWNTs to desired regions via surface modification. By functionalizing the silicon surface using a classic self-assembled monolayer, the catalyst can be selectively dip-coated onto hydrophilic areas of the substrate. This technique was successful in producing both random and aligned SWNTs with various patterns. The precise control of the diameter and morphology of SWNTs, achieved by simple and scalable liquid-based surface chemistry, could greatly facilitate the application of SWNTs as the building blocks of future nano-devices.

LLNL Partners with IBM on Brain-Like Computing Chip

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

Van Essen, Brian

Lawrence Livermore National Laboratory (LLNL) will receive a first-of-a-kind brain-inspired supercomputing platform for deep learning developed by IBM Research. Based on a breakthrough neurosynaptic computer chip called IBM TrueNorth, the scalable platform will process the equivalent of 16 million neurons and 4 billion synapses and consume the energy equivalent of a hearing aid battery – a mere 2.5 watts of power. The brain-like, neural network design of the IBM Neuromorphic System is able to infer complex cognitive tasks such as pattern recognition and integrated sensory processing far more efficiently than conventional chips.

LLNL Partners with IBM on Brain-Like Computing Chip

ScienceCinema

Van Essen, Brian

2018-06-25

Lawrence Livermore National Laboratory (LLNL) will receive a first-of-a-kind brain-inspired supercomputing platform for deep learning developed by IBM Research. Based on a breakthrough neurosynaptic computer chip called IBM TrueNorth, the scalable platform will process the equivalent of 16 million neurons and 4 billion synapses and consume the energy equivalent of a hearing aid battery – a mere 2.5 watts of power. The brain-like, neural network design of the IBM Neuromorphic System is able to infer complex cognitive tasks such as pattern recognition and integrated sensory processing far more efficiently than conventional chips.

Recording polarization gratings with a standing spiral wave

NASA Astrophysics Data System (ADS)

Vernon, Jonathan P.; Serak, Svetlana V.; Hakobyan, Rafik S.; Aleksanyan, Artur K.; Tondiglia, Vincent P.; White, Timothy J.; Bunning, Timothy J.; Tabiryan, Nelson V.

2013-11-01

A scalable and robust methodology for writing cycloidal modulation patterns of optical axis orientation in photosensitive surface alignment layers is demonstrated. Counterpropagating circularly polarized beams, generated by reflection of the input beam from a cholesteric liquid crystal, direct local surface orientation in a photosensitive surface. Purposely introducing a slight angle between the input beam and the photosensitive surface normal introduces a grating period/orientation that is readily controlled and templated. The resulting cycloidal diffractive waveplates offer utility in technologies requiring diffraction over a broad range of angles/wavelengths. This simple methodology of forming polarization gratings offers advantages over conventional fabrication techniques.

Scalable Integrated Region-Based Image Retrieval Using IRM and Statistical Clustering.

ERIC Educational Resources Information Center

Wang, James Z.; Du, Yanping

Statistical clustering is critical in designing scalable image retrieval systems. This paper presents a scalable algorithm for indexing and retrieving images based on region segmentation. The method uses statistical clustering on region features and IRM (Integrated Region Matching), a measure developed to evaluate overall similarity between images…

Temporally Scalable Visual SLAM using a Reduced Pose Graph

DTIC Science & Technology

2012-05-25

m b r i d g e , m a 0 213 9 u s a — w w w. c s a i l . m i t . e d u MIT-CSAIL-TR-2012-013 May 25, 2012 Temporally Scalable Visual SLAM using a...00-00-2012 4. TITLE AND SUBTITLE Temporally Scalable Visual SLAM using a Reduced Pose Graph 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...demonstrate a system for temporally scalable visual SLAM using a reduced pose graph representation. Unlike previous visual SLAM approaches that use

A mutual support mechanism through intercellular movement of CAPRICE and GLABRA3 can pattern the Arabidopsis root epidermis.

PubMed

Savage, Natasha Saint; Walker, Tom; Wieckowski, Yana; Schiefelbein, John; Dolan, Liam; Monk, Nicholas A M

2008-09-23

The patterning of the Arabidopsis root epidermis depends on a genetic regulatory network that operates both within and between cells. Genetic studies have identified a number of key components of this network, but a clear picture of the functional logic of the network is lacking. Here, we integrate existing genetic and biochemical data in a mathematical model that allows us to explore both the sufficiency of known network interactions and the extent to which additional assumptions about the model can account for wild-type and mutant data. Our model shows that an existing hypothesis concerning the autoregulation of WEREWOLF does not account fully for the expression patterns of components of the network. We confirm the lack of WEREWOLF autoregulation experimentally in transgenic plants. Rather, our modelling suggests that patterning depends on the movement of the CAPRICE and GLABRA3 transcriptional regulators between epidermal cells. Our combined modelling and experimental studies show that WEREWOLF autoregulation does not contribute to the initial patterning of epidermal cell fates in the Arabidopsis seedling root. In contrast to a patterning mechanism relying on local activation, we propose a mechanism based on lateral inhibition with feedback. The active intercellular movements of proteins that are central to our model underlie a mechanism for pattern formation in planar groups of cells that is centred on the mutual support of two cell fates rather than on local activation and lateral inhibition.

A Mutual Support Mechanism through Intercellular Movement of CAPRICE and GLABRA3 Can Pattern the Arabidopsis Root Epidermis

PubMed Central

Savage, Natasha Saint; Walker, Tom; Wieckowski, Yana; Schiefelbein, John; Dolan, Liam; Monk, Nicholas A. M

2008-01-01

The patterning of the Arabidopsis root epidermis depends on a genetic regulatory network that operates both within and between cells. Genetic studies have identified a number of key components of this network, but a clear picture of the functional logic of the network is lacking. Here, we integrate existing genetic and biochemical data in a mathematical model that allows us to explore both the sufficiency of known network interactions and the extent to which additional assumptions about the model can account for wild-type and mutant data. Our model shows that an existing hypothesis concerning the autoregulation of WEREWOLF does not account fully for the expression patterns of components of the network. We confirm the lack of WEREWOLF autoregulation experimentally in transgenic plants. Rather, our modelling suggests that patterning depends on the movement of the CAPRICE and GLABRA3 transcriptional regulators between epidermal cells. Our combined modelling and experimental studies show that WEREWOLF autoregulation does not contribute to the initial patterning of epidermal cell fates in the Arabidopsis seedling root. In contrast to a patterning mechanism relying on local activation, we propose a mechanism based on lateral inhibition with feedback. The active intercellular movements of proteins that are central to our model underlie a mechanism for pattern formation in planar groups of cells that is centred on the mutual support of two cell fates rather than on local activation and lateral inhibition. PMID:18816165

The Relationship between Respiration-Related Membrane Potential Slow Oscillations and Discharge Patterns in Mitral/Tufted Cells: What Are the Rules?

PubMed Central

Briffaud, Virginie; Fourcaud-Trocmé, Nicolas; Messaoudi, Belkacem; Buonviso, Nathalie; Amat, Corine

2012-01-01

Background A slow respiration-related rhythm strongly shapes the activity of the olfactory bulb. This rhythm appears as a slow oscillation that is detectable in the membrane potential, the respiration-related spike discharge of the mitral/tufted cells and the bulbar local field potential. Here, we investigated the rules that govern the manifestation of membrane potential slow oscillations (MPSOs) and respiration-related discharge activities under various afferent input conditions and cellular excitability states. Methodology and Principal Findings We recorded the intracellular membrane potential signals in the mitral/tufted cells of freely breathing anesthetized rats. We first demonstrated the existence of multiple types of MPSOs, which were influenced by odor stimulation and discharge activity patterns. Complementary studies using changes in the intracellular excitability state and a computational model of the mitral cell demonstrated that slow oscillations in the mitral/tufted cell membrane potential were also modulated by the intracellular excitability state, whereas the respiration-related spike activity primarily reflected the afferent input. Based on our data regarding MPSOs and spike patterns, we found that cells exhibiting an unsynchronized discharge pattern never exhibited an MPSO. In contrast, cells with a respiration-synchronized discharge pattern always exhibited an MPSO. In addition, we demonstrated that the association between spike patterns and MPSO types appeared complex. Conclusion We propose that both the intracellular excitability state and input strength underlie specific MPSOs, which, in turn, constrain the types of spike patterns exhibited. PMID:22952828

Alternative mechanisms alter the emergent properties of self-organization in mussel beds

PubMed Central

Liu, Quan-Xing; Weerman, Ellen J.; Herman, Peter M. J.; Olff, Han; van de Koppel, Johan

2012-01-01

Theoretical models predict that spatial self-organization can have important, unexpected implications by affecting the functioning of ecosystems in terms of resilience and productivity. Whether and how these emergent effects depend on specific formulations of the underlying mechanisms are questions that are often ignored. Here, we compare two alternative models of regular spatial pattern formation in mussel beds that have different mechanistic descriptions of the facilitative interactions between mussels. The first mechanism involves a reduced mussel loss rate at high density owing to mutual protection between the mussels, which is the basis of prior studies on the pattern formation in mussels. The second mechanism assumes, based on novel experimental evidence, that mussels feed more efficiently on top of mussel-generated hummocks. Model simulations point out that the second mechanism produces very similar types of spatial patterns in mussel beds. Yet the mechanisms predict a strikingly contrasting effect of these spatial patterns on ecosystem functioning, in terms of productivity and resilience. In the first model, where high mussel densities reduce mussel loss rates, patterns are predicted to strongly increase productivity and decrease the recovery time of the bed following a disturbance. When pattern formation is generated by increased feeding efficiency on hummocks, only minor emergent effects of pattern formation on ecosystem functioning are predicted. Our results provide a warning against predictions of the implications and emergent properties of spatial self-organization, when the mechanisms that underlie self-organization are incompletely understood and not based on the experimental study. PMID:22418256

Fractal Patterns of Neural Activity Exist within the Suprachiasmatic Nucleus and Require Extrinsic Network Interactions

PubMed Central

Hu, Kun; Meijer, Johanna H.; Shea, Steven A.; vanderLeest, Henk Tjebbe; Pittman-Polletta, Benjamin; Houben, Thijs; van Oosterhout, Floor; Deboer, Tom; Scheer, Frank A. J. L.

2012-01-01

The mammalian central circadian pacemaker (the suprachiasmatic nucleus, SCN) contains thousands of neurons that are coupled through a complex network of interactions. In addition to the established role of the SCN in generating rhythms of ∼24 hours in many physiological functions, the SCN was recently shown to be necessary for normal self-similar/fractal organization of motor activity and heart rate over a wide range of time scales—from minutes to 24 hours. To test whether the neural network within the SCN is sufficient to generate such fractal patterns, we studied multi-unit neural activity of in vivo and in vitro SCNs in rodents. In vivo SCN-neural activity exhibited fractal patterns that are virtually identical in mice and rats and are similar to those in motor activity at time scales from minutes up to 10 hours. In addition, these patterns remained unchanged when the main afferent signal to the SCN, namely light, was removed. However, the fractal patterns of SCN-neural activity are not autonomous within the SCN as these patterns completely broke down in the isolated in vitro SCN despite persistence of circadian rhythmicity. Thus, SCN-neural activity is fractal in the intact organism and these fractal patterns require network interactions between the SCN and extra-SCN nodes. Such a fractal control network could underlie the fractal regulation observed in many physiological functions that involve the SCN, including motor control and heart rate regulation. PMID:23185285

Rhythm generation, coordination, and initiation in the vocal pathways of male African clawed frogs

PubMed Central

Cavin Barnes, Jessica; Appleby, Todd

2016-01-01

Central pattern generators (CPGs) in the brain stem are considered to underlie vocalizations in many vertebrate species, but the detailed mechanisms underlying how motor rhythms are generated, coordinated, and initiated remain unclear. We addressed these issues using isolated brain preparations of Xenopus laevis from which fictive vocalizations can be elicited. Advertisement calls of male X. laevis that consist of fast and slow trills are generated by vocal CPGs contained in the brain stem. Brain stem central vocal pathways consist of a premotor nucleus [dorsal tegmental area of medulla (DTAM)] and a laryngeal motor nucleus [a homologue of nucleus ambiguus (n.IX-X)] with extensive reciprocal connections between the nuclei. In addition, DTAM receives descending inputs from the extended amygdala. We found that unilateral transection of the projections between DTAM and n.IX-X eliminated premotor fictive fast trill patterns but did not affect fictive slow trills, suggesting that the fast and slow trill CPGs are distinct; the slow trill CPG is contained in n.IX-X, and the fast trill CPG spans DTAM and n.IX-X. Midline transections that eliminated the anterior, posterior, or both commissures caused no change in the temporal structure of fictive calls, but bilateral synchrony was lost, indicating that the vocal CPGs are contained in the lateral halves of the brain stem and that the commissures synchronize the two oscillators. Furthermore, the elimination of the inputs from extended amygdala to DTAM, in addition to the anterior commissure, resulted in autonomous initiation of fictive fast but not slow trills by each hemibrain stem, indicating that the extended amygdala provides a bilateral signal to initiate fast trills. NEW & NOTEWORTHY Central pattern generators (CPGs) are considered to underlie vocalizations in many vertebrate species, but the detailed mechanisms underlying their functions remain unclear. We addressed this question using an isolated brain preparation of African clawed frogs. We discovered that two vocal phases are mediated by anatomically distinct CPGs, that there are a pair of CPGs contained in the left and right half of the brain stem, and that mechanisms underlying initiation of the two vocal phases are distinct. PMID:27760822

Context-dependent plasticity in the subcortical encoding of linguistic pitch patterns

PubMed Central

Lau, Joseph C. Y.; Wong, Patrick C. M.

2016-01-01

We examined the mechanics of online experience-dependent auditory plasticity by assessing the influence of prior context on the frequency-following responses (FFRs), which reflect phase-locked responses from neural ensembles within the subcortical auditory system. FFRs were elicited to a Cantonese falling lexical pitch pattern from 24 native speakers of Cantonese in a variable context, wherein the falling pitch pattern randomly occurred in the context of two other linguistic pitch patterns; in a patterned context, wherein, the falling pitch pattern was presented in a predictable sequence along with two other pitch patterns, and in a repetitive context, wherein the falling pitch pattern was presented with 100% probability. We found that neural tracking of the stimulus pitch contour was most faithful and accurate when listening context was patterned and least faithful when the listening context was variable. The patterned context elicited more robust pitch tracking relative to the repetitive context, suggesting that context-dependent plasticity is most robust when the context is predictable but not repetitive. Our study demonstrates a robust influence of prior listening context that works to enhance online neural encoding of linguistic pitch patterns. We interpret these results as indicative of an interplay between contextual processes that are responsive to predictability as well as novelty in the presentation context. NEW & NOTEWORTHY Human auditory perception in dynamic listening environments requires fine-tuning of sensory signal based on behaviorally relevant regularities in listening context, i.e., online experience-dependent plasticity. Our finding suggests what partly underlie online experience-dependent plasticity are interplaying contextual processes in the subcortical auditory system that are responsive to predictability as well as novelty in listening context. These findings add to the literature that looks to establish the neurophysiological bases of auditory system plasticity, a central issue in auditory neuroscience. PMID:27832606

Context-dependent plasticity in the subcortical encoding of linguistic pitch patterns.

PubMed

Lau, Joseph C Y; Wong, Patrick C M; Chandrasekaran, Bharath

2017-02-01

We examined the mechanics of online experience-dependent auditory plasticity by assessing the influence of prior context on the frequency-following responses (FFRs), which reflect phase-locked responses from neural ensembles within the subcortical auditory system. FFRs were elicited to a Cantonese falling lexical pitch pattern from 24 native speakers of Cantonese in a variable context, wherein the falling pitch pattern randomly occurred in the context of two other linguistic pitch patterns; in a patterned context, wherein, the falling pitch pattern was presented in a predictable sequence along with two other pitch patterns, and in a repetitive context, wherein the falling pitch pattern was presented with 100% probability. We found that neural tracking of the stimulus pitch contour was most faithful and accurate when listening context was patterned and least faithful when the listening context was variable. The patterned context elicited more robust pitch tracking relative to the repetitive context, suggesting that context-dependent plasticity is most robust when the context is predictable but not repetitive. Our study demonstrates a robust influence of prior listening context that works to enhance online neural encoding of linguistic pitch patterns. We interpret these results as indicative of an interplay between contextual processes that are responsive to predictability as well as novelty in the presentation context. Human auditory perception in dynamic listening environments requires fine-tuning of sensory signal based on behaviorally relevant regularities in listening context, i.e., online experience-dependent plasticity. Our finding suggests what partly underlie online experience-dependent plasticity are interplaying contextual processes in the subcortical auditory system that are responsive to predictability as well as novelty in listening context. These findings add to the literature that looks to establish the neurophysiological bases of auditory system plasticity, a central issue in auditory neuroscience. Copyright © 2017 the American Physiological Society.

Kuru

MedlinePlus

... The NINDS funds research to better understand the genetic, molecular, and cellular mechanisms that underlie the TSE diseases. ... The NINDS funds research to better understand the genetic, molecular, and cellular mechanisms that underlie the TSE diseases. ...

Activity of the anterior cingulate cortex and ventral hippocampus underlie increases in contextual fear generalization.

PubMed

Cullen, Patrick K; Gilman, T Lee; Winiecki, Patrick; Riccio, David C; Jasnow, Aaron M

2015-10-01

Memories for context become less specific with time resulting in animals generalizing fear from training contexts to novel contexts. Though much attention has been given to the neural structures that underlie the long-term consolidation of a context fear memory, very little is known about the mechanisms responsible for the increase in fear generalization that occurs as the memory ages. Here, we examine the neural pattern of activation underlying the expression of a generalized context fear memory in male C57BL/6J mice. Animals were context fear conditioned and tested for fear in either the training context or a novel context at recent and remote time points. Animals were sacrificed and fluorescent in situ hybridization was performed to assay neural activation. Our results demonstrate activity of the prelimbic, infralimbic, and anterior cingulate (ACC) cortices as well as the ventral hippocampus (vHPC) underlie expression of a generalized fear memory. To verify the involvement of the ACC and vHPC in the expression of a generalized fear memory, animals were context fear conditioned and infused with 4% lidocaine into the ACC, dHPC, or vHPC prior to retrieval to temporarily inactivate these structures. The results demonstrate that activity of the ACC and vHPC is required for the expression of a generalized fear memory, as inactivation of these regions returned the memory to a contextually precise form. Current theories of time-dependent generalization of contextual memories do not predict involvement of the vHPC. Our data suggest a novel role of this region in generalized memory, which should be incorporated into current theories of time-dependent memory generalization. We also show that the dorsal hippocampus plays a prolonged role in contextually precise memories. Our findings suggest a possible interaction between the ACC and vHPC controls the expression of fear generalization. Copyright © 2015 Elsevier Inc. All rights reserved.

Challenges and Opportunities to Developing Synergies Among Diverse Environmental Observatories: FSML, NEON, and GLEON

NASA Astrophysics Data System (ADS)

Williamson, C. E.; Weathers, K. C.; Knoll, L. B.; Brentrup, J.

2012-12-01

Recent rapid advances in sensor technology and cyberinfrastructure have enabled the development of numerous environmental observatories ranging from local networks at field stations and marine laboratories (FSML) to continental scale observatories such as the National Ecological Observatory Network (NEON) to global scale observatories such as the Global Lake Ecological Observatory Network (GLEON). While divergent goals underlie the initial development of these observatories, and they are often designed to serve different communities, many opportunities for synergies exist. In addition, the use of existing infrastructure may enhance the cost-effectiveness of building and maintaining large scale observatories. For example, FSMLs are established facilities with the staff and infrastructure to host sensor nodes of larger networks. Many field stations have existing staff and long-term databases as well as smaller sensor networks that are the product of a single or small group of investigators with a unique data management system embedded in a local or regional community. These field station based facilities and data are a potentially untapped gold mine for larger continental and global scale observatories; common ecological and environmental challenges centered on understanding the impacts of changing climate, land use, and invasive species often underlie these efforts. The purpose of this talk is to stimulate a dialog on the challenges of merging efforts across these different spatial and temporal scales, as well as addressing how to develop synergies among observatory networks with divergent roots and philosophical approaches. For example, FSMLs have existing long-term databases and facilities, while NEON has sparse past data but a well-developed template and closely coordinated team working in a coherent format across a continental scale. GLEON on the other hand is a grass-roots network of experts in science, information technology, and engineering with a common goal of building a scalable network around the world to understand and predict how lakes respond to global change. Creating synergies among networks at these divergent scales requires open discussions ranging from data collection and management to data serving and sharing. Coordination of these efforts can provide an additional opportunity to educate both students and the public in innovative new ways about the broader continental to global scale of ecological and environmental challenges that they have observed in their more local ecosystems.

Energy-absorption capability and scalability of square cross section composite tube specimens

NASA Technical Reports Server (NTRS)

Farley, Gary L.

1987-01-01

Static crushing tests were conducted on graphite/epoxy and Kevlar/epoxy square cross section tubes to study the influence of specimen geometry on the energy-absorption capability and scalability of composite materials. The tube inside width-to-wall thickness (W/t) ratio was determined to significantly affect the energy-absorption capability of composite materials. As W/t ratio decreases, the energy-absorption capability increases nonlinearly. The energy-absorption capability of Kevlar epoxy tubes was found to be geometrically scalable, but the energy-absorption capability of graphite/epoxy tubes was not geometrically scalable.

Study on Dissemination Patterns in Location-Aware Gossiping Networks

NASA Astrophysics Data System (ADS)

Kami, Nobuharu; Baba, Teruyuki; Yoshikawa, Takashi; Morikawa, Hiroyuki

We study the properties of information dissemination over location-aware gossiping networks leveraging location-based real-time communication applications. Gossiping is a promising method for quickly disseminating messages in a large-scale system, but in its application to information dissemination for location-aware applications, it is important to consider the network topology and patterns of spatial dissemination over the network in order to achieve effective delivery of messages to potentially interested users. To this end, we propose a continuous-space network model extended from Kleinberg's small-world model applicable to actual location-based applications. Analytical and simulation-based study shows that the proposed network achieves high dissemination efficiency resulting from geographically neutral dissemination patterns as well as selective dissemination to proximate users. We have designed a highly scalable location management method capable of promptly updating the network topology in response to node movement and have implemented a distributed simulator to perform dynamic target pursuit experiments as one example of applications that are the most sensitive to message forwarding delay. The experimental results show that the proposed network surpasses other types of networks in pursuit efficiency and achieves the desirable dissemination patterns.

Memristive neural network for on-line learning and tracking with brain-inspired spike timing dependent plasticity.

PubMed

Pedretti, G; Milo, V; Ambrogio, S; Carboni, R; Bianchi, S; Calderoni, A; Ramaswamy, N; Spinelli, A S; Ielmini, D

2017-07-13

Brain-inspired computation can revolutionize information technology by introducing machines capable of recognizing patterns (images, speech, video) and interacting with the external world in a cognitive, humanlike way. Achieving this goal requires first to gain a detailed understanding of the brain operation, and second to identify a scalable microelectronic technology capable of reproducing some of the inherent functions of the human brain, such as the high synaptic connectivity (~10 4 ) and the peculiar time-dependent synaptic plasticity. Here we demonstrate unsupervised learning and tracking in a spiking neural network with memristive synapses, where synaptic weights are updated via brain-inspired spike timing dependent plasticity (STDP). The synaptic conductance is updated by the local time-dependent superposition of pre- and post-synaptic spikes within a hybrid one-transistor/one-resistor (1T1R) memristive synapse. Only 2 synaptic states, namely the low resistance state (LRS) and the high resistance state (HRS), are sufficient to learn and recognize patterns. Unsupervised learning of a static pattern and tracking of a dynamic pattern of up to 4 × 4 pixels are demonstrated, paving the way for intelligent hardware technology with up-scaled memristive neural networks.

Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films

PubMed Central

Shi, Xuesong; Li, Xin; Jiang, Lan; Qu, Liangti; Zhao, Yang; Ran, Peng; Wang, Qingsong; Cao, Qiang; Ma, Tianbao; Lu, Yongfeng

2015-01-01

We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10–50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics. PMID:26615800

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research.

PubMed

Torous, John; Kiang, Mathew V; Lorme, Jeanette; Onnela, Jukka-Pekka

2016-05-05

A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health.

Scalable Inkjet-Based Structural Color Printing by Molding Transparent Gratings on Multilayer Nanostructured Surfaces.

PubMed

Jiang, Hao; Kaminska, Bozena

2018-04-24

To enable customized manufacturing of structural colors for commercial applications, up-scalable, low-cost, rapid, and versatile printing techniques are highly demanded. In this paper, we introduce a viable strategy for scaling up production of custom-input images by patterning individual structural colors on separate layers, which are then vertically stacked and recombined into full-color images. By applying this strategy on molded-ink-on-nanostructured-surface printing, we present an industry-applicable inkjet structural color printing technique termed multilayer molded-ink-on-nanostructured-surface (M-MIONS) printing, in which structural color pixels are molded on multiple layers of nanostructured surfaces. Transparent colorless titanium dioxide nanoparticles were inkjet-printed onto three separate transparent polymer substrates, and each substrate surface has one specific subwavelength grating pattern for molding the deposited nanoparticles into structural color pixels of red, green, or blue primary color. After index-matching lamination, the three layers were vertically stacked and bonded to display a color image. Each primary color can be printed into a range of different shades controlled through a half-tone process, and full colors were achieved by mixing primary colors from three layers. In our experiments, an image size as big as 10 cm by 10 cm was effortlessly achieved, and even larger images can potentially be printed on recombined grating surfaces. In one application example, the M-MIONS technique was used for printing customizable transparent color optical variable devices for protecting personalized security documents. In another example, a transparent diffractive color image printed with the M-MIONS technique was pasted onto a transparent panel for overlaying colorful information onto one's view of reality.

Fabrication of cross-shaped Cu-nanowire resistive memory devices using a rapid, scalable, and designable inorganic-nanowire-digital-alignment technique (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Wentao; Lee, Yeongjun; Min, Sung-Yong; Park, Cheolmin; Lee, Tae-Woo

2016-09-01

Resistive random-access memory (RRAM) is a candidate next generation nonvolatile memory due to its high access speed, high density and ease of fabrication. Especially, cross-point-access allows cross-bar arrays that lead to high-density cells in a two-dimensional planar structure. Use of such designs could be compatible with the aggressive scaling down of memory devices, but existing methods such as optical or e-beam lithographic approaches are too complicated. One-dimensional inorganic nanowires (i-NWs) are regarded as ideal components of nanoelectronics to circumvent the limitations of conventional lithographic approaches. However, post-growth alignment of these i-NWs precisely on a large area with individual control is still a difficult challenge. Here, we report a simple, inexpensive, and rapid method to fabricate two-dimensional arrays of perpendicularly-aligned, individually-conductive Cu-NWs with a nanometer-scale CuxO layer sandwiched at each cross point, by using an inorganic-nanowire-digital-alignment technique (INDAT) and a one-step reduction process. In this approach, the oxide layer is self-formed and patterned, so conventional deposition and lithography are not necessary. INDAT eliminates the difficulties of alignment and scalable fabrication that are encountered when using currently-available techniques that use inorganic nanowires. This simple process facilitates fabrication of cross-point nonvolatile memristor arrays. Fabricated arrays had reproducible resistive switching behavior, high on/off current ratio (Ion/Ioff) 10 6 and extensive cycling endurance. This is the first report of memristors with the resistive switching oxide layer self-formed, self-patterned and self-positioned; we envision that the new features of the technique will provide great opportunities for future nano-electronic circuits.

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research

PubMed Central

Torous, John; Kiang, Mathew V; Lorme, Jeanette

2016-01-01

Background A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Objective Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. Methods We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. Results We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Conclusions Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health. PMID:27150677

Value-added Synthesis of Graphene: Recycling Industrial Carbon Waste into Electrodes for High-Performance Electronic Devices

PubMed Central

Seo, Hong-Kyu; Kim, Tae-Sik; Park, Chibeom; Xu, Wentao; Baek, Kangkyun; Bae, Sang-Hoon; Ahn, Jong-Hyun; Kim, Kimoon; Choi, Hee Cheul; Lee, Tae-Woo

2015-01-01

We have developed a simple, scalable, transfer-free, ecologically sustainable, value-added method to convert inexpensive coal tar pitch to patterned graphene films directly on device substrates. The method, which does not require an additional transfer process, enables direct growth of graphene films on device substrates in large area. To demonstrate the practical applications of the graphene films, we used the patterned graphene grown on a dielectric substrate directly as electrodes of bottom-contact pentacene field-effect transistors (max. field effect mobility ~0.36 cm2·V−1·s−1), without using any physical transfer process. This use of a chemical waste product as a solid carbon source instead of commonly used explosive hydrocarbon gas sources for graphene synthesis has the dual benefits of converting the waste to a valuable product, and reducing pollution. PMID:26567845

Taking a 'Big Data' approach to data quality in a citizen science project.

PubMed

Kelling, Steve; Fink, Daniel; La Sorte, Frank A; Johnston, Alison; Bruns, Nicholas E; Hochachka, Wesley M

2015-11-01

Data from well-designed experiments provide the strongest evidence of causation in biodiversity studies. However, for many species the collection of these data is not scalable to the spatial and temporal extents required to understand patterns at the population level. Only data collected from citizen science projects can gather sufficient quantities of data, but data collected from volunteers are inherently noisy and heterogeneous. Here we describe a 'Big Data' approach to improve the data quality in eBird, a global citizen science project that gathers bird observations. First, eBird's data submission design ensures that all data meet high standards of completeness and accuracy. Second, we take a 'sensor calibration' approach to measure individual variation in eBird participant's ability to detect and identify birds. Third, we use species distribution models to fill in data gaps. Finally, we provide examples of novel analyses exploring population-level patterns in bird distributions.

Alternating current line-filter based on electrochemical capacitor utilizing template-patterned graphene.

PubMed

Wu, Zhenkun; Li, Liyi; Lin, Ziyin; Song, Bo; Li, Zhuo; Moon, Kyoung-Sik; Wong, Ching-Ping; Bai, Shu-Lin

2015-06-17

Aluminum electrolytic capacitors (AECs) are widely used for alternating current (ac) line-filtering. However, their bulky size is becoming more and more incompatible with the rapid development of portable electronics. Here we report a scalable process to fabricate miniaturized graphene-based ac line-filters on flexible substrates at room temperature. In this work, graphene oxide (GO) is reduced by patterned metal interdigits at room temperature and used directly as the electrode material. The as-fabricated device shows a phase angle of -75.4° at 120 Hz with a specific capacitance of 316 µF/cm(2) and a RC time constant of 0.35 ms. In addition, it retains 97.2% of the initial capacitance after 10000 charge/discharge cycles. These outstanding performance characteristics of our device demonstrate its promising to replace the conventional AECs for ac line filtering.

Advanced fast 3D DSA model development and calibration for design technology co-optimization

NASA Astrophysics Data System (ADS)

Lai, Kafai; Meliorisz, Balint; Muelders, Thomas; Welling, Ulrich; Stock, Hans-Jürgen; Marokkey, Sajan; Demmerle, Wolfgang; Liu, Chi-Chun; Chi, Cheng; Guo, Jing

2017-04-01

Direct Optimization (DO) of a 3D DSA model is a more optimal approach to a DTCO study in terms of accuracy and speed compared to a Cahn Hilliard Equation solver. DO's shorter run time (10X to 100X faster) and linear scaling makes it scalable to the area required for a DTCO study. However, the lack of temporal data output, as opposed to prior art, requires a new calibration method. The new method involves a specific set of calibration patterns. The calibration pattern's design is extremely important when temporal data is absent to obtain robust model parameters. A model calibrated to a Hybrid DSA system with a set of device-relevant constructs indicates the effectiveness of using nontemporal data. Preliminary model prediction using programmed defects on chemo-epitaxy shows encouraging results and agree qualitatively well with theoretical predictions from a strong segregation theory.

Nanoscale imaging of photocurrent enhancement by resonator array photovoltaic coatings.

PubMed

Ha, Dongheon; Yoon, Yohan; Zhitenev, Nikolai B

2018-04-06

Nanoscale surface patterning commonly used to increase absorption of solar cells can adversely impact the open-circuit voltage due to increased surface area and recombination. Here, we demonstrate absorptivity and photocurrent enhancement using silicon dioxide (SiO 2 ) nanosphere arrays on a gallium arsenide (GaAs) solar cell that do not require direct surface patterning. Due to the combined effects of thin-film interference and whispering gallery-like resonances within nanosphere arrays, there is more than 20% enhancement in both absorptivity and photocurrent. To determine the effect of the resonance coupling between nanospheres, we perform a scanning photocurrent microscopy based on a near-field scanning optical microscopy measurement and find a substantial local photocurrent enhancement. The nanosphere-based antireflection coating (ARC), made by the Meyer rod rolling technique, is a scalable and a room-temperature process; and, can replace the conventional thin-film-based ARCs requiring expensive high-temperature vacuum deposition.

Nanoscale imaging of photocurrent enhancement by resonator array photovoltaic coatings

NASA Astrophysics Data System (ADS)

Ha, Dongheon; Yoon, Yohan; Zhitenev, Nikolai B.

2018-04-01

Nanoscale surface patterning commonly used to increase absorption of solar cells can adversely impact the open-circuit voltage due to increased surface area and recombination. Here, we demonstrate absorptivity and photocurrent enhancement using silicon dioxide (SiO2) nanosphere arrays on a gallium arsenide (GaAs) solar cell that do not require direct surface patterning. Due to the combined effects of thin-film interference and whispering gallery-like resonances within nanosphere arrays, there is more than 20% enhancement in both absorptivity and photocurrent. To determine the effect of the resonance coupling between nanospheres, we perform a scanning photocurrent microscopy based on a near-field scanning optical microscopy measurement and find a substantial local photocurrent enhancement. The nanosphere-based antireflection coating (ARC), made by the Meyer rod rolling technique, is a scalable and a room-temperature process; and, can replace the conventional thin-film-based ARCs requiring expensive high-temperature vacuum deposition.

Topological Magnon Modes in Patterned Ferrimagnetic Insulator Thin Films.

PubMed

Li, Yun-Mei; Xiao, Jiang; Chang, Kai

2018-05-09

Manipulation of magnons opens an attractive direction in the future energy-efficient information processing devices. Such quasi-particles can transfer and process information free from the troublesome Ohmic loss in conventional electronic devices. Here, we propose to realize topologically protected magnon modes using the interface between the patterned ferrimagnetic insulator thin films of different configurations without the Dzyaloshinskii-Moriya interaction. The interface thus behaves like a perfect waveguide to conduct the magnon modes lying in the band gap. These modes are immune to backscattering even in sharply bent tracks, robust against the disorders, and maintain a high degree of coherence during propagation. We design a magnonic Mach-Zehnder interferometer, which realizes a continuous change of magnon signal with varying external magnetic field or driving frequency. Our results pave a new way for realizing topologically protected magnon waveguide and finally achieving a scalable low-dissipation spintronic devices and even the magnonic integrated circuit.

Nanotextured Shrink Wrap Superhydrophobic Surfaces by Argon Plasma Etching

PubMed Central

Nokes, Jolie M.; Sharma, Himanshu; Tu, Roger; Kim, Monica Y.; Chu, Michael; Siddiqui, Ali; Khine, Michelle

2016-01-01

We present a rapid, simple, and scalable approach to achieve superhydrophobic (SH) substrates directly in commodity shrink wrap film utilizing Argon (Ar) plasma. Ar plasma treatment creates a stiff skin layer on the surface of the shrink film. When the film shrinks, the mismatch in stiffness between the stiff skin layer and bulk shrink film causes the formation of multiscale hierarchical wrinkles with nano-textured features. Scanning electron microscopy (SEM) images confirm the presence of these biomimetic structures. Contact angle (CA) and contact angle hysteresis (CAH) measurements, respectively, defined as values greater than 150° and less than 10°, verified the SH nature of the substrates. Furthermore, we demonstrate the ability to reliably pattern hydrophilic regions onto the SH substrates, allowing precise capture and detection of proteins in urine. Finally, we achieved self-driven microfluidics via patterning contrasting superhydrophilic microchannels on the SH Ar substrates to induce flow for biosensing. PMID:28773318

Nanotextured Shrink Wrap Superhydrophobic Surfaces by Argon Plasma Etching.

PubMed

Nokes, Jolie M; Sharma, Himanshu; Tu, Roger; Kim, Monica Y; Chu, Michael; Siddiqui, Ali; Khine, Michelle

2016-03-14

We present a rapid, simple, and scalable approach to achieve superhydrophobic (SH) substrates directly in commodity shrink wrap film utilizing Argon (Ar) plasma. Ar plasma treatment creates a stiff skin layer on the surface of the shrink film. When the film shrinks, the mismatch in stiffness between the stiff skin layer and bulk shrink film causes the formation of multiscale hierarchical wrinkles with nano-textured features. Scanning electron microscopy (SEM) images confirm the presence of these biomimetic structures. Contact angle (CA) and contact angle hysteresis (CAH) measurements, respectively, defined as values greater than 150° and less than 10°, verified the SH nature of the substrates. Furthermore, we demonstrate the ability to reliably pattern hydrophilic regions onto the SH substrates, allowing precise capture and detection of proteins in urine. Finally, we achieved self-driven microfluidics via patterning contrasting superhydrophilic microchannels on the SH Ar substrates to induce flow for biosensing.

Visualizing Article Similarities via Sparsified Article Network and Map Projection for Systematic Reviews.

PubMed

Ji, Xiaonan; Machiraju, Raghu; Ritter, Alan; Yen, Po-Yin

2017-01-01

Systematic Reviews (SRs) of biomedical literature summarize evidence from high-quality studies to inform clinical decisions, but are time and labor intensive due to the large number of article collections. Article similarities established from textual features have been shown to assist in the identification of relevant articles, thus facilitating the article screening process efficiently. In this study, we visualized article similarities to extend its utilization in practical settings for SR researchers, aiming to promote human comprehension of article distributions and hidden patterns. To prompt an effective visualization in an interpretable, intuitive, and scalable way, we implemented a graph-based network visualization with three network sparsification approaches and a distance-based map projection via dimensionality reduction. We evaluated and compared three network sparsification approaches and the visualization types (article network vs. article map). We demonstrated the effectiveness in revealing article distribution and exhibiting clustering patterns of relevant articles with practical meanings for SRs.

Extension of the dielectric breakdown model for simulation of viscous fingering at finite viscosity ratios.

PubMed

Doorwar, Shashvat; Mohanty, Kishore K

2014-07-01

Immiscible displacement of viscous oil by water in a petroleum reservoir is often hydrodynamically unstable. Due to similarities between the physics of dielectric breakdown and immiscible flow in porous media, we extend the existing dielectric breakdown model to simulate viscous fingering patterns for a wide range of viscosity ratios (μ(r)). At low values of power-law index η, the system behaves like a stable Eden growth model and as the value of η is increased to unity, diffusion limited aggregation-like fractals appear. This model is compared with our two-dimensional (2D) experiments to develop a correlation between the viscosity ratio and the power index, i.e., η = 10(-5)μ(r)(0.8775). The 2D and three-dimensional (3D) simulation data appear scalable. The fingering pattern in 3D simulations at finite viscosity ratios appear qualitatively similar to the few experimental results published in the literature.

Value-added Synthesis of Graphene: Recycling Industrial Carbon Waste into Electrodes for High-Performance Electronic Devices

NASA Astrophysics Data System (ADS)

Seo, Hong-Kyu; Kim, Tae-Sik; Park, Chibeom; Xu, Wentao; Baek, Kangkyun; Bae, Sang-Hoon; Ahn, Jong-Hyun; Kim, Kimoon; Choi, Hee Cheul; Lee, Tae-Woo

2015-11-01

We have developed a simple, scalable, transfer-free, ecologically sustainable, value-added method to convert inexpensive coal tar pitch to patterned graphene films directly on device substrates. The method, which does not require an additional transfer process, enables direct growth of graphene films on device substrates in large area. To demonstrate the practical applications of the graphene films, we used the patterned graphene grown on a dielectric substrate directly as electrodes of bottom-contact pentacene field-effect transistors (max. field effect mobility ~0.36 cm2·V-1·s-1), without using any physical transfer process. This use of a chemical waste product as a solid carbon source instead of commonly used explosive hydrocarbon gas sources for graphene synthesis has the dual benefits of converting the waste to a valuable product, and reducing pollution.

Value-added Synthesis of Graphene: Recycling Industrial Carbon Waste into Electrodes for High-Performance Electronic Devices.

PubMed

Seo, Hong-Kyu; Kim, Tae-Sik; Park, Chibeom; Xu, Wentao; Baek, Kangkyun; Bae, Sang-Hoon; Ahn, Jong-Hyun; Kim, Kimoon; Choi, Hee Cheul; Lee, Tae-Woo

2015-11-16

We have developed a simple, scalable, transfer-free, ecologically sustainable, value-added method to convert inexpensive coal tar pitch to patterned graphene films directly on device substrates. The method, which does not require an additional transfer process, enables direct growth of graphene films on device substrates in large area. To demonstrate the practical applications of the graphene films, we used the patterned graphene grown on a dielectric substrate directly as electrodes of bottom-contact pentacene field-effect transistors (max. field effect mobility ~0.36 cm(2)·V(-1)·s(-1)), without using any physical transfer process. This use of a chemical waste product as a solid carbon source instead of commonly used explosive hydrocarbon gas sources for graphene synthesis has the dual benefits of converting the waste to a valuable product, and reducing pollution.

Disparity : scalable anomaly detection for clusters.

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

Desai, N.; Bradshaw, R.; Lusk, E.

2008-01-01

In this paper, we describe disparity, a tool that does parallel, scalable anomaly detection for clusters. Disparity uses basic statistical methods and scalable reduction operations to perform data reduction on client nodes and uses these results to locate node anomalies. We discuss the implementation of disparity and present results of its use on a SiCortex SC5832 system.

Toward robust phase-locking in Melibe swim central pattern generator models

NASA Astrophysics Data System (ADS)

Jalil, Sajiya; Allen, Dane; Youker, Joseph; Shilnikov, Andrey

2013-12-01

Small groups of interneurons, abbreviated by CPG for central pattern generators, are arranged into neural networks to generate a variety of core bursting rhythms with specific phase-locked states, on distinct time scales, which govern vital motor behaviors in invertebrates such as chewing and swimming. These movements in lower level animals mimic motions of organs in higher animals due to evolutionarily conserved mechanisms. Hence, various neurological diseases can be linked to abnormal movement of body parts that are regulated by a malfunctioning CPG. In this paper, we, being inspired by recent experimental studies of neuronal activity patterns recorded from a swimming motion CPG of the sea slug Melibe leonina, examine a mathematical model of a 4-cell network that can plausibly and stably underlie the observed bursting rhythm. We develop a dynamical systems framework for explaining the existence and robustness of phase-locked states in activity patterns produced by the modeled CPGs. The proposed tools can be used for identifying core components for other CPG networks with reliable bursting outcomes and specific phase relationships between the interneurons. Our findings can be employed for identifying or implementing the conditions for normal and pathological functioning of basic CPGs of animals and artificially intelligent prosthetics that can regulate various movements.

Joint source-channel coding for motion-compensated DCT-based SNR scalable video.

PubMed

Kondi, Lisimachos P; Ishtiaq, Faisal; Katsaggelos, Aggelos K

2002-01-01

In this paper, we develop an approach toward joint source-channel coding for motion-compensated DCT-based scalable video coding and transmission. A framework for the optimal selection of the source and channel coding rates over all scalable layers is presented such that the overall distortion is minimized. The algorithm utilizes universal rate distortion characteristics which are obtained experimentally and show the sensitivity of the source encoder and decoder to channel errors. The proposed algorithm allocates the available bit rate between scalable layers and, within each layer, between source and channel coding. We present the results of this rate allocation algorithm for video transmission over a wireless channel using the H.263 Version 2 signal-to-noise ratio (SNR) scalable codec for source coding and rate-compatible punctured convolutional (RCPC) codes for channel coding. We discuss the performance of the algorithm with respect to the channel conditions, coding methodologies, layer rates, and number of layers.

Scalable software-defined optical networking with high-performance routing and wavelength assignment algorithms.

PubMed

Lee, Chankyun; Cao, Xiaoyuan; Yoshikane, Noboru; Tsuritani, Takehiro; Rhee, June-Koo Kevin

2015-10-19

The feasibility of software-defined optical networking (SDON) for a practical application critically depends on scalability of centralized control performance. The paper, highly scalable routing and wavelength assignment (RWA) algorithms are investigated on an OpenFlow-based SDON testbed for proof-of-concept demonstration. Efficient RWA algorithms are proposed to achieve high performance in achieving network capacity with reduced computation cost, which is a significant attribute in a scalable centralized-control SDON. The proposed heuristic RWA algorithms differ in the orders of request processes and in the procedures of routing table updates. Combined in a shortest-path-based routing algorithm, a hottest-request-first processing policy that considers demand intensity and end-to-end distance information offers both the highest throughput of networks and acceptable computation scalability. We further investigate trade-off relationship between network throughput and computation complexity in routing table update procedure by a simulation study.

Mining of high utility-probability sequential patterns from uncertain databases

PubMed Central

Zhang, Binbin; Fournier-Viger, Philippe; Li, Ting

2017-01-01

High-utility sequential pattern mining (HUSPM) has become an important issue in the field of data mining. Several HUSPM algorithms have been designed to mine high-utility sequential patterns (HUPSPs). They have been applied in several real-life situations such as for consumer behavior analysis and event detection in sensor networks. Nonetheless, most studies on HUSPM have focused on mining HUPSPs in precise data. But in real-life, uncertainty is an important factor as data is collected using various types of sensors that are more or less accurate. Hence, data collected in a real-life database can be annotated with existing probabilities. This paper presents a novel pattern mining framework called high utility-probability sequential pattern mining (HUPSPM) for mining high utility-probability sequential patterns (HUPSPs) in uncertain sequence databases. A baseline algorithm with three optional pruning strategies is presented to mine HUPSPs. Moroever, to speed up the mining process, a projection mechanism is designed to create a database projection for each processed sequence, which is smaller than the original database. Thus, the number of unpromising candidates can be greatly reduced, as well as the execution time for mining HUPSPs. Substantial experiments both on real-life and synthetic datasets show that the designed algorithm performs well in terms of runtime, number of candidates, memory usage, and scalability for different minimum utility and minimum probability thresholds. PMID:28742847

Periodic, chaotic, and doubled earthquake recurrence intervals on the deep San Andreas Fault

USGS Publications Warehouse

Shelly, David R.

2010-01-01

Earthquake recurrence histories may provide clues to the timing of future events, but long intervals between large events obscure full recurrence variability. In contrast, small earthquakes occur frequently, and recurrence intervals are quantifiable on a much shorter time scale. In this work, I examine an 8.5-year sequence of more than 900 recurring low-frequency earthquake bursts composing tremor beneath the San Andreas fault near Parkfield, California. These events exhibit tightly clustered recurrence intervals that, at times, oscillate between ~3 and ~6 days, but the patterns sometimes change abruptly. Although the environments of large and low-frequency earthquakes are different, these observations suggest that similar complexity might underlie sequences of large earthquakes.

On the Self-Organizing Origins of Agency.

PubMed

Kelso, J A Scott

2016-07-01

The question of agency and directedness in living systems has puzzled philosophers and scientists for centuries. What principles and mechanisms underlie the emergence of agency? Analysis and dynamical modeling of experiments on human infants suggest that the birth of agency is due to a eureka-like, pattern-forming phase transition in which the infant suddenly realizes it can make things happen in the world. The main mechanism involves positive feedback: when the baby's initially spontaneous movements cause the world to change, their perceived consequences have a sudden and sustained amplifying effect on the baby's further actions. The baby discovers itself as a causal agent. Some implications of this theory are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Drug Addiction and DNA Modifications.

PubMed

Brown, Amber N; Feng, Jian

2017-01-01

Drug addiction is a complex disorder which can be influenced by both genetic and environmental factors. Research has shown that epigenetic modifications can translate environmental signals into changes in gene expression, suggesting that epigenetic changes may underlie the causes and possibly treatment of substance use disorders. This chapter will focus on epigenetic modifications to DNA, which include DNA methylation and several recently defined additional DNA epigenetic changes. We will discuss the functions of DNA modifications and methods for detecting them, followed by a description of the research investigating the function and consequences of drug-induced changes in DNA methylation patterns. Understanding these epigenetic changes may provide us translational tools for the diagnosis and treatment of addiction in the future.

A multivariate ecogeographic analysis of macaque craniodental variation.

PubMed

Grunstra, Nicole D S; Mitteroecker, Philipp; Foley, Robert A

2018-06-01

To infer the ecogeographic conditions that underlie the evolutionary diversification of macaques, we investigated the within- and between-species relationships of craniodental dimensions, geography, and environment in extant macaque species. We studied evolutionary processes by contrasting macroevolutionary patterns, phylogeny, and within-species associations. Sixty-three linear measurements of the permanent dentition and skull along with data about climate, ecology (environment), and spatial geography were collected for 711 specimens of 12 macaque species and analyzed by a multivariate approach. Phylogenetic two-block partial least squares was used to identify patterns of covariance between craniodental and environmental variation. Phylogenetic reduced rank regression was employed to analyze spatial clines in morphological variation. Between-species associations consisted of two distinct multivariate patterns. The first represents overall craniodental size and is negatively associated with temperature and habitat, but positively with latitude. The second pattern shows an antero-posterior tooth size contrast related to diet, rainfall, and habitat productivity. After controlling for phylogeny, however, the latter dimension was diminished. Within-species analyses neither revealed significant association between morphology, environment, and geography, nor evidence of isolation by distance. We found evidence for environmental adaptation in macaque body and craniodental size, primarily driven by selection for thermoregulation. This pattern cannot be explained by the within-species pattern, indicating an evolved genetic basis for the between-species relationship. The dietary signal in relative tooth size, by contrast, can largely be explained by phylogeny. This cautions against adaptive interpretations of phenotype-environment associations when phylogeny is not explicitly modelled. © 2018 Wiley Periodicals, Inc.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

problems, arising from the proliferation of new data models and distributed technologies for building scalable, available data stores . Architects must...longer are relational databases the de facto standard for building data repositories. Highly distributed, scalable “ NoSQL ” databases [11] have emerged...This is especially challenging at the data storage layer. The multitude of competing NoSQL database technologies creates a complex and rapidly

Scalable and Manageable Storage Systems

DTIC Science & Technology

2000-12-01

Despite our long- distance relationship, my brothers and sisters, Charfeddine, Amel, Ghazi, Hajer, Nabeel , and Ines overwhelmed me with more love and...that enable storage sys - tems to be more cost-effectively scalable. Furthermore, the dissertation proposes an approach to ensure automatic load...and addresses three key technical challenges to making storage sys - tems more cost-effectively scalable and manageable. 1.2 Dissertation research The

Scalable Quantum Networks for Distributed Computing and Sensing

DTIC Science & Technology

2016-04-01

probabilistic measurement , so we developed quantum memories and guided-wave implementations of same, demonstrating controlled delay of a heralded single...Second, fundamental scalability requires a method to synchronize protocols based on quantum measurements , which are inherently probabilistic. To meet...AFRL-AFOSR-UK-TR-2016-0007 Scalable Quantum Networks for Distributed Computing and Sensing Ian Walmsley THE UNIVERSITY OF OXFORD Final Report 04/01

A scalable infrastructure for CMS data analysis based on OpenStack Cloud and Gluster file system

NASA Astrophysics Data System (ADS)

Toor, S.; Osmani, L.; Eerola, P.; Kraemer, O.; Lindén, T.; Tarkoma, S.; White, J.

2014-06-01

The challenge of providing a resilient and scalable computational and data management solution for massive scale research environments requires continuous exploration of new technologies and techniques. In this project the aim has been to design a scalable and resilient infrastructure for CERN HEP data analysis. The infrastructure is based on OpenStack components for structuring a private Cloud with the Gluster File System. We integrate the state-of-the-art Cloud technologies with the traditional Grid middleware infrastructure. Our test results show that the adopted approach provides a scalable and resilient solution for managing resources without compromising on performance and high availability.

Adaptive UEP and Packet Size Assignment for Scalable Video Transmission over Burst-Error Channels

NASA Astrophysics Data System (ADS)

Lee, Chen-Wei; Yang, Chu-Sing; Su, Yih-Ching

2006-12-01

This work proposes an adaptive unequal error protection (UEP) and packet size assignment scheme for scalable video transmission over a burst-error channel. An analytic model is developed to evaluate the impact of channel bit error rate on the quality of streaming scalable video. A video transmission scheme, which combines the adaptive assignment of packet size with unequal error protection to increase the end-to-end video quality, is proposed. Several distinct scalable video transmission schemes over burst-error channel have been compared, and the simulation results reveal that the proposed transmission schemes can react to varying channel conditions with less and smoother quality degradation.

Scalability enhancement of AODV using local link repairing

NASA Astrophysics Data System (ADS)

Jain, Jyoti; Gupta, Roopam; Bandhopadhyay, T. K.

2014-09-01

Dynamic change in the topology of an ad hoc network makes it difficult to design an efficient routing protocol. Scalability of an ad hoc network is also one of the important criteria of research in this field. Most of the research works in ad hoc network focus on routing and medium access protocols and produce simulation results for limited-size networks. Ad hoc on-demand distance vector (AODV) is one of the best reactive routing protocols. In this article, modified routing protocols based on local link repairing of AODV are proposed. Method of finding alternate routes for next-to-next node is proposed in case of link failure. These protocols are beacon-less, means periodic hello message is removed from the basic AODV to improve scalability. Few control packet formats have been changed to accommodate suggested modification. Proposed protocols are simulated to investigate scalability performance and compared with basic AODV protocol. This also proves that local link repairing of proposed protocol improves scalability of the network. From simulation results, it is clear that scalability performance of routing protocol is improved because of link repairing method. We have tested protocols for different terrain area with approximate constant node densities and different traffic load.

Wanted: Scalable Tracers for Diffusion Measurements

PubMed Central

2015-01-01

Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core–shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say “reinforced Ficoll” or “reinforced hyperbranched polyglycerol.” PMID:25319586

A malicious pattern detection engine for embedded security systems in the Internet of Things.

PubMed

Oh, Doohwan; Kim, Deokho; Ro, Won Woo

2014-12-16

With the emergence of the Internet of Things (IoT), a large number of physical objects in daily life have been aggressively connected to the Internet. As the number of objects connected to networks increases, the security systems face a critical challenge due to the global connectivity and accessibility of the IoT. However, it is difficult to adapt traditional security systems to the objects in the IoT, because of their limited computing power and memory size. In light of this, we present a lightweight security system that uses a novel malicious pattern-matching engine. We limit the memory usage of the proposed system in order to make it work on resource-constrained devices. To mitigate performance degradation due to limitations of computation power and memory, we propose two novel techniques, auxiliary shifting and early decision. Through both techniques, we can efficiently reduce the number of matching operations on resource-constrained systems. Experiments and performance analyses show that our proposed system achieves a maximum speedup of 2.14 with an IoT object and provides scalable performance for a large number of patterns.

High fidelity nanopatterning of proteins onto well-defined surfaces through subtractive contact printing

PubMed Central

García, José R.; Singh, Ankur; García, Andrés J.

2016-01-01

In the pursuit to develop enhanced technologies for cellular bioassays as well as understand single cell interactions with its underlying substrate, the field of biotechnology has extensively utilized lithographic techniques to spatially pattern proteins onto surfaces in user-defined geometries. Microcontact printing (μCP) remains an incredibly useful patterning method due to its inexpensive nature, scalability, and the lack of considerable use of specialized clean room equipment. However, as new technologies emerge that necessitate various nano-sized areas of deposited proteins, traditional microcontact printing methods may not be able to supply users with the needed resolution size. Recently, our group developed a modified “subtractive microcontact printing” method which still retains many of the benefits offered by conventional μCP. Using this technique, we have been able to reach resolution sizes of fibronectin as small as 250 nm in largely spaced arrays for cell culture. In this communication, we present a detailed description of our subtractive μCP procedure that expands on many of the little tips and tricks that together make this procedure an easy and effective method for controlling protein patterning. PMID:24439290

Access and Use: Improving Digital Multimedia Consumer Health Information.

PubMed

Thomas, Alex

2016-01-01

This project enabled novel organisational insight into the comparative utility of a portfolio of consumer health information content, by measuring patterns of attrition (abandonment) in content use. The project used as a case study the event activity log of a fully automated digital information kiosk, located in a community health facility. Direct measurements of the duration of content use were derived from the user interface activity recorded in the kiosk log, thus avoiding issues in using other approaches to collecting this type of data, such as sampling and observer bias. The distribution patterns of 1,383 durations of observed abandonments of use for twenty-eight discrete modules of health information content were visualised using Kaplan-Meir survival plots. Clear patterns of abandonment of content use were exhibited. The method of analysis is cost-effective, scalable and provides deep insight into the utility of health promotion content. The impact on the content producers, platform operators and service users is to improve organisational learning and thus increase the confidence in stakeholders that the service is continuously delivering high quality health and wellbeing benefits.

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Statistical modeling of SRAM yield performance and circuit variability

NASA Astrophysics Data System (ADS)

Cheng, Qi; Chen, Yijian

2015-03-01

In this paper, we develop statistical models to investigate SRAM yield performance and circuit variability in the presence of self-aligned multiple patterning (SAMP) process. It is assumed that SRAM fins are fabricated by a positivetone (spacer is line) self-aligned sextuple patterning (SASP) process which accommodates two types of spacers, while gates are fabricated by a more pitch-relaxed self-aligned quadruple patterning (SAQP) process which only allows one type of spacer. A number of possible inverter and SRAM structures are identified and the related circuit multi-modality is studied using the developed failure-probability and yield models. It is shown that SRAM circuit yield is significantly impacted by the multi-modality of fins' spatial variations in a SRAM cell. The sensitivity of 6-transistor SRAM read/write failure probability to SASP process variations is calculated and the specific circuit type with the highest probability to fail in the reading/writing operation is identified. Our study suggests that the 6-transistor SRAM configuration may not be scalable to 7-nm half pitch and more robust SRAM circuit design needs to be researched.

Directed self-assembly of nanorod networks: bringing the top down to the bottom up.

PubMed

Einsle, Joshua F; Scheunert, Gunther; Murphy, Antony; McPhillips, John; Zayats, Anatoly V; Pollard, Robert; Bowman, Robert M

2012-12-21

Self-assembled electrodeposited nanorod materials have been shown to offer an exciting landscape for a wide array of research ranging from nanophotonics through to biosensing and magnetics. However, until now, the scope for site-specific preparation of the nanorods on wafers has been limited to local area definition. Further there is little or no lateral control of nanorod height. In this work we present a scalable method for controlling the growth of the nanorods in the vertical direction as well as their lateral position. A focused ion beam pre-patterns the Au cathode layer prior to the creation of the anodized aluminium oxide (AAO) template on top. When the pre-patterning is of the same dimension as the pore spacing of the AAO template, lines of single nanorods are successfully grown. Further, for sub-200 nm wide features, a relationship between the nanorod height and distance from the non-patterned cathode can be seen to follow a quadratic growth rate obeying Faraday's law of electrodeposition. This facilitates lateral control of nanorod height combined with localized growth of the nanorods.

Software-based data path for raster-scanned multi-beam mask lithography

NASA Astrophysics Data System (ADS)

Rajagopalan, Archana; Agarwal, Ankita; Buck, Peter; Geller, Paul; Hamaker, H. Christopher; Rao, Nagswara

2016-10-01

According to the 2013 SEMATECH Mask Industry Survey,i roughly half of all photomasks are produced using laser mask pattern generator ("LMPG") lithography. LMPG lithography can be used for all layers at mature technology nodes, and for many non-critical and semi-critical masks at advanced nodes. The extensive use of multi-patterning at the 14-nm node significantly increases the number of critical mask layers, and the transition in wafer lithography from positive tone resist to negative tone resist at the 14-nm design node enables the switch from advanced binary masks back to attenuated phase shifting masks that require second level writes to remove unwanted chrome. LMPG lithography is typically used for second level writes due to its high productivity, absence of charging effects, and versatile non-actinic alignment capability. As multi-patterning use expands from double to triple patterning and beyond, the number of LMPG second level writes increases correspondingly. The desire to reserve the limited capacity of advanced electron beam writers for use when essential is another factor driving the demand for LMPG capacity. The increasing demand for cost-effective productivity has kept most of the laser mask writers ever manufactured running in production, sometimes long past their projected lifespan, and new writers continue to be built based on hardware developed some years ago.ii The data path is a case in point. While state-ofthe- art when first introduced, hardware-based data path systems are difficult to modify or add new features to meet the changing requirements of the market. As data volumes increase, design styles change, and new uses are found for laser writers, it is useful to consider a replacement for this critical subsystem. The availability of low-cost, high-performance, distributed computer systems combined with highly scalable EDA software lends itself well to creating an advanced data path system. EDA software, in routine production today, scales well to hundreds or even thousands of CPU-cores, offering the potential for virtually unlimited capacity. Features available in EDA software such as sizing, scaling, tone reversal, OPC, MPC, rasterization, and others are easily adapted to the requirements of a data path system. This paper presents the motivation, requirements, design and performance of an advanced, scalable software data path system suitable to support multi-beam laser mask lithography.

Trustworthiness and Negative Affect Predict Economic Decision-Making.

PubMed

Nguyen, Christopher M; Koenigs, Michael; Yamada, Torricia H; Teo, Shu Hao; Cavanaugh, Joseph E; Tranel, Daniel; Denburg, Natalie L

2011-09-01

The Ultimatum Game (UG) is a widely used and well-studied laboratory model of economic decision-making. Here, we studied 129 healthy adults and compared demographic (i.e., age, gender, education), cognitive (i.e., intelligence, attention/working memory, speed, language, visuospatial, memory, executive functions), and personality (i.e., "Big Five", positive affect, negative affect) variables between those with a "rational" versus an "irrational" response pattern on the UG. Our data indicated that participants with "rational" UG performance (accepting any offer, no matter the fairness) endorsed higher levels of trust, or the belief in the sincerity and good intentions of others, while participants with "irrational" UG performance (rejecting unfair offers) endorsed higher levels of negative affect, such as anger and contempt. These personality variables were the only ones that differentiated the two response patterns-demographic and cognitive factors did not differ between rational and irrational players. The results indicate that the examination of personality and affect is crucial to our understanding of the individual differences that underlie decision-making.

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

PubMed Central

Lettice, Laura A.; Williamson, Iain; Wiltshire, John H.; Peluso, Silvia; Devenney, Paul S.; Hill, Alison E.; Essafi, Abdelkader; Hagman, James; Mort, Richard; Grimes, Graeme; DeAngelis, Carlo L.; Hill, Robert E.

2012-01-01

Summary Sonic hedgehog (Shh) expression during limb development is crucial for specifying the identity and number of digits. The spatial pattern of Shh expression is restricted to a region called the zone of polarizing activity (ZPA), and this expression is controlled from a long distance by the cis-regulator ZRS. Here, members of two groups of ETS transcription factors are shown to act directly at the ZRS mediating a differential effect on Shh, defining its spatial expression pattern. Occupancy at multiple GABPα/ETS1 sites regulates the position of the ZPA boundary, whereas ETV4/ETV5 binding restricts expression outside the ZPA. The ETS gene family is therefore attributed with specifying the boundaries of the classical ZPA. Two point mutations within the ZRS change the profile of ETS binding and activate Shh expression at an ectopic site in the limb bud. These molecular changes define a pathogenetic mechanism that leads to preaxial polydactyly (PPD). PMID:22340503

A New Perspective for Parkinson's Disease: Circadian Rhythm.

PubMed

Li, Siyue; Wang, Yali; Wang, Fen; Hu, Li-Fang; Liu, Chun-Feng

2017-02-01

Circadian rhythm is manifested by the behavioral and physiological changes from day to night, which is controlled by the pacemaker and its regulator. The former is located at the suprachiasmatic nuclei (SCN) in the anterior hypothalamus, while the latter is composed of clock genes present in all tissues. Circadian desynchronization influences normal patterns of day-night rhythms such as sleep and alertness cycles, rest and activity cycles. Parkinson's disease (PD) exhibits diurnal fluctuations. Circadian dysfunction has been observed in PD patients and animal models, which may result in negative consequences to the homeostasis and even exacerbate the disease progression. Therefore, circadian therapies, including light stimulation, physical activity, dietary and social schedules, may be helpful for PD patients. However, the cellular and molecular mechanisms that underlie the circadian dysfunction in PD remain elusive. Further research on circadian patterns is needed. This article summarizes the existing research on the circadian rhythms in PD, focusing on the clinical symptom variations, molecular changes, as well as the available treatment options.

Microglial brain region-dependent diversity and selective regional sensitivities to ageing

PubMed Central

Grabert, Kathleen; Michoel, Tom; Karavolos, Michail H; Clohisey, Sara; Baillie, J Kenneth; Stevens, Mark P; Freeman, Tom C; Summers, Kim M; McColl, Barry W

2015-01-01

Microglia play critical roles in neural development, homeostasis and neuroinflammation and are increasingly implicated in age-related neurological dysfunction. Neurodegeneration often occurs in disease-specific spatially-restricted patterns, the origins of which are unknown. We performed the first genome-wide analysis of microglia from discrete brain regions across the adult lifespan of the mouse and reveal that microglia have distinct region-dependent transcriptional identities and age in a regionally variable manner. In the young adult brain, differences in bioenergetic and immunoregulatory pathways were the major sources of heterogeneity and suggested that cerebellar and hippocampal microglia exist in a more immune vigilant state. Immune function correlated with regional transcriptional patterns. Augmentation of the distinct cerebellar immunophenotype and a contrasting loss in distinction of the hippocampal phenotype among forebrain regions were key features during ageing. Microglial diversity may enable regionally localised homeostatic functions but could also underlie region-specific sensitivities to microglial dysregulation and involvement in age-related neurodegeneration. PMID:26780511

Navigating north: how body mass and winds shape avian flight behaviours across a North American migratory flyway.

PubMed

Horton, Kyle G; Van Doren, Benjamin M; La Sorte, Frank A; Fink, Daniel; Sheldon, Daniel; Farnsworth, Andrew; Kelly, Jeffrey F

2018-05-07

The migratory patterns of birds have been the focus of ecologists for millennia. What behavioural traits underlie these remarkably consistent movements? Addressing this question is central to advancing our understanding of migratory flight strategies and requires the integration of information across levels of biological organisation, e.g. species to communities. Here, we combine species-specific observations from the eBird citizen-science database with observations aggregated from weather surveillance radars during spring migration in central North America. Our results confirm a core prediction of migration theory at an unprecedented national scale: body mass predicts variation in flight strategies across latitudes, with larger-bodied species flying faster and compensating more for wind drift. We also find evidence that migrants travelling northward earlier in the spring increasingly compensate for wind drift at higher latitudes. This integration of information across biological scales provides new insight into patterns and determinants of broad-scale flight strategies of migratory birds. © 2018 John Wiley & Sons Ltd/CNRS.

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

PubMed

Wallberg, Andreas; Han, Fan; Wellhagen, Gustaf; Dahle, Bjørn; Kawata, Masakado; Haddad, Nizar; Simões, Zilá Luz Paulino; Allsopp, Mike H; Kandemir, Irfan; De la Rúa, Pilar; Pirk, Christian W; Webster, Matthew T

2014-10-01

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system- and sperm motility-related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.

Morphomechanics and Developmental Constraints in the Evolution of Ammonites Shell Form.

PubMed

Erlich, Alexander; Moulton, Derek E; Goriely, Alain; Chirat, Regis

2016-11-01

The idea that physical processes involved in biological development underlie morphogenetic rules and channel morphological evolution has been central to the rise of evolutionary developmental biology. Here, we explore this idea in the context of seashell morphogenesis. We show that a morphomechanical model predicts the effects of variations in shell shape on the ornamental pattern in ammonites, a now extinct group of cephalopods with external chambered shell. Our model shows that several seemingly unrelated characteristics of synchronous, ontogenetic, intraspecific, and evolutionary variations in ornamental patterns among various ammonite species may all be understood from the fact that the mechanical forces underlying the oscillatory behavior of the shell secreting system scale with the cross-sectional curvature of the shell aperture. This simple morphogenetic rule, emerging from biophysical interactions during shell formation, introduced a non-random component in the production of phenotypic variation and channeled the morphological evolution of ammonites over millions of years. As such, it provides a paradigm for the concept of "developmental constraints." © 2016 Wiley Periodicals, Inc.

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces.

PubMed

Wang, Gang; Or, Dani

2014-10-24

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.

Prediction in the Processing of Repair Disfluencies: Evidence from the Visual-World Paradigm

PubMed Central

Lowder, Matthew W.; Ferreira, Fernanda

2016-01-01

Two visual-world eye-tracking experiments investigated the role of prediction in the processing of repair disfluencies (e.g., The chef reached for some salt uh I mean some ketchup…). Experiment 1 showed that listeners were more likely to fixate a critical distractor item (e.g., pepper) during the processing of repair disfluencies compared to the processing of coordination structures (e.g., …some salt and also some ketchup…). Experiment 2 replicated the findings of Experiment 1 for disfluency versus coordination constructions and also showed that the pattern of fixations to the critical distractor for disfluency constructions was similar to the fixation patterns for sentences employing contrastive focus (e.g., …not some salt but rather some ketchup…). The results suggest that similar mechanisms underlie the processing of repair disfluencies and contrastive focus, with listeners generating sets of entities that stand in semantic contrast to the reparandum in the case of disfluencies or the negated entity in the case of contrastive focus. PMID:26866657

MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system.

PubMed

Hur, Matthew; Gistelinck, Charlotte A; Huber, Philippe; Lee, Jane; Thompson, Marjorie H; Monstad-Rios, Adrian T; Watson, Claire J; McMenamin, Sarah K; Willaert, Andy; Parichy, David M; Coucke, Paul; Kwon, Ronald Y

2017-09-08

Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

Direct fitness benefits explain mate preference, but not choice, for similarity in heterozygosity levels.

PubMed

Zandberg, Lies; Gort, Gerrit; van Oers, Kees; Hinde, Camilla A

2017-10-01

Under sexual selection, mate preferences can evolve for traits advertising fitness benefits. Observed mating patterns (mate choice) are often assumed to represent preference, even though they result from the interaction between preference, sampling strategy and environmental factors. Correlating fitness with mate choice instead of preference will therefore lead to confounded conclusions about the role of preference in sexual selection. Here we show that direct fitness benefits underlie mate preferences for genetic characteristics in a unique experiment on wild great tits. In repeated mate preference tests, both sexes preferred mates that had similar heterozygosity levels to themselves, and not those with which they would optimise offspring heterozygosity. In a subsequent field experiment where we cross fostered offspring, foster parents with more similar heterozygosity levels had higher reproductive success, despite the absence of assortative mating patterns. These results support the idea that selection for preference persists despite constraints on mate choice. © 2017 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Respiratory-borne Disease Outbreaks in Populations: Contact Networks and the Spread of Disease

NASA Astrophysics Data System (ADS)

Pourbohloul, Babak; Meyers, Lauren A.; Newman, Mark E. J.; Skowronski, Danuta M.

2005-03-01

A large class of infectious diseases spread through direct person-to-person contact. Traditional ``compartmental'' modeling in epidemiology assumes that in population groups every individual has an equal chance of spreading the disease to every other. The patterns of these contacts, however, tend to be highly heterogeneous. Explicit models of the patterns of contact among individuals in a community, contact network models, underlie a powerful approach to predicting and controlling the spread of such infectious disease and provide detailed and valuable insight into the fate and control of an outbreak. We use contact network epidemiology to predict the impact of various control policies for both a mildly contagious disease such as SARS and a more highly contagious disease such as smallpox. We demonstrate how integrating these tools into public health decision-making should facilitate more rational strategies for managing newly emerging diseases, bioterrorism and pandemic influenza in situations where empirical data are not yet available to guide decision making.

Fiber type-specific afferent nerve activity induced by transient contractions of rat bladder smooth muscle in pathological states

PubMed Central

Kuga, Nahoko; Tanioka, Asao; Hagihara, Koichiro; Kawai, Tomoyuki

2017-01-01

Bladder smooth muscle shows spontaneous phasic contractions, which undergo a variety of abnormal changes depending on pathological conditions. How abnormal contractions affect the activity of bladder afferent nerves remains to be fully tested. In this study, we examined the relationship between transient increases in bladder pressure, representing transient contraction of bladder smooth muscle, and spiking patterns of bladder afferent fibers of the L6 dorsal root, in rat pathological models. All recordings were performed at a bladder pressure of approximately 10 cmH2O by maintaining the degree of bladder filling. In the cyclophosphamide-induced model, both Aδ and C fibers showed increased sensitivity to transient bladder pressure increases. In the prostaglandin E2-induced model, Aδ fibers, but not C fibers, specifically showed overexcitation that was time-locked with transient bladder pressure increases. These fiber type-specific changes in nerve spike patterns may underlie the symptoms of urinary bladder diseases. PMID:29267380

Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum

NASA Astrophysics Data System (ADS)

Bäuerle, Felix K.; Kramar, Mirna; Alim, Karen

2017-11-01

Wounding is a severe impairment of function, especially for an exposed organism like the network-forming true slime mould Physarum polycephalum. The tubular network making up the organism’s body plan is entirely interconnected and shares a common cytoplasm. Oscillatory contractions of the enclosing tube walls drive the shuttle streaming of the cytoplasm. Cytoplasmic flows underlie the reorganization of the network for example by movement toward attractive stimuli or away from repellants. Here, we follow the reorganization of P. polycephalum networks after severe wounding. Spatial mapping of the contraction changes in response to wounding reveal a multi-step pattern. Phases of increased activity alternate with cessation of contractions and stalling of flows, giving rise to coordinated transport and growth at the severing site. Overall, severing surprisingly acts like an attractive stimulus enabling healing of severed tubes. The reproducible cessation of contractions arising during this wound-healing response may open up new venues to investigate the biochemical wiring underlying P. polycephalum’s complex behaviours.

Central Body Fat Distribution Associates with Unfavorable Renal Hemodynamics Independent of Body Mass Index

PubMed Central

Zelle, Dorien M.; Bakker, Stephan J.L.; Navis, Gerjan

2013-01-01

Central distribution of body fat is associated with a higher risk of renal disease, but whether it is the distribution pattern or the overall excess weight that underlies this association is not well understood. Here, we studied the association between waist-to-hip ratio (WHR), which reflects central adiposity, and renal hemodynamics in 315 healthy persons with a mean body mass index (BMI) of 24.9 kg/m2 and a mean 125I-iothalamate GFR of 109 ml/min per 1.73 m2. In multivariate analyses, WHR was associated with lower GFR, lower effective renal plasma flow, and higher filtration fraction, even after adjustment for sex, age, mean arterial pressure, and BMI. Multivariate models produced similar results regardless of whether the hemodynamic measures were indexed to body surface area. Thus, these results suggest that central body fat distribution, independent of BMI, is associated with an unfavorable pattern of renal hemodynamic measures that could underlie the increased renal risk reported in observational studies. PMID:23578944

Multi-protein assemblies underlie the mesoscale organization of the plasma membrane

PubMed Central

Saka, Sinem K.; Honigmann, Alf; Eggeling, Christian; Hell, Stefan W.; Lang, Thorsten; Rizzoli, Silvio O.

2014-01-01

Most proteins have uneven distributions in the plasma membrane. Broadly speaking, this may be caused by mechanisms specific to each protein, or may be a consequence of a general pattern that affects the distribution of all membrane proteins. The latter hypothesis has been difficult to test in the past. Here, we introduce several approaches based on click chemistry, through which we study the distribution of membrane proteins in living cells, as well as in membrane sheets. We found that the plasma membrane proteins form multi-protein assemblies that are long lived (minutes), and in which protein diffusion is restricted. The formation of the assemblies is dependent on cholesterol. They are separated and anchored by the actin cytoskeleton. Specific proteins are preferentially located in different regions of the assemblies, from their cores to their edges. We conclude that the assemblies constitute a basic mesoscale feature of the membrane, which affects the patterning of most membrane proteins, and possibly also their activity. PMID:25060237

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.

PubMed

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z; Li, Yuyang; Xu, Qikai; Naxerova, Kamila; Wooten, Eric C; Bernardi, Ronald J; Martin, Timothy D; Chen, Ting; Leng, Yumei; Liang, Anthony C; Scorsone, Kathleen A; Westbrook, Thomas F; Wong, Kwok-Kin; Elledge, Stephen J

2018-04-05

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors. Copyright © 2018 Elsevier Inc. All rights reserved.

YAP is essential for mechanical force production and epithelial cell proliferation during lung branching morphogenesis

PubMed Central

Lin, Chuwen; Yao, Erica; Zhang, Kuan; Jiang, Xuan; Croll, Stacey; Thompson-Peer, Katherine; Chuang, Pao-Tien

2017-01-01

Branching morphogenesis is a fundamental program for tissue patterning. We show that active YAP, a key mediator of Hippo signaling, is distributed throughout the murine lung epithelium and loss of epithelial YAP severely disrupts branching. Failure to branch is restricted to regions where YAP activity is removed. This suggests that YAP controls local epithelial cell properties. In support of this model, mechanical force production is compromised and cell proliferation is reduced in Yap mutant lungs. We propose that defective force generation and insufficient epithelial cell number underlie the branching defects. Through genomic analysis, we also uncovered a feedback control of pMLC levels, which is critical for mechanical force production, likely through the direct induction of multiple regulators by YAP. Our work provides a molecular pathway that could control epithelial cell properties required for proper morphogenetic movement and pattern formation. DOI: http://dx.doi.org/10.7554/eLife.21130.001 PMID:28323616

Vortex arrays and ciliary tangles underlie the feeding-swimming tradeoff in starfish larvae

NASA Astrophysics Data System (ADS)

Gilpin, William; Prakash, Vivek N.; Prakash, Manu

2016-11-01

Many marine invertebrates have larval stages covered in linear arrays of beating cilia, which propel the animal while simultaneously entraining planktonic prey. These bands are strongly conserved across taxa spanning four major superphyla, and they are responsible for the unusual morphologies of many invertebrates. However, few studies have investigated their underlying hydrodynamics. Here, we study the ciliary bands of starfish larvae, and discover a beautiful pattern of slowly-evolving vortices that surrounds the swimming animals. Closer inspection of the bands reveals unusual ciliary "tangles" analogous to topological defects that break-up and re-form as the animal adjusts its swimming stroke. Quantitative experiments and modeling demonstrate that these vortices create a physical tradeoff between feeding and swimming in heterogenous environments, which manifests as distinct flow patterns or "eigenstrokes" representing each behavior-potentially implicating neuronal control of cilia. This quantitative interplay between larval form and hydrodynamic function generalizes to other invertebrates, and illustrates the potential effects of active boundary conditions in other biological and synthetic systems.

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention

PubMed Central

Yu, Chen; Smith, Linda B.

2016-01-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of the present study is to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention – and the sensory-motor behaviors that underlie it – using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention, and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings – like skills in other sensory-motor domains – emerges from multiple pathways to the same functional end. PMID:27016038

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention.

PubMed

Yu, Chen; Smith, Linda B

2017-02-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of this study was to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention-and the sensory-motor behaviors that underlie it-using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings-like skills in other sensory-motor domains-emerges from multiple pathways to the same functional end. Copyright © 2016 Cognitive Science Society, Inc.

A critical analysis of disease-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig

PubMed Central

Ibeagha-Awemu, Eveline M.; Kgwatalala, Patrick; Ibeagha, Aloysius E.

2008-01-01

Genetic variations through their effects on gene expression and protein function underlie disease susceptibility in farm animal species. The variations are in the form of single nucleotide polymorphisms, deletions/insertions of nucleotides or whole genes, gene or whole chromosomal rearrangements, gene duplications, and copy number polymorphisms or variants. They exert varying degrees of effects on gene action, such as substitution of an amino acid for another, shift in reading frame and premature termination of translation, and complete deletion of entire exon(s) or gene(s) in diseased individuals. These factors influence gene function by affecting mRNA splicing pattern or by altering/eliminating protein function. Elucidating the genetic bases of diseases under the control of many genes is very challenging, and it is compounded by several factors, including host × pathogen × environment interactions. In this review, the genetic variations that underlie several diseases of livestock (under monogenic and polygenic control) are analyzed. Also, factors hampering research efforts toward identification of genetic influences on animal disease identification and control are highlighted. A better understanding of the factors analyzed could be better harnessed to effectively identify and control, genetically, livestock diseases. Finally, genetic control of animal diseases can reduce the costs associated with diseases, improve animal welfare, and provide healthy animal products to consumers, and should be given more attention. PMID:18350334

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

PubMed

Rittschof, Clare C; Bukhari, Syed Abbas; Sloofman, Laura G; Troy, Joseph M; Caetano-Anollés, Derek; Cash-Ahmed, Amy; Kent, Molly; Lu, Xiaochen; Sanogo, Yibayiri O; Weisner, Patricia A; Zhang, Huimin; Bell, Alison M; Ma, Jian; Sinha, Saurabh; Robinson, Gene E; Stubbs, Lisa

2014-12-16

Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.

Bioinspired broadband antireflection coatings on GaSb

NASA Astrophysics Data System (ADS)

Min, Wei-Lun; Betancourt, Amaury P.; Jiang, Peng; Jiang, Bin

2008-04-01

We report an inexpensive yet scalable templating technique for fabricating moth-eye antireflection gratings on gallium antimonide substrates. Non-close-packed colloidal monolayers are utilized as etching masks to pattern subwavelength-structured nipple arrays on GaSb. The resulting gratings exhibit superior broadband antireflection properties and thermal stability than conventional multilayer dielectric coatings. The specular reflection of the templated nipple arrays match with the theoretical predictions using a rigorous coupled-wave analysis model. The effect of the nipple shape and size on the antireflection properties has also been investigated by the same model. These biomimetic coatings are of great technological importance in developing efficient thermophotovoltaic cells.

Expanding applications, accuracy, and interpretation of laser speckle contrast imaging of cerebral blood flow

PubMed Central

Kazmi, S M Shams; Richards, Lisa M; Schrandt, Christian J; Davis, Mitchell A; Dunn, Andrew K

2015-01-01

Laser speckle contrast imaging (LSCI) provides a rapid characterization of cortical flow dynamics for functional monitoring of the microcirculation. The technique stems from interactions of laser light with moving particles. These interactions encode the encountered Doppler phenomena within a random interference pattern imaged in widefield, known as laser speckle. Studies of neurovascular function and coupling with LSCI have benefited from the real-time characterization of functional dynamics in the laboratory setting through quantification of perfusion dynamics. While the technique has largely been relegated to acute small animal imaging, its scalability is being assessed and characterized for both chronic and clinical neurovascular imaging. PMID:25944593

Colorimetry Technique for Scalable Characterization of Suspended Graphene.

PubMed

Cartamil-Bueno, Santiago J; Steeneken, Peter G; Centeno, Alba; Zurutuza, Amaia; van der Zant, Herre S J; Houri, Samer

2016-11-09

Previous statistical studies on the mechanical properties of chemical-vapor-deposited (CVD) suspended graphene membranes have been performed by means of measuring individual devices or with techniques that affect the material. Here, we present a colorimetry technique as a parallel, noninvasive, and affordable way of characterizing suspended graphene devices. We exploit Newton's rings interference patterns to study the deformation of a double-layer graphene drum 13.2 μm in diameter when a pressure step is applied. By studying the time evolution of the deformation, we find that filling the drum cavity with air is 2-5 times slower than when it is purged.

Cicada-Wing-Inspired Self-Cleaning Antireflection Coatings on Polymer Substrates.

PubMed

Chen, Ying-Chu; Huang, Zhe-Sheng; Yang, Hongta

2015-11-18

The cicada has transparent wings with remarkable self-cleaning properties and high transmittance over the whole visible spectral range, which is derived from periodic conical structures covering the wing surface. Here we report a scalable self-assembly technique for fabricating multifunctional optical coatings that mimic cicada-wing structures. Spin-coated two-dimensional non-close-packed colloidal crystals are utilized as etching masks to pattern subwavelength-structured cone arrays directly on polymer substrates. The resulting gratings exhibit broadband antireflection performance and superhydrophobic properties after surface modification. The dependence of the cone shape and size on the antireflective and self-cleaning properties has also been investigated in this study.

Smart integrated microsystems: the energy efficiency challenge (Conference Presentation) (Plenary Presentation)

NASA Astrophysics Data System (ADS)

Benini, Luca

2017-06-01

The "internet of everything" envisions trillions of connected objects loaded with high-bandwidth sensors requiring massive amounts of local signal processing, fusion, pattern extraction and classification. From the computational viewpoint, the challenge is formidable and can be addressed only by pushing computing fabrics toward massive parallelism and brain-like energy efficiency levels. CMOS technology can still take us a long way toward this goal, but technology scaling is losing steam. Energy efficiency improvement will increasingly hinge on architecture, circuits, design techniques such as heterogeneous 3D integration, mixed-signal preprocessing, event-based approximate computing and non-Von-Neumann architectures for scalable acceleration.

Conceptual Architecture for Obtaining Cyber Situational Awareness

DTIC Science & Technology

2014-06-01

1-893723-17-8. [10] SKYBOX SECURITY. Developer´s Guide. Skybox View. Manual.Version 11. 2010. [11] SCALABLE Network. EXata communications...E. Understanding command and control. Washington, D.C.: CCRP Publication Series, 2006. 255 p. ISBN 1-893723-17-8. • [10] SKYBOX SECURITY. Developer...s Guide. Skybox View. Manual.Version 11. 2010. • [11] SCALABLE Network. EXata communications simulation platform. Available: <http://www.scalable

Scalable Power-Component Models for Concept Testing

DTIC Science & Technology

2011-08-17

Scalable Power-Component Models for Concept Testing, Mazzola, et al . UNCLASSIFIED: Dist A. Approved for public release 2011 NDIA GROUND VEHICLE...Power-Component Models for Concept Testing, Mazzola, et al . UNCLASSIFIED: Dist A. Approved for public release Page 2 of 8 technology that has yet...Technology Symposium (GVSETS) Scalable Power-Component Models for Concept Testing, Mazzola, et al . UNCLASSIFIED: Dist A. Approved for public release

TriG: Next Generation Scalable Spaceborne GNSS Receiver

NASA Technical Reports Server (NTRS)

Tien, Jeffrey Y.; Okihiro, Brian Bachman; Esterhuizen, Stephan X.; Franklin, Garth W.; Meehan, Thomas K.; Munson, Timothy N.; Robison, David E.; Turbiner, Dmitry; Young, Lawrence E.

2012-01-01

TriG is the next generation NASA scalable space GNSS Science Receiver. It will track all GNSS and additional signals (i.e. GPS, GLONASS, Galileo, Compass and Doris). Scalable 3U architecture and fully software and firmware recofigurable, enabling optimization to meet specific mission requirements. TriG GNSS EM is currently undergoing testing and is expected to complete full performance testing later this year.

A comparative analysis of sex change in Labridae supports the size advantage hypothesis.

PubMed

Kazancioğlu, Erem; Alonzo, Suzanne H

2010-08-01

The size advantage hypothesis (SAH) predicts that the rate of increase in male and female fitness with size (the size advantage) drives the evolution of sequential hermaphroditism or sex change. Despite qualitative agreement between empirical patterns and SAH, only one comparative study tested SAH quantitatively. Here, we perform the first comparative analysis of sex change in Labridae, a group of hermaphroditic and dioecious (non-sex changer) fish with several model sex-changing species. We also estimate, for the first time, rates of evolutionary transitions between sex change and dioecy. Our analyses support SAH and indicate that the evolution of hermaphroditism is correlated to the size advantage. Furthermore, we find that transitions from sex change to dioecy are less likely under stronger size advantage. We cannot determine, however, how the size advantage affects transitions from dioecy to sex change. Finally, contrary to what is generally expected, we find that transitions from dioecy to sex change are more likely than transitions from sex change to dioecy. The similarity of sexual differentiation in hermaphroditic and dioecious labrids might underlie this pattern. We suggest that elucidating the developmental basis of sex change is critical to predict and explain patterns of the evolutionary history of sequential hermaphroditism.

HLA-C expression pattern is spatially different between psoriasis and eczema skin lesions.

PubMed

Carlén, Lina; Sakuraba, Kazuko; Ståhle, Mona; Sánchez, Fabio

2007-02-01

Interactions between genetic and environmental factors underlie the immune dysregulation and keratinocyte abnormalities that characterize psoriasis. Among known psoriasis susceptibility loci (PSORS), PSORS1 on chromosome 6 has the strongest association to disease. Altered expression of some PSORS1 candidate genes has been reported but little is known about HLA-C expression in psoriasis. This study compared expression of major histocompatibility complex class Ia and HLA-C in psoriasis, allergic contact eczema, and normal skin. Although HLA-C was abundant in protein extracts from both eczema and psoriasis, a consistent and intriguing difference in the expression pattern was observed; strong immunoreactivity in the basal cell layer, polarized towards the basement membrane in psoriasis, whereas in eczema lesions HLA-C immunostaining was present mostly in suprabasal cells. Inflammatory cells in the dermis were strongly stained in both diseases. Normal skin epithelium showed less intense but similar HLA-C staining as eczema lesions. HLA class Ia expression overall resembled that of HLA-C in all samples. The distinct HLA-C expression patterns in psoriasis and eczema suggest a functional role in the specific psoriasis immune response and not only a general feature of inflammation.

Microwave assisted scalable synthesis of titanium ferrite nanomaterials

NASA Astrophysics Data System (ADS)

Shukla, Abhishek; Bhardwaj, Abhishek K.; Singh, S. C.; Uttam, K. N.; Gautam, Nisha; Himanshu, A. K.; Shah, Jyoti; Kotnala, R. K.; Gopal, R.

2018-04-01

Titanium ferrite magnetic nanomaterials are synthesized by one-step, one pot, and scalable method assisted by microwave radiation. Effects of titanium content and microwave exposure time on size, shape, morphology, yield, bonding nature, crystalline structure, and magnetic properties of titanium ferrite nanomaterials are studied. As-synthesized nanomaterials are characterized by X-ray diffraction (XRD), ultraviolet-visible absorption spectroscopy (UV-Vis), attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), Raman spectroscopy, transmission electron microscopy (TEM), and vibrating sample magnetometer measurements. XRD measurements depict the presence of two phases of titanium ferrite into the same sample, where crystallite size increases from ˜33 nm to 37 nm with the increase in titanium concentration. UV-Vis measurement showed broad spectrum in the spectral range of 250-600 nm which reveals that its characteristic peaks lie between ultraviolet and visible region; ATR-FTIR and Raman measurements predict iron-titanium oxide structures that are consistent with XRD results. The micrographs of TEM and selected area electron diffraction patterns show formation of hexagonal shaped particles with a high degree of crystallinity and presence of multi-phase. Energy dispersive spectroscopy measurements confirm that Ti:Fe compositional mass ratio can be controlled by tuning synthesis conditions. Increase of Ti defects into titanium ferrite lattice, either by increasing titanium precursor or by increasing exposure time, enhances its magnetic properties.

Exploiting NASA's Cumulus Earth Science Cloud Archive with Services and Computation

NASA Astrophysics Data System (ADS)

Pilone, D.; Quinn, P.; Jazayeri, A.; Schuler, I.; Plofchan, P.; Baynes, K.; Ramachandran, R.

2017-12-01

NASA's Earth Observing System Data and Information System (EOSDIS) houses nearly 30PBs of critical Earth Science data and with upcoming missions is expected to balloon to between 200PBs-300PBs over the next seven years. In addition to the massive increase in data collected, researchers and application developers want more and faster access - enabling complex visualizations, long time-series analysis, and cross dataset research without needing to copy and manage massive amounts of data locally. NASA has started prototyping with commercial cloud providers to make this data available in elastic cloud compute environments, allowing application developers direct access to the massive EOSDIS holdings. In this talk we'll explain the principles behind the archive architecture and share our experience of dealing with large amounts of data with serverless architectures including AWS Lambda, the Elastic Container Service (ECS) for long running jobs, and why we dropped thousands of lines of code for AWS Step Functions. We'll discuss best practices and patterns for accessing and using data available in a shared object store (S3) and leveraging events and message passing for sophisticated and highly scalable processing and analysis workflows. Finally we'll share capabilities NASA and cloud services are making available on the archives to enable massively scalable analysis and computation in a variety of formats and tools.

A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

DOE PAGES

Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; ...

2013-01-01

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in amore » 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.« less

Large Scale Triboelectric Nanogenerator and Self-Powered Pressure Sensor Array Using Low Cost Roll-to-Roll UV Embossing

PubMed Central

Dhakar, Lokesh; Gudla, Sudeep; Shan, Xuechuan; Wang, Zhiping; Tay, Francis Eng Hock; Heng, Chun-Huat; Lee, Chengkuo

2016-01-01

Triboelectric nanogenerators (TENGs) have emerged as a potential solution for mechanical energy harvesting over conventional mechanisms such as piezoelectric and electromagnetic, due to easy fabrication, high efficiency and wider choice of materials. Traditional fabrication techniques used to realize TENGs involve plasma etching, soft lithography and nanoparticle deposition for higher performance. But lack of truly scalable fabrication processes still remains a critical challenge and bottleneck in the path of bringing TENGs to commercial production. In this paper, we demonstrate fabrication of large scale triboelectric nanogenerator (LS-TENG) using roll-to-roll ultraviolet embossing to pattern polyethylene terephthalate sheets. These LS-TENGs can be used to harvest energy from human motion and vehicle motion from embedded devices in floors and roads, respectively. LS-TENG generated a power density of 62.5 mW m−2. Using roll-to-roll processing technique, we also demonstrate a large scale triboelectric pressure sensor array with pressure detection sensitivity of 1.33 V kPa−1. The large scale pressure sensor array has applications in self-powered motion tracking, posture monitoring and electronic skin applications. This work demonstrates scalable fabrication of TENGs and self-powered pressure sensor arrays, which will lead to extremely low cost and bring them closer to commercial production. PMID:26905285

Photoreactive elastin-like proteins for use as versatile bioactive materials and surface coatings

PubMed Central

Raphel, Jordan; Parisi-Amon, Andreina; Heilshorn, Sarah

2012-01-01

Photocrosslinkable, protein-engineered biomaterials combine a rapid, controllable, cytocompatible crosslinking method with a modular design strategy to create a new family of bioactive materials. These materials have a wide range of biomedical applications, including the development of bioactive implant coatings, drug delivery vehicles, and tissue engineering scaffolds. We present the successful functionalization of a bioactive elastin-like protein with photoreactive diazirine moieties. Scalable synthesis is achieved using a standard recombinant protein expression host followed by site-specific modification of lysine residues with a heterobifunctional N-hydroxysuccinimide ester-diazirine crosslinker. The resulting biomaterial is demonstrated to be processable by spin coating, drop casting, soft lithographic patterning, and mold casting to fabricate a variety of two- and three-dimensional photocrosslinked biomaterials with length scales spanning the nanometer to millimeter range. Protein thin films proved to be highly stable over a three-week period. Cell-adhesive functional domains incorporated into the engineered protein materials were shown to remain active post-photo-processing. Human adipose-derived stem cells achieved faster rates of cell adhesion and larger spread areas on thin films of the engineered protein compared to control substrates. The ease and scalability of material production, processing versatility, and modular bioactive functionality make this recombinantly engineered protein an ideal candidate for the development of novel biomaterial coatings, films, and scaffolds. PMID:23015764

Photoreactive elastin-like proteins for use as versatile bioactive materials and surface coatings.

PubMed

Raphel, Jordan; Parisi-Amon, Andreina; Heilshorn, Sarah

2012-10-07

Photocrosslinkable, protein-engineered biomaterials combine a rapid, controllable, cytocompatible crosslinking method with a modular design strategy to create a new family of bioactive materials. These materials have a wide range of biomedical applications, including the development of bioactive implant coatings, drug delivery vehicles, and tissue engineering scaffolds. We present the successful functionalization of a bioactive elastin-like protein with photoreactive diazirine moieties. Scalable synthesis is achieved using a standard recombinant protein expression host followed by site-specific modification of lysine residues with a heterobifunctional N-hydroxysuccinimide ester-diazirine crosslinker. The resulting biomaterial is demonstrated to be processable by spin coating, drop casting, soft lithographic patterning, and mold casting to fabricate a variety of two- and three-dimensional photocrosslinked biomaterials with length scales spanning the nanometer to millimeter range. Protein thin films proved to be highly stable over a three-week period. Cell-adhesive functional domains incorporated into the engineered protein materials were shown to remain active post-photo-processing. Human adipose-derived stem cells achieved faster rates of cell adhesion and larger spread areas on thin films of the engineered protein compared to control substrates. The ease and scalability of material production, processing versatility, and modular bioactive functionality make this recombinantly engineered protein an ideal candidate for the development of novel biomaterial coatings, films, and scaffolds.

Different evolutionary pathways underlie the morphology of wrist bones in hominoids

PubMed Central

2013-01-01

Background The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context. We identify morphological features that principally characterize primate – and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones – the scaphoid, lunate, triquetrum, capitate and hamate – are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Result Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Conclusions Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist bones. These results exemplify a degree of evolutionary and functional independence across different wrist bones, the potential evolvability of skeletal morphology, and help to contextualize the postcranial mosaicism observed in the hominin fossil record. PMID:24148262

Floral heterochrony promotes flexibility of reproductive strategies in the morphologically homogeneous genus Eugenia (Myrtaceae).

PubMed

Vasconcelos, Thais N C; Lucas, Eve J; Faria, Jair E Q; Prenner, Gerhard

2018-01-25

Comparative floral ontogeny represents a valuable tool to understand angiosperm evolution. Such an approach may elucidate subtle changes in development that discretely modify floral architecture and underlie reproductive lability in groups with superficial homogeneous morphology. This study presents a comparative survey of floral development in Eugenia (Myrtaceae), one of the largest genera of angiosperms, and shows how previously undocumented ontogenetic trends help to explain the evolution of its megadiversity in contrast to its apparent flower uniformity. Using scanning electron microscopy, selected steps of the floral ontogeny of a model species (Eugenia punicifolia) are described and compared with 20 further species representing all ten major clades in the Eugenia phylogenetic tree. Additional floral trait data are contrasted for correlation analysis and character reconstructions performed against the Myrtaceae phylogenetic tree. Eugenia flowers show similar organ arrangement patterns: radially symmetrical, (most commonly) tetramerous flowers with variable numbers of stamens and ovules. Despite a similar general organization, heterochrony is evident from size differences between tissues and structures at similar developmental stages. These differences underlie variable levels of investment in protection, subtle modifications to symmetry, herkogamic effects and independent androecium and gynoecium variation, producing a wide spectrum of floral display and contributing to fluctuations in fitness. During Eugenia's bud development, the hypanthium (as defined here) is completely covered by stamen primordia, unusual in other Myrtaceae. This is the likely plesiomorphic state for Myrteae and may have represented a key evolutionary novelty in the tribe. Floral evolution in Eugenia depends on heterochronic patterns rather than changes in complexity to promote flexibility in floral strategies. The successful early establishment of Myrteae, previously mainly linked to the key innovation of fleshy fruit, may also have benefitted from changes in flower structure. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Optimal bit allocation for hybrid scalable/multiple-description video transmission over wireless channels

NASA Astrophysics Data System (ADS)

Jubran, Mohammad K.; Bansal, Manu; Kondi, Lisimachos P.

2006-01-01

In this paper, we consider the problem of optimal bit allocation for wireless video transmission over fading channels. We use a newly developed hybrid scalable/multiple-description codec that combines the functionality of both scalable and multiple-description codecs. It produces a base layer and multiple-description enhancement layers. Any of the enhancement layers can be decoded (in a non-hierarchical manner) with the base layer to improve the reconstructed video quality. Two different channel coding schemes (Rate-Compatible Punctured Convolutional (RCPC)/Cyclic Redundancy Check (CRC) coding and, product code Reed Solomon (RS)+RCPC/CRC coding) are used for unequal error protection of the layered bitstream. Optimal allocation of the bitrate between source and channel coding is performed for discrete sets of source coding rates and channel coding rates. Experimental results are presented for a wide range of channel conditions. Also, comparisons with classical scalable coding show the effectiveness of using hybrid scalable/multiple-description coding for wireless transmission.

Performances of the PIPER scalable child human body model in accident reconstruction

PubMed Central

Giordano, Chiara; Kleiven, Svein

2017-01-01

Human body models (HBMs) have the potential to provide significant insights into the pediatric response to impact. This study describes a scalable/posable approach to perform child accident reconstructions using the Position and Personalize Advanced Human Body Models for Injury Prediction (PIPER) scalable child HBM of different ages and in different positions obtained by the PIPER tool. Overall, the PIPER scalable child HBM managed reasonably well to predict the injury severity and location of the children involved in real-life crash scenarios documented in the medical records. The developed methodology and workflow is essential for future work to determine child injury tolerances based on the full Child Advanced Safety Project for European Roads (CASPER) accident reconstruction database. With the workflow presented in this study, the open-source PIPER scalable HBM combined with the PIPER tool is also foreseen to have implications for improved safety designs for a better protection of children in traffic accidents. PMID:29135997

Power-Scalable Blue-Green Bessel Beams

DTIC Science & Technology

2016-02-23

19b. TELEPHONE NUMBER (Include area code) 02/23/2016 Final Technical JAN 2011 - DEC 2013 Power-Scalable Blue -Green Bessel Beams Siddharth Ramachandran...fiber lasers, non-traditional emission wavelengths, high-power blue -green tunabel lasers U U U SAR 11 Siddharth Ramachandran 617-353-9811 1 Power...Scalable Blue -Green Bessel Beams Siddharth Ramachandran Photonics Center, Boston University, 8 Saint Mary’s Street, Boston, MA 02215 phone: (617) 353

Discretized Streams: A Fault-Tolerant Model for Scalable Stream Processing

DTIC Science & Technology

2012-12-14

Discretized Streams: A Fault-Tolerant Model for Scalable Stream Processing Matei Zaharia Tathagata Das Haoyuan Li Timothy Hunter Scott Shenker Ion...SUBTITLE Discretized Streams: A Fault-Tolerant Model for Scalable Stream Processing 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...time. However, current programming models for distributed stream processing are relatively low-level often leaving the user to worry about consistency of

Modular Universal Scalable Ion-trap Quantum Computer

DTIC Science & Technology

2016-06-02

SECURITY CLASSIFICATION OF: The main goal of the original MUSIQC proposal was to construct and demonstrate a modular and universally- expandable ion...Distribution Unlimited UU UU UU UU 02-06-2016 1-Aug-2010 31-Jan-2016 Final Report: Modular Universal Scalable Ion-trap Quantum Computer The views...P.O. Box 12211 Research Triangle Park, NC 27709-2211 Ion trap quantum computation, scalable modular architectures REPORT DOCUMENTATION PAGE 11

Scalable L-infinite coding of meshes.

PubMed

Munteanu, Adrian; Cernea, Dan C; Alecu, Alin; Cornelis, Jan; Schelkens, Peter

2010-01-01

The paper investigates the novel concept of local-error control in mesh geometry encoding. In contrast to traditional mesh-coding systems that use the mean-square error as target distortion metric, this paper proposes a new L-infinite mesh-coding approach, for which the target distortion metric is the L-infinite distortion. In this context, a novel wavelet-based L-infinite-constrained coding approach for meshes is proposed, which ensures that the maximum error between the vertex positions in the original and decoded meshes is lower than a given upper bound. Furthermore, the proposed system achieves scalability in L-infinite sense, that is, any decoding of the input stream will correspond to a perfectly predictable L-infinite distortion upper bound. An instantiation of the proposed L-infinite-coding approach is demonstrated for MESHGRID, which is a scalable 3D object encoding system, part of MPEG-4 AFX. In this context, the advantages of scalable L-infinite coding over L-2-oriented coding are experimentally demonstrated. One concludes that the proposed L-infinite mesh-coding approach guarantees an upper bound on the local error in the decoded mesh, it enables a fast real-time implementation of the rate allocation, and it preserves all the scalability features and animation capabilities of the employed scalable mesh codec.

Scalability of grid- and subbasin-based land surface modeling approaches for hydrologic simulations

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

Tesfa, Teklu K.; Ruby Leung, L.; Huang, Maoyi

2014-03-27

This paper investigates the relative merits of grid- and subbasin-based land surface modeling approaches for hydrologic simulations, with a focus on their scalability (i.e., abilities to perform consistently across a range of spatial resolutions) in simulating runoff generation. Simulations produced by the grid- and subbasin-based configurations of the Community Land Model (CLM) are compared at four spatial resolutions (0.125o, 0.25o, 0.5o and 1o) over the topographically diverse region of the U.S. Pacific Northwest. Using the 0.125o resolution simulation as the “reference”, statistical skill metrics are calculated and compared across simulations at 0.25o, 0.5o and 1o spatial resolutions of each modelingmore » approach at basin and topographic region levels. Results suggest significant scalability advantage for the subbasin-based approach compared to the grid-based approach for runoff generation. Basin level annual average relative errors of surface runoff at 0.25o, 0.5o, and 1o compared to 0.125o are 3%, 4%, and 6% for the subbasin-based configuration and 4%, 7%, and 11% for the grid-based configuration, respectively. The scalability advantages of the subbasin-based approach are more pronounced during winter/spring and over mountainous regions. The source of runoff scalability is found to be related to the scalability of major meteorological and land surface parameters of runoff generation. More specifically, the subbasin-based approach is more consistent across spatial scales than the grid-based approach in snowfall/rainfall partitioning, which is related to air temperature and surface elevation. Scalability of a topographic parameter used in the runoff parameterization also contributes to improved scalability of the rain driven saturated surface runoff component, particularly during winter. Hence this study demonstrates the importance of spatial structure for multi-scale modeling of hydrological processes, with implications to surface heat fluxes in coupled land-atmosphere modeling.« less

Value Contestations in Development Intervention: Community Development and Sustainable Livelihoods Approaches.

ERIC Educational Resources Information Center

Arce, Alberto

2003-01-01

Both community development and sustainable livelihood approaches ignore value contestations that underlie people's interests and experiences. A case from Bolivia demonstrates that local values, social relations, actions, and language strategies must underlie policy and method in development. (Contains 28 references.) (SK)

Multi-Purpose, Application-Centric, Scalable I/O Proxy Application

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

Miller, M. C.

2015-06-15

MACSio is a Multi-purpose, Application-Centric, Scalable I/O proxy application. It is designed to support a number of goals with respect to parallel I/O performance testing and benchmarking including the ability to test and compare various I/O libraries and I/O paradigms, to predict scalable performance of real applications and to help identify where improvements in I/O performance can be made within the HPC I/O software stack.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

PubMed

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig's scalability over many computing nodes and illustrate its use with example scripts. Available under the open source MIT license at http://sourceforge.net/projects/seqpig/

Scalable Implementation of Finite Elements by NASA _ Implicit (ScIFEi)

NASA Technical Reports Server (NTRS)

Warner, James E.; Bomarito, Geoffrey F.; Heber, Gerd; Hochhalter, Jacob D.

2016-01-01

Scalable Implementation of Finite Elements by NASA (ScIFEN) is a parallel finite element analysis code written in C++. ScIFEN is designed to provide scalable solutions to computational mechanics problems. It supports a variety of finite element types, nonlinear material models, and boundary conditions. This report provides an overview of ScIFEi (\\Sci-Fi"), the implicit solid mechanics driver within ScIFEN. A description of ScIFEi's capabilities is provided, including an overview of the tools and features that accompany the software as well as a description of the input and output le formats. Results from several problems are included, demonstrating the efficiency and scalability of ScIFEi by comparing to finite element analysis using a commercial code.

Scalable Motion Estimation Processor Core for Multimedia System-on-Chip Applications

NASA Astrophysics Data System (ADS)

Lai, Yeong-Kang; Hsieh, Tian-En; Chen, Lien-Fei

2007-04-01

In this paper, we describe a high-throughput and scalable motion estimation processor architecture for multimedia system-on-chip applications. The number of processing elements (PEs) is scalable according to the variable algorithm parameters and the performance required for different applications. Using the PE rings efficiently and an intelligent memory-interleaving organization, the efficiency of the architecture can be increased. Moreover, using efficient on-chip memories and a data management technique can effectively decrease the power consumption and memory bandwidth. Techniques for reducing the number of interconnections and external memory accesses are also presented. Our results demonstrate that the proposed scalable PE-ringed architecture is a flexible and high-performance processor core in multimedia system-on-chip applications.

An MPI-based MoSST core dynamics model

NASA Astrophysics Data System (ADS)

Jiang, Weiyuan; Kuang, Weijia

2008-09-01

Distributed systems are among the main cost-effective and expandable platforms for high-end scientific computing. Therefore scalable numerical models are important for effective use of such systems. In this paper, we present an MPI-based numerical core dynamics model for simulation of geodynamo and planetary dynamos, and for simulation of core-mantle interactions. The model is developed based on MPI libraries. Two algorithms are used for node-node communication: a "master-slave" architecture and a "divide-and-conquer" architecture. The former is easy to implement but not scalable in communication. The latter is scalable in both computation and communication. The model scalability is tested on Linux PC clusters with up to 128 nodes. This model is also benchmarked with a published numerical dynamo model solution.

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

Shamis, Pavel; Graham, Richard L; Gorentla Venkata, Manjunath

The scalability and performance of collective communication operations limit the scalability and performance of many scientific applications. This paper presents two new blocking and nonblocking Broadcast algorithms for communicators with arbitrary communication topology, and studies their performance. These algorithms benefit from increased concurrency and a reduced memory footprint, making them suitable for use on large-scale systems. Measuring small, medium, and large data Broadcasts on a Cray-XT5, using 24,576 MPI processes, the Cheetah algorithms outperform the native MPI on that system by 51%, 69%, and 9%, respectively, at the same process count. These results demonstrate an algorithmic approach to the implementationmore » of the important class of collective communications, which is high performing, scalable, and also uses resources in a scalable manner.« less

Next Generation Non-Vacuum, Maskless, Low Temperature Nanoparticle Ink Laser Digital Direct Metal Patterning for a Large Area Flexible Electronics

PubMed Central

Yeo, Junyeob; Hong, Sukjoon; Lee, Daehoo; Hotz, Nico; Lee, Ming-Tsang; Grigoropoulos, Costas P.; Ko, Seung Hwan

2012-01-01

Flexible electronics opened a new class of future electronics. The foldable, light and durable nature of flexible electronics allows vast flexibility in applications such as display, energy devices and mobile electronics. Even though conventional electronics fabrication methods are well developed for rigid substrates, direct application or slight modification of conventional processes for flexible electronics fabrication cannot work. The future flexible electronics fabrication requires totally new low-temperature process development optimized for flexible substrate and it should be based on new material too. Here we present a simple approach to developing a flexible electronics fabrication without using conventional vacuum deposition and photolithography. We found that direct metal patterning based on laser-induced local melting of metal nanoparticle ink is a promising low-temperature alternative to vacuum deposition– and photolithography-based conventional metal patterning processes. The “digital” nature of the proposed direct metal patterning process removes the need for expensive photomask and allows easy design modification and short turnaround time. This new process can be extremely useful for current small-volume, large-variety manufacturing paradigms. Besides, simple, scalable, fast and low-temperature processes can lead to cost-effective fabrication methods on a large-area polymer substrate. The developed process was successfully applied to demonstrate high-quality Ag patterning (2.1 µΩ·cm) and high-performance flexible organic field effect transistor arrays. PMID:22900011

Next generation non-vacuum, maskless, low temperature nanoparticle ink laser digital direct metal patterning for a large area flexible electronics.

PubMed

Yeo, Junyeob; Hong, Sukjoon; Lee, Daehoo; Hotz, Nico; Lee, Ming-Tsang; Grigoropoulos, Costas P; Ko, Seung Hwan

2012-01-01

Flexible electronics opened a new class of future electronics. The foldable, light and durable nature of flexible electronics allows vast flexibility in applications such as display, energy devices and mobile electronics. Even though conventional electronics fabrication methods are well developed for rigid substrates, direct application or slight modification of conventional processes for flexible electronics fabrication cannot work. The future flexible electronics fabrication requires totally new low-temperature process development optimized for flexible substrate and it should be based on new material too. Here we present a simple approach to developing a flexible electronics fabrication without using conventional vacuum deposition and photolithography. We found that direct metal patterning based on laser-induced local melting of metal nanoparticle ink is a promising low-temperature alternative to vacuum deposition- and photolithography-based conventional metal patterning processes. The "digital" nature of the proposed direct metal patterning process removes the need for expensive photomask and allows easy design modification and short turnaround time. This new process can be extremely useful for current small-volume, large-variety manufacturing paradigms. Besides, simple, scalable, fast and low-temperature processes can lead to cost-effective fabrication methods on a large-area polymer substrate. The developed process was successfully applied to demonstrate high-quality Ag patterning (2.1 µΩ·cm) and high-performance flexible organic field effect transistor arrays.

Direct Interactions Between Gli3, Wnt8b, and Fgfs Underlie Patterning of the Dorsal Telencephalon.

PubMed

Hasenpusch-Theil, Kerstin; Watson, Julia A; Theil, Thomas

2017-02-01

A key step in the development of the cerebral cortex is a patterning process, which subdivides the telencephalon into several molecularly distinct domains and is critical for cortical arealization. This process is dependent on a complex network of interactions between signaling molecules of the Fgf and Wnt gene families and the Gli3 transcription factor gene, but a better knowledge of the molecular basis of the interplay between these factors is required to gain a deeper understanding of the genetic circuitry underlying telencephalic patterning. Using DNA-binding and reporter gene assays, we here investigate the possibility that Gli3 and these signaling molecules interact by directly regulating each other's expression. We show that Fgf signaling is required for Wnt8b enhancer activity in the cortical hem, whereas Wnt/β-catenin signaling represses Fgf17 forebrain enhancer activity. In contrast, Fgf and Wnt/β-catenin signaling cooperate to regulate Gli3 expression. Taken together, these findings indicate that mutual interactions between Gli3, Wnt8b, and Fgf17 are crucial elements of the balance between these factors thereby conferring robustness to the patterning process. Hence, our study provides a framework for understanding the genetic circuitry underlying telencephalic patterning and how defects in this process can affect the formation of cortical areas. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Global biogeography of human infectious diseases.

PubMed

Murray, Kris A; Preston, Nicholas; Allen, Toph; Zambrana-Torrelio, Carlos; Hosseini, Parviez R; Daszak, Peter

2015-10-13

The distributions of most infectious agents causing disease in humans are poorly resolved or unknown. However, poorly known and unknown agents contribute to the global burden of disease and will underlie many future disease risks. Existing patterns of infectious disease co-occurrence could thus play a critical role in resolving or anticipating current and future disease threats. We analyzed the global occurrence patterns of 187 human infectious diseases across 225 countries and seven epidemiological classes (human-specific, zoonotic, vector-borne, non-vector-borne, bacterial, viral, and parasitic) to show that human infectious diseases exhibit distinct spatial grouping patterns at a global scale. We demonstrate, using outbreaks of Ebola virus as a test case, that this spatial structuring provides an untapped source of prior information that could be used to tighten the focus of a range of health-related research and management activities at early stages or in data-poor settings, including disease surveillance, outbreak responses, or optimizing pathogen discovery. In examining the correlates of these spatial patterns, among a range of geographic, epidemiological, environmental, and social factors, mammalian biodiversity was the strongest predictor of infectious disease co-occurrence overall and for six of the seven disease classes examined, giving rise to a striking congruence between global pathogeographic and "Wallacean" zoogeographic patterns. This clear biogeographic signal suggests that infectious disease assemblages remain fundamentally constrained in their distributions by ecological barriers to dispersal or establishment, despite the homogenizing forces of globalization. Pathogeography thus provides an overarching context in which other factors promoting infectious disease emergence and spread are set.

Laser-induced patterns on metals and polymers for biomimetic surface engineering

NASA Astrophysics Data System (ADS)

Kietzig, Anne-Marie; Lehr, Jorge; Matus, Luke; Liang, Fang

2014-03-01

One common feature of many functional surfaces found in nature is their modular composition often exhibiting several length scales. Prominent natural examples for extreme behaviors can be named in various plant leaf (rose, peanut, lotus) or animal toe surfaces (Gecko, tree frog). Influence factors of interest are the surface's chemical composition, its microstructure, its organized or random roughness and hence the resulting surface wetting and adhesion character. Femtosecond (fs) laser micromachining offers a possibility to render all these factors in one single processing step on metallic and polymeric surfaces. Exemplarily, studies on Titanium and PTFE are shown, where the dependence of the resulting feature sizes on lasing intensity is investigated. While Ti surfaces show rigid surface patterns of micrometer scaled features with superimposed nanostructures, PTFE exhibits elastic hairy structures of nanometric diameter, which upon a certain threshold tend to bundle to larger features. Both surface patterns can be adjusted to mimic specific wetting and flow behaviour as seen on natural examples. Therefore, fs-laser micromachining is suggested as an interesting industrially scalable technique to pattern and fine-tune the surface wettability of a surface to the desired extends in one process step. Possible applications can be seen with surfaces, which require specific wetting, fouling, icing, friction or cell adhesion behaviour.

Cognitive Processes that Underlie Mathematical Precociousness in Young Children

ERIC Educational Resources Information Center

Swanson, H. Lee

2006-01-01

The working memory (WM) processes that underlie young children's (ages 6-8 years) mathematical precociousness were examined. A battery of tests that assessed components of WM (phonological loop, visual-spatial sketchpad, and central executive), naming speed, random generation, and fluency was administered to mathematically precocious and…

EUV patterning using CAR or MOX photoresist at low dose exposure for sub 36nm pitch

NASA Astrophysics Data System (ADS)

Thibaut, Sophie; Raley, Angélique; Lazarrino, Frederic; Mao, Ming; De Simone, Danilo; Piumi, Daniele; Barla, Kathy; Ko, Akiteru; Metz, Andrew; Kumar, Kaushik; Biolsi, Peter

2018-04-01

The semiconductor industry has been pushing the limits of scalability by combining 193nm immersion lithography with multi-patterning techniques for several years. Those integrations have been declined in a wide variety of options to lower their cost but retain their inherent variability and process complexity. EUV lithography offers a much desired path that allows for direct print of line and space at 36nm pitch and below and effectively addresses issues like cycle time, intra-level overlay and mask count costs associated with multi-patterning. However it also brings its own sets of challenges. One of the major barrier to high volume manufacturing implementation has been hitting the 250W power exposure required for adequate throughput [1]. Enabling patterning using a lower dose resist could help move us closer to the HVM throughput targets assuming required performance for roughness and pattern transfer can be met. As plasma etching is known to reduce line edge roughness on 193nm lithography printed features [2], we investigate in this paper the level of roughness that can be achieved on EUV photoresist exposed at a lower dose through etch process optimization into a typical back end of line film stack. We will study 16nm lines printed at 32 and 34nm pitch. MOX and CAR photoresist performance will be compared. We will review step by step etch chemistry development to reach adequate selectivity and roughness reduction to successfully pattern the target layer.

Conflict Inhibitory Control Facilitates Pretense Quality in Young Preschoolers

PubMed Central

Van Reet, Jennifer

2013-01-01

The present research explores the role of inhibitory control in young preschoolers’ pretense ability using an ego depletion paradigm. In Experiment 1 (N = 56), children’s pretense ability was assessed either before or after participating in conflict inhibitory control or control tasks, and in Experiment 2 (N = 36), pretense ability was measured after children engaged in either conflict or delay inhibitory control tasks. In both experiments, pretense scores were significantly higher only after engaging in conflict inhibitory control tasks. Further, pretense scores were positively correlated with inhibitory control scores when conflict inhibitory control was not experienced first. This pattern of results suggests that inhibitory control may underlie pretense, and conflict inhibitory control can boost the quality of children’s subsequent pretending. PMID:26074736

Neuroanatomical Substrates of Rodent Social Behavior: The Medial Prefrontal Cortex and Its Projection Patterns.

PubMed

Ko, Jaewon

2017-01-01

Social behavior encompasses a number of distinctive and complex constructs that form the core elements of human imitative culture, mainly represented as either affiliative or antagonistic interactions with conspecifics. Traditionally considered in the realm of psychology, social behavior research has benefited from recent advancements in neuroscience that have accelerated identification of the neural systems, circuits, causative genes and molecular mechanisms that underlie distinct social cognitive traits. In this review article, I summarize recent findings regarding the neuroanatomical substrates of key social behaviors, focusing on results from experiments conducted in rodent models. In particular, I will review the role of the medial prefrontal cortex (mPFC) and downstream subcortical structures in controlling social behavior, and discuss pertinent future research perspectives.

Viral Perturbations of Host Networks Reflect Disease Etiology

PubMed Central

Dricot, Amélie; Padi, Megha; Byrdsong, Danielle; Franchi, Rachel; Lee, Deok-Sun; Rozenblatt-Rosen, Orit; Mar, Jessica C.; Calderwood, Michael A.; Baldwin, Amy; Zhao, Bo; Santhanam, Balaji; Braun, Pascal; Simonis, Nicolas; Huh, Kyung-Won; Hellner, Karin; Grace, Miranda; Chen, Alyce; Rubio, Renee; Marto, Jarrod A.; Christakis, Nicholas A.; Kieff, Elliott; Roth, Frederick P.; Roecklein-Canfield, Jennifer; DeCaprio, James A.; Cusick, Michael E.; Quackenbush, John; Hill, David E.; Münger, Karl; Vidal, Marc; Barabási, Albert-László

2012-01-01

Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated diseases), either in a directly causal manner or by indirect associations. Here we examine whether viral perturbations of host interactome may underlie such virally implicated disease relationships. Using as models two different human viruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV), we find that host targets of viral proteins reside in network proximity to products of disease susceptibility genes. Expression changes in virally implicated disease tissues and comorbidity patterns cluster significantly in the network vicinity of viral targets. The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia. PMID:22761553

Posttranscriptional (Re)programming of Cell Fate: Examples in Stem Cells, Progenitor, and Differentiated Cells.

PubMed

Kanellopoulou, Chrysi; Muljo, Stefan A

2018-01-01

How a single genome can give rise to many different transcriptomes and thus all the different cell lineages in the human body is a fundamental question in biology. While signaling pathways, transcription factors, and chromatin architecture, to name a few determinants, have been established to play critical roles, recently, there is a growing appreciation of the roles of non-coding RNAs and RNA-binding proteins in controlling cell fates posttranscriptionally. Thus, it is vital that these emerging players are also integrated into models of gene regulatory networks that underlie programs of cellular differentiation. Sometimes, we can leverage knowledge about such posttranscriptional circuits to reprogram patterns of gene expression in meaningful ways. Here, we review three examples from our work.

The NIH Science of Behavior Change Program: Transforming the science through a focus on mechanisms of change

PubMed Central

Nielsen, Lisbeth; Riddle, Melissa; King, Jonathan W.; Aklin, Will M.; Chen, Wen; Clark, David; Collier, Elaine; Czajkowski, Susan; Esposito, Layla; Ferrer, Rebecca; Green, Paige; Hunter, Christine; Kehl, Karen; King, Rosalind; Onken, Lisa; Simmons, Janine M.; Stoeckel, Luke; Stoney, Catherine; Tully, Lois; Weber, Wendy

2017-01-01

The goal of the NIH Science of Behavior Change (SOBC) Common Fund Program is to provide the basis for an experimental medicine approach to behavior change that focuses on identifying and measuring the mechanisms that underlie behavioral patterns we are trying to change. This paper frames the development of the program within a discussion of the substantial disease burden in the U.S. attributable to behavioral factors, and details our strategies for breaking down the disease- and condition-focused silos in the behavior change field to accelerate discovery and translation. These principles serve as the foundation for our vision for a unified science of behavior change at the NIH and in the broader research community. PMID:29110885

Neuroanatomical Substrates of Rodent Social Behavior: The Medial Prefrontal Cortex and Its Projection Patterns

PubMed Central

Ko, Jaewon

2017-01-01

Social behavior encompasses a number of distinctive and complex constructs that form the core elements of human imitative culture, mainly represented as either affiliative or antagonistic interactions with conspecifics. Traditionally considered in the realm of psychology, social behavior research has benefited from recent advancements in neuroscience that have accelerated identification of the neural systems, circuits, causative genes and molecular mechanisms that underlie distinct social cognitive traits. In this review article, I summarize recent findings regarding the neuroanatomical substrates of key social behaviors, focusing on results from experiments conducted in rodent models. In particular, I will review the role of the medial prefrontal cortex (mPFC) and downstream subcortical structures in controlling social behavior, and discuss pertinent future research perspectives. PMID:28659766

Population clocks: motor timing with neural dynamics

PubMed Central

Buonomano, Dean V.; Laje, Rodrigo

2010-01-01

An understanding of sensory and motor processing will require elucidation of the mechanisms by which the brain tells time. Open questions relate to whether timing relies on dedicated or intrinsic mechanisms and whether distinct mechanisms underlie timing across scales and modalities. Although experimental and theoretical studies support the notion that neural circuits are intrinsically capable of sensory timing on short scales, few general models of motor timing have been proposed. For one class of models, population clocks, it is proposed that time is encoded in the time-varying patterns of activity of a population of neurons. We argue that population clocks emerge from the internal dynamics of recurrently connected networks, are biologically realistic and account for many aspects of motor timing. PMID:20889368

ON THE PERCEPTION OF PROBABLE THINGS

PubMed Central

Albright, Thomas D.

2012-01-01

SUMMARY Perception is influenced both by the immediate pattern of sensory inputs and by memories acquired through prior experiences with the world. Throughout much of its illustrious history, however, study of the cellular basis of perception has focused on neuronal structures and events that underlie the detection and discrimination of sensory stimuli. Relatively little attention has been paid to the means by which memories interact with incoming sensory signals. Building upon recent neurophysiological/behavioral studies of the cortical substrates of visual associative memory, I propose a specific functional process by which stored information about the world supplements sensory inputs to yield neuronal signals that can account for visual perceptual experience. This perspective represents a significant shift in the way we think about the cellular bases of perception. PMID:22542178

Temporally diverse firing patterns in olfactory receptor neurons underlie spatiotemporal neural codes for odors

PubMed Central

Raman, Baranidharan; Joseph, Joby; Tang, Jeff; Stopfer, Mark

2010-01-01

Odorants are represented as spatiotemporal patterns of spikes in neurons of the antennal lobe (AL, insects) and olfactory bulb (OB, vertebrates). These response patterns have been thought to arise primarily from interactions within the AL/OB, an idea supported, in part, by the assumption that olfactory receptor neurons (ORNs) respond to odorants with simple firing patterns. However, activating the AL directly with simple pulses of current evoked responses in AL neurons that were much less diverse, complex, and enduring than responses elicited by odorants. Similarly, models of the AL driven by simplistic inputs generated relatively simple output. How then are dynamic neural codes for odors generated? Consistent with recent results from several other species, our recordings from locust ORNs showed a great diversity of temporal structure. Further, we found that, viewed as a population, many response features of ORNs were remarkably similar to those observed within the AL. Using a set of computational models constrained by our electrophysiological recordings, we found that the temporal heterogeneity of responses of ORNs critically underlies the generation of spatiotemporal odor codes in the AL. A test then performed in vivo confirmed that, given temporally homogeneous input, the AL cannot create diverse spatiotemporal patterns on its own; however, given temporally heterogeneous input, the AL generated realistic firing patterns. Finally, given the temporally structured input provided by ORNs, we clarified several separate, additional contributions of the AL to olfactory information processing. Thus, our results demonstrate the origin and subsequent reformatting of spatiotemporal neural codes for odors. PMID:20147528

Acute stress evokes sexually dimorphic, stressor-specific patterns of neural activation across multiple limbic brain regions in adult rats.

PubMed

Sood, Ankit; Chaudhari, Karina; Vaidya, Vidita A

2018-03-01

Stress enhances the risk for psychiatric disorders such as anxiety and depression. Stress responses vary across sex and may underlie the heightened vulnerability to psychopathology in females. Here, we examined the influence of acute immobilization stress (AIS) and a two-day short-term forced swim stress (FS) on neural activation in multiple cortical and subcortical brain regions, implicated as targets of stress and in the regulation of neuroendocrine stress responses, in male and female rats using Fos as a neural activity marker. AIS evoked a sex-dependent pattern of neural activation within the cingulate and infralimbic subdivisions of the medial prefrontal cortex (mPFC), lateral septum (LS), habenula, and hippocampal subfields. The degree of neural activation in the mPFC, LS, and habenula was higher in males. Female rats exhibited reduced Fos positive cell numbers in the dentate gyrus hippocampal subfield, an effect not observed in males. We addressed whether the sexually dimorphic neural activation pattern noted following AIS was also observed with the short-term stress of FS. In the paraventricular nucleus of the hypothalamus and the amygdala, FS similar to AIS resulted in robust increases in neural activation in both sexes. The pattern of neural activation evoked by FS was distinct across sexes, with a heightened neural activation noted in the prelimbic mPFC subdivision and hippocampal subfields in females and differed from the pattern noted with AIS. This indicates that the sex differences in neural activation patterns observed within stress-responsive brain regions are dependent on the nature of stressor experience.

Visual Scanning Patterns and Executive Function in Relation to Facial Emotion Recognition in Aging

PubMed Central

Circelli, Karishma S.; Clark, Uraina S.; Cronin-Golomb, Alice

2012-01-01

Objective The ability to perceive facial emotion varies with age. Relative to younger adults (YA), older adults (OA) are less accurate at identifying fear, anger, and sadness, and more accurate at identifying disgust. Because different emotions are conveyed by different parts of the face, changes in visual scanning patterns may account for age-related variability. We investigated the relation between scanning patterns and recognition of facial emotions. Additionally, as frontal-lobe changes with age may affect scanning patterns and emotion recognition, we examined correlations between scanning parameters and performance on executive function tests. Methods We recorded eye movements from 16 OA (mean age 68.9) and 16 YA (mean age 19.2) while they categorized facial expressions and non-face control images (landscapes), and administered standard tests of executive function. Results OA were less accurate than YA at identifying fear (p<.05, r=.44) and more accurate at identifying disgust (p<.05, r=.39). OA fixated less than YA on the top half of the face for disgust, fearful, happy, neutral, and sad faces (p’s<.05, r’s≥.38), whereas there was no group difference for landscapes. For OA, executive function was correlated with recognition of sad expressions and with scanning patterns for fearful, sad, and surprised expressions. Conclusion We report significant age-related differences in visual scanning that are specific to faces. The observed relation between scanning patterns and executive function supports the hypothesis that frontal-lobe changes with age may underlie some changes in emotion recognition. PMID:22616800

Upgrade of the TOTEM DAQ using the Scalable Readout System (SRS)

NASA Astrophysics Data System (ADS)

Quinto, M.; Cafagna, F.; Fiergolski, A.; Radicioni, E.

2013-11-01

The main goals of the TOTEM Experiment at the LHC are the measurements of the elastic and total p-p cross sections and the studies of the diffractive dissociation processes. At LHC, collisions are produced at a rate of 40 MHz, imposing strong requirements for the Data Acquisition Systems (DAQ) in terms of trigger rate and data throughput. The TOTEM DAQ adopts a modular approach that, in standalone mode, is based on VME bus system. The VME based Front End Driver (FED) modules, host mezzanines that receive data through optical fibres directly from the detectors. After data checks and formatting are applied in the mezzanine, data is retransmitted to the VME interface and to another mezzanine card plugged in the FED module. The VME bus maximum bandwidth limits the maximum first level trigger (L1A) to 1 kHz rate. In order to get rid of the VME bottleneck and improve scalability and the overall capabilities of the DAQ, a new system was designed and constructed based on the Scalable Readout System (SRS), developed in the framework of the RD51 Collaboration. The project aims to increase the efficiency of the actual readout system providing higher bandwidth, and increasing data filtering, implementing a second-level trigger event selection based on hardware pattern recognition algorithms. This goal is to be achieved preserving the maximum back compatibility with the LHC Timing, Trigger and Control (TTC) system as well as with the CMS DAQ. The obtained results and the perspectives of the project are reported. In particular, we describe the system architecture and the new Opto-FEC adapter card developed to connect the SRS with the FED mezzanine modules. A first test bench was built and validated during the last TOTEM data taking period (February 2013). Readout of a set of 3 TOTEM Roman Pot silicon detectors was carried out to verify performance in the real LHC environment. In addition, the test allowed a check of data consistency and quality.

Line-frequency doubling of directed self-assembly patterns for single-digit bit pattern media lithography

NASA Astrophysics Data System (ADS)

Patel, K. C.; Ruiz, R.; Lille, J.; Wan, L.; Dobiz, E.; Gao, H.; Robertson, N.; Albrecht, T. R.

2012-03-01

Directed self-assembly is emerging as a promising technology to define sub-20nm features. However, a straightforward path to scale block copolymer lithography to single-digit fabrication remains challenging given the diverse material properties found in the wide spectrum of self-assembling materials. A vast amount of block copolymer research for industrial applications has been dedicated to polystyrene-b-methyl methacrylate (PS-b-PMMA), a model system that displays multiple properties making it ideal for lithography, but that is limited by a weak interaction parameter that prevents it from scaling to single-digit lithography. Other block copolymer materials have shown scalability to much smaller dimensions, but at the expense of other material properties that could delay their insertion into industrial lithographic processes. We report on a line doubling process applied to block copolymer patterns to double the frequency of PS-b-PMMA line/space features, demonstrating the potential of this technique to reach single-digit lithography. We demonstrate a line-doubling process that starts with directed self-assembly of PS-b-PMMA to define line/space features. This pattern is transferred into an underlying sacrificial hard-mask layer followed by a growth of self-aligned spacers which subsequently serve as hard-masks for transferring the 2x frequency doubled pattern to the underlying substrate. We applied this process to two different block copolymer materials to demonstrate line-space patterns with a half pitch of 11nm and 7nm underscoring the potential to reach single-digit critical dimensions. A subsequent patterning step with perpendicular lines can be used to cut the fine line patterns into a 2-D array of islands suitable for bit patterned media. Several integration challenges such as line width control and line roughness are addressed.

Unique Configurations of Compression and Truncation of Neuronal Activity Underlie l-DOPA-Induced Selection of Motor Patterns in Aplysia.

PubMed

Neveu, Curtis L; Costa, Renan M; Homma, Ryota; Nagayama, Shin; Baxter, Douglas A; Byrne, John H

2017-01-01

A key issue in neuroscience is understanding the ways in which neuromodulators such as dopamine modify neuronal activity to mediate selection of distinct motor patterns. We addressed this issue by applying either low or high concentrations of l-DOPA (40 or 250 μM) and then monitoring activity of up to 130 neurons simultaneously in the feeding circuitry of Aplysia using a voltage-sensitive dye (RH-155). l-DOPA selected one of two distinct buccal motor patterns (BMPs): intermediate (low l-DOPA) or bite (high l-DOPA) patterns. The selection of intermediate BMPs was associated with shortening of the second phase of the BMP (retraction), whereas the selection of bite BMPs was associated with shortening of both phases of the BMP (protraction and retraction). Selection of intermediate BMPs was also associated with truncation of individual neuron spike activity (decreased burst duration but no change in spike frequency or burst latency) in neurons active during retraction. In contrast, selection of bite BMPs was associated with compression of spike activity (decreased burst latency and duration and increased spike frequency) in neurons projecting through specific nerves, as well as increased spike frequency of protraction neurons. Finally, large-scale voltage-sensitive dye recordings delineated the spatial distribution of neurons active during BMPs and the modification of that distribution by the two concentrations of l-DOPA.

Unique Configurations of Compression and Truncation of Neuronal Activity Underlie l-DOPA–Induced Selection of Motor Patterns in Aplysia

PubMed Central

Homma, Ryota; Nagayama, Shin; Baxter, Douglas A.

2017-01-01

A key issue in neuroscience is understanding the ways in which neuromodulators such as dopamine modify neuronal activity to mediate selection of distinct motor patterns. We addressed this issue by applying either low or high concentrations of l-DOPA (40 or 250 μM) and then monitoring activity of up to 130 neurons simultaneously in the feeding circuitry of Aplysia using a voltage-sensitive dye (RH-155). l-DOPA selected one of two distinct buccal motor patterns (BMPs): intermediate (low l-DOPA) or bite (high l-DOPA) patterns. The selection of intermediate BMPs was associated with shortening of the second phase of the BMP (retraction), whereas the selection of bite BMPs was associated with shortening of both phases of the BMP (protraction and retraction). Selection of intermediate BMPs was also associated with truncation of individual neuron spike activity (decreased burst duration but no change in spike frequency or burst latency) in neurons active during retraction. In contrast, selection of bite BMPs was associated with compression of spike activity (decreased burst latency and duration and increased spike frequency) in neurons projecting through specific nerves, as well as increased spike frequency of protraction neurons. Finally, large-scale voltage-sensitive dye recordings delineated the spatial distribution of neurons active during BMPs and the modification of that distribution by the two concentrations of l-DOPA. PMID:29071298

Emergent Auditory Feature Tuning in a Real-Time Neuromorphic VLSI System.

PubMed

Sheik, Sadique; Coath, Martin; Indiveri, Giacomo; Denham, Susan L; Wennekers, Thomas; Chicca, Elisabetta

2012-01-01

Many sounds of ecological importance, such as communication calls, are characterized by time-varying spectra. However, most neuromorphic auditory models to date have focused on distinguishing mainly static patterns, under the assumption that dynamic patterns can be learned as sequences of static ones. In contrast, the emergence of dynamic feature sensitivity through exposure to formative stimuli has been recently modeled in a network of spiking neurons based on the thalamo-cortical architecture. The proposed network models the effect of lateral and recurrent connections between cortical layers, distance-dependent axonal transmission delays, and learning in the form of Spike Timing Dependent Plasticity (STDP), which effects stimulus-driven changes in the pattern of network connectivity. In this paper we demonstrate how these principles can be efficiently implemented in neuromorphic hardware. In doing so we address two principle problems in the design of neuromorphic systems: real-time event-based asynchronous communication in multi-chip systems, and the realization in hybrid analog/digital VLSI technology of neural computational principles that we propose underlie plasticity in neural processing of dynamic stimuli. The result is a hardware neural network that learns in real-time and shows preferential responses, after exposure, to stimuli exhibiting particular spectro-temporal patterns. The availability of hardware on which the model can be implemented, makes this a significant step toward the development of adaptive, neurobiologically plausible, spike-based, artificial sensory systems.

Emergent Auditory Feature Tuning in a Real-Time Neuromorphic VLSI System

PubMed Central

Sheik, Sadique; Coath, Martin; Indiveri, Giacomo; Denham, Susan L.; Wennekers, Thomas; Chicca, Elisabetta

2011-01-01

Many sounds of ecological importance, such as communication calls, are characterized by time-varying spectra. However, most neuromorphic auditory models to date have focused on distinguishing mainly static patterns, under the assumption that dynamic patterns can be learned as sequences of static ones. In contrast, the emergence of dynamic feature sensitivity through exposure to formative stimuli has been recently modeled in a network of spiking neurons based on the thalamo-cortical architecture. The proposed network models the effect of lateral and recurrent connections between cortical layers, distance-dependent axonal transmission delays, and learning in the form of Spike Timing Dependent Plasticity (STDP), which effects stimulus-driven changes in the pattern of network connectivity. In this paper we demonstrate how these principles can be efficiently implemented in neuromorphic hardware. In doing so we address two principle problems in the design of neuromorphic systems: real-time event-based asynchronous communication in multi-chip systems, and the realization in hybrid analog/digital VLSI technology of neural computational principles that we propose underlie plasticity in neural processing of dynamic stimuli. The result is a hardware neural network that learns in real-time and shows preferential responses, after exposure, to stimuli exhibiting particular spectro-temporal patterns. The availability of hardware on which the model can be implemented, makes this a significant step toward the development of adaptive, neurobiologically plausible, spike-based, artificial sensory systems. PMID:22347163

On the scalability of the Albany/FELIX first-order Stokes approximation ice sheet solver for large-scale simulations of the Greenland and Antarctic ice sheets

DOE PAGES

Tezaur, Irina K.; Tuminaro, Raymond S.; Perego, Mauro; ...

2015-01-01

We examine the scalability of the recently developed Albany/FELIX finite-element based code for the first-order Stokes momentum balance equations for ice flow. We focus our analysis on the performance of two possible preconditioners for the iterative solution of the sparse linear systems that arise from the discretization of the governing equations: (1) a preconditioner based on the incomplete LU (ILU) factorization, and (2) a recently-developed algebraic multigrid (AMG) preconditioner, constructed using the idea of semi-coarsening. A strong scalability study on a realistic, high resolution Greenland ice sheet problem reveals that, for a given number of processor cores, the AMG preconditionermore » results in faster linear solve times but the ILU preconditioner exhibits better scalability. In addition, a weak scalability study is performed on a realistic, moderate resolution Antarctic ice sheet problem, a substantial fraction of which contains floating ice shelves, making it fundamentally different from the Greenland ice sheet problem. We show that as the problem size increases, the performance of the ILU preconditioner deteriorates whereas the AMG preconditioner maintains scalability. This is because the linear systems are extremely ill-conditioned in the presence of floating ice shelves, and the ill-conditioning has a greater negative effect on the ILU preconditioner than on the AMG preconditioner.« less

Structure Building Predicts Grades in College Psychology and Biology

ERIC Educational Resources Information Center

Arnold, Kathleen M.; Daniel, David B.; Jensen, Jamie L.; McDaniel, Mark A.; Marsh, Elizabeth J.

2016-01-01

Knowing what skills underlie college success can allow students, teachers, and universities to identify and to help at-risk students. One skill that may underlie success across a variety of subject areas is structure building, the ability to create mental representations of narratives (Gernsbacher, Varner, & Faust, 1990). We tested if…

Recognising Value Tensions That Underlie Problems in Inclusive Education

ERIC Educational Resources Information Center

Norwich, Brahm

2014-01-01

This paper aims to examine some tensions that underlie inclusive education as regards pupils with disabilities and difficulties. Two key tensions are analysed: difference as enabling-stigmatising (dilemmas of difference) and participation-protection, both of which can lead to significant dilemmas. Berlin's hedgehog-fox distinction about the unity…

MicROS-drt: supporting real-time and scalable data distribution in distributed robotic systems.

PubMed

Ding, Bo; Wang, Huaimin; Fan, Zedong; Zhang, Pengfei; Liu, Hui

A primary requirement in distributed robotic software systems is the dissemination of data to all interested collaborative entities in a timely and scalable manner. However, providing such a service in a highly dynamic and resource-limited robotic environment is a challenging task, and existing robot software infrastructure has limitations in this aspect. This paper presents a novel robot software infrastructure, micROS-drt, which supports real-time and scalable data distribution. The solution is based on a loosely coupled data publish-subscribe model with the ability to support various time-related constraints. And to realize this model, a mature data distribution standard, the data distribution service for real-time systems (DDS), is adopted as the foundation of the transport layer of this software infrastructure. By elaborately adapting and encapsulating the capability of the underlying DDS middleware, micROS-drt can meet the requirement of real-time and scalable data distribution in distributed robotic systems. Evaluation results in terms of scalability, latency jitter and transport priority as well as the experiment on real robots validate the effectiveness of this work.

BactoGeNIE: A large-scale comparative genome visualization for big displays

DOE PAGES

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; ...

2015-08-13

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

BactoGeNIE: a large-scale comparative genome visualization for big displays

PubMed Central

2015-01-01

Background The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. Results In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. Conclusions BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics. PMID:26329021

BactoGeNIE: A large-scale comparative genome visualization for big displays

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

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

Efficient and scalable ionization of neutral atoms by an orderly array of gold-doped silicon nanowires

NASA Astrophysics Data System (ADS)

Bucay, Igal; Helal, Ahmed; Dunsky, David; Leviyev, Alex; Mallavarapu, Akhila; Sreenivasan, S. V.; Raizen, Mark

2017-04-01

Ionization of atoms and molecules is an important process in many applications and processes such as mass spectrometry. Ionization is typically accomplished by electron bombardment, and while it is scalable to large volumes, is also very inefficient due to the small cross section of electron-atom collisions. Photoionization methods can be highly efficient, but are not scalable due to the small ionization volume. Electric field ionization is accomplished using ultra-sharp conducting tips biased to a few kilovolts, but suffers from a low ionization volume and tip fabrication limitations. We report on our progress towards an efficient, robust, and scalable method of atomic and molecular ionization using orderly arrays of sharp, gold-doped silicon nanowires. As demonstrated in earlier work, the presence of the gold greatly enhances the ionization probability, which was attributed to an increase in available acceptor surface states. We present here a novel process used to fabricate the nanowire array, results of simulations aimed at optimizing the configuration of the array, and our progress towards demonstrating efficient and scalable ionization.

Medusa: A Scalable MR Console Using USB

PubMed Central

Stang, Pascal P.; Conolly, Steven M.; Santos, Juan M.; Pauly, John M.; Scott, Greig C.

2012-01-01

MRI pulse sequence consoles typically employ closed proprietary hardware, software, and interfaces, making difficult any adaptation for innovative experimental technology. Yet MRI systems research is trending to higher channel count receivers, transmitters, gradient/shims, and unique interfaces for interventional applications. Customized console designs are now feasible for researchers with modern electronic components, but high data rates, synchronization, scalability, and cost present important challenges. Implementing large multi-channel MR systems with efficiency and flexibility requires a scalable modular architecture. With Medusa, we propose an open system architecture using the Universal Serial Bus (USB) for scalability, combined with distributed processing and buffering to address the high data rates and strict synchronization required by multi-channel MRI. Medusa uses a modular design concept based on digital synthesizer, receiver, and gradient blocks, in conjunction with fast programmable logic for sampling and synchronization. Medusa is a form of synthetic instrument, being reconfigurable for a variety of medical/scientific instrumentation needs. The Medusa distributed architecture, scalability, and data bandwidth limits are presented, and its flexibility is demonstrated in a variety of novel MRI applications. PMID:21954200

Predicting and Detecting Emerging Cyberattack Patterns Using StreamWorks

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

Chin, George; Choudhury, Sutanay; Feo, John T.

2014-06-30

The number and sophistication of cyberattacks on industries and governments have dramatically grown in recent years. To counter this movement, new advanced tools and techniques are needed to detect cyberattacks in their early stages such that defensive actions may be taken to avert or mitigate potential damage. From a cybersecurity analysis perspective, detecting cyberattacks may be cast as a problem of identifying patterns in computer network traffic. Logically and intuitively, these patterns may take on the form of a directed graph that conveys how an attack or intrusion propagates through the computers of a network. Such cyberattack graphs could providemore » cybersecurity analysts with powerful conceptual representations that are natural to express and analyze. We have been researching and developing graph-centric approaches and algorithms for dynamic cyberattack detection. The advanced dynamic graph algorithms we are developing will be packaged into a streaming network analysis framework known as StreamWorks. With StreamWorks, a scientist or analyst may detect and identify precursor events and patterns as they emerge in complex networks. This analysis framework is intended to be used in a dynamic environment where network data is streamed in and is appended to a large-scale dynamic graph. Specific graphical query patterns are decomposed and collected into a graph query library. The individual decomposed subpatterns in the library are continuously and efficiently matched against the dynamic graph as it evolves to identify and detect early, partial subgraph patterns. The scalable emerging subgraph pattern algorithms will match on both structural and semantic network properties.« less

The Scalable Checkpoint/Restart Library

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

Moody, A.

The Scalable Checkpoint/Restart (SCR) library provides an interface that codes may use to worite our and read in application-level checkpoints in a scalable fashion. In the current implementation, checkpoint files are cached in local storage (hard disk or RAM disk) on the compute nodes. This technique provides scalable aggregate bandwidth and uses storage resources that are fully dedicated to the job. This approach addresses the two common drawbacks of checkpointing a large-scale application to a shared parallel file system, namely, limited bandwidth and file system contention. In fact, on current platforms, SCR scales linearly with the number of compute nodes.more » It has been benchmarked as high as 720GB/s on 1094 nodes of Atlas, which is nearly two orders of magnitude faster thanthe parallel file system.« less

Metal- and Reagent-Free Anodic C-C Cross-Coupling of Phenols with Benzofurans leading to a Furan Metathesis.

PubMed

Lips, Sebastian; Frontana-Uribe, Bernardo Antonio; Dörr, Maurice; Schollmeyer, Dieter; Franke, Robert; Waldvogel, Siegfried R

2018-04-20

Heterobiaryls consisting of a phenol and a benzofuran motif are of significant importance for pharmaceutical applications. An attractive sustainable, metal- and reagent-free, electrosynthetic, and highly efficient method, that allows access to (2-hydroxyphenyl)benzofurans is presented. Upon the electrochemical dehydrogenative C-C cross-coupling reaction, a metathesis of the benzo moiety at the benzofuran occurs. This gives rise to a substitution pattern at the hydroxyphenyl moiety which would not be compatible by a direct coupling process. The single-step protocol is easy to conduct in an undivided electrolysis cell, therefore scalable, and inherently safe. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stacked waveguide reactors with gradient embedded scatterers for high-capacity water cleaning

DOE PAGES

Ahsan, Syed Saad; Gumus, Abdurrahman; Erickson, David

2015-11-04

We present a compact water-cleaning reactor with stacked layers of waveguides containing gradient patterns of optical scatterers that enable uniform light distribution and augmented water-cleaning rates. Previous photocatalytic reactors using immersion, external, or distributive lamps suffer from poor light distribution that impedes scalability. Here, we use an external UV-source to direct photons into stacked waveguide reactors where we scatter the photons uniformly over the length of the waveguide to thin films of TiO 2-catalysts. In conclusion, we also show 4.5 times improvement in activity over uniform scatterer designs, demonstrate a degradation of 67% of the organic dye, and characterize themore » degradation rate constant.« less

Stacked waveguide reactors with gradient embedded scatterers for high-capacity water cleaning

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

Ahsan, Syed Saad; Gumus, Abdurrahman; Erickson, David

We present a compact water-cleaning reactor with stacked layers of waveguides containing gradient patterns of optical scatterers that enable uniform light distribution and augmented water-cleaning rates. Previous photocatalytic reactors using immersion, external, or distributive lamps suffer from poor light distribution that impedes scalability. Here, we use an external UV-source to direct photons into stacked waveguide reactors where we scatter the photons uniformly over the length of the waveguide to thin films of TiO 2-catalysts. In conclusion, we also show 4.5 times improvement in activity over uniform scatterer designs, demonstrate a degradation of 67% of the organic dye, and characterize themore » degradation rate constant.« less

Generic Bistability in Creased Conical Surfaces

NASA Astrophysics Data System (ADS)

Lechenault, F.; Adda-Bedia, M.

2015-12-01

The emerging field of mechanical metamaterials has sought inspiration in the ancient art of origami as archetypal deployable structures that carry geometric rigidity, exhibit exotic material properties, and are potentially scalable. A promising venue to introduce functionality consists in coupling the elasticity of the sheet and the kinematics of the folds. In this spirit, we introduce a scale-free, analytical description of a very general class of snap-through, bistable patterns of creases naturally occurring at the vertices of real origami that can be used as building blocks to program and actuate the overall shape of the decorated sheet. These switches appear at the simplest possible level of creasing and admit straightforward experimental realizations.

High-Precision Photothermal Ablation Using Biocompatible Palladium Nanoparticles and Laser Scanning Microscopy

PubMed Central

2018-01-01

Herein, we report a straightforward method for the scalable preparation of Pd nanoparticles (Pd-NPs) with reduced inherent cytotoxicity and high photothermal conversion capacity. These Pd-NPs are rapidly taken up by cells and able to kill labeled cancer cells upon short exposure to near-infrared (NIR) light. Following cell treatment with Pd-NPs, ablated areas were patterned with high precision by laser scanning microscopy, allowing one to perform cell migration assays with unprecedented accuracy. Using coherent Raman microscopy, cells containing Pd-NPs were simultaneously ablated and imaged. This novel methodology was combined with intravital imaging to mediate microablation of cancerous tissue in tumor xenografts in mice. PMID:29320154

ZnO nanotube waveguide arrays on graphene films for local optical excitation on biological cells

NASA Astrophysics Data System (ADS)

Baek, Hyeonjun; Kwak, Hankyul; Song, Minho S.; Ha, Go Eun; Park, Jongwoo; Tchoe, Youngbin; Hyun, Jerome K.; Park, Hye Yoon; Cheong, Eunji; Yi, Gyu-Chul

2017-04-01

We report on scalable and position-controlled optical nanoprobe arrays using ZnO nanotube waveguides on graphene films for use in local optical excitation. For the waveguide fabrication, position-controlled and well-ordered ZnO nanotube arrays were grown on chemical vapor deposited graphene films with a submicron patterned mask layer and Au prepared between the interspace of nanotubes. Mammalian cells were cultured on the nanotube waveguide arrays and were locally excited by light illuminated through the nanotubes. Fluorescence and optogenetic signals could be excited through the optical nanoprobes. This method offers the ability to investigate cellular behavior with a high spatial resolution that surpasses the current limitation.

Monitoring service for the Gran Telescopio Canarias control system

NASA Astrophysics Data System (ADS)

Huertas, Manuel; Molgo, Jordi; Macías, Rosa; Ramos, Francisco

2016-07-01

The Monitoring Service collects, persists and propagates the Telescope and Instrument telemetry, for the Gran Telescopio CANARIAS (GTC), an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). A new version of the Monitoring Service has been developed in order to improve performance, provide high availability, guarantee fault tolerance and scalability to cope with high volume of data. The architecture is based on a distributed in-memory data store with a Product/Consumer pattern design. The producer generates the data samples. The consumers either persists the samples to a database for further analysis or propagates them to the consoles in the control room to monitorize the state of the whole system.

Plant developmental responses to climate change.

PubMed

Gray, Sharon B; Brady, Siobhan M

2016-11-01

Climate change is multi-faceted, and includes changing concentrations of greenhouse gases in the atmosphere, rising temperatures, changes in precipitation patterns, and increasing frequency of extreme weather events. Here, we focus on the effects of rising atmospheric CO 2 concentrations, rising temperature, and drought stress and their interaction on plant developmental processes in leaves, roots, and in reproductive structures. While in some cases these responses are conserved across species, such as decreased root elongation, perturbation of root growth angle and reduced seed yield in response to drought, or an increase in root biomass in shallow soil in response to elevated CO 2 , most responses are variable within and between species and are dependent on developmental stage. These variable responses include species-specific thresholds that arrest development of reproductive structures, reduce root growth rate and the rate of leaf initiation and expansion in response to elevated temperature. Leaf developmental responses to elevated CO 2 vary by cell type and by species. Variability also exists between C 3 and C 4 species in response to elevated CO 2 , especially in terms of growth and seed yield stimulation. At the molecular level, significantly less is understood regarding conservation and variability in molecular mechanisms underlying these traits. Abscisic acid-mediated changes in cell wall expansion likely underlie reductions in growth rate in response to drought, and changes in known regulators of flowering time likely underlie altered reproductive transitions in response to elevated temperature and CO 2 . Genes that underlie most other organ or tissue-level responses have largely only been identified in a single species in response to a single stress and their level of conservation is unknown. We conclude that there is a need for further research regarding the molecular mechanisms of plant developmental responses to climate change factors in general, and that this lack of data is particularly prevalent in the case of interactive effects of multiple climate change factors. As future growing conditions will likely expose plants to multiple climate change factors simultaneously, with a sum negative influence on global agriculture, further research in this area is critical. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Improved heat dissipation in gallium nitride light-emitting diodes with embedded graphene oxide pattern.

PubMed

Han, Nam; Cuong, Tran Viet; Han, Min; Ryu, Beo Deul; Chandramohan, S; Park, Jong Bae; Kang, Ji Hye; Park, Young-Jae; Ko, Kang Bok; Kim, Hee Yun; Kim, Hyun Kyu; Ryu, Jae Hyoung; Katharria, Y S; Choi, Chel-Jong; Hong, Chang-Hee

2013-01-01

The future of solid-state lighting relies on how the performance parameters will be improved further for developing high-brightness light-emitting diodes. Eventually, heat removal is becoming a crucial issue because the requirement of high brightness necessitates high-operating current densities that would trigger more joule heating. Here we demonstrate that the embedded graphene oxide in a gallium nitride light-emitting diode alleviates the self-heating issues by virtue of its heat-spreading ability and reducing the thermal boundary resistance. The fabrication process involves the generation of scalable graphene oxide microscale patterns on a sapphire substrate, followed by its thermal reduction and epitaxial lateral overgrowth of gallium nitride in a metal-organic chemical vapour deposition system under one-step process. The device with embedded graphene oxide outperforms its conventional counterpart by emitting bright light with relatively low-junction temperature and thermal resistance. This facile strategy may enable integration of large-scale graphene into practical devices for effective heat removal.

Ice Stream Slowdown Will Drive Long-Term Thinning of the Ross Ice Shelf, With or Without Ocean Warming

NASA Astrophysics Data System (ADS)

Campbell, Adam J.; Hulbe, Christina L.; Lee, Choon-Ki

2018-01-01

As time series observations of Antarctic change proliferate, it is imperative that mathematical frameworks through which they are understood keep pace. Here we present a new method of interpreting remotely sensed change using spatial statistics and apply it to the specific case of thickness change on the Ross Ice Shelf. First, a numerical model of ice shelf flow is used together with empirical orthogonal function analysis to generate characteristic patterns of response to specific forcings. Because they are continuous and scalable in space and time, the patterns allow short duration observations to be placed in a longer time series context. Second, focusing only on changes that are statistically significant, the synthetic response surfaces are used to extract magnitude and timing of past events from the observational data. Slowdown of Kamb and Whillans Ice Streams is clearly detectable in remotely sensed thickness change. Moreover, those past events will continue to drive thinning into the future.

Parallel computing in experimental mechanics and optical measurement: A review (II)

NASA Astrophysics Data System (ADS)

Wang, Tianyi; Kemao, Qian

2018-05-01

With advantages such as non-destructiveness, high sensitivity and high accuracy, optical techniques have successfully integrated into various important physical quantities in experimental mechanics (EM) and optical measurement (OM). However, in pursuit of higher image resolutions for higher accuracy, the computation burden of optical techniques has become much heavier. Therefore, in recent years, heterogeneous platforms composing of hardware such as CPUs and GPUs, have been widely employed to accelerate these techniques due to their cost-effectiveness, short development cycle, easy portability, and high scalability. In this paper, we analyze various works by first illustrating their different architectures, followed by introducing their various parallel patterns for high speed computation. Next, we review the effects of CPU and GPU parallel computing specifically in EM & OM applications in a broad scope, which include digital image/volume correlation, fringe pattern analysis, tomography, hyperspectral imaging, computer-generated holograms, and integral imaging. In our survey, we have found that high parallelism can always be exploited in such applications for the development of high-performance systems.

Theory of optical absorption by interlayer excitons in transition metal dichalcogenide heterobilayers

NASA Astrophysics Data System (ADS)

Wu, Fengcheng; Lovorn, Timothy; MacDonald, A. H.

2018-01-01

We present a theory of optical absorption by interlayer excitons in a heterobilayer formed from transition metal dichalcogenides. The theory accounts for the presence of small relative rotations that produce a momentum shift between electron and hole bands located in different layers, and a moiré pattern in real space. Because of the momentum shift, the optically active interlayer excitons are located at the moiré Brillouin zone's corners, instead of at its center, and would have elliptical optical selection rules if the individual layers were translationally invariant. We show that the exciton moiré potential energy restores circular optical selection rules by coupling excitons with different center of mass momenta. A variety of interlayer excitons with both senses of circular optical activity, and energies that are tunable by twist angle, are present at each valley. The lowest energy exciton states are generally localized near the exciton potential energy minima. We discuss the possibility of using the moiré pattern to achieve scalable two-dimensional arrays of nearly identical quantum dots.

Recognition of Arabic Sign Language Alphabet Using Polynomial Classifiers

NASA Astrophysics Data System (ADS)

Assaleh, Khaled; Al-Rousan, M.

2005-12-01

Building an accurate automatic sign language recognition system is of great importance in facilitating efficient communication with deaf people. In this paper, we propose the use of polynomial classifiers as a classification engine for the recognition of Arabic sign language (ArSL) alphabet. Polynomial classifiers have several advantages over other classifiers in that they do not require iterative training, and that they are highly computationally scalable with the number of classes. Based on polynomial classifiers, we have built an ArSL system and measured its performance using real ArSL data collected from deaf people. We show that the proposed system provides superior recognition results when compared with previously published results using ANFIS-based classification on the same dataset and feature extraction methodology. The comparison is shown in terms of the number of misclassified test patterns. The reduction in the rate of misclassified patterns was very significant. In particular, we have achieved a 36% reduction of misclassifications on the training data and 57% on the test data.

In-situ photoluminescence imaging for passivation-layer etching process control for photovoltaics

NASA Astrophysics Data System (ADS)

Lee, J. Z.; Michaelson, L.; Munoz, K.; Tyson, T.; Gallegos, A.; Sullivan, J. T.; Buonassisi, T.

2014-07-01

Light-induced plating (LIP) of solar-cell metal contacts is a scalable alternative to silver paste. However, LIP requires an additional patterning step to create openings in the silicon nitride (SiNx) antireflection coating (ARC) layer prior to metallization. One approach to pattern the SiNx is masking and wet chemical etching. In-situ real-time photoluminescence imaging (PLI) is demonstrated as a process-monitoring method to determine when SiNx has been fully removed during etching. We demonstrate that the change in PLI signal intensity during etching is caused by a combination of (1) decreasing light absorption from the reduction in SiNx ARC layer thickness and (2) decreasing surface lifetime as the SiNx/Si interface transitions to an etch-solution/Si. Using in-situ PLI to guide the etching process, we demonstrate a full-area plated single-crystalline silicon device. In-situ PLI has the potential to be integrated into a commercial processing line to improve process control and reliability.

Buckligami: Actuation of soft structures through mechanical instabilities

NASA Astrophysics Data System (ADS)

Lazarus, Arnaud; Reis, Pedro

2013-03-01

We present a novel mechanism for actuating soft structures, that is triggered through buckling. Our elastomeric samples are rapid-prototyped using digital fabrication and comprise of a cylindrical shell patterned with an array of voids, each of which is covered by a thin membrane. Decreasing the internal pressure of the structure induces local buckling of the ligaments of the pattern, resulting in controllable folding of the global structure. Using rigid inclusions to plug the voids in specific geometric arrangements allows us to excite a variety of different fundamental motions of the cylindrical shell, including flexure and twist. We refer to this new mechanism of buckling-induced folding as ``buckligami.'' Given that geometry, elasticity and buckling are the underlying ingredients of this local folding mechanism, the global actuation is scalable, reversible and repeatable. Characterization and rationalization of our experiments provide crucial fundamental understanding to aid the design of new scale-independent actuators, with potential implications in the field of soft robotics.

Direct growth of graphene-dielectric bi-layer structure on device substrates from Si-based polymer

NASA Astrophysics Data System (ADS)

Seo, Hong-Kyu; Kim, Kyunghun; Min, Sung-Yong; Lee, Yeongjun; Eon Park, Chan; Raj, Rishi; Lee, Tae-Woo

2017-06-01

To facilitate the utilization of graphene films in conventional semiconducting devices (e.g. transistors and memories) which includes an insulating layer such as gate dielectric, facile synthesis of bi-layers composed of a graphene film and an insulating layer by one-step thermal conversion will be very important. We demonstrate a simple, inexpensive, scalable and patternable process to synthesize graphene-dielectric bi-layer films from solution-processed polydimethylsiloxane (PDMS) under a Ni capping layer. This method fabricates graphene-dielectric bi-layer structure simultaneously directly on substrate by thermal conversion of PDMS without using additional graphene transfer and patterning process or formation of an expensive dielectric layer, which makes the device fabrication process much easier. The graphene-dielectric bi-layer on a conducting substrate was used in bottom-contact pentacene field-effect transistors that showed ohmic contact and small hysteresis. Our new method will provide a way to fabricate flexible electronic devices simply and inexpensively.

Optofluidic fabrication for 3D-shaped particles

NASA Astrophysics Data System (ADS)

Paulsen, Kevin S.; di Carlo, Dino; Chung, Aram J.

2015-04-01

Complex three-dimensional (3D)-shaped particles could play unique roles in biotechnology, structural mechanics and self-assembly. Current methods of fabricating 3D-shaped particles such as 3D printing, injection moulding or photolithography are limited because of low-resolution, low-throughput or complicated/expensive procedures. Here, we present a novel method called optofluidic fabrication for the generation of complex 3D-shaped polymer particles based on two coupled processes: inertial flow shaping and ultraviolet (UV) light polymerization. Pillars within fluidic platforms are used to deterministically deform photosensitive precursor fluid streams. The channels are then illuminated with patterned UV light to polymerize the photosensitive fluid, creating particles with multi-scale 3D geometries. The fundamental advantages of optofluidic fabrication include high-resolution, multi-scalability, dynamic tunability, simple operation and great potential for bulk fabrication with full automation. Through different combinations of pillar configurations, flow rates and UV light patterns, an infinite set of 3D-shaped particles is available, and a variety are demonstrated.

A two-in-one process for reliable graphene transistors processed with photo-lithography

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

Ahlberg, P.; Hinnemo, M.; Song, M.

2015-11-16

Research on graphene field-effect transistors (GFETs) has mainly relied on devices fabricated using electron-beam lithography for pattern generation, a method that has known problems with polymer contaminants. GFETs fabricated via photo-lithography suffer even worse from other chemical contaminations, which may lead to strong unintentional doping of the graphene. In this letter, we report on a scalable fabrication process for reliable GFETs based on ordinary photo-lithography by eliminating the aforementioned issues. The key to making this GFET processing compatible with silicon technology lies in a two-in-one process where a gate dielectric is deposited by means of atomic layer deposition. During thismore » deposition step, contaminants, likely unintentionally introduced during the graphene transfer and patterning, are effectively removed. The resulting GFETs exhibit current-voltage characteristics representative to that of intrinsic non-doped graphene. Fundamental aspects pertaining to the surface engineering employed in this work are investigated in the light of chemical analysis in combination with electrical characterization.« less

Mental Disorders among Persons with Heart Disease - Results from the World Mental Health Surveys

PubMed Central

Ormel, Johan; Von Korff, Michael; Burger, Huibert; Scott, Kate; Demyttenaere, Koen; Huang, Yue-qin; Posada-Villa, José; Lepine, Jean Pierre; Angermeyer, Matthias C.; Levinson, Daphna; de Girolamo, Giovanni; Kawakami, Norito; Karam, Elie; Medina-Mora, María Elena; Gureje, Oye; Williams, David; Haro, Josep Maria; Bromet, Evelyn J.; Alonso, Jordi; Kessler, Ron

2007-01-01

Objective While in western countries depression and heart disease often co-occur, less is known about the association of anxiety and alcohol use disorders with heart disease and about the cross-cultural consistency of these associations. Consistency across emotional disorders and cultures would suggest that relatively universal mechanisms underlie the association. Method Surveys in 18 random population samples of household-residing adults in 17 countries in Europe, the Americas, the Middle East, Africa, Asia and the South Pacific. Medically recognized heart disease was ascertained by self-report. Mental disorders were assessed with the WMH-CIDI, a fully structured diagnostic interview. Results Specific mood and anxiety disorders occurred among persons with heart disease at higher rates than among persons without heart disease. Adjusted for gender and age, the pooled odds ratios (95% CI) were 2.1 (1.9,2.5) for mood disorders, 2.2 (1.9,2.5) for anxiety disorders, and 1.4 (1.0,1.9) for alcohol abuse/dependence among persons with versus without heart disease. This pattern was similar across countries. Conclusions An excess of anxiety disorders, as well as mood disorders, is found among persons with heart disease. These associations hold across countries despite substantial between-country differences in culture and mental disorder prevalence rates. These results suggest that similar mechanisms underlie the associations and that a broad spectrum of mood-anxiety disorders should be considered in research on the comorbidity of mental disorders and heart disease. PMID:17591509

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

PubMed Central

Aguilera, Felipe; McDougall, Carmel

2017-01-01

Abstract Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium. PMID:28053006

Quantitative trait loci for response to ethanol in an intercontinental set of recombinant inbred lines of Drosophila melanogaster.

PubMed

Defays, Raquel; Bertoli, Carlos Ignacio

2012-12-01

Alcohol, a drug widely abused, impacts the central nervous system functioning of diverse organisms. The behavioral responses to acute alcohol exposure are remarkably similar among humans and fruit flies. In its natural environment, rich in fermentation products, the fruit fly Drosophila melanogaster encounters relatively high levels of ethanol. The effects of ethanol and its metabolites on Drosophila have been studied for decades, as a model for adaptive evolution. Although extensive work has been done for elucidating patterns of genetic variation, substantially less is known about the genomic regions or genes that underlie the genetic variation of this important trait. To identify regions containing genes involved in the responses to ethanol, we used a mapping population of recombinant inbred (RIL) lines to map quantitative trait loci (QTL) that affect variation in resistance and recovery from ethanol sedation in adults and ethanol resistance in larvae. We mapped fourteen QTL affecting the response to ethanol on the three chromosomes. Seven of the QTL influence the resistance to ethanol in adults, two QTL are related to ethanol-coma recovery in adults and five affect the survival to ethanol in larvae. Most of the QTL were trait specific, suggesting that overlapping but generally unique genetic architectures underlie each trait. Each QTL explained up to 16.8% of the genetic variance among lines. Potential candidate loci contained within our QTL regions were identified and analyzed. Copyright © 2012 Elsevier Inc. All rights reserved.

Neural Basis of Interpersonal Traits in Neurodegenerative Diseases

PubMed Central

Sollberger, Marc; Stanley, Christine M.; Wilson, Stephen M.; Gyurak, Anett; Beckman, Victoria; Growdon, Matthew; Jang, Jung; Weiner, Michael W.; Miller, Bruce L.; Rankin, Katherine P.

2009-01-01

Several functional and structural imaging studies have investigated the neural basis of personality in healthy adults, but human lesions studies are scarce. Personality changes are a common symptom in patients with neurodegenerative diseases like frontotemporal dementia (FTD) and semantic dementia (SD), allowing a unique window into the neural basis of personality. In this study, we used the Interpersonal Adjective Scales to investigate the structural basis of eight interpersonal traits (dominance, arrogance, coldness, introversion, submissiveness, ingenuousness, warmth, and extraversion) in 257 subjects: 214 patients with neurodegenerative diseases such as FTD, SD, progressive non-fluent aphasia, Alzheimer’s disease, amnestic mild cognitive impairment, corticobasal degeneration, and progressive supranuclear palsy and 43 healthy elderly people. Measures of interpersonal traits were correlated with regional atrophy pattern using voxel-based morphometry (VBM) analysis of structural MR images. Interpersonal traits mapped onto distinct brain regions depending on the degree to which they involved agency and affiliation. Interpersonal traits high in agency related to left dorsolateral prefrontal and left lateral frontopolar regions, whereas interpersonal traits high in affiliation related to right ventromedial prefrontal and right anteromedial temporal regions. Consistent with the existing literature on neural networks underlying social cognition, these results indicate that brain regions related to externally-focused, executive control-related processes underlie agentic interpersonal traits such as dominance, whereas brain regions related to internally-focused, emotion- and reward-related processes underlie affiliative interpersonal traits such as warmth. In addition, these findings indicate that interpersonal traits are subserved by complex neural networks rather than discrete anatomic areas. PMID:19540253

A Malicious Pattern Detection Engine for Embedded Security Systems in the Internet of Things

PubMed Central

Oh, Doohwan; Kim, Deokho; Ro, Won Woo

2014-01-01

With the emergence of the Internet of Things (IoT), a large number of physical objects in daily life have been aggressively connected to the Internet. As the number of objects connected to networks increases, the security systems face a critical challenge due to the global connectivity and accessibility of the IoT. However, it is difficult to adapt traditional security systems to the objects in the IoT, because of their limited computing power and memory size. In light of this, we present a lightweight security system that uses a novel malicious pattern-matching engine. We limit the memory usage of the proposed system in order to make it work on resource-constrained devices. To mitigate performance degradation due to limitations of computation power and memory, we propose two novel techniques, auxiliary shifting and early decision. Through both techniques, we can efficiently reduce the number of matching operations on resource-constrained systems. Experiments and performance analyses show that our proposed system achieves a maximum speedup of 2.14 with an IoT object and provides scalable performance for a large number of patterns. PMID:25521382

High fidelity nanopatterning of proteins onto well-defined surfaces through subtractive contact printing.

PubMed

García, José R; Singh, Ankur; García, Andrés J

2014-01-01

In the pursuit to develop enhanced technologies for cellular bioassays as well as understand single cell interactions with its underlying substrate, the field of biotechnology has extensively utilized lithographic techniques to spatially pattern proteins onto surfaces in user-defined geometries. Microcontact printing (μCP) remains an incredibly useful patterning method due to its inexpensive nature, scalability, and the lack of considerable use of specialized clean room equipment. However, as new technologies emerge that necessitate various nano-sized areas of deposited proteins, traditional μCP methods may not be able to supply users with the needed resolution size. Recently, our group developed a modified "subtractive μCP" method which still retains many of the benefits offered by conventional μCP. Using this technique, we have been able to reach resolution sizes of fibronectin as small as 250 nm in largely spaced arrays for cell culture. In this communication, we present a detailed description of our subtractive μCP procedure that expands on many of the little tips and tricks that together make this procedure an easy and effective method for controlling protein patterning. © 2014 Elsevier Inc. All rights reserved.

Sound Morality: Irritating and Icky Noises Amplify Judgments in Divergent Moral Domains

ERIC Educational Resources Information Center

Seidel, Angelika; Prinz, Jesse

2013-01-01

Theoretical models and correlational research suggest that anger and disgust play different roles in moral judgment. Anger is theorized to underlie reactions to crimes against persons, such as battery and unfairness, and disgust is theorized to underlie reactions to crimes against nature, such as sexual transgressions and cannibalism. To date,…

Are ADHD Symptoms Associated with Delay Aversion or Choice Impulsivity? A General Population Study

ERIC Educational Resources Information Center

Paloyelis, Yannis; Asherson, Philip; Kuntsi, Jonna

2009-01-01

The relationship of attention-deficit/hyperactivity disorder (ADHD) with choice impulsivity is examined. Findings were found to indicate that primary constitutional processes that underlie choice impulsivity and their potential role in behavioral inattention are important. It was also found that behavioral and brain processes that underlie choice…

Building emotional resilience over 14 sessions of emotion focused therapy: Micro-longitudinal analyses of productive emotional patterns.

PubMed

Pascual-Leone, A; Yeryomenko, N; Sawashima, T; Warwar, S

2017-05-04

Pascual-Leone and Greenberg's sequential model of emotional processing has been used to explore process in over 24 studies. This line of research shows emotional processing in good psychotherapy often follows a sequential order, supporting a saw-toothed pattern of change within individual sessions (progressing "2-steps-forward, 1-step-back"). However, one cannot assume that local in-session patterns are scalable across an entire course of therapy. Thus, the primary objective of this exploratory study was to consider how the sequential patterns identified by Pascual-Leone, may apply across entire courses of treatment. Intensive emotion coding in two separate single-case designs were submitted for quantitative analyses of longitudinal patterns. Comprehensive coding in these cases involved recording observations for every emotional event in an entire course of treatment (using the Classification of Affective-Meaning States), which were then treated as a 9-point ordinal scale. Applying multilevel modeling to each of the two cases showed significant patterns of change over a large number of sessions, and those patterns were either nested at the within-session level or observed at the broader session-by-session level of change. Examining successful treatment cases showed several theoretically coherent kinds of temporal patterns, although not always in the same case. Clinical or methodological significance of this article: This is the first paper to demonstrate systematic temporal patterns of emotion over the course of an entire treatment. (1) The study offers a proof of concept that longitudinal patterns in the micro-processes of emotion can be objectively derived and quantified. (2) It also shows that patterns in emotion may be identified on the within-session level, as well as the session-by-session level of analysis. (3) Finally, observed processes over time support the ordered pattern of emotional states hypothesized in Pascual-Leone and Greenberg's ( 2007 ) model of emotional processing.

Parallel scalability and efficiency of vortex particle method for aeroelasticity analysis of bluff bodies

NASA Astrophysics Data System (ADS)

Tolba, Khaled Ibrahim; Morgenthal, Guido

2018-01-01

This paper presents an analysis of the scalability and efficiency of a simulation framework based on the vortex particle method. The code is applied for the numerical aerodynamic analysis of line-like structures. The numerical code runs on multicore CPU and GPU architectures using OpenCL framework. The focus of this paper is the analysis of the parallel efficiency and scalability of the method being applied to an engineering test case, specifically the aeroelastic response of a long-span bridge girder at the construction stage. The target is to assess the optimal configuration and the required computer architecture, such that it becomes feasible to efficiently utilise the method within the computational resources available for a regular engineering office. The simulations and the scalability analysis are performed on a regular gaming type computer.

Design of an H.264/SVC resilient watermarking scheme

NASA Astrophysics Data System (ADS)

Van Caenegem, Robrecht; Dooms, Ann; Barbarien, Joeri; Schelkens, Peter

2010-01-01

The rapid dissemination of media technologies has lead to an increase of unauthorized copying and distribution of digital media. Digital watermarking, i.e. embedding information in the multimedia signal in a robust and imperceptible manner, can tackle this problem. Recently, there has been a huge growth in the number of different terminals and connections that can be used to consume multimedia. To tackle the resulting distribution challenges, scalable coding is often employed. Scalable coding allows the adaptation of a single bit-stream to varying terminal and transmission characteristics. As a result of this evolution, watermarking techniques that are robust against scalable compression become essential in order to control illegal copying. In this paper, a watermarking technique resilient against scalable video compression using the state-of-the-art H.264/SVC codec is therefore proposed and evaluated.

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

PubMed Central

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts. Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ Contact: andre.schumacher@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24149054

Evaluation of 3D printed anatomically scalable transfemoral prosthetic knee.

PubMed

Ramakrishnan, Tyagi; Schlafly, Millicent; Reed, Kyle B

2017-07-01

This case study compares a transfemoral amputee's gait while using the existing Ossur Total Knee 2000 and our novel 3D printed anatomically scalable transfemoral prosthetic knee. The anatomically scalable transfemoral prosthetic knee is 3D printed out of a carbon-fiber and nylon composite that has a gear-mesh coupling with a hard-stop weight-actuated locking mechanism aided by a cross-linked four-bar spring mechanism. This design can be scaled using anatomical dimensions of a human femur and tibia to have a unique fit for each user. The transfemoral amputee who was tested is high functioning and walked on the Computer Assisted Rehabilitation Environment (CAREN) at a self-selected pace. The motion capture and force data that was collected showed that there were distinct differences in the gait dynamics. The data was used to perform the Combined Gait Asymmetry Metric (CGAM), where the scores revealed that the overall asymmetry of the gait on the Ossur Total Knee was more asymmetric than the anatomically scalable transfemoral prosthetic knee. The anatomically scalable transfemoral prosthetic knee had higher peak knee flexion that caused a large step time asymmetry. This made walking on the anatomically scalable transfemoral prosthetic knee more strenuous due to the compensatory movements in adapting to the different dynamics. This can be overcome by tuning the cross-linked spring mechanism to emulate the dynamics of the subject better. The subject stated that the knee would be good for daily use and has the potential to be adapted as a running knee.

Scalable hierarchical PDE sampler for generating spatially correlated random fields using nonmatching meshes: Scalable hierarchical PDE sampler using nonmatching meshes

DOE PAGES

Osborn, Sarah; Zulian, Patrick; Benson, Thomas; ...

2018-01-30

This work describes a domain embedding technique between two nonmatching meshes used for generating realizations of spatially correlated random fields with applications to large-scale sampling-based uncertainty quantification. The goal is to apply the multilevel Monte Carlo (MLMC) method for the quantification of output uncertainties of PDEs with random input coefficients on general and unstructured computational domains. We propose a highly scalable, hierarchical sampling method to generate realizations of a Gaussian random field on a given unstructured mesh by solving a reaction–diffusion PDE with a stochastic right-hand side. The stochastic PDE is discretized using the mixed finite element method on anmore » embedded domain with a structured mesh, and then, the solution is projected onto the unstructured mesh. This work describes implementation details on how to efficiently transfer data from the structured and unstructured meshes at coarse levels, assuming that this can be done efficiently on the finest level. We investigate the efficiency and parallel scalability of the technique for the scalable generation of Gaussian random fields in three dimensions. An application of the MLMC method is presented for quantifying uncertainties of subsurface flow problems. Here, we demonstrate the scalability of the sampling method with nonmatching mesh embedding, coupled with a parallel forward model problem solver, for large-scale 3D MLMC simulations with up to 1.9·109 unknowns.« less

Scalable hierarchical PDE sampler for generating spatially correlated random fields using nonmatching meshes: Scalable hierarchical PDE sampler using nonmatching meshes

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

Osborn, Sarah; Zulian, Patrick; Benson, Thomas

This work describes a domain embedding technique between two nonmatching meshes used for generating realizations of spatially correlated random fields with applications to large-scale sampling-based uncertainty quantification. The goal is to apply the multilevel Monte Carlo (MLMC) method for the quantification of output uncertainties of PDEs with random input coefficients on general and unstructured computational domains. We propose a highly scalable, hierarchical sampling method to generate realizations of a Gaussian random field on a given unstructured mesh by solving a reaction–diffusion PDE with a stochastic right-hand side. The stochastic PDE is discretized using the mixed finite element method on anmore » embedded domain with a structured mesh, and then, the solution is projected onto the unstructured mesh. This work describes implementation details on how to efficiently transfer data from the structured and unstructured meshes at coarse levels, assuming that this can be done efficiently on the finest level. We investigate the efficiency and parallel scalability of the technique for the scalable generation of Gaussian random fields in three dimensions. An application of the MLMC method is presented for quantifying uncertainties of subsurface flow problems. Here, we demonstrate the scalability of the sampling method with nonmatching mesh embedding, coupled with a parallel forward model problem solver, for large-scale 3D MLMC simulations with up to 1.9·109 unknowns.« less

ZnO deposition on metal substrates: Relating fabrication, morphology, and wettability

NASA Astrophysics Data System (ADS)

Beaini, Sara S.; Kronawitter, Coleman X.; Carey, Van P.; Mao, Samuel S.

2013-05-01

It is not common practice to deposit thin films on metal substrates, especially copper, which is a common heat exchanger metal and practical engineering material known for its heat transfer properties. While single crystal substrates offer ideal surfaces with uniform structure for compatibility with oxide deposition, metallic surfaces needed for industrial applications exhibit non-idealities that complicate the fabrication of oxide nanostructure arrays. The following study explored different ZnO fabrication techniques to deposit a (super)hydrophobic thin film of ZnO on a metal substrate, specifically copper, in order to explore its feasibility as an enhanced condensing surface. ZnO was selected for its non-toxicity, ability to be made (super)hydrophobic with hierarchical roughness, and its photoinduced hydrophilicity characteristic, which could be utilized to pattern it to have both hydrophobic-hydrophilic regions. We investigated the variation of ZnO's morphology and wetting state, using SEMs and sessile drop contact angle measurements, as a function of different fabrication techniques: sputtering, pulsed laser deposition (PLD), electrodeposition and annealing Zn. We successfully fabricated (super)hydrophobic ZnO on a mirror finish, commercially available copper substrate using the scalable electrodeposition technique. PLD for ZnO deposition did not prove viable, as the ZnO samples on metal substrates were hydrophilic and the process does not lend itself to scalability. The annealed Zn sheets did not exhibit consistent wetting state results.

Embedded ensemble propagation for improving performance, portability, and scalability of uncertainty quantification on emerging computational architectures

DOE PAGES

Phipps, Eric T.; D'Elia, Marta; Edwards, Harold C.; ...

2017-04-18

In this study, quantifying simulation uncertainties is a critical component of rigorous predictive simulation. A key component of this is forward propagation of uncertainties in simulation input data to output quantities of interest. Typical approaches involve repeated sampling of the simulation over the uncertain input data, and can require numerous samples when accurately propagating uncertainties from large numbers of sources. Often simulation processes from sample to sample are similar and much of the data generated from each sample evaluation could be reused. We explore a new method for implementing sampling methods that simultaneously propagates groups of samples together in anmore » embedded fashion, which we call embedded ensemble propagation. We show how this approach takes advantage of properties of modern computer architectures to improve performance by enabling reuse between samples, reducing memory bandwidth requirements, improving memory access patterns, improving opportunities for fine-grained parallelization, and reducing communication costs. We describe a software technique for implementing embedded ensemble propagation based on the use of C++ templates and describe its integration with various scientific computing libraries within Trilinos. We demonstrate improved performance, portability and scalability for the approach applied to the simulation of partial differential equations on a variety of CPU, GPU, and accelerator architectures, including up to 131,072 cores on a Cray XK7 (Titan).« less

Towards Scalable Deep Learning via I/O Analysis and Optimization

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

Pumma, Sarunya; Si, Min; Feng, Wu-Chun

Deep learning systems have been growing in prominence as a way to automatically characterize objects, trends, and anomalies. Given the importance of deep learning systems, researchers have been investigating techniques to optimize such systems. An area of particular interest has been using large supercomputing systems to quickly generate effective deep learning networks: a phase often referred to as “training” of the deep learning neural network. As we scale existing deep learning frameworks—such as Caffe—on these large supercomputing systems, we notice that the parallelism can help improve the computation tremendously, leaving data I/O as the major bottleneck limiting the overall systemmore » scalability. In this paper, we first present a detailed analysis of the performance bottlenecks of Caffe on large supercomputing systems. Our analysis shows that the I/O subsystem of Caffe—LMDB—relies on memory-mapped I/O to access its database, which can be highly inefficient on large-scale systems because of its interaction with the process scheduling system and the network-based parallel filesystem. Based on this analysis, we then present LMDBIO, our optimized I/O plugin for Caffe that takes into account the data access pattern of Caffe in order to vastly improve I/O performance. Our experimental results show that LMDBIO can improve the overall execution time of Caffe by nearly 20-fold in some cases.« less

Recent progress on the scalable fabrication of hybrid polymer/SiO2 nanophotonic cavity arrays with an encapsulated MoS2 film

NASA Astrophysics Data System (ADS)

Hammer, Sebastian; Mangold, Hans-Moritz; Nguyen, Ariana E.; Martinez-Ta, Dominic; Naghibi Alvillar, Sahar; Bartels, Ludwig; Krenner, Hubert J.

2018-02-01

We review1 the fully-scalable fabrication of a large array of hybrid molybdenum disulfide (MoS2) - silicon dioxide (SiO2) one-dimensional (1D), freestanding photonic-crystal cavities (PCCs) capable of enhancement of the MoS2 photoluminescence (PL) at the narrow cavity resonance. As demonstrated in our prior work [S. Hammer et al., Sci. Rep. 7, 7251 (2017)]1, geometric mode tuning over the wide spectral range of MoS2 PL can be achieved by changing the PC period. In this contribution, we provide a step-by-step description of the fabrication process and give additional detailed information on the degradation of MoS2 by XeF2 vapor. We avoid potential damage of the MoS2 monolayer during the crucial XeF2 etch by refraining from stripping the electron beam (e-beam) resist after dry etching of the photonic crystal pattern. The remaining resist on top of the samples encapsulates and protects the MoS2 film during the entire fabrication process. Albeit the thickness of the remaining resists strongly depends on the fabrication process, the resulting encapsulation of the MoS2 layer improves the confinement to the optical modes and gives rise to a potential enhancement of the light-matter interaction.

Connectivity patterns in cognitive control networks predict naturalistic multitasking ability.

PubMed

Wen, Tanya; Liu, De-Cyuan; Hsieh, Shulan

2018-06-01

Multitasking is a fundamental aspect of everyday life activities. To achieve a complex, multi-component goal, the tasks must be subdivided into sub-tasks and component steps, a critical function of prefrontal networks. The prefrontal cortex is considered to be organized in a cascade of executive processes from the sensorimotor to anterior prefrontal cortex, which includes execution of specific goal-directed action, to encoding and maintaining task rules, and finally monitoring distal goals. In the current study, we used a virtual multitasking paradigm to tap into real-world performance and relate it to each individual's resting-state functional connectivity in fMRI. While did not find any correlation between global connectivity of any of the major networks with multitasking ability, global connectivity of the lateral prefrontal cortex (LPFC) was predictive of multitasking ability. Further analysis showed that multivariate connectivity patterns within the sensorimotor network (SMN), and between-network connectivity of the frontoparietal network (FPN) and dorsal attention network (DAN), predicted individual multitasking ability and could be generalized to novel individuals. Together, these results support previous research that prefrontal networks underlie multitasking abilities and show that connectivity patterns in the cascade of prefrontal networks may explain individual differences in performance. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Motor and cognitive stereotypies in the BTBR T+tf/J mouse model of autism

PubMed Central

Pearson, BL; Pobbe, RLH; Defensor, EB; Oasay, L; Bolivar, VJ; Blanchard, DC; Blanchard, RJ

2010-01-01

The BTBR T+tf/J inbred mouse strain displays a variety of persistent phenotypic alterations similar to those exhibited in autism spectrum disorders. The unique genetic background of the BTBR strain is thought to underlie its lack of reciprocal social interactions, elevated repetitive self-directed grooming and restricted exploratory behaviors. In order to clarify the existence, range and mechanisms of abnormal repetitive behaviors within BTBR mice, we performed detailed analyses of the microstructure of self-grooming patterns and noted increased overall grooming, higher percentages of interruptions in grooming bouts and a concomitant decrease in the proportion of incorrect sequence transitions compared to C57BL/6J inbred mice. Analyses of active phase home cage behavior also revealed an increase in stereotypic bar-biting behavior in the BTBR strain relative to B6 mice. Finally, in a novel object investigation task, BTBR mice exhibited greater baseline preference for specific unfamiliar objects as well as more patterned sequences of sequential investigations of those items. These results suggest that the repetitive, stereotyped behavior patterns of BTBR mice are relatively pervasive and reflect both motor and cognitive mechanisms. Furthermore, other pre-clinical mouse models of autism spectrum disorders may benefit from these more detailed analyses of stereotypic behavior. PMID:21040460

Sex differences in motor and cognitive abilities predicted from human evolutionary history with some implications for models of the visual system.

PubMed

Sanders, Geoff

2013-01-01

This article expands the knowledge base available to sex researchers by reviewing recent evidence for sex differences in coincidence-anticipation timing (CAT), motor control with the hand and arm, and visual processing of stimuli in near and far space. In CAT, the differences are between sex and, therefore, typical of other widely reported sex differences. Men perform CAT tasks with greater accuracy and precision than women, who tend to underestimate time to arrival. Null findings arise because significant sex differences are found with easy but not with difficult tasks. The differences in motor control and visual processing are within sex, and they underlie reciprocal patterns of performance in women and men. Motor control is exerted better by women with the hand than the arm. In contrast, men showed the reverse pattern. Visual processing is performed better by women with stimuli within hand reach (near space) as opposed to beyond hand reach (far space); men showed the reverse pattern. The sex differences seen in each of these three abilities are consistent with the evolutionary selection of men for hunting-related skills and women for gathering-related skills. The implications of the sex differences in visual processing for two visual system models of human vision are discussed.

Global patterns and determinants of forest canopy height.

PubMed

Tao, Shengli; Guo, Qinghua; Li, Chao; Wang, Zhiheng; Fang, Jingyun

2016-12-01

Forest canopy height is an important indicator of forest biomass, species diversity, and other ecosystem functions; however, the climatic determinants that underlie its global patterns have not been fully explored. Using satellite LiDAR-derived forest canopy heights and field measurements of the world's giant trees, combined with climate indices, we evaluated the global patterns and determinants of forest canopy height. The mean canopy height was highest in tropical regions, but tall forests (>50 m) occur at various latitudes. Water availability, quantified by the difference between annual precipitation and annual potential evapotranspiration (P-PET), was the best predictor of global forest canopy height, which supports the hydraulic limitation hypothesis. However, in striking contrast with previous studies, the canopy height exhibited a hump-shaped curve along a gradient of P-PET: it initially increased, then peaked at approximately 680 mm of P-PET, and finally declined, which suggests that excessive water supply negatively affects the canopy height. This trend held true across continents and forest types, and it was also validated using forest inventory data from China and the United States. Our findings provide new insights into the climatic controls of the world's giant trees and have important implications for forest management and improvement of forest growth models. © 2016 by the Ecological Society of America.

Genetic Variation in Serotonin Transporter Modulates Tactile Hyperresponsiveness in ASD

PubMed Central

Schauder, Kimberly B.; Muller, Christopher L.; Veenstra-VanderWeele, Jeremy; Cascio, Carissa J.

2014-01-01

Several lines of evidence implicate dysfunction of the serotonin (5-HT) system in autism spectrum disorder (ASD). Specifically, the serotonin transporter (5-HTT, SERT) has been scrutinized as an ASD candidate risk gene. SERT plays key roles in the development of circuits that underlie sensory function, particularly in the somatosensory system. One previous study in ASD found association of a rare, hyperfunctional SERT variant with sensory aversion, but studies of common SERT variants have never examined sensory symptoms in ASD. Using standardized caregiver assessments of sensory function in children, we evaluated patterns of sensory responsiveness in 47 children with ASD and 38 typically developing (TD) children. Study participants were genotyped for the functional SERT promoter polymorphisms, 5-HTTLPR and rs25531, to test the hypothesis that the higher expressing genotypes would be associated with hyperresponsiveness to touch, a common sensory aversion in ASD. All measures of sensory hypo- and hyperresponsiveness were increased in children with ASD, with hyporesponsive sensory patterns negatively correlated to age and hyperresponsive sensory patterns positively correlated to repetitive behavior. Strikingly, high-expressing SERT genotypes were associated with increased tactile hyperresponsiveness in the ASD group. Our findings indicate genetic variation that increases SERT function may specifically impact somatosensory processing in ASD. PMID:25558276

Space-time correlations in urban sprawl.

PubMed

Hernando, A; Hernando, R; Plastino, A

2014-02-06

Understanding demographic and migrational patterns constitutes a great challenge. Millions of individual decisions, motivated by economic, political, demographic, rational and/or emotional reasons underlie the high complexity of demographic dynamics. Significant advances in quantitatively understanding such complexity have been registered in recent years, as those involving the growth of cities but many fundamental issues still defy comprehension. We present here compelling empirical evidence of a high level of regularity regarding time and spatial correlations in urban sprawl, unravelling patterns about the inertia in the growth of cities and their interaction with each other. By using one of the world's most exhaustive extant demographic data basis--that of the Spanish Government's Institute INE, with records covering 111 years and (in 2011) 45 million people, distributed among more than 8000 population nuclei--we show that the inertia of city growth has a characteristic time of 15 years, and its interaction with the growth of other cities has a characteristic distance of 80 km. Distance is shown to be the main factor that entangles two cities (60% of total correlations). The power of our current social theories is thereby enhanced.

A Diffusion Model Analysis of Decision Biases Affecting Delayed Recognition of Emotional Stimuli.

PubMed

Bowen, Holly J; Spaniol, Julia; Patel, Ronak; Voss, Andreas

2016-01-01

Previous empirical work suggests that emotion can influence accuracy and cognitive biases underlying recognition memory, depending on the experimental conditions. The current study examines the effects of arousal and valence on delayed recognition memory using the diffusion model, which allows the separation of two decision biases thought to underlie memory: response bias and memory bias. Memory bias has not been given much attention in the literature but can provide insight into the retrieval dynamics of emotion modulated memory. Participants viewed emotional pictorial stimuli; half were given a recognition test 1-day later and the other half 7-days later. Analyses revealed that emotional valence generally evokes liberal responding, whereas high arousal evokes liberal responding only at a short retention interval. The memory bias analyses indicated that participants experienced greater familiarity with high-arousal compared to low-arousal items and this pattern became more pronounced as study-test lag increased; positive items evoke greater familiarity compared to negative and this pattern remained stable across retention interval. The findings provide insight into the separate contributions of valence and arousal to the cognitive mechanisms underlying delayed emotion modulated memory.

Development and Plasticity of Cortical Processing Architectures

NASA Astrophysics Data System (ADS)

Singer, Wolf

1995-11-01

One of the basic functions of the cerebral cortex is the analysis and representation of relations among the components of sensory and motor patterns. It is proposed that the cortex applies two complementary strategies to cope with the combinatorial problem posed by the astronomical number of possible relations: (i) the analysis and representation of frequently occurring, behaviorally relevant relations by groups of cells with fixed but broadly tuned response properties; and (ii) the dynamic association of these cells into functionally coherent assemblies. Feedforward connections and reciprocal associative connections, respectively, are thought to underlie these two operations. The architectures of both types of connections are susceptible to experience-dependent modifications during development, but they become fixed in the adult. As development proceeds, feedforward connections also appear to lose much of their functional plasticity, whereas the synapses of the associative connections retain a high susceptibility to use-dependent modifications. The reduced plasticity of feedforward connections is probably responsible for the invariance of cognitive categories acquired early in development. The persistent adaptivity of reciprocal connections is a likely substrate for the ability to generate representations for new perceptual objects and motor patterns throughout life.

Speed and segmentation control mechanisms characterized in rhythmically-active circuits created from spinal neurons produced from genetically-tagged embryonic stem cells

PubMed Central

Sternfeld, Matthew J; Hinckley, Christopher A; Moore, Niall J; Pankratz, Matthew T; Hilde, Kathryn L; Driscoll, Shawn P; Hayashi, Marito; Amin, Neal D; Bonanomi, Dario; Gifford, Wesley D; Sharma, Kamal; Goulding, Martyn; Pfaff, Samuel L

2017-01-01

Flexible neural networks, such as the interconnected spinal neurons that control distinct motor actions, can switch their activity to produce different behaviors. Both excitatory (E) and inhibitory (I) spinal neurons are necessary for motor behavior, but the influence of recruiting different ratios of E-to-I cells remains unclear. We constructed synthetic microphysical neural networks, called circuitoids, using precise combinations of spinal neuron subtypes derived from mouse stem cells. Circuitoids of purified excitatory interneurons were sufficient to generate oscillatory bursts with properties similar to in vivo central pattern generators. Inhibitory V1 neurons provided dual layers of regulation within excitatory rhythmogenic networks - they increased the rhythmic burst frequency of excitatory V3 neurons, and segmented excitatory motor neuron activity into sub-networks. Accordingly, the speed and pattern of spinal circuits that underlie complex motor behaviors may be regulated by quantitatively gating the intra-network cellular activity ratio of E-to-I neurons. DOI: http://dx.doi.org/10.7554/eLife.21540.001 PMID:28195039

Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR

PubMed Central

Yang, Fan; Yu, Xiao; Liu, Chuan; Qu, Chang-Xiu; Gong, Zheng; Liu, Hong-Da; Li, Fa-Hui; Wang, Hong-Mei; He, Dong-Fang; Yi, Fan; Song, Chen; Tian, Chang-Lin; Xiao, Kun-Hong; Wang, Jiang-Yun; Sun, Jin-Peng

2015-01-01

Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 ‘reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by 19F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors. PMID:26347956

On species persistence-time distributions.

PubMed

Suweis, S; Bertuzzo, E; Mari, L; Rodriguez-Iturbe, I; Maritan, A; Rinaldo, A

2012-06-21

We present new theoretical and empirical results on the probability distributions of species persistence times in natural ecosystems. Persistence times, defined as the timespans occurring between species' colonization and local extinction in a given geographic region, are empirically estimated from local observations of species' presence/absence. A connected sampling problem is presented, generalized and solved analytically. Species persistence is shown to provide a direct connection with key spatial macroecological patterns like species-area and endemics-area relationships. Our empirical analysis pertains to two different ecosystems and taxa: a herbaceous plant community and a estuarine fish database. Despite the substantial differences in ecological interactions and spatial scales, we confirm earlier evidence on the general properties of the scaling of persistence times, including the predicted effects of the structure of the spatial interaction network. The framework tested here allows to investigate directly nature and extent of spatial effects in the context of ecosystem dynamics. The notable coherence between spatial and temporal macroecological patterns, theoretically derived and empirically verified, is suggested to underlie general features of the dynamic evolution of ecosystems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Patent ductus arteriosus in mice with smooth muscle-specific Jag1 deletion

PubMed Central

Feng, Xuesong; Krebs, Luke T.; Gridley, Thomas

2010-01-01

The ductus arteriosus is an arterial vessel that shunts blood flow away from the lungs during fetal life, but normally occludes after birth to establish the adult circulation pattern. Failure of the ductus arteriosus to close after birth is termed patent ductus arteriosus and is one of the most common congenital heart defects. Mice with smooth muscle cell-specific deletion of Jag1, which encodes a Notch ligand, die postnatally from patent ductus arteriosus. These mice exhibit defects in contractile smooth muscle cell differentiation in the vascular wall of the ductus arteriosus and adjacent descending aorta. These defects arise through an inability to propagate the JAG1-Notch signal via lateral induction throughout the width of the vascular wall. Both heterotypic endothelial smooth muscle cell interactions and homotypic vascular smooth muscle cell interactions are required for normal patterning and differentiation of the ductus arteriosus and adjacent descending aorta. This new model for a common congenital heart defect provides novel insights into the genetic programs that underlie ductus arteriosus development and closure. PMID:21068062

Beyond Columnar Organization: Cell Type- and Target Layer-Specific Principles of Horizontal Axon Projection Patterns in Rat Vibrissal Cortex

PubMed Central

Narayanan, Rajeevan T.; Egger, Robert; Johnson, Andrew S.; Mansvelder, Huibert D.; Sakmann, Bert; de Kock, Christiaan P.J.; Oberlaender, Marcel

2015-01-01

Vertical thalamocortical afferents give rise to the elementary functional units of sensory cortex, cortical columns. Principles that underlie communication between columns remain however unknown. Here we unravel these by reconstructing in vivo-labeled neurons from all excitatory cell types in the vibrissal part of rat primary somatosensory cortex (vS1). Integrating the morphologies into an exact 3D model of vS1 revealed that the majority of intracortical (IC) axons project far beyond the borders of the principal column. We defined the corresponding innervation volume as the IC-unit. Deconstructing this structural cortical unit into its cell type-specific components, we found asymmetric projections that innervate columns of either the same whisker row or arc, and which subdivide vS1 into 2 orthogonal [supra-]granular and infragranular strata. We show that such organization could be most effective for encoding multi whisker inputs. Communication between columns is thus organized by multiple highly specific horizontal projection patterns, rendering IC-units as the primary structural entities for processing complex sensory stimuli. PMID:25838038

Vortex arrays and ciliary tangles underlie the feeding-swimming trade-off in starfish larvae

NASA Astrophysics Data System (ADS)

Gilpin, William; Prakash, Vivek N.; Prakash, Manu

2017-04-01

Many marine invertebrates have larval stages covered in linear arrays of beating cilia, which propel the animal while simultaneously entraining planktonic prey. These bands are strongly conserved across taxa spanning four major superphyla, and they are responsible for the unusual morphologies of many invertebrate larvae. However, few studies have investigated their underlying hydrodynamics. Here, we study the ciliary bands of starfish larvae, and discover a beautiful pattern of slowly evolving vortices that surrounds the swimming animals. Closer inspection of the bands reveals unusual ciliary `tangles' analogous to topological defects that break up and re-form as the animal adjusts its swimming stroke. Quantitative experiments and modelling demonstrate that these vortices create a physical trade-off between feeding and swimming in heterogeneous environments, which manifests as distinct flow patterns or `eigenstrokes' representing each behaviour--potentially implicating neuronal control of cilia. This quantitative interplay between larval form and hydrodynamic function may generalize to other invertebrates with ciliary bands, and illustrates the potential effects of active boundary conditions in other biological and synthetic systems.

Parallel processing architecture for H.264 deblocking filter on multi-core platforms

NASA Astrophysics Data System (ADS)

Prasad, Durga P.; Sonachalam, Sekar; Kunchamwar, Mangesh K.; Gunupudi, Nageswara Rao

2012-03-01

Massively parallel computing (multi-core) chips offer outstanding new solutions that satisfy the increasing demand for high resolution and high quality video compression technologies such as H.264. Such solutions not only provide exceptional quality but also efficiency, low power, and low latency, previously unattainable in software based designs. While custom hardware and Application Specific Integrated Circuit (ASIC) technologies may achieve lowlatency, low power, and real-time performance in some consumer devices, many applications require a flexible and scalable software-defined solution. The deblocking filter in H.264 encoder/decoder poses difficult implementation challenges because of heavy data dependencies and the conditional nature of the computations. Deblocking filter implementations tend to be fixed and difficult to reconfigure for different needs. The ability to scale up for higher quality requirements such as 10-bit pixel depth or a 4:2:2 chroma format often reduces the throughput of a parallel architecture designed for lower feature set. A scalable architecture for deblocking filtering, created with a massively parallel processor based solution, means that the same encoder or decoder will be deployed in a variety of applications, at different video resolutions, for different power requirements, and at higher bit-depths and better color sub sampling patterns like YUV, 4:2:2, or 4:4:4 formats. Low power, software-defined encoders/decoders may be implemented using a massively parallel processor array, like that found in HyperX technology, with 100 or more cores and distributed memory. The large number of processor elements allows the silicon device to operate more efficiently than conventional DSP or CPU technology. This software programing model for massively parallel processors offers a flexible implementation and a power efficiency close to that of ASIC solutions. This work describes a scalable parallel architecture for an H.264 compliant deblocking filter for multi core platforms such as HyperX technology. Parallel techniques such as parallel processing of independent macroblocks, sub blocks, and pixel row level are examined in this work. The deblocking architecture consists of a basic cell called deblocking filter unit (DFU) and dependent data buffer manager (DFM). The DFU can be used in several instances, catering to different performance needs the DFM serves the data required for the different number of DFUs, and also manages all the neighboring data required for future data processing of DFUs. This approach achieves the scalability, flexibility, and performance excellence required in deblocking filters.

Fabrication of Scalable Indoor Light Energy Harvester and Study for Agricultural IoT Applications

NASA Astrophysics Data System (ADS)

Watanabe, M.; Nakamura, A.; Kunii, A.; Kusano, K.; Futagawa, M.

2015-12-01

A scalable indoor light energy harvester was fabricated by microelectromechanical system (MEMS) and printing hybrid technology and evaluated for agricultural IoT applications under different environmental input power density conditions, such as outdoor farming under the sun, greenhouse farming under scattered lighting, and a plant factory under LEDs. We fabricated and evaluated a dye- sensitized-type solar cell (DSC) as a low cost and “scalable” optical harvester device. We developed a transparent conductive oxide (TCO)-less process with a honeycomb metal mesh substrate fabricated by MEMS technology. In terms of the electrical and optical properties, we achieved scalable harvester output power by cell area sizing. Second, we evaluated the dependence of the input power scalable characteristics on the input light intensity, spectrum distribution, and light inlet direction angle, because harvested environmental input power is unstable. The TiO2 fabrication relied on nanoimprint technology, which was designed for optical optimization and fabrication, and we confirmed that the harvesters are robust to a variety of environments. Finally, we studied optical energy harvesting applications for agricultural IoT systems. These scalable indoor light harvesters could be used in many applications and situations in smart agriculture.

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

DOE PAGES

Desai, Ajit; Khalil, Mohammad; Pettit, Chris; ...

2017-09-21

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolutionmore » in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.« less

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

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

Desai, Ajit; Khalil, Mohammad; Pettit, Chris

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolutionmore » in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.« less

Theoretical and Empirical Analysis of a Spatial EA Parallel Boosting Algorithm.

PubMed

Kamath, Uday; Domeniconi, Carlotta; De Jong, Kenneth

2018-01-01

Many real-world problems involve massive amounts of data. Under these circumstances learning algorithms often become prohibitively expensive, making scalability a pressing issue to be addressed. A common approach is to perform sampling to reduce the size of the dataset and enable efficient learning. Alternatively, one customizes learning algorithms to achieve scalability. In either case, the key challenge is to obtain algorithmic efficiency without compromising the quality of the results. In this article we discuss a meta-learning algorithm (PSBML) that combines concepts from spatially structured evolutionary algorithms (SSEAs) with concepts from ensemble and boosting methodologies to achieve the desired scalability property. We present both theoretical and empirical analyses which show that PSBML preserves a critical property of boosting, specifically, convergence to a distribution centered around the margin. We then present additional empirical analyses showing that this meta-level algorithm provides a general and effective framework that can be used in combination with a variety of learning classifiers. We perform extensive experiments to investigate the trade-off achieved between scalability and accuracy, and robustness to noise, on both synthetic and real-world data. These empirical results corroborate our theoretical analysis, and demonstrate the potential of PSBML in achieving scalability without sacrificing accuracy.

Progressive Dictionary Learning with Hierarchical Predictive Structure for Scalable Video Coding.

PubMed

Dai, Wenrui; Shen, Yangmei; Xiong, Hongkai; Jiang, Xiaoqian; Zou, Junni; Taubman, David

2017-04-12

Dictionary learning has emerged as a promising alternative to the conventional hybrid coding framework. However, the rigid structure of sequential training and prediction degrades its performance in scalable video coding. This paper proposes a progressive dictionary learning framework with hierarchical predictive structure for scalable video coding, especially in low bitrate region. For pyramidal layers, sparse representation based on spatio-temporal dictionary is adopted to improve the coding efficiency of enhancement layers (ELs) with a guarantee of reconstruction performance. The overcomplete dictionary is trained to adaptively capture local structures along motion trajectories as well as exploit the correlations between neighboring layers of resolutions. Furthermore, progressive dictionary learning is developed to enable the scalability in temporal domain and restrict the error propagation in a close-loop predictor. Under the hierarchical predictive structure, online learning is leveraged to guarantee the training and prediction performance with an improved convergence rate. To accommodate with the stateof- the-art scalable extension of H.264/AVC and latest HEVC, standardized codec cores are utilized to encode the base and enhancement layers. Experimental results show that the proposed method outperforms the latest SHVC and HEVC simulcast over extensive test sequences with various resolutions.

Scalable hybrid computation with spikes.

PubMed

Sarpeshkar, Rahul; O'Halloran, Micah

2002-09-01

We outline a hybrid analog-digital scheme for computing with three important features that enable it to scale to systems of large complexity: First, like digital computation, which uses several one-bit precise logical units to collectively compute a precise answer to a computation, the hybrid scheme uses several moderate-precision analog units to collectively compute a precise answer to a computation. Second, frequent discrete signal restoration of the analog information prevents analog noise and offset from degrading the computation. And, third, a state machine enables complex computations to be created using a sequence of elementary computations. A natural choice for implementing this hybrid scheme is one based on spikes because spike-count codes are digital, while spike-time codes are analog. We illustrate how spikes afford easy ways to implement all three components of scalable hybrid computation. First, as an important example of distributed analog computation, we show how spikes can create a distributed modular representation of an analog number by implementing digital carry interactions between spiking analog neurons. Second, we show how signal restoration may be performed by recursive spike-count quantization of spike-time codes. And, third, we use spikes from an analog dynamical system to trigger state transitions in a digital dynamical system, which reconfigures the analog dynamical system using a binary control vector; such feedback interactions between analog and digital dynamical systems create a hybrid state machine (HSM). The HSM extends and expands the concept of a digital finite-state-machine to the hybrid domain. We present experimental data from a two-neuron HSM on a chip that implements error-correcting analog-to-digital conversion with the concurrent use of spike-time and spike-count codes. We also present experimental data from silicon circuits that implement HSM-based pattern recognition using spike-time synchrony. We outline how HSMs may be used to perform learning, vector quantization, spike pattern recognition and generation, and how they may be reconfigured.

TU-CD-BRB-05: Radiation Damage Signature of White Matter Fiber Bundles Using Diffusion Tensor Imaging (DTI)

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

Zhu, T; Chapman, C; Lawrence, T

2015-06-15

Purpose: To develop an automated and scalable approach and identify temporal, spatial and dosimetric patterns of radiation damage of white matter (WM) fibers following partial brain irradiation. Methods: An automated and scalable approach was developed to extract DTI features of 22 major WM fibers from 33 patients with low-grade/benign tumors treated by radiation therapy (RT). DTI scans of the patients were performed pre-RT, 3- and 6-week during RT, and 1, 6 and 18 months after RT. The automated tractography analysis was applied to 198 datasets as: (1) intra-subject registration of longitudinal DTI, (2) spatial normalization of individual-patient DTI to themore » Johns Hopkins WM Atlas, (3) automatic fiber tracking regulated by the WM Atlas, and (4) segmentation of WM into 22 major tract profiles. Longitudinal percentage changes in fractional anisotropy (FA), and mean, axial and radial diffusivity (MD/AD/RD) of each tract from pre-RT were quantified and correlated to 95%, 90% and 80% percentiles of doses and mean doses received by the tract. Heatmaps were used to identify clusters of significant correlation and reveal temporal, spatial and dosimetric signatures of WM damage. A multivariate linear regression was further carried out to determine influence of clinical factors. Results: Of 22 tracts, AD/MD changes in 12 tracts had significant correlation with doses, especially at 6 and 18 months post-RT, indicating progressive radiation damage after RT. Most interestingly, the DTI-index changes in the elongated tracts were associated with received maximum doses, suggesting a serial-structure behavior; while short association fibers were affected by mean doses, indicating a parallel-structure response. Conclusion: Using an automated DTI-tractography analysis of whole brain WM fibers, we reveal complex radiation damage patterns of WM fibers. Damage in WM fibers that play an important role in the neural network could be associated with late neurocognitive function declines after brain irradiation. NIH NS064973.« less

Providing scalable system software for high-end simulations

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

Greenberg, D.

1997-12-31

Detailed, full-system, complex physics simulations have been shown to be feasible on systems containing thousands of processors. In order to manage these computer systems it has been necessary to create scalable system services. In this talk Sandia`s research on scalable systems will be described. The key concepts of low overhead data movement through portals and of flexible services through multi-partition architectures will be illustrated in detail. The talk will conclude with a discussion of how these techniques can be applied outside of the standard monolithic MPP system.

The development of a scalable parallel 3-D CFD algorithm for turbomachinery. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Luke, Edward Allen

1993-01-01

Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.

Bath salts and synthetic cathinones: An emerging designer drug phenomenon

PubMed Central

German, Christopher L.; Fleckenstein, Annette E.; Hanson, Glen R.

2014-01-01

The synthetic cathinones are an emerging class of designer drugs abused for psychostimulant and hallucinogenic effects similar to cocaine, methylenedioxymethamphetamine (MDMA), or other amphetamines. Abuse of synthetic cathinones, frequently included in products sold as ‘bath salts’, became prevalent in early 2009, leading to legislative classification throughout Europe in 2010 and schedule I classification within the United States in 2011. Recent pre-clinical and clinical studies indicate dysregulation of central monoamine systems are a principal mechanism of synthetic cathinone action and presumably underlie the behavioral effects and abuse liability associated with these drugs. This review provides insight into the development of synthetic cathinones as substances of abuse, current patterns of their abuse, known mechanisms of their action and toxicology, and the benefits and drawbacks of their classification. PMID:23911668

A new look at Op art: towards a simple explanation of illusory motion.

PubMed

Zanker, Johannes M; Walker, Robin

2004-04-01

Vivid motion illusions created by some Op art paintings are at the centre of a lively scientific debate about possible mechanisms that might underlie these phenomena. Here we review emerging evidence from a new approach that combines perceptual judgements of the illusion and observations of eye movements with simulations of the induced optic flow. This work suggests that the small involuntary saccades which participants make when viewing such Op art patterns would generate an incoherent distribution of motion signals that resemble the perceptual effects experienced by the observers. The combined experimental and computational evidence supports the view that the illusion is indeed caused by involuntary image displacements picked up by low-level motion detectors, and further suggests that coherent motion signals are crucial to perceive a stable world.

A new look at Op art: towards a simple explanation of illusory motion

NASA Astrophysics Data System (ADS)

Zanker, Johannes M.; Walker, Robin

Vivid motion illusions created by some Op art paintings are at the centre of a lively scientific debate about possible mechanisms that might underlie these phenomena. Here we review emerging evidence from a new approach that combines perceptual judgements of the illusion and observations of eye movements with simulations of the induced optic flow. This work suggests that the small involuntary saccades which participants make when viewing such Op art patterns would generate an incoherent distribution of motion signals that resemble the perceptual effects experienced by the observers. The combined experimental and computational evidence supports the view that the illusion is indeed caused by involuntary image displacements picked up by low-level motion detectors, and further suggests that coherent motion signals are crucial to perceive a stable world.

Psychological characteristics of Internet dating service users: the effect of self-esteem, involvement, and sociability on the use of Internet dating services.

PubMed

Kim, Mikyoung; Kwon, Kyoung-Nan; Lee, Mira

2009-08-01

This study explores the three major consumer characteristics that underlie the use of Internet dating services: self-esteem, involvement in romantic relationships, and sociability. A significant three-way interaction effect among these factors emerged. Among sociable people, individuals with high self-esteem are more likely to use Internet dating services than are those with low self-esteem when they are highly involved in romantic relationships. The opposite pattern was revealed for sociable people, however, when they are less involved in romantic relationships. That is, individuals with low self-esteem used Internet dating services more often than did those with high self-esteem when romantic relationships were not important. The implications for academic researchers and practitioners are discussed.

The NIH Science of Behavior Change Program: Transforming the science through a focus on mechanisms of change.

PubMed

Nielsen, Lisbeth; Riddle, Melissa; King, Jonathan W; Aklin, Will M; Chen, Wen; Clark, David; Collier, Elaine; Czajkowski, Susan; Esposito, Layla; Ferrer, Rebecca; Green, Paige; Hunter, Christine; Kehl, Karen; King, Rosalind; Onken, Lisa; Simmons, Janine M; Stoeckel, Luke; Stoney, Catherine; Tully, Lois; Weber, Wendy

2018-02-01

The goal of the NIH Science of Behavior Change (SOBC) Common Fund Program is to provide the basis for an experimental medicine approach to behavior change that focuses on identifying and measuring the mechanisms that underlie behavioral patterns we are trying to change. This paper frames the development of the program within a discussion of the substantial disease burden in the U.S. attributable to behavioral factors, and details our strategies for breaking down the disease- and condition-focused silos in the behavior change field to accelerate discovery and translation. These principles serve as the foundation for our vision for a unified science of behavior change at the NIH and in the broader research community. Copyright © 2017. Published by Elsevier Ltd.

Turning Mechanics During Swimming by Oblate Hydromedusae

NASA Astrophysics Data System (ADS)

Costello, J.; Colin, S.; Sutherland, K.; Gemmell, B. J.

2016-02-01

Maneuverability is critical to the success of many species. Selective forces acting over millions of years have resulted in a range of capabilities currently unmatched by machines. Thus, understanding animal control of fluids for maneuvering has both biological and engineering applications. Medusae are radially symmetrical swimmers that must use asymmetric body motions to change direction during turning maneuvers. But what types of asymmetric motions are useful and how do they interact with surrounding fluids to generate rotational forces? We used high speed digital particle image velocimetry (DPIV) to investigate comparative swimming patterns of three hydromedusan species (Aequorea victoria, Clytia gregaria and Mitrocoma cellularia). We provide evidence for consistent animal-fluid interactions that underlie turning mechanics of oblate hydromedusae and provide new insights into the modulation and control of vorticity for low-speed animal maneuvering.

Event-related potential evidence of processing lexical pitch-accent in auditory Japanese sentences.

PubMed

Koso, Ayumi; Hagiwara, Hiroko

2009-09-23

Neural mechanisms that underlie the processing of lexical pitch-accent in auditory Japanese were investigated by using event-related potentials. Native speakers of Japanese listened to two types of short sentences, both consisting of a noun and a verb. The sentences ended with a verb with either congruous or incongruous pitch-accent pattern, where pitch-accent violations occur at the verb in the incongruent condition. The event-related potentials of the incongruent condition showed an increased widespread negativity that started 400 ms after the onset of the deviant lexical item and lasted for about 400 ms. These results suggest that the negativity evoked by violations in lexical-pitch accent indicates electrophysiological evidence for the online processing of lexical-pitch accent in auditory Japanese.

Reliable, responsive pacemaking and pattern generation with minimal cell numbers: the crustacean cardiac ganglion.

PubMed

Cooke, Ian M

2002-04-01

Investigations of the electrophysiology of crustacean cardiac ganglia over the last half-century are reviewed for their contributions to elucidating the cellular mechanisms and interactions by which a small (as few as nine cells) neuronal network accomplishes extremely reliable, rhythmical, patterned activation of muscular activity-in this case, beating of the neurogenic heart. This ganglion is thus a model for pacemaking and central pattern generation. Favorable anatomy has permitted voltage- and space-clamp analyses of voltage-dependent ionic currents that endow each neuron with the intrinsic ability to respond with rhythmical, patterned impulse activity to nonpatterned stimulation. The crustacean soma and initial axon segment do not support impulse generation but integrate input from stretch-sensitive dendrites and electrotonic and chemically mediated synapses on axonal processes in neuropils. The soma and initial axon produce a depolarization-activated, calcium-mediated, sustained potential, the "driver potential," so-called because it drives a train of impulses at the "trigger zone" of the axon. Extreme reliability results from redundancy and the electrotonic coupling and synaptic interaction among all the neurons. Complex modulation by central nervous system inputs and by neurohormones to adjust heart pumping to physiological demands has long been demonstrated, but much remains to be learned about the cellular and molecular mechanisms of action. The continuing relevance of the crustacean cardiac ganglion as a relatively simple model for pacemaking and central pattern generation is confirmed by the rapidly widening documentation of intrinsic potentials such as plateau potentials in neurons of all major animal groups. The suite of ionic currents (a slowly inactivating calcium current and various potassium currents, with variations) observed for the crustacean cardiac ganglion have been implicated in or proven to underlie a majority of the intrinsic potentials of neurons involved in pattern generation.

Learning new sequential stepping patterns requires striatal plasticity during the earliest phase of acquisition.

PubMed

Nakamura, Toru; Nagata, Masatoshi; Yagi, Takeshi; Graybiel, Ann M; Yamamori, Tetsuo; Kitsukawa, Takashi

2017-04-01

Animals including humans execute motor behavior to reach their goals. For this purpose, they must choose correct strategies according to environmental conditions and shape many parameters of their movements, including their serial order and timing. To investigate the neurobiology underlying such skills, we used a multi-sensor equipped, motor-driven running wheel with adjustable sequences of foothold pegs on which mice ran to obtain water reward. When the peg patterns changed from a familiar pattern to a new pattern, the mice had to learn and implement new locomotor strategies in order to receive reward. We found that the accuracy of stepping and the achievement of water reward improved with the new learning after changes in the peg-pattern, and c-Fos expression levels assayed after the first post-switch session were high in both dorsolateral striatum and motor cortex, relative to post-switch plateau levels. Combined in situ hybridization and immunohistochemistry of striatal sections demonstrated that both enkephalin-positive (indirect pathway) neurons and substance P-positive (direct pathway) neurons were recruited specifically after the pattern switches, as were interneurons expressing neuronal nitric oxide synthase. When we blocked N-methyl-D-aspartate (NMDA) receptors in the dorsolateral striatum by injecting the NMDA receptor antagonist, D-2-amino-5-phosphonopentanoic acid (AP5), we found delays in early post-switch improvement in performance. These findings suggest that the dorsolateral striatum is activated on detecting shifts in environment to adapt motor behavior to the new context via NMDA-dependent plasticity, and that this plasticity may underlie forming and breaking skills and habits as well as to behavioral difficulties in clinical disorders. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

[Geographic patterns and ecological factors correlates of snake species richness in China].

PubMed

Cai, Bo; Huang, Yong; Chen, Yue-Ying; Hu, Jun-Hua; Guo, Xian-Guang; Wang, Yue-Zhao

2012-08-01

Understanding large-scale geographic patterns of species richness as well its underlying mechanisms are among the most significant objectives of macroecology and biogeography. The ecological hypothesis is one of the most accepted explanations of this mechanism. Here, we studied the geographic patterns of snakes and investigated the relationships between species richness and ecological factors in China at a spatial resolution of 100 km×100 km. We obtained the eigenvector-based spatial filters by Principal Coordinates Neighbor Matrices, and then analyzed ecological factors by multiple regression analysis. The results indicated several things: (1) species richness of snakes showed multi-peak patterns along both the latitudinal and longitudinal gradient. The areas of highest richness of snake are tropics and subtropical areas of Oriental realm in China while the areas of lowest richness are Qinghai-Tibet Plateau, the grasslands and deserts in northern China, Yangtze-Huai Plain, Two-lake Plain, and the Poyang-lake Plain; (2) results of multiple regression analysis explained a total of 56.5% variance in snake richness. Among ecological factors used to explore the species richness patterns, we found the best factors were the normalized difference vegetation index, precipitation in the coldest quarter and temperature annual range ; (3) our results indicated that the model based on the significant variables that (P<0.05) uses a combination of precipitation of coldest quarter, normalized difference vegetation index and temperature annual range is the most parsimonious model for explaining the mechanism of snake richness in China. This finding demonstrates that different ecological factors work together to affect the geographic distribution of snakes in China. Studying the mechanisms that underlie these geographic patterns are complex, so we must carefully consider the choice of impact-factors and the influence of human activities.

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

Janjusic, Tommy; Kartsaklis, Christos

Memory scalability is an enduring problem and bottleneck that plagues many parallel codes. Parallel codes designed for High Performance Systems are typically designed over the span of several, and in some instances 10+, years. As a result, optimization practices which were appropriate for earlier systems may no longer be valid and thus require careful optimization consideration. Specifically, parallel codes whose memory footprint is a function of their scalability must be carefully considered for future exa-scale systems. In this paper we present a methodology and tool to study the memory scalability of parallel codes. Using our methodology we evaluate an applicationmore » s memory footprint as a function of scalability, which we coined memory efficiency, and describe our results. In particular, using our in-house tools we can pinpoint the specific application components which contribute to the application s overall memory foot-print (application data- structures, libraries, etc.).« less

A novel processing platform for post tape out flows

NASA Astrophysics Data System (ADS)

Vu, Hien T.; Kim, Soohong; Word, James; Cai, Lynn Y.

2018-03-01

As the computational requirements for post tape out (PTO) flows increase at the 7nm and below technology nodes, there is a need to increase the scalability of the computational tools in order to reduce the turn-around time (TAT) of the flows. Utilization of design hierarchy has been one proven method to provide sufficient partitioning to enable PTO processing. However, as the data is processed through the PTO flow, its effective hierarchy is reduced. The reduction is necessary to achieve the desired accuracy. Also, the sequential nature of the PTO flow is inherently non-scalable. To address these limitations, we are proposing a quasi-hierarchical solution that combines multiple levels of parallelism to increase the scalability of the entire PTO flow. In this paper, we describe the system and present experimental results demonstrating the runtime reduction through scalable processing with thousands of computational cores.

Scalable architecture for a room temperature solid-state quantum information processor.

PubMed

Yao, N Y; Jiang, L; Gorshkov, A V; Maurer, P C; Giedke, G; Cirac, J I; Lukin, M D

2012-04-24

The realization of a scalable quantum information processor has emerged over the past decade as one of the central challenges at the interface of fundamental science and engineering. Here we propose and analyse an architecture for a scalable, solid-state quantum information processor capable of operating at room temperature. Our approach is based on recent experimental advances involving nitrogen-vacancy colour centres in diamond. In particular, we demonstrate that the multiple challenges associated with operation at ambient temperature, individual addressing at the nanoscale, strong qubit coupling, robustness against disorder and low decoherence rates can be simultaneously achieved under realistic, experimentally relevant conditions. The architecture uses a novel approach to quantum information transfer and includes a hierarchy of control at successive length scales. Moreover, it alleviates the stringent constraints currently limiting the realization of scalable quantum processors and will provide fundamental insights into the physics of non-equilibrium many-body quantum systems.

Scalable free energy calculation of proteins via multiscale essential sampling

NASA Astrophysics Data System (ADS)

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2010-12-01

A multiscale simulation method, "multiscale essential sampling (MSES)," is proposed for calculating free energy surface of proteins in a sizable dimensional space with good scalability. In MSES, the configurational sampling of a full-dimensional model is enhanced by coupling with the accelerated dynamics of the essential degrees of freedom. Applying the Hamiltonian exchange method to MSES can remove the biasing potential from the coupling term, deriving the free energy surface of the essential degrees of freedom. The form of the coupling term ensures good scalability in the Hamiltonian exchange. As a test application, the free energy surface of the folding process of a miniprotein, chignolin, was calculated in the continuum solvent model. Results agreed with the free energy surface derived from the multicanonical simulation. Significantly improved scalability with the MSES method was clearly shown in the free energy calculation of chignolin in explicit solvent, which was achieved without increasing the number of replicas in the Hamiltonian exchange.

Non-peristaltic patterns of motor activity in the guinea-pig proximal colon.

PubMed

Hennig, G W; Gregory, S; Brookes, S J H; Costa, M

2010-06-01

The guinea-pig proximal colon contains semi-solid feces which are propelled by intermittent neural peristaltic waves to the distal colon, where solid pellets are formed. Between propulsive periods, complex motor patterns underlie fluid re-absorption and mixing of contents. Spatio-temporal analysis of video recordings were used to investigate neural and myogenic patterns of non-peristaltic motor activity. At low distension (6 cmH(2)O), two major motor patterns were seen. Narrow rings of constriction (abrupt contractions) occurred at 19 cpm. These previously undescribed contractions occurred, almost simultaneously, at many points along the preparation, with a calculated propagation velocity of 110 mm s(-1). They were abolished by hexamethonium and by tetrodotoxin, indicating they were neurally mediated. Inhibition of nitric oxide synthase resulted in increased frequency of 'abrupt contractions' suggesting ongoing inhibitory modulation by endogenous nitric oxide. After tetrodotoxin, another distinct motor pattern was revealed; 'ripples'(1) consisted of shallow rings of contraction, occurring at 18 cpm and propagating at 2.7-2.9 mm s(-1) orally or aborally from multiple initiation sites. The frequency of 'ripples' increased as intraluminal pressure was raised, becoming very irregular at high distensions. L-type calcium channel blockers and openers affected the amplitude of 'ripples'. No frequency gradient of 'ripples' along the proximal colon was detected. This absence explains the multiple initiation sites which often shifted over time, and the oral and aboral propagation of 'ripples'. The interaction of myogenic 'ripples' with neurogenic 'abrupt contractions' generates localized alternating rings of contractions and dilatation, well suited to effective mixing of contents.

Integration of an intelligent systems behavior simulator and a scalable soldier-machine interface

NASA Astrophysics Data System (ADS)

Johnson, Tony; Manteuffel, Chris; Brewster, Benjamin; Tierney, Terry

2007-04-01

As the Army's Future Combat Systems (FCS) introduce emerging technologies and new force structures to the battlefield, soldiers will increasingly face new challenges in workload management. The next generation warfighter will be responsible for effectively managing robotic assets in addition to performing other missions. Studies of future battlefield operational scenarios involving the use of automation, including the specification of existing and proposed technologies, will provide significant insight into potential problem areas regarding soldier workload. The US Army Tank Automotive Research, Development, and Engineering Center (TARDEC) is currently executing an Army technology objective program to analyze and evaluate the effect of automated technologies and their associated control devices with respect to soldier workload. The Human-Robotic Interface (HRI) Intelligent Systems Behavior Simulator (ISBS) is a human performance measurement simulation system that allows modelers to develop constructive simulations of military scenarios with various deployments of interface technologies in order to evaluate operator effectiveness. One such interface is TARDEC's Scalable Soldier-Machine Interface (SMI). The scalable SMI provides a configurable machine interface application that is capable of adapting to several hardware platforms by recognizing the physical space limitations of the display device. This paper describes the integration of the ISBS and Scalable SMI applications, which will ultimately benefit both systems. The ISBS will be able to use the Scalable SMI to visualize the behaviors of virtual soldiers performing HRI tasks, such as route planning, and the scalable SMI will benefit from stimuli provided by the ISBS simulation environment. The paper describes the background of each system and details of the system integration approach.

Using the eServices platform for detecting behavior patterns deviation in the elderly assisted living: a case study.

PubMed

Marcelino, Isabel; Lopes, David; Reis, Michael; Silva, Fernando; Laza, Rosalía; Pereira, António

2015-01-01

World's aging population is rising and the elderly are increasingly isolated socially and geographically. As a consequence, in many situations, they need assistance that is not granted in time. In this paper, we present a solution that follows the CRISP-DM methodology to detect the elderly's behavior pattern deviations that may indicate possible risk situations. To obtain these patterns, many variables are aggregated to ensure the alert system reliability and minimize eventual false positive alert situations. These variables comprehend information provided by body area network (BAN), by environment sensors, and also by the elderly's interaction in a service provider platform, called eServices--Elderly Support Service Platform. eServices is a scalable platform aggregating a service ecosystem developed specially for elderly people. This pattern recognition will further activate the adequate response. With the system evolution, it will learn to predict potential danger situations for a specified user, acting preventively and ensuring the elderly's safety and well-being. As the eServices platform is still in development, synthetic data, based on real data sample and empiric knowledge, is being used to populate the initial dataset. The presented work is a proof of concept of knowledge extraction using the eServices platform information. Regardless of not using real data, this work proves to be an asset, achieving a good performance in preventing alert situations.

Using the eServices Platform for Detecting Behavior Patterns Deviation in the Elderly Assisted Living: A Case Study

PubMed Central

Marcelino, Isabel; Laza, Rosalía

2015-01-01

World's aging population is rising and the elderly are increasingly isolated socially and geographically. As a consequence, in many situations, they need assistance that is not granted in time. In this paper, we present a solution that follows the CRISP-DM methodology to detect the elderly's behavior pattern deviations that may indicate possible risk situations. To obtain these patterns, many variables are aggregated to ensure the alert system reliability and minimize eventual false positive alert situations. These variables comprehend information provided by body area network (BAN), by environment sensors, and also by the elderly's interaction in a service provider platform, called eServices—Elderly Support Service Platform. eServices is a scalable platform aggregating a service ecosystem developed specially for elderly people. This pattern recognition will further activate the adequate response. With the system evolution, it will learn to predict potential danger situations for a specified user, acting preventively and ensuring the elderly's safety and well-being. As the eServices platform is still in development, synthetic data, based on real data sample and empiric knowledge, is being used to populate the initial dataset. The presented work is a proof of concept of knowledge extraction using the eServices platform information. Regardless of not using real data, this work proves to be an asset, achieving a good performance in preventing alert situations. PMID:25874219

Level-2 Milestone 3504: Scalable Applications Preparations and Outreach for the Sequoia ID (Dawn)

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

Futral, W. Scott; Gyllenhaal, John C.; Hedges, Richard M.

2010-07-02

This report documents LLNL SAP project activities in anticipation of the ASC Sequoia system, ASC L2 milestone 3504: Scalable Applications Preparations and Outreach for the Sequoia ID (Dawn), due June 30, 2010.

Scalable Metadata Management for a Large Multi-Source Seismic Data Repository

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

Gaylord, J. M.; Dodge, D. A.; Magana-Zook, S. A.

In this work, we implemented the key metadata management components of a scalable seismic data ingestion framework to address limitations in our existing system, and to position it for anticipated growth in volume and complexity.

Long-Term Synaptic Changes in Two Input Pathways into the Lateral Nucleus of the Amygdala Underlie Fear Extinction

ERIC Educational Resources Information Center

Park, Junchol; Choi, June-Seek

2010-01-01

Plasticity in two input pathways into the lateral nucleus of the amygdala (LA), the medial prefrontal cortex (mPFC) and the sensory thalamus, have been suggested to underlie extinction, suppression of a previously acquired conditioned response (CR) following repeated presentations of the conditioned stimulus (CS). However, little is known about…

Temporal and Spatial Variations in Transcriptional Patterns among Closely Related Marine Microbial Taxa

NASA Astrophysics Data System (ADS)

Shilova, I. N.; Robidart, J.; DeLong, E.; Zehr, J. P.

2016-02-01

Marine microbial communities are complex, and even closely related marine microbial populations are genetically and physiologically diverse. Despite such great diversity, conserved and highly synchronized rhythmic transcriptional patterns have been observed in microbial communities worldwide. The current widely used approaches analyzing high-throughput sequence data from microbiomes are not designed to differentiate transcription at strain or ecotype level. We used a novel MicroArray-inspired Gene-Centric (MAGC) bioinformatics approach to discern daily transcription by individual strains in previously analyzed metatranscriptomes from two oceanic regions, California Current System and central North Pacific. The results demonstrated that marine microbial taxa (within cyanobacteria Prochlorococcus and Synechococcus, Alphaproteobacterium Pelagibacter and picoeukaryote Ostreococcus) have unique transcription patterns and respond differentially to variability in space and time in the ocean. For example, the timing of maximum transcription for the photosynthesis and pigments genes varied among Synechococcus strains in the California Current study, likely for optimizing light utilization based on their differences in genetics and physiology. While several Prochlorococcus genotypes were present in the North Pacific study, transcription of the phosphate transporter gene, pstS, in specific genotypes was negatively correlated with phosphate concentrations. These individual transcriptional patterns underlie whole microbial community responses and may be sensitive indicators of environmental conditions, including those associated with long-term environmental change. The MAGC applied here to ocean ecosystems is a promising complementary approach that can enhance the ability to analyze metatranscriptomic data from a variety of environmental microbiomes.