Computational search for hypotheses concerning the endocannabinoid contribution to the extinction of fear conditioning

PubMed Central

Anastasio, Thomas J.

2013-01-01

Fear conditioning, in which a cue is conditioned to elicit a fear response, and extinction, in which a previously conditioned cue no longer elicits a fear response, depend on neural plasticity occurring within the amygdala. Projection neurons in the basolateral amygdala (BLA) learn to respond to the cue during fear conditioning, and they mediate fear responding by transferring cue signals to the output stage of the amygdala. Some BLA projection neurons retain their cue responses after extinction. Recent work shows that activation of the endocannabinoid system is necessary for extinction, and it leads to long-term depression (LTD) of the GABAergic synapses that inhibitory interneurons make onto BLA projection neurons. Such GABAergic LTD would enhance the responses of the BLA projection neurons that mediate fear responding, so it would seem to oppose, rather than promote, extinction. To address this paradox, a computational analysis of two well-known conceptual models of amygdaloid plasticity was undertaken. The analysis employed exhaustive state-space search conducted within a declarative programming environment. The analysis reveals that GABAergic LTD actually increases the number of synaptic strength configurations that achieve extinction while preserving the cue responses of some BLA projection neurons in both models. The results suggest that GABAergic LTD helps the amygdala retain cue memory during extinction even as the amygdala learns to suppress the previously conditioned response. The analysis also reveals which features of both models are essential for their ability to achieve extinction with some cue memory preservation, and suggests experimental tests of those features. PMID:23761759

The relative effectiveness of extinction and counter-conditioning in diminishing children's fear.

PubMed

Newall, Carol; Watson, Tiffany; Grant, Kerry-Ann; Richardson, Rick

2017-08-01

Two behavioural strategies for reducing learned fear are extinction and counter-conditioning, and in this study we compared the relative effectiveness of the two procedures at diminishing fear in children. Seventy-three children aged 7-12 years old (M = 9.30, SD = 1.62) were exposed to pictures of two novel animals on a computer screen during the fear acquisition phase. One of these animals was paired with a picture of a scared human face (CS+) while the other was not (CS-). The children were then randomly assigned to one of three conditions: counter-conditioning (animal paired with a happy face), extinction (animal without scared face), or control (no fear reduction procedure). Changes in fear beliefs and behavioural avoidance of the animal were measured. Counter-conditioning was more effective at reducing fear to the CS + than extinction. The findings are discussed in terms of implications for behavioural treatments of childhood anxiety disorders. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Social Networks Users: Fear of Missing out in Preservice Teachers

ERIC Educational Resources Information Center

Gezgin, Deniz Mertkan; Hamutoglu, Nazire Burcin; Gemikonakli, Orhan; Raman, Ilhan

2017-01-01

As mobile computing and smartphones become an integrated part of our lives, the time individuals spend on social networks has significantly increased. Moreover, a link has been established between the uncontrolled use of social networks to the development of undesirable habits and behaviors including addictions. One such behavior, namely, fear of…

"FearNot!": A Computer-Based Anti-Bullying-Programme Designed to Foster Peer Intervention

ERIC Educational Resources Information Center

Vannini, Natalie; Enz, Sibylle; Sapouna, Maria; Wolke, Dieter; Watson, Scott; Woods, Sarah; Dautenhahn, Kerstin; Hall, Lynne; Paiva, Ana; Andre, Elizabeth; Aylett, Ruth; Schneider, Wolfgang

2011-01-01

Bullying is widespread in European schools, despite multiple intervention strategies having been proposed over the years. The present study investigates the effects of a novel virtual learning strategy ("FearNot!") to tackle bullying in both UK and German samples. The approach is intended primarily for victims to increase their coping…

Computer-Assisted Exposure Treatment for Flight Phobia

ERIC Educational Resources Information Center

Tortella-Feliu, Miguel; Bornas, Xavier; Llabres, Jordi

2008-01-01

This review introduces the state of the art in computer-assisted treatment for behavioural disorders. The core of the paper is devoted to describe one of these interventions providing computer-assisted exposure for flight phobia treatment, the Computer-Assisted Fear of Flying Treatment (CAFFT). The rationale, contents and structure of the CAFFT…

Two-Dimensional Finite Element Ablative Thermal Response Analysis of an Arcjet Stagnation Test

NASA Technical Reports Server (NTRS)

Dec, John A.; Laub, Bernard; Braun, Robert D.

2011-01-01

The finite element ablation and thermal response (FEAtR, hence forth called FEAR) design and analysis program simulates the one, two, or three-dimensional ablation, internal heat conduction, thermal decomposition, and pyrolysis gas flow of thermal protection system materials. As part of a code validation study, two-dimensional axisymmetric results from FEAR are compared to thermal response data obtained from an arc-jet stagnation test in this paper. The results from FEAR are also compared to the two-dimensional axisymmetric computations from the two-dimensional implicit thermal response and ablation program under the same arcjet conditions. The ablating material being used in this arcjet test is phenolic impregnated carbon ablator with an LI-2200 insulator as backup material. The test is performed at the NASA, Ames Research Center Interaction Heating Facility. Spatially distributed computational fluid dynamics solutions for the flow field around the test article are used for the surface boundary conditions.

Fear of communicating fear versus fear of terrorism: A human rights violation or a sign of our time?

PubMed

Anyanwu, Chika

2018-02-01

At its very first session, the United Nations General Assembly, adopted Resolution 59(I) which states that "freedom of information is a fundamental human right and … the touchstone of all the freedoms to which the United Nations is consecrated". In 1948, it proclaimed the Universal Declaration of Human Rights in Paris. Article 19 of that Declaration states that "everyone has the right to freedom of opinion and expression; this right includes freedom to hold opinions without interference and to seek, receive and impart information and ideas through any media and regardless of frontiers". When we place these basic human rights against current global terror threats, and consequent restrictive antiterror legislations to combat them, the question becomes whether Article 19 is still relevant in the context of today's changed security landscape. The aim of this paper is to explore ways that anti-terror legislations can balance between national security, and the protection of freedom of information.

Meta assembler enhancements and generalized linkage editor

NASA Technical Reports Server (NTRS)

1979-01-01

A meta Assembler for NASA was developed. The initial development of the Meta Assembler for the SUMC was performed. The capabilities included assembly for both main and micro level programs. A period of checkout and utilization to verify the performance of the Meta Assembler was undertaken. Additional enhancements were made to the Meta Assembler which expanded the target computer family to include architectures represented by the PDP-11, MODCOMP 2, and Raytheon 706 computers.

Domesticating the Personal Computer: The Mainstreaming of a New Technology and the Cultural Management of a Widespread Technophobia, 1964-.

ERIC Educational Resources Information Center

Reed, Lori

2000-01-01

Uses discourses on "computer-phobia" and "computer addiction" to describe the cultural work involved and marketing strategies used between 1960s-1990s regarding management of computer fear. Draws on popular discourses, advertisements, and advice literature to explore how the personal computer was successfully connected to middle-class family…

CARL: a LabVIEW 3 computer program for conducting exposure therapy for the treatment of dental injection fear.

PubMed

Coldwell, S E; Getz, T; Milgrom, P; Prall, C W; Spadafora, A; Ramsay, D S

1998-04-01

This paper describes CARL (Computer Assisted Relaxation Learning), a computerized, exposure-based therapy program for the treatment of dental injection fear. The CARL program operates primarily in two different modes; in vitro, which presents a video-taped exposure hierarchy, and in vivo, which presents scripts for a dentist or hygienist to use while working with a subject. Two additional modes are used to train subjects to use the program and to administer behavioral assessment tests. The program contains five different modules, which function to register a subject, train subjects to use physical and cognitive relaxation techniques, deliver an exposure hierarchy, question subjects about the helpfulness of each of the therapy components, and test for memory effects of anxiolytic medication. Nine subjects have completed the CARL therapy program and 1-yr follow-up as participants in a placebo-controlled clinical trial examining the effects of alprazolam on exposure therapy for dental injection phobia. All nine subjects were able to receive two dental injections, and all reduced their general fear of dental injections. Initial results therefore indicate that the CARL program successfully reduces dental injection fear.

From "Fear-Based" Choice to "Freedom-Based" Choice: Georgia's Tuition Grants Act, 1960-1997

ERIC Educational Resources Information Center

Wearne, Eric

2013-01-01

Georgia's General Assembly passed the 1961 "Tuition Grants Act" as a method for avoiding school desegregation. In 1993, an Atlanta attorney attempted to use the Act to provide private school vouchers. This study compares and contrasts arguments for and against the Act, and public support for the Act, in 1961 and 1993, using Robinson's…

Neural assembly computing.

PubMed

Ranhel, João

2012-06-01

Spiking neurons can realize several computational operations when firing cooperatively. This is a prevalent notion, although the mechanisms are not yet understood. A way by which neural assemblies compute is proposed in this paper. It is shown how neural coalitions represent things (and world states), memorize them, and control their hierarchical relations in order to perform algorithms. It is described how neural groups perform statistic logic functions as they form assemblies. Neural coalitions can reverberate, becoming bistable loops. Such bistable neural assemblies become short- or long-term memories that represent the event that triggers them. In addition, assemblies can branch and dismantle other neural groups generating new events that trigger other coalitions. Hence, such capabilities and the interaction among assemblies allow neural networks to create and control hierarchical cascades of causal activities, giving rise to parallel algorithms. Computing and algorithms are used here as in a nonstandard computation approach. In this sense, neural assembly computing (NAC) can be seen as a new class of spiking neural network machines. NAC can explain the following points: 1) how neuron groups represent things and states; 2) how they retain binary states in memories that do not require any plasticity mechanism; and 3) how branching, disbanding, and interaction among assemblies may result in algorithms and behavioral responses. Simulations were carried out and the results are in agreement with the hypothesis presented. A MATLAB code is available as a supplementary material.

More Colleges Eye outside Companies to Run Their Computer Operations.

ERIC Educational Resources Information Center

DeLoughry, Thomas J.

1993-01-01

Increasingly, budget pressures and rapid technological change are causing colleges to consider "outsourcing" for computer operations management, particularly for administrative purposes. Supporters see the trend as similar to hiring experts for other, ancillary services. Critics fear loss of control of the institution's vital computer systems.…

Prospective Students' Reactions to the Presentation of the Computer Science Major

ERIC Educational Resources Information Center

Weaver, Daniel Scott

2010-01-01

The number of students enrolling in Computer Science in colleges and Universities has declined since its peak in the early 2000s. Some claim contributing factors that intimate that prospective students fear the lack of employment opportunities if they study computing in college. However, the lack of understanding of what Computer Science is and…

Computerized Dental Injection Fear Treatment

PubMed Central

Heaton, L.J.; Leroux, B.G.; Ruff, P.A.; Coldwell, S.E.

2013-01-01

One in four adults reports a clinically significant fear of dental injections, leading many to avoid dental care. While systematic desensitization is the most common therapeutic method for treating specific phobias such as fear of dental injections, lack of access to trained therapists, as well as dentists’ lack of training and time in providing such a therapy, means that most fearful individuals are not able to receive the therapy needed to be able to receive necessary dental treatment. Computer Assisted Relaxation Learning (CARL) is a self-paced computerized treatment based on systematic desensitization for dental injection fear. This multicenter, block-randomized, dentist-blind, parallel-group study conducted in 8 sites in the United States compared CARL with an informational pamphlet in reducing fear of dental injections. Participants completing CARL reported significantly greater reduction in self-reported general and injection-specific dental anxiety measures compared with control individuals (p < .001). Twice as many CARL participants (35.3%) as controls (17.6%) opted to receive a dental injection after the intervention, although this was not statistically significant. CARL, therefore, led to significant changes in self-reported fear in study participants, but no significant differences in the proportion of participants having a dental injection (ClinicalTrials.gov, NCT00609648). PMID:23690352

Dentate Gyrus Contributes to Retrieval as well as Encoding: Evidence from Context Fear Conditioning, Recall, and Extinction

PubMed Central

Krasne, Franklin B.

2017-01-01

Dentate gyrus (DG) is widely thought to provide a teaching signal that enables hippocampal encoding of memories, but its role during retrieval is poorly understood. Some data and models suggest that DG plays no role in retrieval; others encourage the opposite conclusion. To resolve this controversy, we evaluated the effects of optogenetic inhibition of dorsal DG during context fear conditioning, recall, generalization, and extinction in male mice. We found that (1) inhibition during training impaired context fear acquisition; (2) inhibition during recall did not impair fear expression in the training context, unless mice had to distinguish between similar feared and neutral contexts; (3) inhibition increased generalization of fear to an unfamiliar context that was similar to a feared one and impaired fear expression in the conditioned context when it was similar to a neutral one; and (4) inhibition impaired fear extinction. These effects, as well as several seemingly contradictory published findings, could be reproduced by BACON (Bayesian Context Fear Algorithm), a physiologically realistic hippocampal model positing that acquisition and retrieval both involve coordinated activity in DG and CA3. Our findings thus suggest that DG contributes to retrieval and extinction, as well as to the initial establishment of context fear. SIGNIFICANCE STATEMENT Despite abundant evidence that the hippocampal dentate gyrus (DG) plays a critical role in memory, it remains unclear whether the role of DG relates to memory acquisition or retrieval. Using contextual fear conditioning and optogenetic inhibition, we show that DG contributes to both of these processes. Using computational simulations, we identify specific mechanisms through which the suppression of DG affects memory performance. Finally, we show that DG contributes to fear extinction learning, a process in which learned fear is attenuated through exposures to a fearful context in the absence of threat. Our data resolve a long-standing question about the role of DG in memory and provide insight into how disorders affecting DG, including aging, stress, and depression, influence cognitive processes. PMID:28546308

Design of a Neurally Plausible Model of Fear Learning

PubMed Central

Krasne, Franklin B.; Fanselow, Michael S.; Zelikowsky, Moriel

2011-01-01

A neurally oriented conceptual and computational model of fear conditioning manifested by freezing behavior (FRAT), which accounts for many aspects of delay and context conditioning, has been constructed. Conditioning and extinction are the result of neuromodulation-controlled LTP at synapses of thalamic, cortical, and hippocampal afferents on principal cells and inhibitory interneurons of lateral and basal amygdala. The phenomena accounted for by the model (and simulated by the computational version) include conditioning, secondary reinforcement, blocking, the immediate shock deficit, extinction, renewal, and a range of empirically valid effects of pre- and post-training ablation or inactivation of hippocampus or amygdala nuclei. PMID:21845175

The present and future of de novo whole-genome assembly.

PubMed

Sohn, Jang-Il; Nam, Jin-Wu

2018-01-01

As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The central extended amygdala in fear and anxiety: Closing the gap between mechanistic and neuroimaging research.

PubMed

Fox, Andrew S; Shackman, Alexander J

2017-11-30

Anxiety disorders impose a staggering burden on public health, underscoring the need to develop a deeper understanding of the distributed neural circuits underlying extreme fear and anxiety. Recent work highlights the importance of the central extended amygdala, including the central nucleus of the amygdala (Ce) and neighboring bed nucleus of the stria terminalis (BST). Anatomical data indicate that the Ce and BST form a tightly interconnected unit, where different kinds of threat-relevant information can be integrated to assemble states of fear and anxiety. Neuroimaging studies show that the Ce and BST are engaged by a broad spectrum of potentially threat-relevant cues. Mechanistic work demonstrates that the Ce and BST are critically involved in organizing defensive responses to a wide range of threats. Studies in rodents have begun to reveal the specific molecules, cells, and microcircuits within the central extended amygdala that underlie signs of fear and anxiety, but the relevance of these tantalizing discoveries to human experience and disease remains unclear. Using a combination of focal perturbations and whole-brain imaging, a new generation of nonhuman primate studies is beginning to close this gap. This work opens the door to discovering the mechanisms underlying neuroimaging measures linked to pathological fear and anxiety, to understanding how the Ce and BST interact with one another and with distal brain regions to govern defensive responses to threat, and to developing improved intervention strategies. Copyright © 2017. Published by Elsevier B.V.

Frances: A Tool for Understanding Computer Architecture and Assembly Language

ERIC Educational Resources Information Center

Sondag, Tyler; Pokorny, Kian L.; Rajan, Hridesh

2012-01-01

Students in all areas of computing require knowledge of the computing device including software implementation at the machine level. Several courses in computer science curricula address these low-level details such as computer architecture and assembly languages. For such courses, there are advantages to studying real architectures instead of…

The Overdominance of Computers

ERIC Educational Resources Information Center

Monke, Lowell W.

2006-01-01

Most schools are unwilling to consider decreasing computer use at school because they fear that without screen time, students will not be prepared for the demands of a high-tech 21st century. Monke argues that having young children spend a significant amount of time on computers in school is harmful, particularly when children spend so much…

Study of Employee Leave for School Service. Report of the Department of Education to the Governor and the General Assembly of Virginia. House Document No. 55.

ERIC Educational Resources Information Center

Virginia State Dept. of Education, Richmond.

Research reveals that parental involvement in their children's education improves attendance, increases academic achievement, improves student behavior and study habits, and generates positive attitudes toward schools. The demands of work and family can act as barriers to involvement. Some parents are discouraged by a fear of incompetence and…

Microstructure of cotton fibrous assemblies based on computed tomography

NASA Astrophysics Data System (ADS)

Jing, Hui; Yu, Weidong

2017-12-01

This paper describes for the first time the analysis of inner microstructure of cotton fibrous assemblies using computed tomography. Microstructure parameters such as packing density, fractal dimension as well as porosity including open porosity, closed porosity and total porosity are calculated based on 2D data from computed tomography. Values of packing density and fractal dimension are stable in random oriented fibrous assemblies, and there exists a satisfactory approximate linear relationship between them. Moreover, poles analysis indicates that porosity represents the tightness of fibrous assemblies and open poles are main existence.

21st International Conference on DNA Computing and Molecular Programming: 8.1 Biochemistry

DTIC Science & Technology

include information storage and biological applications of DNA systems, biomolecular chemical reaction networks, applications of self -assembled DNA...nanostructures, tile self -assembly and computation, principles and models of self -assembly, and strand displacement and biomolecular circuits. The fund

A common neural network differentially mediates direct and social fear learning.

PubMed

Lindström, Björn; Haaker, Jan; Olsson, Andreas

2018-02-15

Across species, fears often spread between individuals through social learning. Yet, little is known about the neural and computational mechanisms underlying social learning. Addressing this question, we compared social and direct (Pavlovian) fear learning showing that they showed indistinguishable behavioral effects, and involved the same cross-modal (self/other) aversive learning network, centered on the amygdala, the anterior insula (AI), and the anterior cingulate cortex (ACC). Crucially, the information flow within this network differed between social and direct fear learning. Dynamic causal modeling combined with reinforcement learning modeling revealed that the amygdala and AI provided input to this network during direct and social learning, respectively. Furthermore, the AI gated learning signals based on surprise (associability), which were conveyed to the ACC, in both learning modalities. Our findings provide insights into the mechanisms underlying social fear learning, with implications for understanding common psychological dysfunctions, such as phobias and other anxiety disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Intelligent electrical harness connector assembly using Bell Helicopter Textron's 'Wire Harness Automated Manufacturing System'

NASA Astrophysics Data System (ADS)

Springer, D. W.

Bell Helicopter Textron, Incorporated (BHTI) installed two Digital Equipment Corporation PDP-11 computers and an American Can Inc. Ink Jet printer in 1980 as the cornerstone of the Wire Harness Automated Manufacturing System (WHAMS). WHAMS is based upon the electrical assembly philosophy of continuous filament harness forming. This installation provided BHTI with a 3 to 1 return-on-investment by reducing wire and cable identification cycle time by 80 percent and harness forming, on dedicated layout tooling, by 40 percent. Yet, this improvement in harness forming created a bottle neck in connector assembly. To remove this bottle neck, BHTI has installed a prototype connector assembly cell that integrates the WHAMS' data base and innovative computer technologies to cut harness connector assembly cycle time. This novel connector assembly cell uses voice recognition, laser identification, and animated computer graphics to help the electrician in the correct assembly of harness connectors.

Dentate Gyrus Contributes to Retrieval as well as Encoding: Evidence from Context Fear Conditioning, Recall, and Extinction.

PubMed

Bernier, Brian E; Lacagnina, Anthony F; Ayoub, Adam; Shue, Francis; Zemelman, Boris V; Krasne, Franklin B; Drew, Michael R

2017-06-28

Dentate gyrus (DG) is widely thought to provide a teaching signal that enables hippocampal encoding of memories, but its role during retrieval is poorly understood. Some data and models suggest that DG plays no role in retrieval; others encourage the opposite conclusion. To resolve this controversy, we evaluated the effects of optogenetic inhibition of dorsal DG during context fear conditioning, recall, generalization, and extinction in male mice. We found that (1) inhibition during training impaired context fear acquisition; (2) inhibition during recall did not impair fear expression in the training context, unless mice had to distinguish between similar feared and neutral contexts; (3) inhibition increased generalization of fear to an unfamiliar context that was similar to a feared one and impaired fear expression in the conditioned context when it was similar to a neutral one; and (4) inhibition impaired fear extinction. These effects, as well as several seemingly contradictory published findings, could be reproduced by BACON (Bayesian Context Fear Algorithm), a physiologically realistic hippocampal model positing that acquisition and retrieval both involve coordinated activity in DG and CA3. Our findings thus suggest that DG contributes to retrieval and extinction, as well as to the initial establishment of context fear. SIGNIFICANCE STATEMENT Despite abundant evidence that the hippocampal dentate gyrus (DG) plays a critical role in memory, it remains unclear whether the role of DG relates to memory acquisition or retrieval. Using contextual fear conditioning and optogenetic inhibition, we show that DG contributes to both of these processes. Using computational simulations, we identify specific mechanisms through which the suppression of DG affects memory performance. Finally, we show that DG contributes to fear extinction learning, a process in which learned fear is attenuated through exposures to a fearful context in the absence of threat. Our data resolve a long-standing question about the role of DG in memory and provide insight into how disorders affecting DG, including aging, stress, and depression, influence cognitive processes. Copyright © 2017 the authors 0270-6474/17/376359-13$15.00/0.

An IBM 370 assembly language program verifier

NASA Technical Reports Server (NTRS)

Maurer, W. D.

1977-01-01

The paper describes a program written in SNOBOL which verifies the correctness of programs written in assembly language for the IBM 360 and 370 series of computers. The motivation for using assembly language as a source language for a program verifier was the realization that many errors in programs are caused by misunderstanding or ignorance of the characteristics of specific computers. The proof of correctness of a program written in assembly language must take these characteristics into account. The program has been compiled and is currently running at the Center for Academic and Administrative Computing of The George Washington University.

Theory of Connectivity: Nature and Nurture of Cell Assemblies and Cognitive Computation.

PubMed

Li, Meng; Liu, Jun; Tsien, Joe Z

2016-01-01

Richard Semon and Donald Hebb are among the firsts to put forth the notion of cell assembly-a group of coherently or sequentially-activated neurons-to represent percept, memory, or concept. Despite the rekindled interest in this century-old idea, the concept of cell assembly still remains ill-defined and its operational principle is poorly understood. What is the size of a cell assembly? How should a cell assembly be organized? What is the computational logic underlying Hebbian cell assemblies? How might Nature vs. Nurture interact at the level of a cell assembly? In contrast to the widely assumed randomness within the mature but naïve cell assembly, the Theory of Connectivity postulates that the brain consists of the developmentally pre-programmed cell assemblies known as the functional connectivity motif (FCM). Principal cells within such FCM is organized by the power-of-two-based mathematical principle that guides the construction of specific-to-general combinatorial connectivity patterns in neuronal circuits, giving rise to a full range of specific features, various relational patterns, and generalized knowledge. This pre-configured canonical computation is predicted to be evolutionarily conserved across many circuits, ranging from these encoding memory engrams and imagination to decision-making and motor control. Although the power-of-two-based wiring and computational logic places a mathematical boundary on an individual's cognitive capacity, the fullest intellectual potential can be brought about by optimized nature and nurture. This theory may also open up a new avenue to examining how genetic mutations and various drugs might impair or improve the computational logic of brain circuits.

Biologically based neural circuit modelling for the study of fear learning and extinction

NASA Astrophysics Data System (ADS)

Nair, Satish S.; Paré, Denis; Vicentic, Aleksandra

2016-11-01

The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.

Extreme-Scale De Novo Genome Assembly

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

Georganas, Evangelos; Hofmeyr, Steven; Egan, Rob

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and themore » large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.« less

Habenula and interpeduncular nucleus differentially modulate predator odor-induced innate fear behavior in rats.

PubMed

Vincenz, Daniel; Wernecke, Kerstin E A; Fendt, Markus; Goldschmidt, Jürgen

2017-08-14

Fear is an important behavioral system helping humans and animals to survive potentially dangerous situations. Fear can be innate or learned. Whereas the neural circuits underlying learned fear are already well investigated, the knowledge about the circuits mediating innate fear is still limited. We here used a novel, unbiased approach to image in vivo the spatial patterns of neural activity in odor-induced innate fear behavior in rats. We intravenously injected awake unrestrained rats with a 99m-technetium labeled blood flow tracer (99mTc-HMPAO) during ongoing exposure to fox urine or water as control, and mapped the brain distribution of the trapped tracer using single-photon emission computed tomography (SPECT). Upon fox urine exposure blood flow increased in a number of brain regions previously associated with odor-induced innate fear such as the amygdala, ventromedial hypothalamus and dorsolateral periaqueductal grey, but, unexpectedly, decreased at higher significance levels in the interpeduncular nucleus (IPN). Significant flow changes were found in regions monosynaptically connected to the IPN. Flow decreased in the dorsal tegmentum and entorhinal cortex. Flow increased in the habenula (Hb) and correlated with odor effects on behavioral defensive strategy. Hb lesions reduced avoidance of but increased approach to the fox urine while IPN lesions only reduced avoidance behavior without approach behavior. Our study identifies a new component, the IPN, of the neural circuit mediating odor-induced innate fear behavior in mammals and suggests that the evolutionarily conserved Hb-IPN system, which has recently been implicated in cued fear, also forms an integral part of the innate fear circuitry. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Virtual reality in anxiety disorders: the past and the future.

PubMed

Gorini, Alessandra; Riva, Giuseppe

2008-02-01

One of the most effective treatments of anxiety is exposure therapy: a person is exposed to specific feared situations or objects that trigger anxiety. This exposure process may be done through actual exposure, with visualization, by imagination or using virtual reality (VR), that provides users with computer simulated environments with and within which they can interact. VR is made possible by the capability of computers to synthesize a 3D graphical environment from numerical data. Furthermore, because input devices sense the subject's reactions and motions, the computer can modify the synthetic environment accordingly, creating the illusion of interacting with, and thus being immersed within the environment. Starting from 1995, different experimental studies have been conducted in order to investigate the effect of VR exposure in the treatment of subclinical fears and anxiety disorders. This review will discuss their outcome and provide guidelines for the use of VR exposure for the treatment of anxious patients.

A Context-Aware Ubiquitous Learning Approach for Providing Instant Learning Support in Personal Computer Assembly Activities

ERIC Educational Resources Information Center

Hsu, Ching-Kun; Hwang, Gwo-Jen

2014-01-01

Personal computer assembly courses have been recognized as being essential in helping students understand computer structure as well as the functionality of each computer component. In this study, a context-aware ubiquitous learning approach is proposed for providing instant assistance to individual students in the learning activity of a…

Modeling biological problems in computer science: a case study in genome assembly.

PubMed

Medvedev, Paul

2018-01-30

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A survey of emergency physicians' fear of malpractice and its association with the decision to order computed tomography scans for children with minor head trauma.

PubMed

Wong, Andrew C; Kowalenko, Terry; Roahen-Harrison, Stephanie; Smith, Barbara; Maio, Ronald F; Stanley, Rachel M

2011-03-01

The objective of the study was to determine whether fear of malpractice is associated with emergency physicians' decision to order head computed tomography (CT) in 3 age-specific scenarios of pediatric minor head trauma. We hypothesized that physicians with higher fear of malpractice scores will be more likely to order head CT scans. Board-eligible/board-certified members of the Michigan College of Emergency Physicians were sent a 2-part survey consisting of case scenarios and demographic questions. Effect of fear of malpractice on the decision to order a CT scan was evaluated using a cumulative logit model. Two hundred forty-six members (36.5%) completed the surveys. In scenario 1 (infant), being a male and working in a university setting were associated with reduced odds of ordering a CT scan (odds ratio [OR], 0.40; 95% confidence interval [CI], 0.18-0.88; and OR, 0.35; 95% CI, 0.13-0.96, respectively). In scenario 2 (toddler), working for 15 years or more, at multiple hospitals, and for a private group were associated with reduced odds of ordering a CT scan (OR, 0.46; 95% CI, 0.26-0.79; OR, 0.36; 95% CI, 0.16-0.80; and OR, 0.51; 95% CI, 0.27-0.94, respectively). No demographic variables were significantly associated with ordering a CT scan in scenario 3 (teen). Overall, the fear of malpractice was not significantly associated with ordering a CT scan (OR, 1.28; 95% CI, 0.73-2.26; and OR, 1.70; 95% CI, 0.97-3.0). Only in scenario 2 was high fear significantly associated with increased odds of ordering a CT scan (OR, 2.09; 95% CI, 1.08-4.05). Members of Michigan College of Emergency Physicians with a higher fear of malpractice score tended to order more head CT scans in pediatric minor head trauma. However, this trend was shown to be statistically significant only in 1 case and not overall.

Immersive 3D exposure-based treatment for spider fear: A randomized controlled trial.

PubMed

Minns, Sean; Levihn-Coon, Andrew; Carl, Emily; Smits, Jasper A J; Miller, Wayne; Howard, Don; Papini, Santiago; Quiroz, Simon; Lee-Furman, Eunjung; Telch, Michael; Carlbring, Per; Xanthopoulos, Drew; Powers, Mark B

2018-06-04

Stereoscopic 3D gives the viewer the same shape, size, perspective and depth they would experience viewing the real world and could mimic the perceptual threat cues present in real life. This is the first study to investigate whether an immersive stereoscopic 3D video exposure-based treatment would be effective in reducing fear of spiders. Participants with a fear of spiders (N = 77) watched two psychoeducational videos with facts about spiders and phobias. They were then randomized to a treatment condition that watched a single session of a stereoscopic 3D immersive video exposure-based treatment (six 5-min exposures) delivered through a virtual reality headset or a psychoeducation only control condition that watched a 30-min neutral video (2D documentary) presented on a computer monitor. Assessments of spider fear (Fear of Spiders Questionnaire [FSQ], Behavioral Approach Task [BAT], & subjective ratings of fear) were completed pre- and post-treatment. Consistent with prediction, the stereoscopic 3D video condition outperformed the control condition in reducing fear of spiders showing a large between-group effect size on the FSQ (Cohen's d = 0.85) and a medium between-group effect size on the BAT (Cohen's d = 0.47). This provides initial support for stereoscopic 3D video in treating phobias. Copyright © 2018 Elsevier Ltd. All rights reserved.

Theory of Connectivity: Nature and Nurture of Cell Assemblies and Cognitive Computation

PubMed Central

Li, Meng; Liu, Jun; Tsien, Joe Z.

2016-01-01

Richard Semon and Donald Hebb are among the firsts to put forth the notion of cell assembly—a group of coherently or sequentially-activated neurons—to represent percept, memory, or concept. Despite the rekindled interest in this century-old idea, the concept of cell assembly still remains ill-defined and its operational principle is poorly understood. What is the size of a cell assembly? How should a cell assembly be organized? What is the computational logic underlying Hebbian cell assemblies? How might Nature vs. Nurture interact at the level of a cell assembly? In contrast to the widely assumed randomness within the mature but naïve cell assembly, the Theory of Connectivity postulates that the brain consists of the developmentally pre-programmed cell assemblies known as the functional connectivity motif (FCM). Principal cells within such FCM is organized by the power-of-two-based mathematical principle that guides the construction of specific-to-general combinatorial connectivity patterns in neuronal circuits, giving rise to a full range of specific features, various relational patterns, and generalized knowledge. This pre-configured canonical computation is predicted to be evolutionarily conserved across many circuits, ranging from these encoding memory engrams and imagination to decision-making and motor control. Although the power-of-two-based wiring and computational logic places a mathematical boundary on an individual’s cognitive capacity, the fullest intellectual potential can be brought about by optimized nature and nurture. This theory may also open up a new avenue to examining how genetic mutations and various drugs might impair or improve the computational logic of brain circuits. PMID:27199674

AutoAssemblyD: a graphical user interface system for several genome assemblers.

PubMed

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

Iran After the Bomb: How Would a Nuclear-Armed Tehran Behave?

DTIC Science & Technology

2013-01-01

Ayatollah Khamenei, who constantly warns of a repeat of the 2009 “ sedition ,” fears that a replay of the 2009 Green uprising could present a grave...opposition and has adopted policies similar to those of other Arab autocratic regimes, including attempts to limit freedom of thought and speech (Ulrichsen... speech to the UN General Assembly, Israeli Prime Minister Netanyahu claimed that Rafsanjani’s words illustrate Iran’s supposed willingness to use

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation

PubMed Central

Smith, Gregory R.; Xie, Lu; Schwartz, Russell

2016-01-01

The environment of a living cell is vastly different from that of an in vitro reaction system, an issue that presents great challenges to the use of in vitro models, or computer simulations based on them, for understanding biochemistry in vivo. Virus capsids make an excellent model system for such questions because they typically have few distinct components, making them amenable to in vitro and modeling studies, yet their assembly can involve complex networks of possible reactions that cannot be resolved in detail by any current experimental technology. We previously fit kinetic simulation parameters to bulk in vitro assembly data to yield a close match between simulated and real data, and then used the simulations to study features of assembly that cannot be monitored experimentally. The present work seeks to project how assembly in these simulations fit to in vitro data would be altered by computationally adding features of the cellular environment to the system, specifically the presence of nucleic acid about which many capsids assemble. The major challenge of such work is computational: simulating fine-scale assembly pathways on the scale and in the parameter domains of real viruses is far too computationally costly to allow for explicit models of nucleic acid interaction. We bypass that limitation by applying analytical models of nucleic acid effects to adjust kinetic rate parameters learned from in vitro data to see how these adjustments, singly or in combination, might affect fine-scale assembly progress. The resulting simulations exhibit surprising behavioral complexity, with distinct effects often acting synergistically to drive efficient assembly and alter pathways relative to the in vitro model. The work demonstrates how computer simulations can help us understand how assembly might differ between the in vitro and in vivo environments and what features of the cellular environment account for these differences. PMID:27244559

Overcoming Computer Anxiety: A Three-Step Process for Adult Learners

ERIC Educational Resources Information Center

Sivakumaran, Thillainatarajan; Lux, Allison C.

2011-01-01

Many adult learners returning to school later in life have discovered that technology is heavily embedded in the learning environment. Learning both course contents and technology in unison can be a daunting task for students who feel intimidated by technology. Computer anxiety is a term that describes resistance, fear or anxieties towards…

German Adult Education and the New Technology.

ERIC Educational Resources Information Center

Dohmen, Gunther

Although adults in Germany see positive benefits coming from the introduction of new technology, especially computers, they also fear that the technology will bring about more control of their work and private lives. They also dislike the perceived dangers of dehumanization that computers could have on society. Adult educators in Germany see two…

ICALL's Relevance to CALL

ERIC Educational Resources Information Center

Ward, Monica

2017-01-01

The term Intelligent Computer Assisted Language Learning (ICALL) covers many different aspects of CALL that add something extra to a CALL resource. This could be with the use of computational linguistics or Artificial Intelligence (AI). ICALL tends to be not very well understood within the CALL community. There may also be the slight fear factor…

A Proposed Programming System for Knuth's Mix Computer.

ERIC Educational Resources Information Center

Akers, Max Neil

A programing system using a hypothetical computer is proposed for use in teaching machine and assembly language programing courses. Major components such as monitor, assembler, interpreter, grader, and diagnostics are described. The interpreter is programed and documented for use on an IBM 360/67 computer. The interpreter can be used for teaching…

LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.

PubMed

El-Metwally, Sara; Zakaria, Magdi; Hamza, Taher

2016-11-01

The deluge of current sequenced data has exceeded Moore's Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory. LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of [Formula: see text]-spaced sequenced [Formula: see text]-mers and the other holding [Formula: see text]-mers classified as likely correct, using a simple statistical test. LightAssembler contains a light implementation of the graph traversal and simplification modules that achieves comparable assembly accuracy and contiguity to other competing tools. Our method reduces the memory usage by [Formula: see text] compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemblathon projects. While LightAssembler can be considered as a gap-based sequence assembler, different gap sizes result in an almost constant assembly size and genome coverage. https://github.com/SaraEl-Metwally/LightAssembler CONTACT: sarah_almetwally4@mans.edu.egSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Logical NAND and NOR Operations Using Algorithmic Self-assembly of DNA Molecules

NASA Astrophysics Data System (ADS)

Wang, Yanfeng; Cui, Guangzhao; Zhang, Xuncai; Zheng, Yan

DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. It has been demonstrated that the simple binary arithmetic and logical operations can be computed by the process of self assembly of DNA tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute five steps of a logical NAND and NOR operations on a string of binary bits. To achieve this, abstract tiles were translated into DNA tiles based on triple-crossover motifs. Serving as input for the computation, long single stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. Our method shows that engineered DNA self-assembly can be treated as a bottom-up design techniques, and can be capable of designing DNA computer organization and architecture.

MR Angiography (MRA)

MedlinePlus

... resonance angiography (MRA), a powerful magnetic field, radio frequency waves and a computer produce detailed images of ... test. If you have claustrophobia (fear of enclosed spaces) or anxiety, you may want to ask your ...

Computed Tomography Measuring Inside Machines

NASA Technical Reports Server (NTRS)

Wozniak, James F.; Scudder, Henry J.; Anders, Jeffrey E.

1995-01-01

Computed tomography applied to obtain approximate measurements of radial distances from centerline of turbopump to leading edges of diffuser vanes in turbopump. Use of computed tomography has significance beyond turbopump application: example of general concept of measuring internal dimensions of assembly of parts without having to perform time-consuming task of taking assembly apart and measuring internal parts on coordinate-measuring machine.

Safety Behaviors and Stuttering.

PubMed

Lowe, Robyn; Helgadottir, Fjola; Menzies, Ross; Heard, Rob; O'Brian, Sue; Packman, Ann; Onslow, Mark

2017-05-24

Those who are socially anxious may use safety behaviors during feared social interactions to prevent negative outcomes. Safety behaviors are associated with anxiety maintenance and poorer treatment outcomes because they prevent fear extinction. Social anxiety disorder is often comorbid with stuttering. Speech pathologists reported in a recent publication (Helgadottir, Menzies, Onslow, Packman, & O'Brian, 2014a) that they often recommended procedures for clients that could be safety behaviors. This study investigated the self-reported use of safety behaviors by adults who stutter. Participants were 133 adults who stutter enrolled in an online cognitive-behavior therapy program. Participants completed a questionnaire about their use of potential safety behaviors when anxious during social encounters. Correlations were computed between safety behaviors and pretreatment scores on measures of fear of negative evaluation and negative cognitions. Of 133 participants, 132 reported that they used safety behaviors. Many of the safety behaviors correlated with higher scores for fear of negative evaluation and negative cognitions. Adults who stutter report using safety behaviors, and their use is associated with pretreatment fear of negative evaluation and unhelpful thoughts about stuttering. These results suggest that the negative effects of safety behaviors may extend to those who stutter, and further research is needed.

Occupational stress in human computer interaction.

PubMed

Smith, M J; Conway, F T; Karsh, B T

1999-04-01

There have been a variety of research approaches that have examined the stress issues related to human computer interaction including laboratory studies, cross-sectional surveys, longitudinal case studies and intervention studies. A critical review of these studies indicates that there are important physiological, biochemical, somatic and psychological indicators of stress that are related to work activities where human computer interaction occurs. Many of the stressors of human computer interaction at work are similar to those stressors that have historically been observed in other automated jobs. These include high workload, high work pressure, diminished job control, inadequate employee training to use new technology, monotonous tasks, por supervisory relations, and fear for job security. New stressors have emerged that can be tied primarily to human computer interaction. These include technology breakdowns, technology slowdowns, and electronic performance monitoring. The effects of the stress of human computer interaction in the workplace are increased physiological arousal; somatic complaints, especially of the musculoskeletal system; mood disturbances, particularly anxiety, fear and anger; and diminished quality of working life, such as reduced job satisfaction. Interventions to reduce the stress of computer technology have included improved technology implementation approaches and increased employee participation in implementation. Recommendations for ways to reduce the stress of human computer interaction at work are presented. These include proper ergonomic conditions, increased organizational support, improved job content, proper workload to decrease work pressure, and enhanced opportunities for social support. A model approach to the design of human computer interaction at work that focuses on the system "balance" is proposed.

Fearing Prying U.S. Eyes, Canada's Colleges Crack Down On Computing

ERIC Educational Resources Information Center

Carnevale, Dan

2007-01-01

The USA Patriot Act is having far-reaching effects on the kinds of data that wind up on some academics' computers in Canada. Canadian colleges, responding to provincial laws passed in reaction to the Patriot Act, are preventing professors from entering the United States with students' private data on their laptops and limiting the locations of…

Exposure-based Interventions for the management of individuals with high levels of needle fear across the lifespan: a clinical practice guideline and call for further research

PubMed Central

McMurtry, C. Meghan; Taddio, Anna; Noel, Melanie; Antony, Martin M.; Chambers, Christine T.; Asmundson, Gordon J. G.; Pillai Riddell, Rebecca; Shah, Vibhuti; MacDonald, Noni E.; Rogers, Jess; Bucci, Lucie M.; Mousmanis, Patricia; Lang, Eddy; Halperin, Scott; Bowles, Susan; Halpert, Christine; Ipp, Moshe; Rieder, Michael J.; Robson, Kate; Uleryk, Elizabeth; Votta Bleeker, Elizabeth; Dubey, Vinita; Hanrahan, Anita; Lockett, Donna; Scott, Jeffrey

2016-01-01

Abstract Needle fear typically begins in childhood and represents an important health-related issue across the lifespan. Individuals who are highly fearful of needles frequently avoid health care. Although guidance exists for managing needle pain and fear during procedures, the most highly fearful may refuse or abstain from such procedures. The purpose of a clinical practice guideline (CPG) is to provide actionable instruction on the management of a particular health concern; this guidance emerges from a systematic process. Using evidence from a rigorous systematic review interpreted by an expert panel, this CPG provides recommendations on exposure-based interventions for high levels of needle fear in children and adults. The AGREE-II, GRADE, and Cochrane methodologies were used. Exposure-based interventions were included. The included evidence was very low quality on average. Strong recommendations include the following. In vivo (live/in person) exposure-based therapy is recommended (vs. no treatment) for children seven years and older and adults with high levels of needle fear. Non-in vivo (imaginal, computer-based) exposure (vs. no treatment) is recommended for individuals (over seven years of age) who are unwilling to undergo in vivo exposure. Although there were no included trials which examined children < 7 years, exposure-based interventions are discussed as good clinical practice. Implementation considerations are discussed and clinical tools are provided. Utilization of these recommended practices may lead to improved health outcomes due to better health care compliance. Research on the understanding and treatment of high levels of needle fear is urgently needed; specific recommendations are provided. PMID:27007463

Exposure-based Interventions for the management of individuals with high levels of needle fear across the lifespan: a clinical practice guideline and call for further research.

PubMed

McMurtry, C Meghan; Taddio, Anna; Noel, Melanie; Antony, Martin M; Chambers, Christine T; Asmundson, Gordon J G; Pillai Riddell, Rebecca; Shah, Vibhuti; MacDonald, Noni E; Rogers, Jess; Bucci, Lucie M; Mousmanis, Patricia; Lang, Eddy; Halperin, Scott; Bowles, Susan; Halpert, Christine; Ipp, Moshe; Rieder, Michael J; Robson, Kate; Uleryk, Elizabeth; Votta Bleeker, Elizabeth; Dubey, Vinita; Hanrahan, Anita; Lockett, Donna; Scott, Jeffrey

2016-04-01

Needle fear typically begins in childhood and represents an important health-related issue across the lifespan. Individuals who are highly fearful of needles frequently avoid health care. Although guidance exists for managing needle pain and fear during procedures, the most highly fearful may refuse or abstain from such procedures. The purpose of a clinical practice guideline (CPG) is to provide actionable instruction on the management of a particular health concern; this guidance emerges from a systematic process. Using evidence from a rigorous systematic review interpreted by an expert panel, this CPG provides recommendations on exposure-based interventions for high levels of needle fear in children and adults. The AGREE-II, GRADE, and Cochrane methodologies were used. Exposure-based interventions were included. The included evidence was very low quality on average. Strong recommendations include the following. In vivo (live/in person) exposure-based therapy is recommended (vs. no treatment) for children seven years and older and adults with high levels of needle fear. Non-in vivo (imaginal, computer-based) exposure (vs. no treatment) is recommended for individuals (over seven years of age) who are unwilling to undergo in vivo exposure. Although there were no included trials which examined children < 7 years, exposure-based interventions are discussed as good clinical practice. Implementation considerations are discussed and clinical tools are provided. Utilization of these recommended practices may lead to improved health outcomes due to better health care compliance. Research on the understanding and treatment of high levels of needle fear is urgently needed; specific recommendations are provided.

Computational and theoretical modeling of pH and flow effects on the early-stage non-equilibrium self-assembly of optoelectronic peptides

NASA Astrophysics Data System (ADS)

Mansbach, Rachael; Ferguson, Andrew

Self-assembling π-conjugated peptides are attractive candidates for the fabrication of bioelectronic materials possessing optoelectronic properties due to electron delocalization over the conjugated peptide groups. We present a computational and theoretical study of an experimentally-realized optoelectronic peptide that displays triggerable assembly in low pH to resolve the microscopic effects of flow and pH on the non-equilibrium morphology and kinetics of assembly. Using a combination of molecular dynamics simulations and hydrodynamic modeling, we quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to influence assembly. We also show that there is a critical pH below which aggregation proceeds irreversibly, and quantify the relationship between pH, charge density, and aggregate size. Our work provides new fundamental understanding of pH and flow of non-equilibrium π-conjugated peptide assembly, and lays the groundwork for the rational manipulation of environmental conditions and peptide chemistry to control assembly and the attendant emergent optoelectronic properties. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award # DE-SC0011847, and by the Computational Science and Engineering Fellowship from the University of Illinois at Urbana-Champaign.

Maladaptive behavioral consequences of conditioned fear-generalization: a pronounced, yet sparsely studied, feature of anxiety pathology.

PubMed

van Meurs, Brian; Wiggert, Nicole; Wicker, Isaac; Lissek, Shmuel

2014-06-01

Fear-conditioning experiments in the anxiety disorders focus almost exclusively on passive-emotional, Pavlovian conditioning, rather than active-behavioral, instrumental conditioning. Paradigms eliciting both types of conditioning are needed to study maladaptive, instrumental behaviors resulting from Pavlovian abnormalities found in clinical anxiety. One such Pavlovian abnormality is generalization of fear from a conditioned danger-cue (CS+) to resembling stimuli. Though lab-based findings repeatedly link overgeneralized Pavlovian-fear to clinical anxiety, no study assesses the degree to which Pavlovian overgeneralization corresponds with maladaptive, overgeneralized instrumental-avoidance. The current effort fills this gap by validating a novel fear-potentiated startle paradigm including Pavlovian and instrumental components. The paradigm is embedded in a computer game during which shapes appear on the screen. One shape paired with electric-shock serves as CS+, and other resembling shapes, presented in the absence of shock, serve as generalization stimuli (GSs). During the game, participants choose whether to behaviorally avoid shock at the cost of poorer performance. Avoidance during CS+ is considered adaptive because shock is a real possibility. By contrast, avoidance during GSs is considered maladaptive because shock is not a realistic prospect and thus unnecessarily compromises performance. Results indicate significant Pavlovian-instrumental relations, with greater generalization of Pavlovian fear associated with overgeneralization of maladaptive instrumental-avoidance. Copyright © 2014 Elsevier Ltd. All rights reserved.

Digital Representation for Communication of Product Definition Data. Revision

DTIC Science & Technology

1990-04-30

Treuhandgesellschaft Electrical Thomas C . Estervog Boeing Computer Services John C . Faulkner S D R C Ayron L. Fears IBM Corp. ix MEMBERS OF THE IGES/PDES...Force Eugene F. Gurga Computervision C . Hayden Hamilton III PDA Engineering William Hammon Tandem Computer Yosef Haridim Boeing Electronics Co. C ...British Aerospace Raphael McBain General Dynamics Corp. Dennis McBurney L-ueing Military Airplane Co Patrick McFadden Boeing Computer Services C . Kevin

A computer-oriented system for assembling and displaying land management information

Treesearch

Elliot L. Amidon

1964-01-01

Maps contain information basic to land management planning. By transforming conventional map symbols into numbers which are punched into cards, the land manager can have a computer assemble and display information required for a specific job. He can let a computer select information from several maps, combine it with such nonmap data as treatment cost or benefit per...

Computational path planner for product assembly in complex environments

NASA Astrophysics Data System (ADS)

Shang, Wei; Liu, Jianhua; Ning, Ruxin; Liu, Mi

2013-03-01

Assembly path planning is a crucial problem in assembly related design and manufacturing processes. Sampling based motion planning algorithms are used for computational assembly path planning. However, the performance of such algorithms may degrade much in environments with complex product structure, narrow passages or other challenging scenarios. A computational path planner for automatic assembly path planning in complex 3D environments is presented. The global planning process is divided into three phases based on the environment and specific algorithms are proposed and utilized in each phase to solve the challenging issues. A novel ray test based stochastic collision detection method is proposed to evaluate the intersection between two polyhedral objects. This method avoids fake collisions in conventional methods and degrades the geometric constraint when a part has to be removed with surface contact with other parts. A refined history based rapidly-exploring random tree (RRT) algorithm which bias the growth of the tree based on its planning history is proposed and employed in the planning phase where the path is simple but the space is highly constrained. A novel adaptive RRT algorithm is developed for the path planning problem with challenging scenarios and uncertain environment. With extending values assigned on each tree node and extending schemes applied, the tree can adapts its growth to explore complex environments more efficiently. Experiments on the key algorithms are carried out and comparisons are made between the conventional path planning algorithms and the presented ones. The comparing results show that based on the proposed algorithms, the path planner can compute assembly path in challenging complex environments more efficiently and with higher success. This research provides the references to the study of computational assembly path planning under complex environments.

Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.

PubMed

Kleftogiannis, Dimitrios; Kalnis, Panos; Bajic, Vladimir B

2013-01-01

A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.

Attention regulates anger and fear to predict changes in adolescent risk-taking behaviors

PubMed Central

Kim-Spoon, Jungmeen; Holmes, Christopher; Deater-Deckard, Kirby

2014-01-01

Background Regulation of negative affect is critical to healthy development in childhood and adolescence. We conducted a longitudinal study examining the moderating role of attention control in the effects of anger and fear on changes in risk-taking behaviors from early to middle adolescence. Method The sample involved participants from the Study of Early Child Care and Youth Development (SECCYD), assessed at 9, 11, and 15 years of age. Composite scores for anger, fear, and attention control were computed using indicators from multiple informants, and risk-taking behaviors were assessed based on adolescents’ self-reports. Results Latent difference score analysis indicated significant moderating effects of attention control showing that increased anger between 9 and 11 years was related to increases in risk-taking behaviors between 11 and 15 years only for adolescents with low attention control but not for adolescents with high attention control. In contrast, significant moderating effects of attention control for the link between fear and risk-taking behaviors suggested increased fear between 9 and 11 years tended to be associated with decreases in risk-taking behaviors between 11 and 15 years only for adolescents with high attention control but not for adolescents with low attention control. Conclusions Attention control regulates the connections between negative affect such as anger and fear with changes in adolescent risk-taking behaviors. Our data suggest the protective role of strong attention control against the development of risk-taking behaviors in adolescence as it demotes the effects of anger and promotes the effects of fear. PMID:25280179

An automatic recording system for the study of escape from fear in rats.

PubMed

Li, Ming; He, Wei

2013-11-01

Escape from fear (EFF) is an active response to a conditioned stimulus (CS) previously paired with an unconditioned fearful stimulus (US), which typically leads to the termination of the CS. In this paradigm, animals acquire two distinct associations: S-S [CS-US] and R-O [response-outcome] through Pavlovian and instrumental conditioning, respectively. The present study describes a computer controlled automatic recording system that captures the development of EFF and allows the determination of the respective roles of S-S and R-O associations in this process. We validated this system by showing that only rats subjected to a simultaneous CS-US conditioning (i.e., CS and US occur together at the beginning of each trial) acquired EFF, not those subjected to an unpaired CS-US conditioning. Paired rats had a progressively increased number of EFF and significantly shorter escape latencies than unpaired rats across the 5-trial blocks on the test day. However, during the conditioning phase, the unpaired rats emitted more 22kHz ultrasonic vocalizations, a validated measure of conditioned reactive fear responses. Our results demonstrate that the acquisition of EFF is contingent upon pairing of the CS with the US, not simply the consequence of a high level of generalized fear. Because this commercially available system is capable of examining both conditioned active and reactive fear responses in a single setup, it could be used to determine the relative roles of S-S and R-O associations in EFF, the neurobiology of conditioned active fear response and neuropharmacology of psychotherapeutic drugs. Copyright © 2013 Elsevier B.V. All rights reserved.

Biased Intensity Judgements of Visceral Sensations After Learning to Fear Visceral Stimuli: A Drift Diffusion Approach.

PubMed

Zaman, Jonas; Madden, Victoria J; Iven, Julie; Wiech, Katja; Weltens, Nathalie; Ly, Huynh Giao; Vlaeyen, Johan W S; Van Oudenhove, Lukas; Van Diest, Ilse

2017-10-01

A growing body of research has identified fear of visceral sensations as a potential mechanism in the development and maintenance of visceral pain disorders. However, the extent to which such learned fear affects visceroception remains unclear. To address this question, we used a differential fear conditioning paradigm with nonpainful esophageal balloon distensions of 2 different intensities as conditioning stimuli (CSs). The experiment comprised of preacquisition, acquisition, and postacquisition phases during which participants categorized the CSs with respect to their intensity. The CS+ was always followed by a painful electrical stimulus (unconditioned stimulus) during the acquisition phase and in 60% of the trials during postacquisition. The second stimulus (CS-) was never associated with pain. Analyses of galvanic skin and startle eyeblink responses as physiological markers of successful conditioning showed increased fear responses to the CS+ compared with the CS-, but only in the group with the low-intensity stimulus as CS+. Computational modeling of response times and response accuracies revealed that differential fear learning affected perceptual decision-making about the intensities of visceral sensations such that sensations were more likely to be categorized as more intense. These results suggest that associative learning might indeed contribute to visceral hypersensitivity in functional gastrointestinal disorders. This study shows that associative fear learning biases intensity judgements of visceral sensations toward perceiving such sensations as more intense. Learning-induced alterations in visceroception might therefore contribute to the development or maintenance of visceral pain. Copyright © 2017 American Pain Society. Published by Elsevier Inc. All rights reserved.

Human Fear Conditioning Conducted in Full Immersion 3-Dimensional Virtual Reality

PubMed Central

Huff, Nicole C.; Zielinski, David J.; Fecteau, Matthew E.; Brady, Rachael; LaBar, Kevin S.

2010-01-01

Fear conditioning is a widely used paradigm in non-human animal research to investigate the neural mechanisms underlying fear and anxiety. A major challenge in conducting conditioning studies in humans is the ability to strongly manipulate or simulate the environmental contexts that are associated with conditioned emotional behaviors. In this regard, virtual reality (VR) technology is a promising tool. Yet, adapting this technology to meet experimental constraints requires special accommodations. Here we address the methodological issues involved when conducting fear conditioning in a fully immersive 6-sided VR environment and present fear conditioning data. In the real world, traumatic events occur in complex environments that are made up of many cues, engaging all of our sensory modalities. For example, cues that form the environmental configuration include not only visual elements, but aural, olfactory, and even tactile. In rodent studies of fear conditioning animals are fully immersed in a context that is rich with novel visual, tactile and olfactory cues. However, standard laboratory tests of fear conditioning in humans are typically conducted in a nondescript room in front of a flat or 2D computer screen and do not replicate the complexity of real world experiences. On the other hand, a major limitation of clinical studies aimed at reducing (extinguishing) fear and preventing relapse in anxiety disorders is that treatment occurs after participants have acquired a fear in an uncontrolled and largely unknown context. Thus the experimenters are left without information about the duration of exposure, the true nature of the stimulus, and associated background cues in the environment1. In the absence of this information it can be difficult to truly extinguish a fear that is both cue and context-dependent. Virtual reality environments address these issues by providing the complexity of the real world, and at the same time allowing experimenters to constrain fear conditioning and extinction parameters to yield empirical data that can suggest better treatment options and/or analyze mechanistic hypotheses. In order to test the hypothesis that fear conditioning may be richly encoded and context specific when conducted in a fully immersive environment, we developed distinct virtual reality 3-D contexts in which participants experienced fear conditioning to virtual snakes or spiders. Auditory cues co-occurred with the CS in order to further evoke orienting responses and a feeling of "presence" in subjects 2 . Skin conductance response served as the dependent measure of fear acquisition, memory retention and extinction. PMID:20736913

MIADS2 ... an alphanumeric map information assembly and display system for a large computer

Treesearch

Elliot L. Amidon

1966-01-01

A major improvement and extension of the Map Information Assembly and Display System (MIADS) developed in 1964 is described. Basic principles remain unchanged, but the computer programs have been expanded and rewritten for a large computer, in Fortran IV and MAP languages. The code system is extended from 99 integers to about 2,200 alphanumeric 2-character codes. Hand-...

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

DOE PAGES

Mills, Jeremy H.; Sheffler, William; Ener, Maraia E.; ...

2016-12-08

Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here in this paper, we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala) 3] 2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystalmore » structure for the residues at the protein interface is ~1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.« less

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

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

Mills, Jeremy H.; Sheffler, William; Ener, Maraia E.

Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here in this paper, we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala) 3] 2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystalmore » structure for the residues at the protein interface is ~1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.« less

Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells.

PubMed

Chen, Feng; Bai, Min; Cao, Ke; Zhao, Yue; Cao, Xiaowen; Wei, Jing; Wu, Na; Li, Jiang; Wang, Lihua; Fan, Chunhai; Zhao, Yongxi

2017-12-26

Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO 2 nanosheets as both DNA carriers and source of Mn 2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.

Higher threat avoidance costs reduce avoidance behaviour which in turn promotes fear extinction in humans.

PubMed

Rattel, Julina A; Miedl, Stephan F; Blechert, Jens; Wilhelm, Frank H

2017-09-01

Theoretical models specifying the underlying mechanisms of the development and maintenance of anxiety and related disorders state that fear responses acquired through classical Pavlovian conditioning are maintained by repeated avoidance behaviour; thus, it is assumed that avoidance prevents fear extinction. The present study investigated behavioural avoidance decisions as a function of avoidance costs in a naturalistic fear conditioning paradigm. Ecologically valid avoidance costs - manipulated between participant groups - were represented via time-delays during a detour in a gamified computer task. After differential acquisitions of shock-expectancy to a predictive conditioned stimulus (CS+), participants underwent extinction where they could either take a risky shortcut, while anticipating shock signaled by the CS+, or choose a costly avoidance option (lengthy detour); thus, they were faced with an approach-avoidance conflict. Groups with higher avoidance costs (longer detours) showed lower proportions of avoiders. Avoiders gave heightened shock-expectancy ratings post-extinction, demonstrating 'protecting from extinction', i.e. failure to extinguish. Moreover, there was an indirect effect of avoidance costs on protection from extinction through avoidance behaviour. No moderating role of trait-anxiety was found. Theoretical implications of avoidance behaviour are discussed, considering the involvement of instrumental learning in the maintenance of fear responses. Copyright © 2016 Elsevier Ltd. All rights reserved.

A multi-component cognitive behavioural intervention for the treatment of fear of falling after hip fracture (FIT-HIP): protocol of a randomised controlled trial.

PubMed

Scheffers-Barnhoorn, Maaike N; van Haastregt, Jolanda C M; Schols, Jos M G A; Kempen, Gertrudis I J M; van Balen, Romke; Visschedijk, Jan H M; van den Hout, Wilbert B; Dumas, Eve M; Achterberg, Wilco P; van Eijk, Monica

2017-03-20

Hip fracture is a common injury in the geriatric population. Despite surgical repair and subsequent rehabilitation programmes, functional recovery is often limited, particularly in individuals with multi-morbidity. This leads to high care dependency and subsequent use of healthcare services. Fear of falling has a negative influence on recovery after hip fracture, due to avoidance of activity and subsequent restriction in mobility. Although fear of falling is highly prevalent after hip fracture, no structured treatment programme is currently available. This trial will evaluate whether targeted treatment of fear of falling in geriatric rehabilitation after hip fracture using a multi-component cognitive behavioural intervention (FIT-HIP), is feasible and (cost) effective in reducing fear of falling and associated activity restriction and thereby improves physical functioning. This multicentre cluster randomised controlled trial will be conducted among older patients with hip fracture and fear of falling who are admitted to a multidisciplinary inpatient geriatric rehabilitation programme in eleven post-acute geriatric rehabilitation units. Fifteen participants will be recruited from each site. Recruitment sites will be allocated by computer randomisation to either the control group, receiving usual care, or to the intervention group receiving the FIT-HIP intervention in addition to usual care. The FIT-HIP intervention is conducted by physiotherapists and will be embedded in usual care. It consists of various elements of cognitive behavioural therapy, including guided exposure to feared activities (that are avoided by the participants). Participants and outcome assessors are blinded to group allocation. Follow-up measurements will be performed at 3 and 6 months after discharge from geriatric rehabilitation. (Cost)-effectiveness and feasibility of the intervention will be evaluated. Primary outcome measures are fear of falling and mobility. Targeted treatment of fear of falling may improve recovery and physical and social functioning after hip fracture, thereby offering benefits for patients and reducing healthcare costs. Results of this study will provide insight into whether fear of falling is modifiable in the (geriatric) rehabilitation after hip fracture and whether the intervention is feasible. Netherlands Trial Register: NTR 5695 .

Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer (7th Annual SFAF Meeting, 2012)

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

Copeland, Alex

2012-06-01

Alex Copeland on "Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

19 CFR 10.14 - Fabricated components subject to the exemption.

Code of Federal Regulations, 2012 CFR

2012-04-01

....14 Section 10.14 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY... assembly for a computer is assembled in the United States by soldering American-made and foreign-made... electronic function and is ready for incorporation into the computer. The foreign-made components have...

19 CFR 10.14 - Fabricated components subject to the exemption.

Code of Federal Regulations, 2014 CFR

2014-04-01

....14 Section 10.14 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY... assembly for a computer is assembled in the United States by soldering American-made and foreign-made... electronic function and is ready for incorporation into the computer. The foreign-made components have...

19 CFR 10.14 - Fabricated components subject to the exemption.

Code of Federal Regulations, 2013 CFR

2013-04-01

....14 Section 10.14 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY... assembly for a computer is assembled in the United States by soldering American-made and foreign-made... electronic function and is ready for incorporation into the computer. The foreign-made components have...

19 CFR 10.14 - Fabricated components subject to the exemption.

Code of Federal Regulations, 2011 CFR

2011-04-01

....14 Section 10.14 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY... assembly for a computer is assembled in the United States by soldering American-made and foreign-made... electronic function and is ready for incorporation into the computer. The foreign-made components have...

Computer Aided Tests.

ERIC Educational Resources Information Center

Steinke, Elisabeth

An approach to using the computer to assemble German tests is described. The purposes of the system would be: (1) an expansion of the bilingual lexical memory bank to list and store idioms of all degrees of difficulty, with frequency data and with complete and sophisticated retrieval possibility for assembly; (2) the creation of an…

Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer (7th Annual SFAF Meeting, 2012)

ScienceCinema

Copeland, Alex [DOE JGI

2017-12-09

Alex Copeland on "Assembly of large metagenome data sets using a Convey HC-1 hybrid core computer" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

The Development of a Technology-Based Hierarchy to Assess Chronic Low Back Pain and Pain-Related Anxiety From a Fear-Avoidance Model.

PubMed

Springer, Kristen S; George, Steven Z; Robinson, Michael E

2016-08-01

Previous studies have not examined the assessment of chronic low back pain (CLBP) and pain-related anxiety from a fear avoidance model through the use of motion-capture software and virtual human technologies. The aim of this study was to develop and assess the psychometric properties of an interactive, technologically based hierarchy that can be used to assess patients with pain and pain-related anxiety. We enrolled 30 licensed physical therapists and 30 participants with CLBP. Participants rated 21 video clips of a 3-D animated character (avatar) engaging in activities that are typically feared by patients with CLBP. The results of the study indicate that physical therapists found the virtual hierarchy clips acceptable and depicted realistic patient experiences. Most participants with CLBP reported at least 1 video clip as being sufficiently anxiety-provoking for use clinically. Therefore, this study suggests a hierarchy of fears can be created out of 21 virtual patient video clips paving the way for future clinical use in patients with CLBP. This report describes the development of a computer-based virtual patient system for the assessment of back pain-related fear and anxiety. Results show that people with back pain as well as physical therapists found the avatar to be realistic, and the depictions of behavior anxiety- and fear-provoking. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.

Intraosseous anesthesia using a computer-controlled system during non-surgical periodontal therapy (root planing): Two case reports.

PubMed

Han, Keumah; Kim, Jongbin

2018-02-01

Local anesthesia is administered to control pain, but it may induce fear and anxiety. Root planing is a non-surgical periodontal therapy; however, when it is performed in an extensive manner, some tissue removal is inevitable. Notably, this removal may be so painful that local anesthesia is required to be administered to the area scheduled for the treatment. Although patients tend to accept root planing easily, they frequently express a fear of local anesthesia. Intraosseous anesthesia (IA) is an intraosseous injection technique, whereby local anesthetic is injected into the cancellous bone supporting the teeth. A computer-controlled IA system (CIAS) exhibits multiple benefits, such as less painful anesthesia, reduced soft tissue numbness, and the provision of palatal or lingual, as well as buccal, anesthesia via single needle penetration. In this report, we present two cases of root planing that were performed under local anesthesia, using a CIAS.

Intraosseous anesthesia using a computer-controlled system during non-surgical periodontal therapy (root planing): Two case reports

PubMed Central

2018-01-01

Local anesthesia is administered to control pain, but it may induce fear and anxiety. Root planing is a non-surgical periodontal therapy; however, when it is performed in an extensive manner, some tissue removal is inevitable. Notably, this removal may be so painful that local anesthesia is required to be administered to the area scheduled for the treatment. Although patients tend to accept root planing easily, they frequently express a fear of local anesthesia. Intraosseous anesthesia (IA) is an intraosseous injection technique, whereby local anesthetic is injected into the cancellous bone supporting the teeth. A computer-controlled IA system (CIAS) exhibits multiple benefits, such as less painful anesthesia, reduced soft tissue numbness, and the provision of palatal or lingual, as well as buccal, anesthesia via single needle penetration. In this report, we present two cases of root planing that were performed under local anesthesia, using a CIAS. PMID:29556561

Virtual Reality-Enhanced Extinction of Phobias and Post-Traumatic Stress.

PubMed

Maples-Keller, Jessica L; Yasinski, Carly; Manjin, Nicole; Rothbaum, Barbara Olasov

2017-07-01

Virtual reality (VR) refers to an advanced technological communication interface in which the user is actively participating in a computer-generated 3-dimensional virtual world that includes computer sensory input devices used to simulate real-world interactive experiences. VR has been used within psychiatric treatment for anxiety disorders, particularly specific phobias and post-traumatic stress disorder, given several advantages that VR provides for use within treatment for these disorders. Exposure therapy for anxiety disorder is grounded in fear-conditioning models, in which extinction learning involves the process through which conditioned fear responses decrease or are inhibited. The present review will provide an overview of extinction training and anxiety disorder treatment, advantages for using VR within extinction training, a review of the literature regarding the effectiveness of VR within exposure therapy for specific phobias and post-traumatic stress disorder, and limitations and future directions of the extant empirical literature.

Discrete State Change Model of Manufacturing Quality to Aid Assembly Process Design

NASA Astrophysics Data System (ADS)

Koga, Tsuyoshi; Aoyama, Kazuhiro

This paper proposes a representation model of the quality state change in an assembly process that can be used in a computer-aided process design system. In order to formalize the state change of the manufacturing quality in the assembly process, the functions, operations, and quality changes in the assembly process are represented as a network model that can simulate discrete events. This paper also develops a design method for the assembly process. The design method calculates the space of quality state change and outputs a better assembly process (better operations and better sequences) that can be used to obtain the intended quality state of the final product. A computational redesigning algorithm of the assembly process that considers the manufacturing quality is developed. The proposed method can be used to design an improved manufacturing process by simulating the quality state change. A prototype system for planning an assembly process is implemented and applied to the design of an auto-breaker assembly process. The result of the design example indicates that the proposed assembly process planning method outputs a better manufacturing scenario based on the simulation of the quality state change.

Toward a molecular programming language for algorithmic self-assembly

NASA Astrophysics Data System (ADS)

Patitz, Matthew John

Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square 'tiles' are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, high-level programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing self-assembling systems, we hope to increase the complexity which is attainable. These tools provide a solid foundation for future work in both the Tile Assembly Model and explorations into more advanced models.

Validation of the Childbirth Attitudes Questionnaire in Greek and psychosocial characteristics of pregnant women with fear of childbirth.

PubMed

Gourounti, Kleanthi; Kouklaki, Eleni; Lykeridou, Katerina

2015-09-01

Fear of childbirth has been found to be a factor that influences women's decision about their choice of delivery. The investigation of psychological factors that relate to fear of childbirth as well as the validation of the Childbirth Attitudes Questionnaire (CAQ) can help identify pregnant women with high fear of childbirth. This study aimed to (a) translate and validate the Childbirth Attitude Questionnaire in Greek and (b) explore how fear of childbirth was related to childbirth self-efficacy, state anxiety, depression, neuroticism, self-esteem and optimism. 145 nulliparous pregnant women, in late pregnancy, attending routine antenatal visit in a private maternity clinic participated. All participants completed the CAQ (fear of childbirth) and other self-report questionnaires that measured childbirth self-efficacy, self-esteem, optimism, neuroticism, state anxiety and depressive symptomatology. Factor structure was investigated using principal axis factoring. Cronbach's α was used to measure internal consistency reliability. Pearson's correlation coefficients were calculated between all study variables, followed by multiple linear regression. The factor analysis suggested the existence of one-factor structure. Construct validity was confirmed by computing correlations between the CAQ and childbirth self-efficacy, self-esteem and optimism. Multivariate analysis showed that childbirth self-efficacy, self-esteem and optimism were negatively and significantly associated with fear of childbirth. The Greek version of the CAQ is a reliable and valid measure. The clinical use of CAQ may enable midwives and other health care professionals to identify pregnant women with low childbirth confidence and to provide information and support. Copyright © 2015 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

Fear of darkness, the full moon and the nocturnal ecology of African lions.

PubMed

Packer, Craig; Swanson, Alexandra; Ikanda, Dennis; Kushnir, Hadas

2011-01-01

Nocturnal carnivores are widely believed to have played an important role in human evolution, driving the need for night-time shelter, the control of fire and our innate fear of darkness. However, no empirical data are available on the effects of darkness on the risks of predation in humans. We performed an extensive analysis of predatory behavior across the lunar cycle on the largest dataset of lion attacks ever assembled and found that African lions are as sensitive to moonlight when hunting humans as when hunting herbivores and that lions are most dangerous to humans when the moon is faint or below the horizon. At night, people are most active between dusk and 10:00 pm, thus most lion attacks occur in the first weeks following the full moon (when the moon rises at least an hour after sunset). Consequently, the full moon is a reliable indicator of impending danger, perhaps helping to explain why the full moon has been the subject of so many myths and misconceptions.

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

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

King, Neil P.; Sheffler, William; Sawaya, Michael R.

2015-09-17

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method canmore » be used to design a wide variety of self-assembling protein nanomaterials.« less

Use of an Automatic Problem Generator to Teach Basic Skills in a First Course in Assembly Language.

ERIC Educational Resources Information Center

Benander, Alan; And Others

1989-01-01

Discussion of the use of computer aided instruction (CAI) and instructional software in college level courses highlights an automatic problem generator, AUTOGEN, that was written for computer science students learning assembly language. Design of the software is explained, and student responses are reported. (nine references) (LRW)

Development of a virtual speaking simulator using Image Based Rendering.

PubMed

Lee, J M; Kim, H; Oh, M J; Ku, J H; Jang, D P; Kim, I Y; Kim, S I

2002-01-01

The fear of speaking is often cited as the world's most common social phobia. The rapid growth of computer technology has enabled the use of virtual reality (VR) for the treatment of the fear of public speaking. There are two techniques for building virtual environments for the treatment of this fear: a model-based and a movie-based method. Both methods have the weakness that they are unrealistic and not controllable individually. To understand these disadvantages, this paper presents a virtual environment produced with Image Based Rendering (IBR) and a chroma-key simultaneously. IBR enables the creation of realistic virtual environments where the images are stitched panoramically with the photos taken from a digital camera. And the use of chroma-keys puts virtual audience members under individual control in the environment. In addition, real time capture technique is used in constructing the virtual environments enabling spoken interaction between the subject and a therapist or another subject.

Distributed collaborative response surface method for mechanical dynamic assembly reliability design

NASA Astrophysics Data System (ADS)

Bai, Guangchen; Fei, Chengwei

2013-11-01

Because of the randomness of many impact factors influencing the dynamic assembly relationship of complex machinery, the reliability analysis of dynamic assembly relationship needs to be accomplished considering the randomness from a probabilistic perspective. To improve the accuracy and efficiency of dynamic assembly relationship reliability analysis, the mechanical dynamic assembly reliability(MDAR) theory and a distributed collaborative response surface method(DCRSM) are proposed. The mathematic model of DCRSM is established based on the quadratic response surface function, and verified by the assembly relationship reliability analysis of aeroengine high pressure turbine(HPT) blade-tip radial running clearance(BTRRC). Through the comparison of the DCRSM, traditional response surface method(RSM) and Monte Carlo Method(MCM), the results show that the DCRSM is not able to accomplish the computational task which is impossible for the other methods when the number of simulation is more than 100 000 times, but also the computational precision for the DCRSM is basically consistent with the MCM and improved by 0.40˜4.63% to the RSM, furthermore, the computational efficiency of DCRSM is up to about 188 times of the MCM and 55 times of the RSM under 10000 times simulations. The DCRSM is demonstrated to be a feasible and effective approach for markedly improving the computational efficiency and accuracy of MDAR analysis. Thus, the proposed research provides the promising theory and method for the MDAR design and optimization, and opens a novel research direction of probabilistic analysis for developing the high-performance and high-reliability of aeroengine.

Greed and Fear in Network Reciprocity: Implications for Cooperation among Organizations.

PubMed

Kitts, James A; Leal, Diego F; Felps, Will; Jones, Thomas M; Berman, Shawn L

2016-01-01

Extensive interdisciplinary literatures have built on the seminal spatial dilemmas model, which depicts the evolution of cooperation on regular lattices, with strategies propagating locally by relative fitness. In this model agents may cooperate with neighbors, paying an individual cost to enhance their collective welfare, or they may exploit cooperative neighbors and diminish collective welfare. Recent research has extended the model in numerous ways, incorporating behavioral noise, implementing other network topologies or adaptive networks, and employing alternative dynamics of replication. Although the underlying dilemma arises from two distinct dimensions-the gains for exploiting cooperative partners (Greed) and the cost of cooperating with exploitative partners (Fear)-most work following from the spatial dilemmas model has argued or assumed that the dilemma can be represented with a single parameter: This research has typically examined Greed or Fear in isolation, or a composite such as the K-index of Cooperation or the ratio of the benefit to cost of cooperation. We challenge this claim on theoretical grounds-showing that embedding interaction in networks generally leads Greed and Fear to have divergent, interactive, and highly nonlinear effects on cooperation at the macro level, even when individuals respond identically to Greed and Fear. Using computational experiments, we characterize both dynamic local behavior and long run outcomes across regions of this space. We also simulate interventions to investigate changes of Greed and Fear over time, showing how model behavior changes asymmetrically as boundaries in payoff space are crossed, leading some interventions to have irreversible effects on cooperation. We then replicate our experiments on inter-organizational network data derived from links through shared directors among 2,400 large US corporations, thus demonstrating our findings for Greed and Fear on a naturally-occurring network. In closing, we discuss implications of our main findings regarding Greed and Fear for the problem of cooperation on inter-organizational networks.

Greed and Fear in Network Reciprocity: Implications for Cooperation among Organizations

PubMed Central

Kitts, James A.; Leal, Diego F.; Felps, Will; Jones, Thomas M.; Berman, Shawn L.

2016-01-01

Extensive interdisciplinary literatures have built on the seminal spatial dilemmas model, which depicts the evolution of cooperation on regular lattices, with strategies propagating locally by relative fitness. In this model agents may cooperate with neighbors, paying an individual cost to enhance their collective welfare, or they may exploit cooperative neighbors and diminish collective welfare. Recent research has extended the model in numerous ways, incorporating behavioral noise, implementing other network topologies or adaptive networks, and employing alternative dynamics of replication. Although the underlying dilemma arises from two distinct dimensions—the gains for exploiting cooperative partners (Greed) and the cost of cooperating with exploitative partners (Fear)–most work following from the spatial dilemmas model has argued or assumed that the dilemma can be represented with a single parameter: This research has typically examined Greed or Fear in isolation, or a composite such as the K-index of Cooperation or the ratio of the benefit to cost of cooperation. We challenge this claim on theoretical grounds—showing that embedding interaction in networks generally leads Greed and Fear to have divergent, interactive, and highly nonlinear effects on cooperation at the macro level, even when individuals respond identically to Greed and Fear. Using computational experiments, we characterize both dynamic local behavior and long run outcomes across regions of this space. We also simulate interventions to investigate changes of Greed and Fear over time, showing how model behavior changes asymmetrically as boundaries in payoff space are crossed, leading some interventions to have irreversible effects on cooperation. We then replicate our experiments on inter-organizational network data derived from links through shared directors among 2,400 large US corporations, thus demonstrating our findings for Greed and Fear on a naturally-occurring network. In closing, we discuss implications of our main findings regarding Greed and Fear for the problem of cooperation on inter-organizational networks. PMID:26863540

Local rules simulation of the kinetics of virus capsid self-assembly.

PubMed

Schwartz, R; Shor, P W; Prevelige, P E; Berger, B

1998-12-01

A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.

Spent nuclear fuel assembly inspection using neutron computed tomography

NASA Astrophysics Data System (ADS)

Pope, Chad Lee

The research presented here focuses on spent nuclear fuel assembly inspection using neutron computed tomography. Experimental measurements involving neutron beam transmission through a spent nuclear fuel assembly serve as benchmark measurements for an MCNP simulation model. Comparison of measured results to simulation results shows good agreement. Generation of tomography images from MCNP tally results was accomplished using adapted versions of built in MATLAB algorithms. Multiple fuel assembly models were examined to provide a broad set of conclusions. Tomography images revealing assembly geometric information including the fuel element lattice structure and missing elements can be obtained using high energy neutrons. A projection difference technique was developed which reveals the substitution of unirradiated fuel elements for irradiated fuel elements, using high energy neutrons. More subtle material differences such as altering the burnup of individual elements can be identified with lower energy neutrons provided the scattered neutron contribution to the image is limited. The research results show that neutron computed tomography can be used to inspect spent nuclear fuel assemblies for the purpose of identifying anomalies such as missing elements or substituted elements. The ability to identify anomalies in spent fuel assemblies can be used to deter diversion of material by increasing the risk of early detection as well as improve reprocessing facility operations by confirming the spent fuel configuration is as expected or allowing segregation if anomalies are detected.

Genome assembly reborn: recent computational challenges

PubMed Central

2009-01-01

Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain. PMID:19482960

Two criteria for the selection of assembly plans - Maximizing the flexibility of sequencing the assembly tasks and minimizing the assembly time through parallel execution of assembly tasks

NASA Technical Reports Server (NTRS)

Homem De Mello, Luiz S.; Sanderson, Arthur C.

1991-01-01

The authors introduce two criteria for the evaluation and selection of assembly plans. The first criterion is to maximize the number of different sequences in which the assembly tasks can be executed. The second criterion is to minimize the total assembly time through simultaneous execution of assembly tasks. An algorithm that performs a heuristic search for the best assembly plan over the AND/OR graph representation of assembly plans is discussed. Admissible heuristics for each of the two criteria introduced are presented. Some implementation issues that affect the computational efficiency are addressed.

Threat visibility modulates the defensive brain circuit underlying fear and anxiety.

PubMed

Rigoli, Francesco; Ewbank, Michael; Dalgleish, Tim; Calder, Andrew

2016-01-26

Recent theories distinguish anxiety from fear in the brain. Anxiety is associated with activation in ventromedial prefrontal cortex and hippocampus, while fear is associated with activation in periaqueductal gray, with amygdala involved in processing aspects of both emotional responses. These theories propose that the amount of information available about threat determines which of the two defensive responses is elicited, with fear and anxiety associated with well-defined and uncertain threats respectively. However, a direct test of this hypothesis is lacking. Here we provide such a test using fMRI to record participants' brain activity while they performed a computer-based task which required to press a button to move an artificial agent to a target position while an artificial predator chased the agent. In one condition (associated with fear) the predator was visible, while in another condition (associated with anxiety) the predator was invisible. Ventromedial prefrontal cortex, hippocampus, and amygdala showed increased activity when the predator was invisible compared to visible, while the opposite effect was observed in periaqueductal gray. We also observed that participants with high but not low trait-anxiety showed an hippocampal activation with invisible threat at an earlier time stage during the trial. These findings help clarify the neural mechanisms that underlie different defensive emotions and shed light on how these mechanisms may contribute to exaggerated anxiety. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Advanced Computer Simulations of Military Incinerators

DTIC Science & Technology

2004-12-01

Reaction Engineering International (REI) has developed advanced computer simulation tools for analyzing chemical demilitarization incinerators. The...Manager, 2003a: Summary of Engineering Design Study Projectile Washout System (PWS) Testing. Assembled Chemical Weapons Alternatives (ACWA), Final... Engineering Design Studies for Demilitarization of Assembled Chemical Weapons at Pueblo Chemical Depot. O’Shea, L. et al, 2003: RIM 57 – Monitoring in

Combining Self-Explaining with Computer Architecture Diagrams to Enhance the Learning of Assembly Language Programming

ERIC Educational Resources Information Center

Hung, Y.-C.

2012-01-01

This paper investigates the impact of combining self explaining (SE) with computer architecture diagrams to help novice students learn assembly language programming. Pre- and post-test scores for the experimental and control groups were compared and subjected to covariance (ANCOVA) statistical analysis. Results indicate that the SE-plus-diagram…

An Easily Assembled Laboratory Exercise in Computed Tomography

ERIC Educational Resources Information Center

Mylott, Elliot; Klepetka, Ryan; Dunlap, Justin C.; Widenhorn, Ralf

2011-01-01

In this paper, we present a laboratory activity in computed tomography (CT) primarily composed of a photogate and a rotary motion sensor that can be assembled quickly and partially automates data collection and analysis. We use an enclosure made with a light filter that is largely opaque in the visible spectrum but mostly transparent to the near…

TUMOR HAPLOTYPE ASSEMBLY ALGORITHMS FOR CANCER GENOMICS

PubMed Central

AGUIAR, DEREK; WONG, WENDY S.W.; ISTRAIL, SORIN

2014-01-01

The growing availability of inexpensive high-throughput sequence data is enabling researchers to sequence tumor populations within a single individual at high coverage. But, cancer genome sequence evolution and mutational phenomena like driver mutations and gene fusions are difficult to investigate without first reconstructing tumor haplotype sequences. Haplotype assembly of single individual tumor populations is an exceedingly difficult task complicated by tumor haplotype heterogeneity, tumor or normal cell sequence contamination, polyploidy, and complex patterns of variation. While computational and experimental haplotype phasing of diploid genomes has seen much progress in recent years, haplotype assembly in cancer genomes remains uncharted territory. In this work, we describe HapCompass-Tumor a computational modeling and algorithmic framework for haplotype assembly of copy number variable cancer genomes containing haplotypes at different frequencies and complex variation. We extend our polyploid haplotype assembly model and present novel algorithms for (1) complex variations, including copy number changes, as varying numbers of disjoint paths in an associated graph, (2) variable haplotype frequencies and contamination, and (3) computation of tumor haplotypes using simple cycles of the compass graph which constrain the space of haplotype assembly solutions. The model and algorithm are implemented in the software package HapCompass-Tumor which is available for download from http://www.brown.edu/Research/Istrail_Lab/. PMID:24297529

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly.

PubMed

Kumar, M Senthil; Schwartz, Russell

2010-12-09

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

NASA Astrophysics Data System (ADS)

Senthil Kumar, M.; Schwartz, Russell

2010-12-01

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

Interpretive computer simulator for the NASA Standard Spacecraft Computer-2 (NSSC-2)

NASA Technical Reports Server (NTRS)

Smith, R. S.; Noland, M. S.

1979-01-01

An Interpretive Computer Simulator (ICS) for the NASA Standard Spacecraft Computer-II (NSSC-II) was developed as a code verification and testing tool for the Annular Suspension and Pointing System (ASPS) project. The simulator is written in the higher level language PASCAL and implented on the CDC CYBER series computer system. It is supported by a metal assembler, a linkage loader for the NSSC-II, and a utility library to meet the application requirements. The architectural design of the NSSC-II is that of an IBM System/360 (S/360) and supports all but four instructions of the S/360 standard instruction set. The structural design of the ICS is described with emphasis on the design differences between it and the NSSC-II hardware. The program flow is diagrammed, with the function of each procedure being defined; the instruction implementation is discussed in broad terms; and the instruction timings used in the ICS are listed. An example of the steps required to process an assembly level language program on the ICS is included. The example illustrates the control cards necessary to assemble, load, and execute assembly language code; the sample program to to be executed; the executable load module produced by the loader; and the resulting output produced by the ICS.

Conquer fear: protocol of a randomised controlled trial of a psychological intervention to reduce fear of cancer recurrence.

PubMed

Butow, Phyllis N; Bell, Melanie L; Smith, Allan B; Fardell, Joanna E; Thewes, Belinda; Turner, Jane; Gilchrist, Jemma; Beith, Jane; Girgis, Afaf; Sharpe, Louise; Shih, Sophy; Mihalopoulos, Cathrine

2013-04-23

Up to 70% of cancer survivors report clinically significant levels of fear of cancer recurrence (FCR). Despite the known negative impact of FCR on psychological wellbeing and quality of life, little research has investigated interventions for high FCR. Our team has developed and piloted a novel intervention (Conquer Fear) based on the Self-Regulatory Executive Function Model and Relational Frame Theory and is evaluating Conquer Fear in a randomised controlled trial (RCT). We aim to compare the efficacy and cost-efficacy of the Conquer Fear Intervention and relaxation training in reducing the impact of FCR. This study is a multi-centre RCT with 260 participants randomised either to the Conquer Fear Intervention or relaxation training. Both interventions will be delivered in five sessions over 10 weeks by trained psychologists, psychiatrists and social workers with five or more years experience in oncology. Conquer Fear sessions use attentional training, detached mindfulness, meta-cognitive therapy, values clarification and psycho-education to help patients change the way they regulate and respond to thoughts about cancer recurrence. Relaxation training includes training in progressive and passive muscle relaxation, meditative relaxation, visualisation and "quick relaxation" techniques. Relaxation was chosen to control for therapist time and attention and has good face-validity as an intervention. The primary outcome is fear of cancer recurrence. Secondary outcomes include distress, quality of life, unmet needs, and health care utilisation. Participants complete questionnaires prior to starting the intervention, immediately after completing the intervention, 3 and 6 months later. Eligible participants are early-stage breast or colorectal cancer survivors who have completed hospital-based treatment between 2 months and 5 years prior to study entry and report a score in the clinical range on the Fear of Cancer Recurrence Inventory. The biostatistician is blinded to group allocation and participants are blinded to which intervention is being evaluated. Randomisation is computer generated, stratified by therapist, and uses sequentially numbered sealed envelopes. If successful, the study will provide an evidence-based intervention to reduce psychological morbidity in cancer survivors, and reduce overall health care costs due to more appropriate use of follow-up care and other health services in this very large population. ACTRN12612000404820.

Conquer fear: protocol of a randomised controlled trial of a psychological intervention to reduce fear of cancer recurrence

PubMed Central

2013-01-01

Background Up to 70% of cancer survivors report clinically significant levels of fear of cancer recurrence (FCR). Despite the known negative impact of FCR on psychological wellbeing and quality of life, little research has investigated interventions for high FCR. Our team has developed and piloted a novel intervention (Conquer Fear) based on the Self-Regulatory Executive Function Model and Relational Frame Theory and is evaluating Conquer Fear in a randomised controlled trial (RCT). We aim to compare the efficacy and cost-efficacy of the Conquer Fear Intervention and relaxation training in reducing the impact of FCR. Methods/design This study is a multi-centre RCT with 260 participants randomised either to the Conquer Fear Intervention or relaxation training. Both interventions will be delivered in five sessions over 10 weeks by trained psychologists, psychiatrists and social workers with five or more years experience in oncology. Conquer Fear sessions use attentional training, detached mindfulness, meta-cognitive therapy, values clarification and psycho-education to help patients change the way they regulate and respond to thoughts about cancer recurrence. Relaxation training includes training in progressive and passive muscle relaxation, meditative relaxation, visualisation and “quick relaxation” techniques. Relaxation was chosen to control for therapist time and attention and has good face-validity as an intervention. The primary outcome is fear of cancer recurrence. Secondary outcomes include distress, quality of life, unmet needs, and health care utilisation. Participants complete questionnaires prior to starting the intervention, immediately after completing the intervention, 3 and 6 months later. Eligible participants are early-stage breast or colorectal cancer survivors who have completed hospital-based treatment between 2 months and 5 years prior to study entry and report a score in the clinical range on the Fear of Cancer Recurrence Inventory. The biostatistician is blinded to group allocation and participants are blinded to which intervention is being evaluated. Randomisation is computer generated, stratified by therapist, and uses sequentially numbered sealed envelopes. Discussion If successful, the study will provide an evidence-based intervention to reduce psychological morbidity in cancer survivors, and reduce overall health care costs due to more appropriate use of follow-up care and other health services in this very large population. Trial registration Trial registration: ACTRN12612000404820 PMID:23617696

Virtual reality system for treatment of the fear of public speaking using image-based rendering and moving pictures.

PubMed

Lee, Jae M; Ku, Jeong H; Jang, Dong P; Kim, Dong H; Choi, Young H; Kim, In Y; Kim, Sun I

2002-06-01

The fear of speaking is often cited as the world's most common social phobia. The rapid growth of computer technology enabled us to use virtual reality (VR) for the treatment of the fear of public speaking. There have been two techniques used to construct a virtual environment for the treatment of the fear of public speaking: model-based and movie-based. Virtual audiences and virtual environments made by model-based technique are unrealistic and unnatural. The movie-based technique has a disadvantage in that each virtual audience cannot be controlled respectively, because all virtual audiences are included in one moving picture file. To address this disadvantage, this paper presents a virtual environment made by using image-based rendering (IBR) and chroma keying simultaneously. IBR enables us to make the virtual environment realistic because the images are stitched panoramically with the photos taken from a digital camera. And the use of chroma keying allows a virtual audience to be controlled individually. In addition, a real-time capture technique was applied in constructing the virtual environment to give the subjects more interaction, in that they can talk with a therapist or another subject.

Programmable full-adder computations in communicating three-dimensional cell cultures.

PubMed

Ausländer, David; Ausländer, Simon; Pierrat, Xavier; Hellmann, Leon; Rachid, Leila; Fussenegger, Martin

2018-01-01

Synthetic biologists have advanced the design of trigger-inducible gene switches and their assembly into input-programmable circuits that enable engineered human cells to perform arithmetic calculations reminiscent of electronic circuits. By designing a versatile plug-and-play molecular-computation platform, we have engineered nine different cell populations with genetic programs, each of which encodes a defined computational instruction. When assembled into 3D cultures, these engineered cell consortia execute programmable multicellular full-adder logics in response to three trigger compounds.

Formulation of advanced consumables management models: Environmental control and electrical power system performance models requirements

NASA Technical Reports Server (NTRS)

Daly, J. K.; Torian, J. G.

1979-01-01

Software design specifications for developing environmental control and life support system (ECLSS) and electrical power system (EPS) programs into interactive computer programs are presented. Specifications for the ECLSS program are at the detail design level with respect to modification of an existing batch mode program. The FORTRAN environmental analysis routines (FEAR) are the subject batch mode program. The characteristics of the FEAR program are included for use in modifying batch mode programs to form interactive programs. The EPS program specifications are at the preliminary design level. Emphasis is on top-down structuring in the development of an interactive program.

Alternatives for Saving and Viewing CAD Graphics for the Web.

ERIC Educational Resources Information Center

Harris, La Verne Abe; Sadowski, Mary A.

2001-01-01

Introduces some alternatives for preparing and viewing computer aided design (CAD) graphics for Internet output on a budget, without the fear of copyright infringement, and without having to go back to college to learn a complex graphic application. (Author/YDS)

Future Work II.

ERIC Educational Resources Information Center

Harris, Philip R.

1985-01-01

Looks at changes in the manager's role due to technological advancement in the workplace. Discusses wider range of uses for computers (analysis, decision making, communications, planning, tracking trends), importance of supervisor training, cyberphobia (fear of new technology), cyberphrenia (addiction to new technology), and the effect of a work…

Hybrid reduced order modeling for assembly calculations

DOE PAGES

Bang, Youngsuk; Abdel-Khalik, Hany S.; Jessee, Matthew A.; ...

2015-08-14

While the accuracy of assembly calculations has greatly improved due to the increase in computer power enabling more refined description of the phase space and use of more sophisticated numerical algorithms, the computational cost continues to increase which limits the full utilization of their effectiveness for routine engineering analysis. Reduced order modeling is a mathematical vehicle that scales down the dimensionality of large-scale numerical problems to enable their repeated executions on small computing environment, often available to end users. This is done by capturing the most dominant underlying relationships between the model's inputs and outputs. Previous works demonstrated the usemore » of the reduced order modeling for a single physics code, such as a radiation transport calculation. This paper extends those works to coupled code systems as currently employed in assembly calculations. Finally, numerical tests are conducted using realistic SCALE assembly models with resonance self-shielding, neutron transport, and nuclides transmutation/depletion models representing the components of the coupled code system.« less

Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

PubMed

Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

2017-03-07

Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

NASA Astrophysics Data System (ADS)

Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L.; Wagner, Jef; Himes, Benjamin A.; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun

2016-12-01

HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

The A, C, G, and T of Genome Assembly.

PubMed

Wajid, Bilal; Sohail, Muhammad U; Ekti, Ali R; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

A Bayesian context fear learning algorithm/automaton

PubMed Central

Krasne, Franklin B.; Cushman, Jesse D.; Fanselow, Michael S.

2015-01-01

Contextual fear conditioning is thought to involve the synaptic plasticity-dependent establishment in hippocampus of representations of to-be-conditioned contexts which can then become associated with USs in the amygdala. A conceptual and computational model of this process is proposed in which contextual attributes are assumed to be sampled serially and randomly during contextual exposures. Given this assumption, moment-to-moment information about such attributes will often be quite different from one exposure to another and, in particular, between exposures during which representations are created, exposures during which conditioning occurs, and during recall sessions. This presents challenges to current conceptual models of hippocampal function. In order to meet these challenges, our model's hippocampus was made to operate in different modes during representation creation and recall, and non-hippocampal machinery was constructed that controlled these hippocampal modes. This machinery uses a comparison between contextual information currently observed and information associated with existing hippocampal representations of familiar contexts to compute the Bayesian Weight of Evidence that the current context is (or is not) a known one, and it uses this value to assess the appropriateness of creation or recall modes. The model predicts a number of known phenomena such as the immediate shock deficit, spurious fear conditioning to contexts that are absent but similar to actually present ones, and modulation of conditioning by pre-familiarization with contexts. It also predicts a number of as yet unknown phenomena. PMID:26074792

A Scheduling Algorithm for Computational Grids that Minimizes Centralized Processing in Genome Assembly of Next-Generation Sequencing Data

PubMed Central

Lima, Jakelyne; Cerdeira, Louise Teixeira; Bol, Erick; Schneider, Maria Paula Cruz; Silva, Artur; Azevedo, Vasco; Abelém, Antônio Jorge Gomes

2012-01-01

Improvements in genome sequencing techniques have resulted in generation of huge volumes of data. As a consequence of this progress, the genome assembly stage demands even more computational power, since the incoming sequence files contain large amounts of data. To speed up the process, it is often necessary to distribute the workload among a group of machines. However, this requires hardware and software solutions specially configured for this purpose. Grid computing try to simplify this process of aggregate resources, but do not always offer the best performance possible due to heterogeneity and decentralized management of its resources. Thus, it is necessary to develop software that takes into account these peculiarities. In order to achieve this purpose, we developed an algorithm aimed to optimize the functionality of de novo assembly software ABySS in order to optimize its operation in grids. We run ABySS with and without the algorithm we developed in the grid simulator SimGrid. Tests showed that our algorithm is viable, flexible, and scalable even on a heterogeneous environment, which improved the genome assembly time in computational grids without changing its quality. PMID:22461785

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

The A, C, G, and T of Genome Assembly

PubMed Central

Wajid, Bilal; Sohail, Muhammad U.; Ekti, Ali R.; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research. PMID:27247941

Application of a personal computer for the uncoupled vibration analysis of wind turbine blade and counterweight assemblies

NASA Technical Reports Server (NTRS)

White, P. R.; Little, R. R.

1985-01-01

A research effort was undertaken to develop personal computer based software for vibrational analysis. The software was developed to analytically determine the natural frequencies and mode shapes for the uncoupled lateral vibrations of the blade and counterweight assemblies used in a single bladed wind turbine. The uncoupled vibration analysis was performed in both the flapwise and chordwise directions for static rotor conditions. The effects of rotation on the uncoupled flapwise vibration of the blade and counterweight assemblies were evaluated for various rotor speeds up to 90 rpm. The theory, used in the vibration analysis codes, is based on a lumped mass formulation for the blade and counterweight assemblies. The codes are general so that other designs can be readily analyzed. The input for the codes is generally interactive to facilitate usage. The output of the codes is both tabular and graphical. Listings of the codes are provided. Predicted natural frequencies of the first several modes show reasonable agreement with experimental results. The analysis codes were originally developed on a DEC PDP 11/34 minicomputer and then downloaded and modified to run on an ITT XTRA personal computer. Studies conducted to evaluate the efficiency of running the programs on a personal computer as compared with the minicomputer indicated that, with the proper combination of hardware and software options, the efficiency of using a personal computer exceeds that of a minicomputer.

Extinction of Conditioned Fear is Better Learned and Recalled in the Morning than in the Evening

PubMed Central

Pace-Schott, Edward F.; Spencer, Rebecca M.C.; Vijayakumar, Shilpa; Ahmed, Nafis; Verga, Patrick W.; Orr, Scott P.; Pitman, Roger K.; Milad, Mohammed R.

2013-01-01

Sleep helps emotional memories consolidate and may promote generalization of fear extinction memory. We examined whether extinction learning and memory might differ in the morning and evening due, potentially, to circadian and/or sleep-homeostatic factors. Healthy men (N=109) in 6 groups completed a 2-session protocol. In Session 1, fear conditioning was followed by extinction learning. Partial reinforcement with mild electric shock produced conditioned skin conductance responses (SCR) to 2 differently colored lamps (CS+), but not a third color (CS−), within the computer image of a room (conditioning context). One CS+ (CS+E) but not the other (CS+U) was immediately extinguished by un-reinforced presentations in a different room (extinction context). Delay durations of 3 hr (within AM or PM), 12 hr (morning-to-evening or evening-to-morning) or 24 hr (morning-to-morning or evening-to-evening) followed. In Session 2, extinction recall and contextual fear renewal were tested. We observed no significant effects of the delay interval on extinction memory but did observe an effect of time-of-day. Fear extinction was significantly better if learned in the morning (p=.002). Collapsing across CS+ type, there was smaller morning differential SCR at both extinction recall (p=.003) and fear renewal (p=.005). Morning extinction recall showed better generalization from the CS+E to CS+U with the response to the CS+U significantly larger than to the CS+E only in the evening (p=.028). Thus, extinction is learned faster and its memory is better generalized in the morning. Cortisol and testosterone showed the expected greater salivary levels in the morning when higher testosterone/cortisol ratio also predicting better extinction learning. Circadian factors may promote morning extinction. Alternatively, evening homeostatic sleep pressure may impede extinction and favor recall of conditioned fear. PMID:23992769

Extinction of conditioned fear is better learned and recalled in the morning than in the evening.

PubMed

Pace-Schott, Edward F; Spencer, Rebecca M C; Vijayakumar, Shilpa; Ahmed, Nafis A K; Verga, Patrick W; Orr, Scott P; Pitman, Roger K; Milad, Mohammed R

2013-11-01

Sleep helps emotional memories consolidate and may promote generalization of fear extinction memory. We examined whether extinction learning and memory might differ in the morning and evening due, potentially, to circadian and/or sleep-homeostatic factors. Healthy men (N = 109) in 6 groups completed a 2-session protocol. In Session 1, fear conditioning was followed by extinction learning. Partial reinforcement with mild electric shock produced conditioned skin conductance responses (SCRs) to 2 differently colored lamps (CS+), but not a third color (CS-), within the computer image of a room (conditioning context). One CS+ (CS + E) but not the other (CS + U) was immediately extinguished by un-reinforced presentations in a different room (extinction context). Delay durations of 3 h (within AM or PM), 12 h (morning-to-evening or evening-to-morning) or 24 h (morning-to-morning or evening-to-evening) followed. In Session 2, extinction recall and contextual fear renewal were tested. We observed no significant effects of the delay interval on extinction memory but did observe an effect of time-of-day. Fear extinction was significantly better if learned in the morning (p = .002). Collapsing across CS + type, there was smaller morning differential SCR at both extinction recall (p = .003) and fear renewal (p = .005). Morning extinction recall showed better generalization from the CS + E to CS + U with the response to the CS + U significantly larger than to the CS + E only in the evening (p = .028). Thus, extinction is learned faster and its memory is better generalized in the morning. Cortisol and testosterone showed the expected greater salivary levels in the morning when higher testosterone/cortisol ratio also predicted better extinction learning. Circadian factors may promote morning extinction. Alternatively, evening homeostatic sleep pressure may impede extinction and favor recall of conditioned fear. Copyright © 2013 Elsevier Ltd. All rights reserved.

Threatening communication: a critical re-analysis and a revised meta-analytic test of fear appeal theory.

PubMed

Peters, Gjalt-Jorn Ygram; Ruiter, Robert A C; Kok, Gerjo

2013-05-01

Despite decades of research, consensus regarding the dynamics of fear appeals remains elusive. A meta-analysis was conducted that was designed to resolve this controversy. Publications that were included in previous meta-analyses were re-analysed, and a number of additional publications were located. The inclusion criteria were full factorial orthogonal manipulations of threat and efficacy, and measurement of behaviour as an outcome. Fixed and random effects models were used to compute mean effect size estimates. Meta-analysis of the six studies that satisfied the inclusion criteria clearly showed a significant interaction between threat and efficacy, such that threat only had an effect under high efficacy (d = 0.31), and efficacy only had an effect under high threat (d = 0.71). Inconsistency in results regarding the effectiveness of threatening communication can likely be attributed to flawed methodology. Proper tests of fear appeal theory yielded the theoretically hypothesised interaction effect. Threatening communication should exclusively be used when pilot studies indicate that an intervention successfully enhances efficacy.

Threatening communication: a critical re-analysis and a revised meta-analytic test of fear appeal theory

PubMed Central

Peters, Gjalt-Jorn Ygram; Ruiter, Robert A.C.; Kok, Gerjo

2013-01-01

Despite decades of research, consensus regarding the dynamics of fear appeals remains elusive. A meta-analysis was conducted that was designed to resolve this controversy. Publications that were included in previous meta-analyses were re-analysed, and a number of additional publications were located. The inclusion criteria were full factorial orthogonal manipulations of threat and efficacy, and measurement of behaviour as an outcome. Fixed and random effects models were used to compute mean effect size estimates. Meta-analysis of the six studies that satisfied the inclusion criteria clearly showed a significant interaction between threat and efficacy, such that threat only had an effect under high efficacy (d = 0.31), and efficacy only had an effect under high threat (d = 0.71). Inconsistency in results regarding the effectiveness of threatening communication can likely be attributed to flawed methodology. Proper tests of fear appeal theory yielded the theoretically hypothesised interaction effect. Threatening communication should exclusively be used when pilot studies indicate that an intervention successfully enhances efficacy. PMID:23772231

A fast sequence assembly method based on compressed data structures.

PubMed

Liang, Peifeng; Zhang, Yancong; Lin, Kui; Hu, Jinglu

2014-01-01

Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, a memory and time efficient assembler is presented from applying FM-index in JR-Assembler, called FMJ-Assembler, where FM stand for FMR-index derived from the FM-index and BWT and J for jumping extension. The FMJ-Assembler uses expanded FM-index and BWT to compress data of reads to save memory and jumping extension method make it faster in CPU time. An extensive comparison of the FMJ-Assembler with current assemblers shows that the FMJ-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less CPU time. All these advantages of the FMJ-Assembler indicate that the FMJ-Assembler will be an efficient assembly method in next generation sequencing technology.

2-d and 1-d Nanomaterials Construction through Peptide Computational Design and Solution Assembly

NASA Astrophysics Data System (ADS)

Pochan, Darrin

Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic/H-bonding/hydrophobic interactions to define hierarchical material structure and consequent properties. Importantly, while biomimicry has been a successful strategy for the design of new peptide molecules for intermolecular assembly, computational tools have been developed to de novo design peptide molecules required for construction of pre-determined, desired nanostructures and materials. A new system comprised of coiled coil bundle motifs theoretically designed to assemble into designed, one and two-dimensional nanostructures will be introduced. The strategy provides the opportunity for arbitrary nanostructure formation, i.e. structures not observed in nature, with peptide molecules. Importantly, the desired nanostructure was chosen first while the peptides needed for coiled coil formation and subsequent nanomaterial formation were determined computationally. Different interbundle, two-dimensional nanostructures are stabilized by differences in amino acid composition exposed on the exterior of the coiled coil bundles. Computation was able to determine molecules required for different interbundle symmetries within two-dimensional sheets stabilized by subtle differences in amino acid composition of the inherent peptides. Finally, polymers were also created through covalent interactions between bundles that allowed formation of architectures spanning flexible network forming chains to ultra-stiff polymers, all with the same building block peptides. The success of the computational design strategy is manifested in the nanomaterial results as characterized by electron microscopy, scattering methods, and biophysical techniques. Support from NSF DMREF program under awards DMR-1234161 and DMR-1235084.

Forced response of mistuned bladed disk assemblies

NASA Technical Reports Server (NTRS)

Watson, Brian C.; Kamat, Manohar P.; Murthy, Durbha V.

1993-01-01

A complete analytic model of mistuned bladed disk assemblies, designed to simulate the dynamical behavior of these systems, is analyzed. The model incorporates a generalized method for describing the mistuning of the assembly through the introduction of specific mistuning modes. The model is used to develop a computational bladed disk assembly model for a series of parametric studies. Results are presented demonstrating that the response amplitudes of bladed disk assemblies depend both on the excitation mode and on the mistune mode.

Technostress in Libraries: Causes, Effects and Solutions.

ERIC Educational Resources Information Center

Bichteler, Julie

1987-01-01

Examines some of the fears, frustrations, and misconceptions of library staff and patrons that hamper the effective use of computers in libraries. Strategies that library administrators could use to alleviate stress are outlined, including staff participation in the automation process, well-designed workstations, and adequate training for staff…

The meaning of computers to a group of men who are homeless.

PubMed

Miller, Kathleen Swenson; Bunch-Harrison, Stacey; Brumbaugh, Brett; Kutty, Rekha Sankaran; FitzGerald, Kathleen

2005-01-01

The purpose of this pilot study was to explore the experience with computers and the meaning of computers to a group of homeless men living in a long-term shelter. This descriptive exploratory study used semistructured interviews with seven men who had been given access to computers and had participated in individually tailored occupation based interventions through a Work Readiness Program. Three themes emerged from analyzing the interviews: access to computers, computers as a bridge to life-skill development, and changed self-perceptions as a result of connecting to technology. Because they lacked computer knowledge and feared failure, the majority of study participants had not sought out computers available through public access. The need for access to computers, the potential use of computers as a medium for intervention, and the meaning of computers to these men who represent the digital divide are described in this study.

Computational studies of the 2D self-assembly of bacterial microcompartment shell proteins

NASA Astrophysics Data System (ADS)

Mahalik, Jyoti; Brown, Kirsten; Cheng, Xiaolin; Fuentes-Cabrera, Miguel

Bacterial microcomartments (BMCs) are subcellular organelles that exist within wide variety of bacteria and function like nano-reactors. Among the different types of BMCs known, the carboxysome has been studied the most. The carboxysomes plays an important role in the transport of metabolites across its outer proteinaceous shell. Plenty of studies have investigated the structure of this shell, yet little is known about its self-assembly . Understanding the self-assembly process of BMCs' shell might allow disrupting their functioning and designing new synthetic nano-reactors. We have investigated the self-assembly process of a major protein component of the carboxysome's shell using a Monte Carlo technique that employed a coarse-grained protein model that was calibrated with the all-atomistic potential of mean force. The simulations reveal that this protein self-assembles into clusters that resemble what were seen experimentally in 2D layers. Further analysis of the simulation results suggests that the 2D self-assembly of carboxysome's facets is driven by nucleation-growth process, which in turn could play an important role in the hierarchical self-assembly of BMCs' shell in general. 1. Science Undergraduate Laboratory Internships, ORNL 2. Oak Ridge Leadership Computing Facility, ORNL.

Experiments to evolve toward a tangible user interface for computer-aided design parts assembly

NASA Astrophysics Data System (ADS)

Legardeur, Jeremy; Garreau, Ludovic; Couture, Nadine

2004-05-01

In this paper, we present the concepts of the ESKUA (Experimentation of a Kinesics System Usable for Assembly) platform that allows designers to carry out the assembly of mechanical CAD (Computer Aided Design) parts. This platform, based on tangible user interface lead taking into account assembly constraints from the beginning of the design phase and especially during the phase of CAD models manipulation. Our goal is to propose a working environment where the designer is confronted with real assembly constraints which are currently masked by existing CAD software functionalities. Thus, the platform is based on the handling of physical objects, called tangible interactors, which enable having a physical perception of the assembly constraints. In this goal, we have defined a typology of interactors based on concepts proposed in Design For Assembly methods. We present here the results of studies that led to the evolution of this first interactors set. One is concerning an experiment to evaluate the cognitive aspects of the use of interactors. The other is about an analysis of existing mechanical product and fasteners. We will show how these studies lead to the evolution of the interactors based on the functional surfaces use.

The Self-Assembly of Particles with Multipolar Interactions

DTIC Science & Technology

2004-01-01

the LATEX template in which this thesis has been written. I also thank Kevin Van Workum and Jack Douglas for contributing simulation work and some...of the computational expense of simulating such complex self-assembly systems at the molecular level and a desire to understand the self-assembly at...Dissertation directed by: Professor Wolfgang Losert Department of Physics In this thesis , we describe results from investigations of the self-assembly of

Method and system rapid piece handling

DOEpatents

Spletzer, Barry L.

1996-01-01

The advent of high-speed fabric cutters has made necessary the development of automated techniques for the collection and sorting of garment pieces into collated piles of pieces ready for assembly. The present invention enables a new method for such handling and sorting of garment parts, and to apparatus capable of carrying out this new method. The common thread is the application of computer-controlled shuttling bins, capable of picking up a desired piece of fabric and dropping it in collated order for assembly. Such apparatus with appropriate computer control relieves the bottleneck now presented by the sorting and collation procedure, thus greatly increasing the overall rate at which garments can be assembled.

Large-scale parallel genome assembler over cloud computing environment.

PubMed

Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

2017-06-01

The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

Interference assembly and fretting wear analysis of hollow shaft.

PubMed

Han, Chuanjun; Zhang, Jie

2014-01-01

Fretting damage phenomenon often appears in the interference fit assembly. The finite element model of hollow shaft and shaft sleeve was established, and the equivalent stress and contact stress were computed after interference assembly. The assembly body of hollow shaft and shaft sleeve was in whirling bending load, and the contact status (sticking, sliding, and opening) and the distribution of stress along one typical contact line were computed under different loads, interferences, hollow degrees, friction coefficient, and wear quantity. Judgment formula of contact state was fixed by introducing the corrected coefficient k. The computation results showed that the "edge effect" appears in the contact surface after interference fit. The size of slip zone is unchanged along with the increase of bending load. The greater the interference value, the bigger the wear range. The hollow degree does not influence the size of stick zone but controls the position of the junction point of slip-open. Tangential contact stress increases with the friction coefficient, which has a little effect on normal contact stress. The relationship between open size and wear capacity is approximately linear.

Computational design of co-assembling protein-DNA nanowires

NASA Astrophysics Data System (ADS)

Mou, Yun; Yu, Jiun-Yann; Wannier, Timothy M.; Guo, Chin-Lin; Mayo, Stephen L.

2015-09-01

Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein-DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein-DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein-DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein-DNA framework presented here.

Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

PubMed Central

Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

2015-01-01

Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly systems in the literature. PMID:26421616

Virtual reality therapy: an effective treatment for phobias.

PubMed

North, M M; North, S M; Coble, J R

1998-01-01

Behavioral therapy techniques for treating phobias often includes graded exposure of the patient to anxiety-producing stimuli (Systematic Desensitization). However, in utilizing systematic desensitization, research reviews demonstrate that many patients appear to have difficulty in applying imaginative techniques. This chapter describes the Virtual Reality Therapy (VRT), a new therapeutical approach that can be used to overcome some of the difficulties inherent in the traditional treatment of phobias. VRT, like current imaginal and in vivo modalities, can generate stimuli that could be utilized in desensitization therapy. Like systematic desensitization therapy, VRT can provide stimuli for patients who have difficulty in imagining scenes and/or are too phobic to experience real situations. As far as we know, the idea of using virtual reality technology to combat psychological disorders was first conceived within the Human-Computer Interaction Group at Clark Atlanta University in November 1992. Since then, we have successfully conducted the first known pilot experiments in the use of virtual reality technologies in the treatment of specific phobias: fear of flying, fear of heights, fear of being in certain situations (such as a dark barn, an enclosed bridge over a river, and in the presence of an animal [a black cat] in a dark room), and fear of public speaking. The results of these experiments are described.

Biased Facial Expression Interpretation in Shy Children

ERIC Educational Resources Information Center

Kokin, Jessica; Younger, Alastair; Gosselin, Pierre; Vaillancourt, Tracy

2016-01-01

The relationship between shyness and the interpretations of the facial expressions of others was examined in a sample of 123 children aged 12 to 14?years. Participants viewed faces displaying happiness, fear, anger, disgust, sadness, surprise, as well as a neutral expression, presented on a computer screen. The children identified each expression…

Effective Use of New Communication Technologies.

ERIC Educational Resources Information Center

Fauley, Franz E.

Until the last two or three years, three forces inhibited the acceptance of computer-assisted instruction (CAI). These were the fear on the part of traditional trainers of displacement by machines, the poor quality of existing courseware and limited capability of accompanying hardware, and the poor price and performance characteristics of existing…

Computerized LCC/ORLA methodology. [Life cycle cost/optimum repair level analysis

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

Henderson, J.T.

1979-01-01

The effort by Sandia Laboratories in developing CDC6600 computer programs for Optimum Repair Level Analysis (ORLA) and Life Cycle Cost (LCC) analysis is described. Investigation of the three repair-level strategies referenced in AFLCM/AFSCM 800-4 (base discard of subassemblies, base repair of subassemblies, and depot repair of subassemblies) was expanded to include an additional three repair-level strategies (base discard of complete assemblies and, upon shipment of complete assemblies to the depot, depot repair of assemblies by subassembly repair, and depot repair of assemblies by subassembly discard). The expanded ORLA was used directly in an LCC model that was procedurally altered tomore » accommodate the ORLA input data. Available from the LCC computer run was an LCC value corresponding to the strategy chosen from the ORLA. 2 figures.« less

A Review Study on Cloud Computing Issues

NASA Astrophysics Data System (ADS)

Kanaan Kadhim, Qusay; Yusof, Robiah; Sadeq Mahdi, Hamid; Al-shami, Sayed Samer Ali; Rahayu Selamat, Siti

2018-05-01

Cloud computing is the most promising current implementation of utility computing in the business world, because it provides some key features over classic utility computing, such as elasticity to allow clients dynamically scale-up and scale-down the resources in execution time. Nevertheless, cloud computing is still in its premature stage and experiences lack of standardization. The security issues are the main challenges to cloud computing adoption. Thus, critical industries such as government organizations (ministries) are reluctant to trust cloud computing due to the fear of losing their sensitive data, as it resides on the cloud with no knowledge of data location and lack of transparency of Cloud Service Providers (CSPs) mechanisms used to secure their data and applications which have created a barrier against adopting this agile computing paradigm. This study aims to review and classify the issues that surround the implementation of cloud computing which a hot area that needs to be addressed by future research.

Modular space station, phase B extension. Information management advanced development. Volume 4: Data processing assembly

NASA Technical Reports Server (NTRS)

Gerber, C. R.

1972-01-01

The computation and logical functions which are performed by the data processing assembly of the modular space station are defined. The subjects discussed are: (1) requirements analysis, (2) baseline data processing assembly configuration, (3) information flow study, (4) throughput simulation, (5) redundancy study, (6) memory studies, and (7) design requirements specification.

An assembler for the MOS Technology 6502 microprocessor as implemented in jolt (TM) and KIM-1 (TM)

NASA Technical Reports Server (NTRS)

Lilley, R. W.

1976-01-01

Design of low-cost, microcomputer-based navigation receivers, and the assembler are described. The development of computer software for microprocessors is materially aided by the assembler program using mnemonic variable names. The flexibility of the environment provided by the IBM's Virtual Machine Facility and the Conversational Monitor System, make possible the convenient assembler access. The implementation of the assembler for the microprocessor chip serves a part of the present need and forms a model for support of other microprocessors.

Kinetically controlled transition from disordered aggregates to ordered lattices of a computationally designed peptide sequence.

NASA Astrophysics Data System (ADS)

Tian, Yu; Zhang, Huixi; Kiick, Kristi; Saven, Jeffrey; Pochan, Darrin

Peptides with well-defined secondary-structures have the ability to exhibit specific, local shapes, which enables the design of complex nanostructures through intermolecular assembly. Our computationally designed coiled-coil homotetrameric peptide building block can self-assemble into 2-D nanomaterial lattices with predetermined symmetries by control of the coiled-coil bundle exterior amino acid residues. And the assemblies can be controlled kinetically. Firstly, the solution pH influences the assembly by affecting the external charged state of peptide bundles which can lead the bundles to be either repulsive or attractive to each other. At room temperature when peptides are under the least charged pH conditions, disordered aggregates are formed that slowly transformed into the desired 2-D lattice structures over long periods of time (weeks). Around neutral pH, even subtle charge differences that come from small pH changes can have an influence on the thickness of afterwards formed plates. Secondly, the solution temperature can largely eliminate the formation of disordered aggregates and accelerate the assembling of matured, desired nanomaterial plates by providing extra energy for the organization process of assembly building blocks. The ability to control the assembly process kinetically makes our peptide plate assemblies very promising templates for further applications to develop inorganic-organic hybrid materials. Funding acknowledged from NSF DMREF program under awards DMR-1234161 and DMR-1235084.

Effect of polarity of electric current on friction behavior of two gallium-lubricated tantalum slipring assemblies

NASA Technical Reports Server (NTRS)

Przybyszewski, J.

1972-01-01

Computer-processed data from low-speed (10 rpm) slipring experiments with two similar (but of opposite polarity) gallium-lubricated tantalum slipring assemblies (hemisphere against disk) carrying 50 amperes dc in vacuum (10 to the minus 9th power torr) showed that the slipring assembly with the anodic hemisphere had significantly lower peak-to-peak values and standard deviations of coefficient-of-friction samples (a measure of smoothness of operation) than the slipring assembly with the cathodic hemisphere. Similar data from an experiment with the same slipring assemblies running currentless showed more random differences in the frictional behavior between the two assemblies.

Comparing de novo genome assembly: the long and short of it.

PubMed

Narzisi, Giuseppe; Mishra, Bud

2011-04-29

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers--both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies--are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing "next-generation" assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium.

Information management advanced development. Volume 1: Summary

NASA Technical Reports Server (NTRS)

Gerber, C. R.

1972-01-01

The information management systems designed for the modular space station are discussed. Subjects presented are: (1) communications terminal breadboard configuration, (2) digital data bus breadboard configuration, (3) data processing assembly definition, and (4) computer program (software) assembly definition.

Optimisation of assembly scheduling in VCIM systems using genetic algorithm

NASA Astrophysics Data System (ADS)

Dao, Son Duy; Abhary, Kazem; Marian, Romeo

2017-09-01

Assembly plays an important role in any production system as it constitutes a significant portion of the lead time and cost of a product. Virtual computer-integrated manufacturing (VCIM) system is a modern production system being conceptually developed to extend the application of traditional computer-integrated manufacturing (CIM) system to global level. Assembly scheduling in VCIM systems is quite different from one in traditional production systems because of the difference in the working principles of the two systems. In this article, the assembly scheduling problem in VCIM systems is modeled and then an integrated approach based on genetic algorithm (GA) is proposed to search for a global optimised solution to the problem. Because of dynamic nature of the scheduling problem, a novel GA with unique chromosome representation and modified genetic operations is developed herein. Robustness of the proposed approach is verified by a numerical example.

Computer-aided design of nano-filter construction using DNA self-assembly

NASA Astrophysics Data System (ADS)

Mohammadzadegan, Reza; Mohabatkar, Hassan

2007-01-01

Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules.

Comparison of Accelerated Testing with Modeling to Predict Lifetime of CPV Solder Layers (Presentation)

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

Silverman, T. J.; Bosco, N.; Kurtz, S.

2012-03-01

Concentrating photovoltaic (CPV) cell assemblies can fail due to thermomechanical fatigue in the die-attach layer. In this presentation, we show the latest results from our computational model of thermomechanical fatigue. The model is used to estimate the relative lifetime of cell assemblies exposed to various temperature histories consistent with service and with accelerated testing. We also present early results from thermal cycling experiments designed to help validate the computational model.

Red-Hot Library Lust

ERIC Educational Resources Information Center

Benton, Thomas H.

2007-01-01

Thomas Benton (a pseudonym of an associate professor of English at a Midwestern liberal-arts college) describes most college libraries of today as being clean and well-lighted, with metal shelving, veneered tabletops, and banks of computers. He fears that in 20 years, college students will regard books as a "quaint technology"--the way they now…

Video Games Take Testing to the Next Level

ERIC Educational Resources Information Center

Rothman, Robert

2011-01-01

Young people playing "Halo" or "World of Warcraft" might not realize it, but they are working on the prototypes for a future generation of student tests. The increasing popularity of video and computer games may cause concern among parents, who fear their children are spending too much time on them. However, educators and researchers increasingly…

Five C Framework: A Student-Centered Approach for Teaching Programming Courses to Students with Diverse Disciplinary Background

ERIC Educational Resources Information Center

Tom, Mary

2015-01-01

The already existing complexities of teaching and learning computer programming are increased where students are diverse in their disciplinary backgrounds, language skills, and culture. Learners experience emotional issues of anxiety, fear or boredom. Identifying opportunities for improvement and applying theoretical and empirical evidence found…

Millennium bug

NASA Astrophysics Data System (ADS)

Showstack, Randy

After global fears of computer snafus prompted billions of dollars of remedial action, the Y2K bug appears to have vanished with barely a trace. But on January l, taxonomists with the entomology division of Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO) reported the discovery of an insect whose scientific and common names will be the "millennium bug."

The Benefits, and Fear, of Cookie Technology

ERIC Educational Resources Information Center

Goldsborough, Reid

2004-01-01

"Cookies" are tiny Web browser helpers and are an example of how the useful can get tossed in with the dangerous through the near hysteria brought about by the real threats of computer viruses, hacking, spyware, spam and phishing. This article briefly discusses antispyware legislation by Congress and the pros and cons of past and future…

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

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

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

DOE PAGES

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh; ...

2016-08-24

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Mapping Flexibility and the Assembly Switch of Cell Division Protein FtsZ by Computational and Mutational Approaches*♦

PubMed Central

Martín-Galiano, Antonio J.; Buey, Rubén M.; Cabezas, Marta; Andreu, José M.

2010-01-01

The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal β-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723. PMID:20472561

Mapping flexibility and the assembly switch of cell division protein FtsZ by computational and mutational approaches.

PubMed

Martín-Galiano, Antonio J; Buey, Rubén M; Cabezas, Marta; Andreu, José M

2010-07-16

The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal beta-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723.

Realistic inversion of diffraction data for an amorphous solid: The case of amorphous silicon

NASA Astrophysics Data System (ADS)

Pandey, Anup; Biswas, Parthapratim; Bhattarai, Bishal; Drabold, D. A.

2016-12-01

We apply a method called "force-enhanced atomic refinement" (FEAR) to create a computer model of amorphous silicon (a -Si) based upon the highly precise x-ray diffraction experiments of Laaziri et al. [Phys. Rev. Lett. 82, 3460 (1999), 10.1103/PhysRevLett.82.3460]. The logic underlying our calculation is to estimate the structure of a real sample a -Si using experimental data and chemical information included in a nonbiased way, starting from random coordinates. The model is in close agreement with experiment and also sits at a suitable energy minimum according to density-functional calculations. In agreement with experiments, we find a small concentration of coordination defects that we discuss, including their electronic consequences. The gap states in the FEAR model are delocalized compared to a continuous random network model. The method is more efficient and accurate, in the sense of fitting the diffraction data, than conventional melt-quench methods. We compute the vibrational density of states and the specific heat, and we find that both compare favorably to experiments.

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes. PMID:29329283

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

Pattern formation in binary colloidal assemblies: hidden symmetries in a kaleidoscope of structures.

PubMed

Lotito, Valeria; Zambelli, Tomaso

2018-06-10

In this study we present a detailed investigation of the morphology of binary colloidal structures formed by self-assembly at air/water interface of particles of two different sizes, with a size ratio such that the larger particles do not retain a hexagonal arrangement in the binary assembly. While the structure and symmetry of binary mixtures in which such hexagonal order is preserved has been thoroughly scrutinized, binary colloids in the regime of non-preservation of the hexagonal order have not been examined with the same level of detail due also to the difficulty in finding analysis tools suitable to recognize hidden symmetries in seemingly amorphous and disordered arrangements. For this purpose, we resorted to a combination of different analysis tools based on computational geometry and computational topology in order to get a comprehensive picture of the morphology of the assemblies. By carrying out an extensive investigation of binary assemblies in this regime with variable concentration of smaller particles with respect to larger particles, we identify the main patterns that coexist in the apparently disordered assemblies and detect transitions in the symmetries upon increase in the number of small particles. As the concentration of small particles increases, large particle arrangements become more dilute and a transition from hexagonal to rhombic and square symmetries occurs, accompanied also by an increase in clusters of small particles; the relative weight of each specific symmetry can be controlled by varying the composition of the assemblies. The demonstration of the possibility to control the morphology of apparently disordered binary colloidal assemblies by varying experimental conditions and the definition of a route for the investigation of disordered assemblies are precious for future studies of complex colloidal patterns to understand self-assembly mechanisms and to tailor physical properties of colloidal assemblies.

[Disintegration of the prison system, public security and social exclusion].

PubMed

Freixo, Marcelo

2016-06-01

The defense of human rights, namely one of the most important duties of the legislature, is a considerable challenge in the day-to-day business of parliament. The opinions and practices of elected representatives reflect the security concerns and fears of society that engender a vast process of social exclusion. In this context, the defense of the right to health of persons deprived of liberty seems an especially difficult task, as shown in the interview of State Congressman Marcelo Freixo, the Coordinator of the Human Rights Commission of the Legislative Assembly in Rio de Janeiro and creator of the State Mechanism for Preventing and Combating Torture.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PubMed Central

2013-01-01

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. PMID:23320958

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

Aleman, S.E.

The task was to compute the maximum aluminum-oxide and oxide-coolant temperatures of assemblies cladded in 99+ percent aluminum. The assemblies considered were the Mark VB, VE, V5, 15 and 25. These assemblies consist of nested slug columns with individual uranium slugs cladded in aluminum cans. The CREDIT code was modified to calculate the oxide film thickness and the aluminum-oxide temperature at each axial increment. This information in this report will be used to evaluate the potential for cladding corrosion of the Mark 25 assembly.

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

Aleman, S.E.

The task was to compute the maximum aluminum-oxide and oxide-coolant temperatures of assemblies cladded in 99 plus percent aluminum. The assemblies considered were the Mark VB, VE, V5, 15 and 25. These assemblies consist of nested slug columns with individual uranium slugs cladded in aluminum cans. The CREDIT code was modified to calculate the oxide film thickness and the aluminum-oxide temperature at each axial increment. The information in this report will be used to evaluate the potential for cladding corrosion of the Mark 25 assembly.

Translating dynamic defense patterns from rodents to people.

PubMed

Blanchard, D Caroline

2017-05-01

Specific defensive behaviors of rodents are shaped by features of the eliciting threat stimuli and situation. Threat scenarios confirmed these relationships in people, with results substantially replicated in 4 additional scenario studies. Subsequent human studies involve computer games measuring fear as flight from threat stimuli and anxiety as alternation between two threats. Stabilometric studies have shown reduction in sway (freezing) to inescapable (e.g. with gun pointed at subject) threatening photographs; but enhanced lateral sway (flight attempts) to escapable threats; (gun pointed away from subject). Relationships between threat ambiguity, risk assessment, and anxiety have been validated by identification of videos of facial expressions to ambiguous threats, as anxiety; and systematic biases toward threat stimuli by anxious individuals. Enhanced rumination, interpretable as unsuccessful risk assessment, is a dynamic component of both anxiety and depression, particularly in women. While there is less experimental work on defensive threat/attack, a transdiagnostic "Fear of Harm" phenotype of aggression associated with fear suggests that this is a component of pathological as well as normal human defensive behavior. Copyright © 2016. Published by Elsevier Ltd.

Computing Legacy Software Behavior to Understand Functionality and Security Properties: An IBM/370 Demonstration

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

Linger, Richard C; Pleszkoch, Mark G; Prowell, Stacy J

Organizations maintaining mainframe legacy software can benefit from code modernization and incorporation of security capabilities to address the current threat environment. Oak Ridge National Laboratory is developing the Hyperion system to compute the behavior of software as a means to gain understanding of software functionality and security properties. Computation of functionality is critical to revealing security attributes, which are in fact specialized functional behaviors of software. Oak Ridge is collaborating with MITRE Corporation to conduct a demonstration project to compute behavior of legacy IBM Assembly Language code for a federal agency. The ultimate goal is to understand functionality and securitymore » vulnerabilities as a basis for code modernization. This paper reports on the first phase, to define functional semantics for IBM Assembly instructions and conduct behavior computation experiments.« less

Implementing the UCSD PASCAL system on the MODCOMP computer. [deep space network

NASA Technical Reports Server (NTRS)

Wolfe, T.

1980-01-01

The implementation of an interactive software development system (UCSD PASCAL) on the MODCOMP computer is discussed. The development of an interpreter for the MODCOMP II and the MODCOMP IV computers, written in MODCOMP II assembly language, is described. The complete Pascal programming system was run successfully on a MODCOMP II and MODCOMP IV under both the MAX II/III and MAX IV operating systems. The source code for an 8080 microcomputer version of the interpreter was used as the design for the MODCOMP interpreter. A mapping of the functions within the 8080 interpreter into MODCOMP II assembly language was the method used to code the interpreter.

Metagenomic Assembly: Overview, Challenges and Applications

PubMed Central

Ghurye, Jay S.; Cepeda-Espinoza, Victoria; Pop, Mihai

2016-01-01

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems. PMID:27698619

Self-assembled Nanomaterials for Hybrid Electronic and Photonic Systems

DTIC Science & Technology

2015-05-15

storage media.  Project 3. Self‐assembling Circuit Defect Modeling The self‐assembly of  nanoelectronic  devices provide an opportunity to achieve... nanoelectronics . This work will be useful in predicting the potential success of defect‐ tolerance techniques for DNA self‐assembled  nanoelectronic  substrates...program with integrated circuit emphasis simulations for DNA self-assembled nanoelectronics ." IET Computers and Digital Techniques 3, no. 6 (2009): 553-569.        

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

DOE PAGES

Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin; ...

2015-01-31

We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible tomore » construct a mapping population.« less

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

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

Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin

We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible tomore » construct a mapping population.« less

Thermal Hydraulic Computational Fluid Dynamics Simulations and Experimental Investigation of Deformed Fuel Assemblies

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

Mays, Brian; Jackson, R. Brian

2017-03-08

The project, Toward a Longer Life Core: Thermal Hydraulic CFD Simulations and Experimental Investigation of Deformed Fuel Assemblies, DOE Project code DE-NE0008321, was a verification and validation project for flow and heat transfer through wire wrapped simulated liquid metal fuel assemblies that included both experiments and computational fluid dynamics simulations of those experiments. This project was a two year collaboration between AREVA, TerraPower, Argonne National Laboratory and Texas A&M University. Experiments were performed by AREVA and Texas A&M University. Numerical simulations of these experiments were performed by TerraPower and Argonne National Lab. Project management was performed by AREVA Federal Services.more » The first of a kind project resulted in the production of both local point temperature measurements and local flow mixing experiment data paired with numerical simulation benchmarking of the experiments. The project experiments included the largest wire-wrapped pin assembly Mass Index of Refraction (MIR) experiment in the world, the first known wire-wrapped assembly experiment with deformed duct geometries and the largest numerical simulations ever produced for wire-wrapped bundles.« less

Application of X-Ray Computer Tomography for Observing the Central Void Formations and the Fuel Pin Deformations of Irradiated FBR Fuel Assemblies

NASA Astrophysics Data System (ADS)

Katsuyama, Kozo; Nagamine, Tsuyoshi; Furuya, Hirotaka

2010-10-01

In order to observe the structural change in the interior of irradiated fuel assemblies, a non-destructive post-irradiation examination (PIE) technique using X-ray computer tomography (X-ray CT) was developed. This X-ray CT technique was applied to observe the central void formations and fuel pin deformations of fuel assemblies which had been irradiated at high linear heat rating. The central void sizes in all fuel pins were measured on five cross sections of the core fuel column as a parameter for evaluating fuel thermal performance. In addition, the fuel pin deformations were analyzed from X-ray CT images obtained along the axial direction of a fuel assembly at the same separation interval. A dependence of void size on the linear heat rating was seen in the fuel assembly irradiated at high linear heat rating. In addition, significant undulations of the fuel pin were observed along the axial direction, coinciding with the wrapping wire pitch in the core fuel column. Application of the developed technique should provide enhanced resolution of measurements and simplify fuel PIEs.

Self-assembled nanocages based on the coiled coil bundle motif

NASA Astrophysics Data System (ADS)

Sinha, Nairiti; Villegas, Jose; Saven, Jeffery; Kiick, Kristi; Pochan, Darrin

Computational design of coiled coil peptide bundles that undergo solution phase self-assembly presents a diverse toolbox for engineering new materials with tunable and pre-determined nanostructures that can have various end applications such as in drug delivery, biomineralization and electronics. Self-assembled cages are especially advantageous as the cage geometry provides three distinct functional sites: the interior, the exterior and the solvent-cage interface. In this poster, syntheses and characterization of a peptide cage based on computationally designed homotetrameric coiled coil bundles as building blocks is discussed. Techniques such as Transmission Electron Microscopy (TEM), Small-Angle Neutron Scattering (SANS) and Analytical Ultracentrifugation (AUC) are employed to characterize the size, shape and molecular weight of the self-assembled peptide cages under different pH and temperature conditions. Various self-assembly pathways such as dialysis and thermal quenching are shown to have a significant impact on the final structure of these peptides in solution. Comparison of results with the target cage design can be used to iteratively improve the peptide design and provide greater understanding of its interactions and folding.

A Survey of Robotic Technology.

DTIC Science & Technology

1983-07-01

developed the following definition of a robot: A robot is a reprogrammable multifunctional manipulator designed to move material, parts, tools, or specialized...subroutines subroutines commands to specific actuators, computations based on sensor data, etc. For instance, the job might be to assemble an automobile ...the set-up developed at Draper Labs to enable a robot to assemble an automobile alternator. The assembly operation is impressive to watch. The number

Berthing mechanism final test report and program assessment

NASA Technical Reports Server (NTRS)

1988-01-01

The purpose is to document the testing performed on both hardware and software developed under the Space Station Berthing Mechanisms Program. Testing of the mechanism occurred at three locations. Several system components, e.g., actuators and computer systems, were functionally tested before assembly. A series of post assembly tests were performed. The post assembly tests, as well as the dynamic testing of the mechanism, are presented.

Advanced On-Board Processor (AOP). [for future spacecraft applications

NASA Technical Reports Server (NTRS)

1973-01-01

Advanced On-board Processor the (AOP) uses large scale integration throughout and is the most advanced space qualified computer of its class in existence today. It was designed to satisfy most spacecraft requirements which are anticipated over the next several years. The AOP design utilizes custom metallized multigate arrays (CMMA) which have been designed specifically for this computer. This approach provides the most efficient use of circuits, reduces volume, weight, assembly costs and provides for a significant increase in reliability by the significant reduction in conventional circuit interconnections. The required 69 CMMA packages are assembled on a single multilayer printed circuit board which together with associated connectors constitutes the complete AOP. This approach also reduces conventional interconnections thus further reducing weight, volume and assembly costs.

Variation simulation for compliant sheet metal assemblies with applications

NASA Astrophysics Data System (ADS)

Long, Yufeng

Sheet metals are widely used in discrete products, such as automobiles, aircraft, furniture and electronics appliances, due to their good manufacturability and low cost. A typical automotive body assembly consists of more than 300 parts welded together in more than 200 assembly fixture stations. Such an assembly system is usually quite complex, and takes a long time to develop. As the automotive customer demands products of increasing quality in a shorter time, engineers in automotive industry turn to computer-aided engineering (CAE) tools for help. Computers are an invaluable resource for engineers, not only to simplify and automate the design process, but also to share design specifications with manufacturing groups so that production systems can be tooled up quickly and efficiently. Therefore, it is beneficial to develop computerized simulation and evaluation tools for development of automotive body assembly systems. It is a well-known fact that assembly architectures (joints, fixtures, and assembly lines) have a profound impact on dimensional quality of compliant sheet metal assemblies. To evaluate sheet metal assembly architectures, a special dimensional analysis tool need be developed for predicting dimensional variation of the assembly. Then, the corresponding systematic tools can be established to help engineers select the assembly architectures. In this dissertation, a unified variation model is developed to predict variation in compliant sheet metal assemblies by considering fixture-induced rigid-body motion, deformation and springback. Based on the unified variation model, variation propagation models in multiple assembly stations with various configurations are established. To evaluate the dimensional capability of assembly architectures, quantitative indices are proposed based on the sensitivity matrix, which are independent of the variation level of the process. Examples are given to demonstrate their applications in selecting robust assembly architectures, and some useful guidelines for selection of assembly architectures are summarized. In addition, to enhance the fault diagnosis, a systematic methodology is proposed for selection of measurement configurations. Specifically, principles involved in selecting measurements are generalized first; then, the corresponding quantitative indices are developed to evaluate the measurement configurations, and finally, examples are present.

Modeling Viral Capsid Assembly

PubMed Central

2014-01-01

I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened. PMID:25663722

Feedback Inhibition Shapes Emergent Computational Properties of Cortical Microcircuit Motifs.

PubMed

Jonke, Zeno; Legenstein, Robert; Habenschuss, Stefan; Maass, Wolfgang

2017-08-30

Cortical microcircuits are very complex networks, but they are composed of a relatively small number of stereotypical motifs. Hence, one strategy for throwing light on the computational function of cortical microcircuits is to analyze emergent computational properties of these stereotypical microcircuit motifs. We are addressing here the question how spike timing-dependent plasticity shapes the computational properties of one motif that has frequently been studied experimentally: interconnected populations of pyramidal cells and parvalbumin-positive inhibitory cells in layer 2/3. Experimental studies suggest that these inhibitory neurons exert some form of divisive inhibition on the pyramidal cells. We show that this data-based form of feedback inhibition, which is softer than that of winner-take-all models that are commonly considered in theoretical analyses, contributes to the emergence of an important computational function through spike timing-dependent plasticity: The capability to disentangle superimposed firing patterns in upstream networks, and to represent their information content through a sparse assembly code. SIGNIFICANCE STATEMENT We analyze emergent computational properties of a ubiquitous cortical microcircuit motif: populations of pyramidal cells that are densely interconnected with inhibitory neurons. Simulations of this model predict that sparse assembly codes emerge in this microcircuit motif under spike timing-dependent plasticity. Furthermore, we show that different assemblies will represent different hidden sources of upstream firing activity. Hence, we propose that spike timing-dependent plasticity enables this microcircuit motif to perform a fundamental computational operation on neural activity patterns. Copyright © 2017 the authors 0270-6474/17/378511-13$15.00/0.

Electron beam diagnostic for profiling high power beams

DOEpatents

Elmer, John W [Danville, CA; Palmer, Todd A [Livermore, CA; Teruya, Alan T [Livermore, CA

2008-03-25

A system for characterizing high power electron beams at power levels of 10 kW and above is described. This system is comprised of a slit disk assembly having a multitude of radial slits, a conducting disk with the same number of radial slits located below the slit disk assembly, a Faraday cup assembly located below the conducting disk, and a start-stop target located proximate the slit disk assembly. In order to keep the system from over-heating during use, a heat sink is placed in close proximity to the components discussed above, and an active cooling system, using water, for example, can be integrated into the heat sink. During use, the high power beam is initially directed onto a start-stop target and after reaching its full power is translated around the slit disk assembly, wherein the beam enters the radial slits and the conducting disk radial slits and is detected at the Faraday cup assembly. A trigger probe assembly can also be integrated into the system in order to aid in the determination of the proper orientation of the beam during reconstruction. After passing over each of the slits, the beam is then rapidly translated back to the start-stop target to minimize the amount of time that the high power beam comes in contact with the slit disk assembly. The data obtained by the system is then transferred into a computer system, where a computer tomography algorithm is used to reconstruct the power density distribution of the beam.

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

Computer-controlled local anesthetic delivery for painless anesthesia: a literature review

PubMed Central

Kwak, Eun-Jung; Pang, Nan-Sim; Cho, Jin-Hyung; Jung, Bock-Young; Kim, Kee-Deog

2016-01-01

Local anesthesia is administered to reduce pain during dental treatments, but may itself cause pain and contribute to increased dental fear. Computer-controlled local anesthetic delivery (CCLAD) is one the method to reduce patient pain during local anesthesia; it is a device that slowly administers anesthetics by using a computerized device to control the injection speed. This literature review aims to provide an objective assessment of the usefulness of CCLAD for controlling pain by reviewing papers published to date that have used CCLAD. PMID:28879299

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

PubMed

Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

Cumulative childhood interpersonal trauma is associated with reduced cortical differentiation between threat and non-threat faces in posttraumatic stress disorder adults.

PubMed

Chu, Denise A; Bryant, Richard A; Gatt, Justine M; Harris, Anthony Wf

2018-03-01

Posttraumatic stress disorder and childhood trauma frequently co-occur. Both are associated with abnormal neural responses to salient emotion stimuli. As childhood trauma is a risk factor for posttraumatic stress disorder, differentiating between their neurophysiological effects is necessary to elucidate the neural pathways by which childhood trauma exposure contributes to increased posttraumatic stress disorder risks. Face-specific N170 evoked response potentials for backward-masked (non-conscious) and conscious threat (fear, angry) and non-threat (happy) faces were measured in 77 adults (18-64 years old, 64% women, 78% right-handed) symptomatic for posttraumatic stress disorder. Differences in N170 peak amplitudes for fear-versus-happy and angry-versus-happy faces at bilateral temporo-occipital (T5, T6) sites were computed. The effect of cumulative exposure to childhood interpersonal trauma, other childhood trauma, adult trauma, depression and posttraumatic stress disorder symptom severity on the N170 response was assessed using hierarchical multiple regression analyses. T5 N170 peak amplitudes for non-conscious fear-versus-happy faces were inversely related to cumulative childhood interpersonal trauma after accounting for socio-demographic, clinical symptom and other trauma factors. Posttraumatic stress disorder Avoidance was positively associated with N170 peak amplitudes for non-conscious fear-versus-happy faces, primarily due to reduced N170 responsivity to happy faces. Childhood interpersonal trauma exposure is associated with reduced discrimination between fear and happy faces, while avoidance symptom severity is associated with dampened responsivity to automatically processed happy faces in posttraumatic stress disorder adults. Results are discussed in terms of the likely contributions of impaired threat discrimination and deficient reward processing during neural processing of salient emotion stimuli, to increased risks of posttraumatic stress disorder onset and chronicity in childhood interpersonal trauma-exposed adults.

A Framework for the Development of Automatic DFA Method to Minimize the Number of Components and Assembly Reorientations

NASA Astrophysics Data System (ADS)

Alfadhlani; Samadhi, T. M. A. Ari; Ma’ruf, Anas; Setiasyah Toha, Isa

2018-03-01

Assembly is a part of manufacturing processes that must be considered at the product design stage. Design for Assembly (DFA) is a method to evaluate product design in order to make it simpler, easier and quicker to assemble, so that assembly cost is reduced. This article discusses a framework for developing a computer-based DFA method. The method is expected to aid product designer to extract data, evaluate assembly process, and provide recommendation for the product design improvement. These three things are desirable to be performed without interactive process or user intervention, so product design evaluation process could be done automatically. Input for the proposed framework is a 3D solid engineering drawing. Product design evaluation is performed by: minimizing the number of components; generating assembly sequence alternatives; selecting the best assembly sequence based on the minimum number of assembly reorientations; and providing suggestion for design improvement.

Distributed collaborative probabilistic design for turbine blade-tip radial running clearance using support vector machine of regression

NASA Astrophysics Data System (ADS)

Fei, Cheng-Wei; Bai, Guang-Chen

2014-12-01

To improve the computational precision and efficiency of probabilistic design for mechanical dynamic assembly like the blade-tip radial running clearance (BTRRC) of gas turbine, a distribution collaborative probabilistic design method-based support vector machine of regression (SR)(called as DCSRM) is proposed by integrating distribution collaborative response surface method and support vector machine regression model. The mathematical model of DCSRM is established and the probabilistic design idea of DCSRM is introduced. The dynamic assembly probabilistic design of aeroengine high-pressure turbine (HPT) BTRRC is accomplished to verify the proposed DCSRM. The analysis results reveal that the optimal static blade-tip clearance of HPT is gained for designing BTRRC, and improving the performance and reliability of aeroengine. The comparison of methods shows that the DCSRM has high computational accuracy and high computational efficiency in BTRRC probabilistic analysis. The present research offers an effective way for the reliability design of mechanical dynamic assembly and enriches mechanical reliability theory and method.

At the Crossroads: Portrait of an Undergraduate Composition Teacher Whose Heuristics Were Transformed by Computer-Technology

ERIC Educational Resources Information Center

Grover, Susan Hendricks

2010-01-01

Heuristics are deeply-held, tacit knowledge structures connected to our feelings. A heuristic study explores a phenomenon crucial to the researcher's self-discovery (Moustakas, 1990). Like me, many undergraduate composition instructors feel both fear and hope at the crossroads of composition and technology. Technology and composition shape one…

Millennium bug

NASA Astrophysics Data System (ADS)

Showstack, Randy

After global fears of computer snafus prompted billions of dollars of remedial action, the Y2K bug appears to have vanished with barely a trace. But on January l, taxonomists with the entomology division of Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO) reported the discovery of an insect whose scientific and common names will be the “millennium bug.”

An Assessment of User Response to Phishing Attacks: The Effects of Fear and Self-Confidence

ERIC Educational Resources Information Center

House, Deanna

2013-01-01

Phishing attacks have threatened the security of both home users and organizations in recent years. Individuals of varying levels of computer proficiency are potential targets for a phishing attack; all that is needed is an email address and Internet access. Phishing uses social engineering to fraudulently obtain information that is confidential…

Cyber-Security Concerns Mount as Student Hacking Hits Schools: Districts Straining to Safeguard Online Networks

ERIC Educational Resources Information Center

Borja, Rhea R.

2006-01-01

While schools rightly fear break-ins to their computer systems by professional criminals, students are increasingly giving educators almost as much to worry about. Reports of students' gaining access to school networks to change grades, delete teachers' files, or steal data are becoming more common, experts say, and many districts remain highly…

Machine learning assembly landscapes from particle tracking data.

PubMed

Long, Andrew W; Zhang, Jie; Granick, Steve; Ferguson, Andrew L

2015-11-07

Bottom-up self-assembly offers a powerful route for the fabrication of novel structural and functional materials. Rational engineering of self-assembling systems requires understanding of the accessible aggregation states and the structural assembly pathways. In this work, we apply nonlinear machine learning to experimental particle tracking data to infer low-dimensional assembly landscapes mapping the morphology, stability, and assembly pathways of accessible aggregates as a function of experimental conditions. To the best of our knowledge, this represents the first time that collective order parameters and assembly landscapes have been inferred directly from experimental data. We apply this technique to the nonequilibrium self-assembly of metallodielectric Janus colloids in an oscillating electric field, and quantify the impact of field strength, oscillation frequency, and salt concentration on the dominant assembly pathways and terminal aggregates. This combined computational and experimental framework furnishes new understanding of self-assembling systems, and quantitatively informs rational engineering of experimental conditions to drive assembly along desired aggregation pathways.

Microcomputer software development facilities

NASA Technical Reports Server (NTRS)

Gorman, J. S.; Mathiasen, C.

1980-01-01

A more efficient and cost effective method for developing microcomputer software is to utilize a host computer with high-speed peripheral support. Application programs such as cross assemblers, loaders, and simulators are implemented in the host computer for each of the microcomputers for which software development is a requirement. The host computer is configured to operate in a time share mode for multiusers. The remote terminals, printers, and down loading capabilities provided are based on user requirements. With this configuration a user, either local or remote, can use the host computer for microcomputer software development. Once the software is developed (through the code and modular debug stage) it can be downloaded to the development system or emulator in a test area where hardware/software integration functions can proceed. The microcomputer software program sources reside in the host computer and can be edited, assembled, loaded, and then downloaded as required until the software development project has been completed.

Computational Modeling of Tissue Self-Assembly

NASA Astrophysics Data System (ADS)

Neagu, Adrian; Kosztin, Ioan; Jakab, Karoly; Barz, Bogdan; Neagu, Monica; Jamison, Richard; Forgacs, Gabor

As a theoretical framework for understanding the self-assembly of living cells into tissues, Steinberg proposed the differential adhesion hypothesis (DAH) according to which a specific cell type possesses a specific adhesion apparatus that combined with cell motility leads to cell assemblies of various cell types in the lowest adhesive energy state. Experimental and theoretical efforts of four decades turned the DAH into a fundamental principle of developmental biology that has been validated both in vitro and in vivo. Based on computational models of cell sorting, we have developed a DAH-based lattice model for tissues in interaction with their environment and simulated biological self-assembly using the Monte Carlo method. The present brief review highlights results on specific morphogenetic processes with relevance to tissue engineering applications. Our own work is presented on the background of several decades of theoretical efforts aimed to model morphogenesis in living tissues. Simulations of systems involving about 105 cells have been performed on high-end personal computers with CPU times of the order of days. Studied processes include cell sorting, cell sheet formation, and the development of endothelialized tubes from rings made of spheroids of two randomly intermixed cell types, when the medium in the interior of the tube was different from the external one. We conclude by noting that computer simulations based on mathematical models of living tissues yield useful guidelines for laboratory work and can catalyze the emergence of innovative technologies in tissue engineering.

Do personal computers make doctors less personal?

PubMed Central

Rethans, Jan-Joost; Höppener, Paul; Wolfs, George; Diederiks, Jos

1988-01-01

Ten months after the installation of a computer in a general practice surgery a postal survey (piloted questionnaire) was sent to 390 patients. The patients' views of their relationship with their doctor after the computer was introduced were compared with their view of their relationship before the installation of the computer. More than 96% of the patients (n=263) stated that contact with their doctor was as easy and as personal as before. Most stated that the computer did not influence the duration of the consultation. Eighty one patients (30%) stated, however, that they thought that their privacy was reduced. Unlike studies of patients' attitudes performed before any actual experience of use of a computer in general practice, this study found that patients have little difficulty in accepting the presence of a computer in the consultation room. Nevertheless, doctors should inform their patients about any connections between their computer and other, external computers to allay fears about a decrease in privacy. PMID:3132287

Interactive debug program for evaluation and modification of assembly-language software

NASA Technical Reports Server (NTRS)

Arpasi, D. J.

1979-01-01

An assembly-language debug program written for the Honeywell HDC-601 and DDP-516/316 computers is described. Names and relative addressing to improve operator-machine interaction are used. Features include versatile display, on-line assembly, and improved program execution and analysis. The program is discussed from both a programmer's and an operator's standpoint. Functional diagrams are included to describe the program, and each command is illustrated.

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.

PubMed

Bonizzoni, Paola; Vedova, Gianluca Della; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella

2016-03-01

The large amount of short read data that has to be assembled in future applications, such as in metagenomics or cancer genomics, strongly motivates the investigation of disk-based approaches to index next-generation sequencing (NGS) data. Positive results in this direction stimulate the investigation of efficient external memory algorithms for de novo assembly from NGS data. Our article is also motivated by the open problem of designing a space-efficient algorithm to compute a string graph using an indexing procedure based on the Burrows-Wheeler transform (BWT). We have developed a disk-based algorithm for computing string graphs in external memory: the light string graph (LSG). LSG relies on a new representation of the FM-index that is exploited to use an amount of main memory requirement that is independent from the size of the data set. Moreover, we have developed a pipeline for genome assembly from NGS data that integrates LSG with the assembly step of SGA (Simpson and Durbin, 2012 ), a state-of-the-art string graph-based assembler, and uses BEETL for indexing the input data. LSG is open source software and is available online. We have analyzed our implementation on a 875-million read whole-genome dataset, on which LSG has built the string graph using only 1GB of main memory (reducing the memory occupation by a factor of 50 with respect to SGA), while requiring slightly more than twice the time than SGA. The analysis of the entire pipeline shows an important decrease in memory usage, while managing to have only a moderate increase in the running time.

Reply [to “Comment on ‘Policy offers protection from harassment” by Marcia McNutt”

NASA Astrophysics Data System (ADS)

McNutt, Marcia

I certainly agree with the second paragraph of the accompanying reply. I cringe when a friend says that he would have liked to comment on a female colleague's stunning blue jacket, but feared that his compliment would be misinterpreted. Or when an AGU member hesitates to walk his female dinner companion back to her hotel for fear that she would resent being considered a potential victim. I think that the entire country has lost its common sense when it comes to male/female issues. I hope my male coworkers will always feel comfortable offering to carry my new computer if I cannot lift it, and I hope that they will not be offended if I insist on actually wiring it up.

Evaluation of Visual Computer Simulator for Computer Architecture Education

ERIC Educational Resources Information Center

Imai, Yoshiro; Imai, Masatoshi; Moritoh, Yoshio

2013-01-01

This paper presents trial evaluation of a visual computer simulator in 2009-2011, which has been developed to play some roles of both instruction facility and learning tool simultaneously. And it illustrates an example of Computer Architecture education for University students and usage of e-Learning tool for Assembly Programming in order to…

Wait, are you sad or angry? Large exposure time differences required for the categorization of facial expressions of emotion

PubMed Central

Du, Shichuan; Martinez, Aleix M.

2013-01-01

Abstract Facial expressions of emotion are essential components of human behavior, yet little is known about the hierarchical organization of their cognitive analysis. We study the minimum exposure time needed to successfully classify the six classical facial expressions of emotion (joy, surprise, sadness, anger, disgust, fear) plus neutral as seen at different image resolutions (240 × 160 to 15 × 10 pixels). Our results suggest a consistent hierarchical analysis of these facial expressions regardless of the resolution of the stimuli. Happiness and surprise can be recognized after very short exposure times (10–20 ms), even at low resolutions. Fear and anger are recognized the slowest (100–250 ms), even in high-resolution images, suggesting a later computation. Sadness and disgust are recognized in between (70–200 ms). The minimum exposure time required for successful classification of each facial expression correlates with the ability of a human subject to identify it correctly at low resolutions. These results suggest a fast, early computation of expressions represented mostly by low spatial frequencies or global configural cues and a later, slower process for those categories requiring a more fine-grained analysis of the image. We also demonstrate that those expressions that are mostly visible in higher-resolution images are not recognized as accurately. We summarize implications for current computational models. PMID:23509409

Meraculous2

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

2014-06-01

meraculous2 is a whole genome shotgun assembler for short-reads that is capable of assembling large, polymorphic genomes with modest computational requirements. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. Additional features include (1) handling of allelic variation using "bubble" structures within the deBruijn graph, (2) gap closing of repetitive and low quality regions using localized assemblies, and (3) an improved scaffolding algorithm that produces more complete assemblies without compromising onmore » scaffolding accuracy« less

Self-assembled software and method of overriding software execution

DOEpatents

Bouchard, Ann M.; Osbourn, Gordon C.

2013-01-08

A computer-implemented software self-assembled system and method for providing an external override and monitoring capability to dynamically self-assembling software containing machines that self-assemble execution sequences and data structures. The method provides an external override machine that can be introduced into a system of self-assembling machines while the machines are executing such that the functionality of the executing software can be changed or paused without stopping the code execution and modifying the existing code. Additionally, a monitoring machine can be introduced without stopping code execution that can monitor specified code execution functions by designated machines and communicate the status to an output device.

Modeling the self-assembly of ordered nanoporous materials

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

Monson, Peter; Auerbach, Scott

This report describes progress on a collaborative project on the multiscale modeling of the assembly processes in the synthesis of nanoporous materials. Such materials are of enormous importance in modern technology with application in the chemical process industries, biomedicine and biotechnology as well as microelectronics. The project focuses on two important classes of materials: i) microporous crystalline materials, such as zeolites, and ii) ordered mesoporous materials. In the first case the pores are part of the crystalline structure, while in the second the structures are amorphous on the atomistic length scale but where surfactant templating gives rise to order onmore » the length scale of 2 - 20 nm. We have developed a modeling framework that encompasses both these kinds of materials. Our models focus on the assembly of corner sharing silica tetrahedra in the presence of structure directing agents. We emphasize a balance between sufficient realism in the models and computational tractibility given the complex many-body phenomena. We use both on-lattice and off-lattice models and the primary computational tools are Monte Carlo simulations with sampling techniques and ensembles appropriate to specific situations. Our modeling approach is the first to capture silica polymerization, nanopore crystallization, and mesopore formation through computer-simulated self assembly.« less

Software for Building Models of 3D Objects via the Internet

NASA Technical Reports Server (NTRS)

Schramer, Tim; Jensen, Jeff

2003-01-01

The Virtual EDF Builder (where EDF signifies Electronic Development Fixture) is a computer program that facilitates the use of the Internet for building and displaying digital models of three-dimensional (3D) objects that ordinarily comprise assemblies of solid models created previously by use of computer-aided-design (CAD) programs. The Virtual EDF Builder resides on a Unix-based server computer. It is used in conjunction with a commercially available Web-based plug-in viewer program that runs on a client computer. The Virtual EDF Builder acts as a translator between the viewer program and a database stored on the server. The translation function includes the provision of uniform resource locator (URL) links to other Web-based computer systems and databases. The Virtual EDF builder can be used in two ways: (1) If the client computer is Unix-based, then it can assemble a model locally; the computational load is transferred from the server to the client computer. (2) Alternatively, the server can be made to build the model, in which case the server bears the computational load and the results are downloaded to the client computer or workstation upon completion.

Robust and efficient overset grid assembly for partitioned unstructured meshes

NASA Astrophysics Data System (ADS)

Roget, Beatrice; Sitaraman, Jayanarayanan

2014-03-01

This paper presents a method to perform efficient and automated Overset Grid Assembly (OGA) on a system of overlapping unstructured meshes in a parallel computing environment where all meshes are partitioned into multiple mesh-blocks and processed on multiple cores. The main task of the overset grid assembler is to identify, in parallel, among all points in the overlapping mesh system, at which points the flow solution should be computed (field points), interpolated (receptor points), or ignored (hole points). Point containment search or donor search, an algorithm to efficiently determine the cell that contains a given point, is the core procedure necessary for accomplishing this task. Donor search is particularly challenging for partitioned unstructured meshes because of the complex irregular boundaries that are often created during partitioning.

Conceptual Designing of a Reduced Moderation Pressurized Water Reactor by Use of MVP and MVP-BURN

NASA Astrophysics Data System (ADS)

Kugo, T.

A conceptual design of a seed-blanket assembly PWR core with a complicated geometry and a strong heterogeneity has been carried forward by use of the continuous-energy Monte Carlo method. Through parametric survey calculations by repeated use of MVP and a lattice burn-up calculation by MVP-BURN, a seed-blanket assembly configuration suitable for a concept of RMWR has been established, by evaluating precisely reactivity, a conversion ratio and a coolant void reactivity coefficient in a realistic computation time on a super computer.

Effects of a midwife psycho-education intervention to reduce childbirth fear on women's birth outcomes and postpartum psychological wellbeing.

PubMed

Fenwick, Jennifer; Toohill, Jocelyn; Gamble, Jenny; Creedy, Debra K; Buist, Anne; Turkstra, Erika; Sneddon, Anne; Scuffham, Paul A; Ryding, Elsa L

2015-10-30

High levels of childbirth fear impact birth preparation, obstetric outcomes and emotional wellbeing for around one in five women living in developed countries. Higher rates of obstetric intervention and caesarean section (CS) are experienced in fearful women. The efficacy of interventions to reduce childbirth fear is unclear, with no previous randomised controlled trials reporting birth outcomes or postnatal psychological wellbeing following a midwife led intervention. Between May 2012 and June 2013 women in their second trimester of pregnancy were recruited. Women with a fear score ≥ 66 on the Wijma Delivery Expectancy / Experience Questionnaire (W-DEQ) were randomised to receive telephone psycho-education by a midwife, or usual maternity care. A two armed non-blinded parallel (1:1) multi-site randomised controlled trial with participants allocated in blocks of ten and stratified by hospital site and parity using an electronic centralised computer service. The outcomes of the RCT on obstetric outcomes, maternal psychological well-being, parenting confidence, birth satisfaction, and future birth preference were analysed by intention to treat and reported here. 1410 women were screened for high childbirth fear (W-DEQ ≥66). Three hundred and thirty-nine (n = 339) women were randomised (intervention n = 170; controls n = 169). One hundred and eighty-four women (54 %) returned data for final analysis at 6 weeks postpartum (intervention n = 91; controls n = 93). Compared to controls the intervention group had a clinically meaningful but not statistically significant reduction in overall caesarean section (34 % vs 42 %, p = 0.27) and emergency CS rates (18 % vs 25 %, p = 0.23). Fewer women in the intervention group preferred caesarean section for a future pregnancy (18 % vs 30 %, p = 0.04). All other obstetric variables remained similar. There were no differences in postnatal depression symptoms scores, parenting confidence, or satisfaction with maternity care between groups, but a lower incidence of flashbacks about their birth in the intervention group compared to controls (14 % vs 26 %, p = 0.05). Postnatally women who received psycho-education reported that the 'decision aid' helped reduce their fear (53 % vs 37 %, p = 0.02). Following a brief antenatal midwife-led psycho-education intervention for childbirth fear women were less likely to experience distressing flashbacks of birth and preferred a normal birth in a future pregnancy. A reduction in overall CS rates was also found. Psycho-education for fearful women has clinical benefits for the current birth and expectations of future pregnancies. Australian New Zealand Controlled Trials Registry ACTRN12612000526875 , 17th May 2012.

A parallel algorithm for generation and assembly of finite element stiffness and mass matrices

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Carmona, E. A.; Nguyen, D. T.; Baddourah, M. A.

1991-01-01

A new algorithm is proposed for parallel generation and assembly of the finite element stiffness and mass matrices. The proposed assembly algorithm is based on a node-by-node approach rather than the more conventional element-by-element approach. The new algorithm's generality and computation speed-up when using multiple processors are demonstrated for several practical applications on multi-processor Cray Y-MP and Cray 2 supercomputers.

Classroom Laboratory Report: Using an Image Database System in Engineering Education.

ERIC Educational Resources Information Center

Alam, Javed; And Others

1991-01-01

Describes an image database system assembled using separate computer components that was developed to overcome text-only computer hardware storage and retrieval limitations for a pavement design class. (JJK)

DNA-programmed dynamic assembly of quantum dots for molecular computation.

PubMed

He, Xuewen; Li, Zhi; Chen, Muzi; Ma, Nan

2014-12-22

Despite the widespread use of quantum dots (QDs) for biosensing and bioimaging, QD-based bio-interfaceable and reconfigurable molecular computing systems have not yet been realized. DNA-programmed dynamic assembly of multi-color QDs is presented for the construction of a new class of fluorescence resonance energy transfer (FRET)-based QD computing systems. A complete set of seven elementary logic gates (OR, AND, NOR, NAND, INH, XOR, XNOR) are realized using a series of binary and ternary QD complexes operated by strand displacement reactions. The integration of different logic gates into a half-adder circuit for molecular computation is also demonstrated. This strategy is quite versatile and straightforward for logical operations and would pave the way for QD-biocomputing-based intelligent molecular diagnostics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

DOE PAGES

Howe, Adina; Chain, Patrick S. G.

2015-07-09

Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, theymore » present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.« less

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

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

Howe, Adina; Chain, Patrick S. G.

Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, theymore » present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.« less

Intergroup Biases in Fear-induced Aggression

PubMed Central

Mifune, Nobuhiro; Simunovic, Dora; Yamagishi, Toshio

2017-01-01

Using a recently created preemptive strike game (PSG) with 176 participants, we investigated if the motivations of spite and/or fear promotes aggression that requires a small cost to the aggressor and imposes a larger cost on the opponent, and confirmed the earlier finding that fear does but spite does not promote intergroup aggression when the groups are characterized as minimal groups; additionally, the rate of intergroup aggression did not vary according to the group membership of the opponent. The PSG represents a situation in which both the motivations of spite and of fear can logically drive players to choose an option of aggression against an opponent. Participants decide whether or not to attack another participant, who also has the same capability. The decision is made in real time, using a computer. We discuss theoretical implications of our findings on the evolutionary foundations of intragroup cooperation and intergroup aggression. The evolutionary model of intergroup aggression, or the parochial altruism model, posits that intragroup cooperation and intergroup aggression have co-evolved, and thus it predicts both intragroup cooperation and intergroup aggression to emerge even in a minimal group devoid of a history of intergroup relationships. The finding that only intragroup cooperation but not intergroup aggression emerged in the minimal group experiments strongly suggests that intergroup aggression involves a psychological mechanism that is independent from that of intragroup cooperation. We further discuss the implications of these findings on real-world politics and military strategy. PMID:28174553

Workshop on Education in Computer Security (WECS6) (6th): Avoiding Fear, Uncertainty and Doubt Through Effective Security Education, Held in Monterey, California on 12-16 July 2004

DTIC Science & Technology

2004-07-01

Melissa ) is created in the controlled environment and propagated. The students learn how viruses are written, how they are propagated via mediums like...vulnerabilities and threats, establishing disaster response and recovery procedures. Joseph Giordano , Technical Advisor, Information Warfare Branch, AFRL 60 The

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

PubMed Central

Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner. PMID:28531174

Fast-SG: an alignment-free algorithm for hybrid assembly.

PubMed

Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro

2018-05-01

Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

DSS 14 64-meter antenna. Computed RF pathlength changes under gravity loadings

NASA Technical Reports Server (NTRS)

Katow, M. S.

1981-01-01

Using a computer model of the reflector structure and its supporting assembly of the 64-m antenna rotating about the elevation axis, the radio frequency (RF) pathlengths changes resulting from gravity loadings were computed. A check on the computed values was made by comparing the computed foci offsets with actual field readings of the Z or axial focussing required for elevation angle changes.

An experiment on fear of public speaking in virtual reality.

PubMed

Pertaub, D P; Slater, M; Barker, C

2001-01-01

Can virtual reality exposure therapy be used to treat people with social phobia? To answer this question it is vital to known if people will respond to virtual humans (avatars) in a virtual social setting in the same way they would to real humans. If someone is extremely anxious with real people, will they also be anxious when faced with simulated people, despite knowing that the avatars are computer generated? In [17] we described a small pilot study that placed 10 people before a virtual audience. The purpose was to assess the extent to which social anxiety, specifically fear of public speaking, was induced by the virtual audience and the extent of influence of degree of immersion (head mounted display or desktop monitor. The current paper describes a follow up study conducted with 40 subjects and the results clearly show that not only is social anxiety induced by the audience, but the degree of anxiety experienced is directly related to the type of virtual audience feedback the speaker receives. In particular, a hostile negative audience scenario was found to generate strong affect in speakers, regardless of whether or not they normally suffered from fear of public speaking.

Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H2O@C60 assemblies

NASA Astrophysics Data System (ADS)

Felker, Peter M.; Bačić, Zlatko

2017-09-01

We present methodology for variational calculation of the 6 n -dimensional translation-rotation (TR) eigenstates of assemblies of n H2O@C60 moieties coupled by dipole-dipole interactions. We show that the TR Hamiltonian matrix for any n can be constructed from dipole-dipole matrix elements computed for n = 2 . We present results for linear H2O@C60 assemblies. Two classes of eigenstates are revealed. One class comprises excitations of the 111 rotational level of H2O. The lowest-energy 111 -derived eigenstate for each assembly exhibits significant dipole ordering and shifts down in energy with the assembly size.

Personal-Computer Video-Terminal Emulator

NASA Technical Reports Server (NTRS)

Buckley, R. H.; Koromilas, A.; Smith, R. M.; Lee, G. E.; Giering, E. W.

1985-01-01

OWL-1200 video terminal emulator has been written for IBM Personal Computer. The OWL-1200 is a simple user terminal with some intelligent capabilities. These capabilities include screen formatting and block transmission of data. Emulator is written in PASCAL and Assembler for the IBM Personal Computer operating under DOS 1.1.

The IBM PC as an Online Search Machine--Part 2: Physiology for Searchers.

ERIC Educational Resources Information Center

Kolner, Stuart J.

1985-01-01

Enumerates "hardware problems" associated with use of the IBM personal computer as an online search machine: purchase of machinery, unpacking of parts, and assembly into a properly functioning computer. Components that allow transformations of computer into a search machine (combination boards, printer, modem) and diagnostics software…

A Theoretical and Experimental Study of DNA Self-assembly

NASA Astrophysics Data System (ADS)

Chandran, Harish

The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software. We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.

Many-molecule encapsulation by an icosahedral shell

PubMed Central

Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F

2016-01-01

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515

Analysis and Design of a Double-Divert Spiral Groove Seal

NASA Technical Reports Server (NTRS)

Zheng, Xiaoqing; Berard, Gerald

2007-01-01

This viewgraph presentation describes the design and analysis of a double spiral groove seal. The contents include: 1) Double Spiral Design Features; 2) Double Spiral Operational Features; 3) Mating Ring/Rotor Assembly; 4) Seal Ring Assembly; 5) Insert Segment Joints; 6) Rotor Assembly Completed Prototype Parts; 7) Seal Assembly Completed Prototype Parts; 8) Finite Element Analysis; 9) Computational Fluid Dynamics (CFD) Analysis; 10) Restrictive Orifice Design; 11) Orifice CFD Model; 12) Orifice Results; 13) Restrictive Orifice; 14) Seal Face Coning; 15) Permanent Magnet Analysis; 16) Magnetic Repulsive Force; 17) Magnetic Repulsive Test Results; 18) Spin Testing; and 19) Testing and Validation.

Building block synthesis using the polymerase chain assembly method.

PubMed

Marchand, Julie A; Peccoud, Jean

2012-01-01

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

Concentrator optical characterization using computer mathematical modelling and point source testing

NASA Technical Reports Server (NTRS)

Dennison, E. W.; John, S. L.; Trentelman, G. F.

1984-01-01

The optical characteristics of a paraboloidal solar concentrator are analyzed using the intercept factor curve (a format for image data) to describe the results of a mathematical model and to represent reduced data from experimental testing. This procedure makes it possible not only to test an assembled concentrator, but also to evaluate single optical panels or to conduct non-solar tests of an assembled concentrator. The use of three-dimensional ray tracing computer programs to calculate the mathematical model is described. These ray tracing programs can include any type of optical configuration from simple paraboloids to array of spherical facets and can be adapted to microcomputers or larger computers, which can graphically display real-time comparison of calculated and measured data.

Design and implementation of a compliant robot with force feedback and strategy planning software

NASA Technical Reports Server (NTRS)

Premack, T.; Strempek, F. M.; Solis, L. A.; Brodd, S. S.; Cutler, E. P.; Purves, L. R.

1984-01-01

Force-feedback robotics techniques are being developed for automated precision assembly and servicing of NASA space flight equipment. Design and implementation of a prototype robot which provides compliance and monitors forces is in progress. Computer software to specify assembly steps and makes force feedback adjustments during assembly are coded and tested for three generically different precision mating problems. A model program demonstrates that a suitably autonomous robot can plan its own strategy.

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

PubMed

Parker, Nicolas J; Parker, Andrew G

2008-04-18

The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.

Transport synthetic acceleration for long-characteristics assembly-level transport problems

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

Zika, M.R.; Adams, M.L.

2000-02-01

The authors apply the transport synthetic acceleration (TSA) scheme to the long-characteristics spatial discretization for the two-dimensional assembly-level transport problem. This synthetic method employs a simplified transport operator as its low-order approximation. Thus, in the acceleration step, the authors take advantage of features of the long-characteristics discretization that make it particularly well suited to assembly-level transport problems. The main contribution is to address difficulties unique to the long-characteristics discretization and produce a computationally efficient acceleration scheme. The combination of the long-characteristics discretization, opposing reflecting boundary conditions (which are present in assembly-level transport problems), and TSA presents several challenges. The authorsmore » devise methods for overcoming each of them in a computationally efficient way. Since the boundary angular data exist on different grids in the high- and low-order problems, they define restriction and prolongation operations specific to the method of long characteristics to map between the two grids. They implement the conjugate gradient (CG) method in the presence of opposing reflection boundary conditions to solve the TSA low-order equations. The CG iteration may be applied only to symmetric positive definite (SPD) matrices; they prove that the long-characteristics discretization yields an SPD matrix. They present results of the acceleration scheme on a simple test problem, a typical pressurized water reactor assembly, and a typical boiling water reactor assembly.« less

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

C. Priniski, T. Dodson, M. Duco, S. Raftopoulos, R. Ellis, and A. Brooks

In support of the National Compact Stellerator Experiment (NCSX), stellerator assembly activities continued this past year at the Princeton Plasma Physics Laboratory (PPPL) in partnership with the Oak Ridge National Laboratory (ORNL). The construction program saw the completion of the first two Half Field-Period Assemblies (HPA), each consisting of three modular coils. The full machine includes six such sub-assemblies. A single HPA consists of three of the NCSX modular coils wound and assembled at PPPL. These geometrically-complex threedimensional coils were wound using computer-aided metrology and CAD models to tolerances within +/- 0.5mm. The assembly of these coils required similar accuracymore » on a larger scale with the added complexity of more individual parts and fewer degrees of freedom for correction. Several new potential positioning issues developed for which measurement and control techniques were developed. To accomplish this, CAD coordinate-based computer metrology equipment and software similar to the solutions employed for winding the modular coils was used. Given the size of the assemblies, the primary tools were both interferometeraided and Absolute Distance Measurement (ADM)-only based laser trackers. In addition, portable Coordinate Measurement Machine (CMM) arms and some novel indirect measurement techniques were employed. This paper will detail both the use of CAD coordinate-based metrology technology and the techniques developed and employed for dimensional control of NSCX subassemblies. The results achieved and possible improvements to techniques will be discussed.« less

Diversity of bilateral synaptic assemblies for binaural computation in midbrain single neurons.

PubMed

He, Na; Kong, Lingzhi; Lin, Tao; Wang, Shaohui; Liu, Xiuping; Qi, Jiyao; Yan, Jun

2017-11-01

Binaural hearing confers many beneficial functions but our understanding of its underlying neural substrates is limited. This study examines the bilateral synaptic assemblies and binaural computation (or integration) in the central nucleus of the inferior colliculus (ICc) of the auditory midbrain, a key convergent center. Using in-vivo whole-cell patch-clamp, the excitatory and inhibitory postsynaptic potentials (EPSPs/IPSPs) of single ICc neurons to contralateral, ipsilateral and bilateral stimulation were recorded. According to the contralateral and ipsilateral EPSP/IPSP, 7 types of bilateral synaptic assemblies were identified. These include EPSP-EPSP (EE), E-IPSP (EI), E-no response (EO), II, IE, IO and complex-mode (CM) neurons. The CM neurons showed frequency- and/or amplitude-dependent EPSPs/IPSPs to contralateral or ipsilateral stimulation. Bilateral stimulation induced EPSPs/IPSPs that could be larger than (facilitation), similar to (ineffectiveness) or smaller than (suppression) those induced by contralateral stimulation. Our findings have allowed our group to characterize novel neural circuitry for binaural computation in the midbrain. Copyright © 2017 Elsevier B.V. All rights reserved.

Fear patterns: a new approach to designing road safety advertisements.

PubMed

Algie, Jennifer; Rossiter, John R

2010-01-01

This research studies fear patterns within fear appeal anti-speeding television commercials. A pattern of fear is the sequence of fear arousal and fear reduction, if any, that is felt by the viewing audience when exposed to a fear appeal advertisement. Many road safety advertisers use fear appeals, such as "shock" advertising, that result in fear arousal, leaving the viewer feeling extremely tense. The moment-to-moment reactions of young drivers to 12 road safety commercials are gauged using a dynamic, temporal measure of fear. The fear patterns generated from each ad are analyzed and a new perspective on creating fear appeal road safety advertisements, with an emphasis on fear-relief, fear-partial relief, and fear-only patterns, is discussed.

Pathways for virus assembly around nucleic acids

PubMed Central

Perlmutter, Jason D; Perkett, Matthew R

2014-01-01

Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single molecule fluorescence correlation spectroscopy or bulk time resolved small angle x-ray scattering experiments. PMID:25036288

Interrogating viral capsid assembly with ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Uetrecht, Charlotte; Barbu, Ioana M.; Shoemaker, Glen K.; van Duijn, Esther; Heck, Albert J. R.

2011-02-01

Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.

The Shadow of Physical Harm? Examining the Unique and Gendered Relationship Between Fear of Murder Versus Fear of Sexual Assault on Fear of Violent Crime.

PubMed

Riggs, Samantha; Cook, Carrie L

2015-09-01

The shadow hypothesis regarding the impact of fear of sexual assault on fear of violent crime suggests that female fear of crime is characterized by concern about sexual assault as a contemporaneous victimization event during a violent crime event. Recent research has found that other types of crime, namely physical assault, may also be feared as a contemporaneous offense. We know of no research that has examined the unique impact of fear of murder versus fear of sexual assault on fear of violent crime. There is also a lack of research that explores how these two types of fear uniquely affect men and women. In addition to gender, we examine factors that have been suggested in previous research to correlate with fear of crime: race, victimization, vicarious victimization, and perceived risk. Through survey methodology, this research examines the unique relationship between both fear of murder and fear of sexual assault and fear of three types of violent crime for men and women. Results suggest differences in how fear of murder and fear of sexual assault are related to fear of other types of violence for men and women. Specifically, fear of murder is important in estimating male fear of robbery and aggravated assault. However, fear of sexual assault is almost as important as fear of murder for men in estimating fear of home invasion. Similarly, for women, fear of sexual assault and fear of murder both are significant factors associated with fear of violent crime, and differences between the levels of significance are marginal. This study is a first to examine whether murder may also be feared as a contemporaneous offense. The results are informative in identifying what drives fear of crime, particularly violent crime, for both men and women. Avenues for future research are discussed. © The Author(s) 2014.

Blockade of CB1 receptors prevents retention of extinction but does not increase low preincubated conditioned fear in the fear incubation procedure.

PubMed

Pickens, Charles L; Theberge, Florence R

2014-02-01

We recently developed a procedure to study fear incubation, in which rats given 100 tone-shock pairings over 10 days show low fear 2 days after conditioned fear training and high fear after 30 days. Notably, fear 2 days after 10 sessions of fear conditioning is lower than fear seen 2 days after a single session of fear conditioning, suggesting that fear is suppressed. Here, we investigate the potential role of CB1 receptor activation by endocannabinoids in this fear suppression. We subjected rats to 10 days of fear conditioning and then administered systemic injections of the CB1 receptor antagonist SR141716 before a conditioned fear test was conducted 2 days later under extinction conditions. A second test was conducted without any injections on the following day (3 days after training) to examine retention of fear extinction. SR141716 injections did not increase fear expression 2 days after extended fear conditioning or affect within-session extinction; however, it impaired retention of between-session fear extinction in the day 3 test. These data suggest that CB1 receptor activation does not suppress fear soon after extended fear conditioning in the fear incubation task. The data also add to the existing literature on the role of CB1 receptors in extinction of conditioned fear.

Blockade of CB1 receptors prevents retention of extinction but does not increase low pre-incubated conditioned fear in the fear incubation procedure

PubMed Central

Pickens, Charles L.; Theberge, Florence R.

2015-01-01

We recently developed a procedure to study fear incubation in which rats given 100 tone-shock pairings over 10 days show low fear 2 days after conditioned fear training and high fear after 30 days. Notably, fear 2 days after 10 sessions of fear conditioning is lower than fear seen 2 days after a single session of fear conditioning, suggesting that fear is suppressed. Here, we investigate the potential role of CB1 receptor activation by endocannabinoids in this fear suppression. We gave rats 10 days of fear conditioning and then gave systemic injections of the CB1 receptor antagonist SR141716 before a conditioned fear test conducted 2 days later under extinction conditions. A second test was conducted without any injections on the following day (3 days post-training) to examine fear extinction retention. SR141716 injections did not increase fear expression 2 days after extended fear conditioning or affect within-session extinction, but impaired retention of between-session fear extinction in the day 3 test. These data suggest that CB1 receptor activation is not suppressing fear soon after extended fear conditioning in the fear incubation task. The data also add to an existing literature on the effects of CB1 receptors in extinction of conditioned fear. PMID:24346290

Minimal Absent Words in Four Human Genome Assemblies

PubMed Central

Garcia, Sara P.; Pinho, Armando J.

2011-01-01

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species. PMID:22220210

Computer Tomography Analysis of Fastrac Composite Thrust Chamber Assemblies

NASA Technical Reports Server (NTRS)

Beshears, Ronald D.

2000-01-01

Computed tomography (CT) inspection has been integrated into the production process for NASA's Fastrac composite thrust chamber assemblies (TCAs). CT has been proven to be uniquely qualified to detect the known critical flaw for these nozzles, liner cracks that are adjacent to debonds between the liner and overwrap. CT is also being used as a process monitoring tool through analysis of low density indications in the nozzle overwraps. 3d reconstruction of CT images to produce models of flawed areas is being used to give program engineers better insight into the location and nature of nozzle flaws.

On Patterns in Affective Media

NASA Astrophysics Data System (ADS)

ADAMATZKY, ANDREW

In computational experiments with cellular automaton models of affective solutions, where chemical species represent happiness, anger, fear, confusion and sadness, we study phenomena of space time dynamic of emotions. We demonstrate feasibility of the affective solution paradigm in example of emotional abuse therapy. Results outlined in the present paper offer unconventional but promising technique to design, analyze and interpret spatio-temporal dynamic of mass moods in crowds.

The Impact of Software on Associate Degree Programs in Electronic Engineering Technology.

ERIC Educational Resources Information Center

Hata, David M.

1986-01-01

Assesses the range and extent of computer assisted instruction software available in electronic engineering technology education. Examines the need for software skills in four areas: (1) high-level languages; (2) assembly language; (3) computer-aided engineering; and (4) computer-aided instruction. Outlines strategies for the future in three…

Inventorying national forest resources...for planning-programing-budgeting system

Treesearch

Miles R. Hill; Elliot L. Amidon

1968-01-01

New systems for analyzing resource management problems, such as Planning-Programing-Budgeting, will require automated procedures to collect and assemble resource inventory data. A computer - oriented system called Map Information Assembly and Display System developed for this purpose was tested on a National Forest in California. It provided information on eight forest...

Computer Assisted Assembly of Tests at Educational Testing Service.

ERIC Educational Resources Information Center

Educational Testing Service, Princeton, NJ.

Two basic requirements for the successful initiation of a program for test assembly are the development of detailed item content classification systems and the delineation of the professional judgements made in building a test from a pool of items to detailed content, ability, and statistical specifications in terms precise enough to be translated…

A data base processor semantics specification package

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1983-01-01

A Semantics Specification Package (DBPSSP) for the Intel Data Base Processor (DBP) is defined. DBPSSP serves as a collection of cross assembly tools that allow the analyst to assemble request blocks on the host computer for passage to the DBP. The assembly tools discussed in this report may be effectively used in conjunction with a DBP compatible data communications protocol to form a query processor, precompiler, or file management system for the database processor. The source modules representing the components of DBPSSP are fully commented and included.

Activity-induced synaptic delivery of the GluN2A-containing NMDA receptor is dependent on endoplasmic reticulum chaperone Bip and involved in fear memory

PubMed Central

Zhang, Xiao-min; Yan, Xun-yi; Zhang, Bin; Yang, Qian; Ye, Mao; Cao, Wei; Qiang, Wen-bin; Zhu, Li-jun; Du, Yong-lan; Xu, Xing-xing; Wang, Jia-sheng; Xu, Fei; Lu, Wei; Qiu, Shuang; Yang, Wei; Luo, Jian-hong

2015-01-01

The N-methyl-D-aspartate receptor (NMDAR) in adult forebrain is a heterotetramer mainly composed of two GluN1 subunits and two GluN2A and/or GluN2B subunits. The synaptic expression and relative numbers of GluN2A- and GluN2B-containing NMDARs play critical roles in controlling Ca2+-dependent signaling and synaptic plasticity. Previous studies have suggested that the synaptic trafficking of NMDAR subtypes is differentially regulated, but the precise molecular mechanism is not yet clear. In this study, we demonstrated that Bip, an endoplasmic reticulum (ER) chaperone, selectively interacted with GluN2A and mediated the neuronal activity-induced assembly and synaptic incorporation of the GluN2A-containing NMDAR from dendritic ER. Furthermore, the GluN2A-specific synaptic trafficking was effectively disrupted by peptides interrupting the interaction between Bip and GluN2A. Interestingly, fear conditioning in mice was disrupted by intraperitoneal injection of the interfering peptide before training. In summary, we have uncovered a novel mechanism for the activity-dependent supply of synaptic GluN2A-containing NMDARs, and demonstrated its relevance to memory formation. PMID:26088419

Recent advances in sequence assembly: principles and applications.

PubMed

Chen, Qingfeng; Lan, Chaowang; Zhao, Liang; Wang, Jianxin; Chen, Baoshan; Chen, Yi-Ping Phoebe

2017-11-01

The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphism occur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered. It focuses on how individual processes, such as optimal k-mer determination and error correction in assembly, rely on intelligent strategies or high-performance computation. We also survey primary algorithms/software and offer a discussion on the emerging challenges in assembly. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

3D investigation on polystyrene colloidal crystals by floatage self-assembly with mixed solvent via synchrotron radiation x-ray phase-contrast computed tomography

NASA Astrophysics Data System (ADS)

Fu, Yanan; Xie, Honglan; Deng, Biao; Du, Guohao; Xiao, Tiqiao

2017-06-01

The floatage self-assembly method was introduced with mixed solvent as the medium of polystyrene sphere suspension to fabricate the colloidal crystal. The three dimensional (3D) void system of the colloidal crystal was noninvasively characterized by synchrotron radiation phase-contrast computed tomography, and the quantitative image analysis was implemented aiming to the polystyrene sphere colloidal crystal. Comparing with gravity sedimentation method, the three samples fabricated from floatage self-assembly with mixed solvents have the lowest porosity, and when ethylene glycol and water were mixed with ratio of 1:1, the lowest porosity of 27.49% could be achieved, that has been very close to the minimum porosity of ordered 3D monodisperse sphere array (26%). In single slices, the porosities and fractal dimension for the voids were calculated. The results showed that two factors would significantly influence the porosity of the whole colloidal crystal: the first deposited sphere layer's orderliness and the sedimentation speed of the spheres. The floatage self-assembly could induce a stable close-packing process, resulted from the powerful nucleation force-lateral capillary force coupled with the mixed solvent to regulate the floating upward speed for purpose of matching the assembly rate.

Ray Meta: scalable de novo metagenome assembly and profiling

PubMed Central

2012-01-01

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

Parallel In Vivo DNA Assembly by Recombination: Experimental Demonstration and Theoretical Approaches

PubMed Central

Shi, Zhenyu; Wedd, Anthony G.; Gras, Sally L.

2013-01-01

The development of synthetic biology requires rapid batch construction of large gene networks from combinations of smaller units. Despite the availability of computational predictions for well-characterized enzymes, the optimization of most synthetic biology projects requires combinational constructions and tests. A new building-brick-style parallel DNA assembly framework for simple and flexible batch construction is presented here. It is based on robust recombination steps and allows a variety of DNA assembly techniques to be organized for complex constructions (with or without scars). The assembly of five DNA fragments into a host genome was performed as an experimental demonstration. PMID:23468883

Computational design of a self-assembling symmetrical β-propeller protein.

PubMed

Voet, Arnout R D; Noguchi, Hiroki; Addy, Christine; Simoncini, David; Terada, Daiki; Unzai, Satoru; Park, Sam-Yong; Zhang, Kam Y J; Tame, Jeremy R H

2014-10-21

The modular structure of many protein families, such as β-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical β-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.

Automated standardization technique for an inductively-coupled plasma emission spectrometer

USGS Publications Warehouse

Garbarino, John R.; Taylor, Howard E.

1982-01-01

The manifold assembly subsystem described permits real-time computer-controlled standardization and quality control of a commercial inductively-coupled plasma atomic emission spectrometer. The manifold assembly consists of a branch-structured glass manifold, a series of microcomputer-controlled solenoid valves, and a reservoir for each standard. Automated standardization involves selective actuation of each solenoid valve that permits a specific mixed standard solution to be pumped to the nebulizer of the spectrometer. Quality control is based on the evaluation of results obtained for a mixed standard containing 17 analytes, that is measured periodically with unknown samples. An inaccurate standard evaluation triggers restandardization of the instrument according to a predetermined protocol. Interaction of the computer-controlled manifold assembly hardware with the spectrometer system is outlined. Evaluation of the automated standardization system with respect to reliability, simplicity, flexibility, and efficiency is compared to the manual procedure. ?? 1982.

Normalizing effect of heroin maintenance treatment on stress-induced brain connectivity

PubMed Central

Walter, Marc; Gerber, Hana; Seifritz, Erich; Brenneisen, Rudolf; Wiesbeck, Gerhard A.; Riecher-Rössler, Anita; Lang, Undine E.; Borgwardt, Stefan

2015-01-01

Recent evidence has shown that a single maintenance dose of heroin attenuates psychophysiological stress responses in heroin-dependent patients, probably reflecting the effectiveness of heroin-assisted therapies for the treatment of severe heroin addiction. However, the underlying neural circuitry of these effects has not yet been investigated. Using a cross-over, double-blind, vehicle-controlled design, 22 heroin-dependent and heroin-maintained outpatients from the Centre of Substance Use Disorders at the University Hospital of Psychiatry in Basel were studied after heroin and placebo administration, while 17 healthy controls from the general population were included for placebo administration only. Functional magnetic resonance imaging was used to detect brain responses to fearful faces and dynamic causal modelling was applied to compute fear-induced modulation of connectivity within the emotional face network. Stress responses were assessed by hormone releases and subjective ratings. Relative to placebo, heroin acutely reduced the fear-induced modulation of connectivity from the left fusiform gyrus to the left amygdala and from the right amygdala to the right orbitofrontal cortex in dependent patients. Both of these amygdala-related connectivity strengths were significantly increased in patients after placebo treatment (acute withdrawal) compared to healthy controls, whose connectivity estimates did not differ from those of patients after heroin injection. Moreover, we found positive correlations between the left fusiform gyrus to amygdala connectivity and different stress responses, as well as between the right amygdala to orbitofrontal cortex connectivity and levels of craving. Our findings indicate that the increased amygdala-related connectivity during fearful face processing after the placebo treatment in heroin-dependent patients transiently normalizes after acute heroin maintenance treatment. Furthermore, this study suggests that the assessment of amygdala-related connectivity during fear processing may provide a prognostic tool to assess stress levels in heroin-dependent patients and to quantify the efficacy of maintenance treatments in drug addiction. PMID:25414039

Fear of water in children and adults: etiology and familial effects.

PubMed

Graham, J; Gaffan, E A

1997-02-01

Water-fearful children (non-swimmers. 5-8 yrs and adults (non-swimmers or late learners, 23-73 yr) were compared with non-fearful controls of similar swimming ability. Parallel assessments were carried out with children and adults to investigate water-related experiences, water fear and competence in parents and siblings, and the relationship of water fear to other fear dimensions. Children were assessed behaviorally and by self and mother's report, adults by self-report. In neither children nor adults was there clear evidence that fearful and non-fearful groups differed in incidence of aversive water-related experience before fear onset. Parents usually believed that children's fear was present at first contact. In both samples, we found parent-offspring and sibling resemblances in fear. Analysis of details of children's contact with parents suggested that social learning within the family decreased water fear rather than increasing it; when both child and parent showed fear, that was as likely to reflect genetic influences as modeling. Young children's water fear forms part of a generic cluster, fear of the Unknown or Danger, while in adults it becomes independent of generic fears.

Allosteric Control of Icosahedral Capsid Assembly

PubMed Central

Lazaro, Guillermo R.

2017-01-01

During the lifecycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data. PMID:27117092

The Mechanization of Design and Manufacturing.

ERIC Educational Resources Information Center

Gunn, Thomas G.

1982-01-01

Describes changes in the design of products and in planning, managing, and coordinating their manufacture. Focuses on discrete-products manufacturing industries, encompassing the fabrication and assembly of automobiles, aircraft, computers and microelectric components of computers, furniture, appliances, foods, clothing, building materials, and…

Nanoparticles Stabilize Thin Polymer Films: A Fundamental Study to Understand the Phenomenon

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

Michael E. Mackay

2009-03-04

A new understanding of thermodynamics at the nanoscale resulted in a recently discovered first order phase transition that nanoparticles in a polymer film will all segregate to the supporting substrate. This is an unusual phase transition that was predicted using a modeling technique developed at Sandia National Laboratories and required the equivalent of many computational years on one computer. This project is a collaboration between Prof. Michael Mackay's group and Dr. Amalie Frischknecht (Sandia National Laboratories) where experimental observation and theoretical rationalization and prediction are brought together. Other discoveries were that this phase transition could be avoided by changing themore » nanoparticle properties yielding control of the assembly process at the nanoscale. In fact, the nanoparticles could be made to assemble to the supporting substrate, to the air interface or not assemble at all within a thin polymer film of order 100 nm in thickness. However, when the assembly process is present it is so robust that it is possible to make rough liquid films at the nanoscale due to nanoparticles assembling around three-dimensional objects. From this knowledge we are able to design and manufacture new coatings with particular emphasis on polymer-based solar cells. Careful control of the morphology at the nanoscale is expected to provide more efficient devices since the physics of these systems is dictated at this length scale and assembly of nanoparticles to various interfaces is critical to operation.« less

Mathematical modeling of HIV-like particle assembly in vitro.

PubMed

Liu, Yuewu; Zou, Xiufen

2017-06-01

In vitro, the recombinant HIV-1 Gag protein can generate spherical particles with a diameter of 25-30 nm in a fully defined system. It has approximately 80 building blocks, and its intermediates for assembly are abundant in geometry. Accordingly, there are a large number of nonlinear equations in the classical model. Therefore, it is difficult to compute values of geometry parameters for intermediates and make the mathematical analysis using the model. In this work, we develop a new model of HIV-like particle assembly in vitro by using six-fold symmetry of HIV-like particle assembly to decrease the number of geometry parameters. This method will greatly reduce computational costs and facilitate the application of the model. Then, we prove the existence and uniqueness of the positive equilibrium solution for this model with 79 nonlinear equations. Based on this model, we derive the interesting result that concentrations of all intermediates at equilibrium are independent of three important parameters, including two microscopic on-rate constants and the size of nucleating structure. Before equilibrium, these three parameters influence the concentration variation rates of all intermediates. We also analyze the relationship between the initial concentration of building blocks and concentrations of all intermediates. Furthermore, the bounds of concentrations of free building blocks and HIV-like particles are estimated. These results will be helpful to guide HIV-like particle assembly experiments and improve our understanding of the assembly dynamics of HIV-like particles in vitro. Copyright © 2017 Elsevier Inc. All rights reserved.

A Short-Term Population Model of the Suicide Risk: The Case of Spain.

PubMed

De la Poza, Elena; Jódar, Lucas

2018-06-14

A relevant proportion of deaths by suicide have been attributed to other causes that produce the number of suicides remains hidden. The existence of a hidden number of cases is explained by the nature of the problem. Problems like this involve violence, and produce fear and social shame in victims' families. The existence of violence, fear and social shame experienced by victims favours a considerable number of suicides, identified as accidents or natural deaths. This paper proposes a short time discrete compartmental mathematical model to measure the suicidal risk for the case of Spain. The compartment model classifies and quantifies the amount of the Spanish population within the age intervals (16, 78) by their degree of suicide risk and their changes over time. Intercompartmental transits are due to the combination of quantitative and qualitative factors. Results are computed and simulations are performed to analyze the sensitivity of the model under uncertain coefficients.

Supporting Undergraduate Computer Architecture Students Using a Visual MIPS64 CPU Simulator

ERIC Educational Resources Information Center

Patti, D.; Spadaccini, A.; Palesi, M.; Fazzino, F.; Catania, V.

2012-01-01

The topics of computer architecture are always taught using an Assembly dialect as an example. The most commonly used textbooks in this field use the MIPS64 Instruction Set Architecture (ISA) to help students in learning the fundamentals of computer architecture because of its orthogonality and its suitability for real-world applications. This…

Modular space station, phase B extension. Information management advanced development. Volume 5: Software assembly

NASA Technical Reports Server (NTRS)

Gerber, C. R.

1972-01-01

The development of uniform computer program standards and conventions for the modular space station is discussed. The accomplishments analyzed are: (1) development of computer program specification hierarchy, (2) definition of computer program development plan, and (3) recommendations for utilization of all operating on-board space station related data processing facilities.

Illuminating the Black Box of Genome Sequence Assembly: A Free Online Tool to Introduce Students to Bioinformatics

ERIC Educational Resources Information Center

Taylor, D. Leland; Campbell, A. Malcolm; Heyer, Laurie J.

2013-01-01

Next-generation sequencing technologies have greatly reduced the cost of sequencing genomes. With the current sequencing technology, a genome is broken into fragments and sequenced, producing millions of "reads." A computer algorithm pieces these reads together in the genome assembly process. PHAST is a set of online modules…

Development of a laboratory model to assess fear and anxiety in cats.

PubMed

de Rivera, Christina; Ley, Jacqui; Milgram, Bill; Landsberg, Gary

2017-06-01

Objectives The objectives of this study were: (1) to develop a laboratory-based model to assess fear and anxiety in cats using the feline open-field test (OFT) and the feline human interaction test (HIT); and (2) to validate the model using diazepam, a known anxiolytic. Methods Laboratory-housed cats (n = 41) were first classified as fearful, mildly fearful or non-fearful by a technician familiar with the cats and also by veterinary behaviorists (GL, JL), by assessing the cats' behavior in their home rooms. In experiment 1, each cat's behavior was assessed in an OFT and an HIT. In experiment 2, after administration of the anxiolytic diazepam, a subset of the cats was re-tested. Results In experiment 1, the OFT revealed significant group effects on two measures: duration of inactivity, and vocalization. Fearful animals had significantly longer periods of inactivity than non-fearful animals. Non-fearful and mildly fearful cats vocalized more frequently than fearful cats. In the HIT, fearful cats travelled less than non-fearful and mildly fearful cats. Fearful and mildly fearful animals had significantly longer durations of inactivity, and non-fearful and mildly fearful cats had a significantly higher frequency of vocalization compared with fearful cats. In experiment 2, in the OFT, treatment with diazepam caused an increase in distance travelled, shorter durations of inactivity, and more frequent inactivity and vocalization. In the HIT, diazepam increased distance travelled and decreased duration of inactivity. Fearful cats spent significantly less time near the human compared with non-fearful cats, and this persisted under diazepam. Conclusions and relevance The feline OFT and feline HIT can be used jointly to assess the effects of medications or other therapies on fear and anxiety in the domestic cat.

Generalization of conditioned fear along a dimension of increasing fear intensity

PubMed Central

Dunsmoor, Joseph E.; Mitroff, Stephen R.; LaBar, Kevin S.

2009-01-01

The present study investigated the extent to which fear generalization in humans is determined by the amount of fear intensity in nonconditioned stimuli relative to a perceptually similar conditioned stimulus. Stimuli consisted of graded emotionally expressive faces of the same identity morphed between neutral and fearful endpoints. Two experimental groups underwent discriminative fear conditioning between a face stimulus of 55% fear intensity (conditioned stimulus, CS+), reinforced with an electric shock, and a second stimulus that was unreinforced (CS−). In Experiment 1 the CS− was a relatively neutral face stimulus, while in Experiment 2 the CS− was the most fear-intense stimulus. Before and following fear conditioning, skin conductance responses (SCR) were recorded to different morph values along the neutral-to-fear dimension. Both experimental groups showed gradients of generalization following fear conditioning that increased with the fear intensity of the stimulus. In Experiment 1 a peak shift in SCRs extended to the most fear-intense stimulus. In contrast, generalization to the most fear-intense stimulus was reduced in Experiment 2, suggesting that discriminative fear learning procedures can attenuate fear generalization. Together, the findings indicate that fear generalization is broadly tuned and sensitive to the amount of fear intensity in nonconditioned stimuli, but that fear generalization can come under stimulus control. These results reveal a novel form of fear generalization in humans that is not merely based on physical similarity to a conditioned exemplar, and may have implications for understanding generalization processes in anxiety disorders characterized by heightened sensitivity to nonthreatening stimuli. PMID:19553384

Specific and social fears in children and adolescents: separating normative fears from problem indicators and phobias.

PubMed

Laporte, Paola P; Pan, Pedro M; Hoffmann, Mauricio S; Wakschlag, Lauren S; Rohde, Luis A; Miguel, Euripedes C; Pine, Daniel S; Manfro, Gisele G; Salum, Giovanni A

2017-01-01

To distinguish normative fears from problematic fears and phobias. We investigated 2,512 children and adolescents from a large community school-based study, the High Risk Study for Psychiatric Disorders. Parent reports of 18 fears and psychiatric diagnosis were investigated. We used two analytical approaches: confirmatory factor analysis (CFA)/item response theory (IRT) and nonparametric receiver operating characteristic (ROC) curve. According to IRT and ROC analyses, social fears are more likely to indicate problems and phobias than specific fears. Most specific fears were normative when mild; all specific fears indicate problems when pervasive. In addition, the situational fear of toilets and people who look unusual were highly indicative of specific phobia. Among social fears, those not restricted to performance and fear of writing in front of others indicate problems when mild. All social fears indicate problems and are highly indicative of social phobia when pervasive. These preliminary findings provide guidance for clinicians and researchers to determine the boundaries that separate normative fears from problem indicators in children and adolescents, and indicate a differential severity threshold for specific and social fears.

Portrait of a Digital Native: Are Digital-Age Students Fundamentally Different from the Rest of Us?

ERIC Educational Resources Information Center

McHale, Tom

2005-01-01

Meredith Fear sits in her room doing her homework. Books are scattered about, and a computer monitor glows before her. She is working on two Word documents and has four Web sites open. She checks her school e-mail account, her Bloglines news aggregator, and Furls of an online article for her independent study. She quickly transitions from this to…

The influence of animal fear on attentional capture by fear-relevant animal stimuli in children.

PubMed

Waters, Allison M; Lipp, Ottmar V

2008-01-01

The present study demonstrated that pictures of fear-relevant animals, snakes and spiders, presented among backgrounds of other animal stimuli captured attention and interfered in the detection of a neutral target to the same extent in a large sample of unselected children (N=81). Moreover, detection of a neutral target animal was slowed more in the presence of a feared fear-relevant distracter, e.g., a snake for snake fearful children, than in the presence of a not feared fear-relevant distracter, e.g., a spider for snake fearful children. These results indicate attentional capture by phylogenetically fear-relevant animal stimuli in children and the selective enhancement of this effect by fear of these animals. These findings are consistent with current models of preferential processing of phylogenetically prepared threat stimuli and with cognitive models of anxiety that propose an enhancing effect of fear in the processing of fear-related stimuli.

Qualitative Analysis of Infant Safe Sleep Public Campaign Messaging.

PubMed

Peacock, Nadine R; Altfeld, Susan; Rosenthal, Allison L; Garland, Caitlin E; Massino, Jill M; Smith, Sherri L; Rowe, Hillary L; Wagener, Sarah E

2018-03-01

The 1994 Back to Sleep public education campaign resulted in dramatic reductions in sleep-related infant deaths, but comparable progress in recent years has been elusive. We conducted qualitative analyses of recent safe sleep campaigns from 13 U.S. cities. Goals were to (a) determine whether the campaigns reflect the full range of American Academy of Pediatrics (AAP) 2011 safe sleep recommendations, (b) describe tone and framing of the messages (e.g., use of fear appeals), (c) describe targeting/tailoring of messages to priority populations, and (d) ascertain whether the campaigns have been evaluated for reach and/or effectiveness. Methods included computer-assisted analyses of campaign materials and key informant interviews. All campaigns included "ABC" (Alone, Back, Crib) messaging; many ignored other AAP recommendations such as breastfeeding, room-sharing, immunizations, and avoiding smoke exposure. Campaigns frequently targeted priority populations such as African Americans. Fear appeals were used in three quarters of the campaigns, and 60% of the fear-based campaigns used guilt/blame messaging. We did not find published evaluation data for any of the campaigns. More attention is needed in public education campaigns to the full range of AAP recommendations, and evaluations are needed to determine the impact of these interventions on knowledge, behavior, and health outcomes.

OSLay: optimal syntenic layout of unfinished assemblies.

PubMed

Richter, Daniel C; Schuster, Stephan C; Huson, Daniel H

2007-07-01

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure. To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly. OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay.

Vector assembly of colloids on monolayer substrates

NASA Astrophysics Data System (ADS)

Jiang, Lingxiang; Yang, Shenyu; Tsang, Boyce; Tu, Mei; Granick, Steve

2017-06-01

The key to spontaneous and directed assembly is to encode the desired assembly information to building blocks in a programmable and efficient way. In computer graphics, raster graphics encodes images on a single-pixel level, conferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape information into vectors that allow small file sizes and operational transformations. Here, we adapt this raster/vector concept to a 2D colloidal system and realize `vector assembly' by manipulating particles on a colloidal monolayer substrate with optical tweezers. In contrast to raster assembly that assigns optical tweezers to each particle, vector assembly requires a minimal number of optical tweezers that allow operations like chain elongation and shortening. This vector approach enables simple uniform particles to form a vast collection of colloidal arenes and colloidenes, the spontaneous dissociation of which is achieved with precision and stage-by-stage complexity by simply removing the optical tweezers.

Quantitative self-assembly prediction yields targeted nanomedicines

NASA Astrophysics Data System (ADS)

Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

2018-02-01

Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

PubMed Central

Pan, Keyao; Kim, Do-Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark

2014-01-01

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. PMID:25470497

Free-floating dual-arm robots for space assembly

NASA Technical Reports Server (NTRS)

Agrawal, Sunil Kumar; Chen, M. Y.

1994-01-01

Freely moving systems in space conserve linear and angular momentum. As moving systems collide, the velocities get altered due to transfer of momentum. The development of strategies for assembly in a free-floating work environment requires a good understanding of primitives such as self motion of the robot, propulsion of the robot due to onboard thrusters, docking of the robot, retrieval of an object from a collection of objects, and release of an object in an object pool. The analytics of such assemblies involve not only kinematics and rigid body dynamics but also collision and impact dynamics of multibody systems. In an effort to understand such assemblies in zero gravity space environment, we are currently developing at Ohio University a free-floating assembly facility with a dual-arm planar robot equipped with thrusters, a free-floating material table, and a free-floating assembly table. The objective is to pick up workpieces from the material table and combine them into prespecified assemblies. This paper presents analytical models of assembly primitives and strategies for overall assembly. A computer simulation of an assembly is developed using the analytical models. The experiment facility will be used to verify the theoretical predictions.

Design and evaluation of brushless electrical generators

NASA Technical Reports Server (NTRS)

Collins, F. A.; Ellis, J. N.

1970-01-01

Ten design manuals assembled and nine computer programs are developed for evaluation of proposed designs of brushless rotating electrical generators. Design manual package provides all information required for generator design, and computer programs permit calculation of performance of specific designs including effects of materials.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PubMed Central

Patmanidis, Ilias

2018-01-01

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation. PMID:29688238

Neural response patterns in spider, blood-injection-injury and social fearful individuals: new insights from a simultaneous EEG/ECG-fMRI study.

PubMed

Michałowski, Jarosław M; Matuszewski, Jacek; Droździel, Dawid; Koziejowski, Wojciech; Rynkiewicz, Andrzej; Jednoróg, Katarzyna; Marchewka, Artur

2017-06-01

In the present simultaneous EEG/ECG-fMRI study we compared the temporal and spatial characteristics of the brain responses and the cardiac activity during fear picture processing between spider, blood-injection-injury (BII) and social fearful as well as healthy (non-fearful) volunteers. All participants were presented with two neutral and six fear-related blocks of pictures: two social, two spider and two blood/injection fear blocks. In a social fear block neutral images were occasionally interspersed with photographs of angry faces and social exposure scenes. In spider and blood/injection fear blocks neutral pictures were interspersed with spider fear-relevant and blood/injection pictures, respectively. When compared to healthy controls the social fear group responded with increased activations in the anterior orbital, middle/anterior cingulate and middle/superior temporal areas for pictures depicting angry faces and with a few elevated superior frontal activations for social exposure scenes. In the blood/injection fear group, heart rate was decreased and the activity in the middle/inferior frontal and visual processing regions was increased for blood/injection pictures. The HR decrease for blood/injection pictures correlated with increased frontal responses. In the spider fear group, spider fear-relevant pictures triggered increased activations within a broad subcortical and cortical neural fear network. The HR response for spider fear-relevant stimuli was increased and correlated with an increased insula and hippocampus activity. When compared to healthy controls, all fear groups showed higher LPP amplitudes for their feared cues and an overall greater P1 hypervigilance effect. Contrasts against the fear control groups showed that the increased responses for fear-specific stimuli are mostly related to specific fears and not to general anxiety proneness. The results suggest different engagement of cognitive evaluation and down-regulation strategies and an overall increased sensitization of the fear system in the three fear groups.

Inverse Problem in Self-assembly

NASA Astrophysics Data System (ADS)

Tkachenko, Alexei

2012-02-01

By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.

Monodisperse self-assembly in a model with protein-like interactions

NASA Astrophysics Data System (ADS)

Wilber, Alex W.; Doye, Jonathan P. K.; Louis, Ard A.; Lewis, Anna C. F.

2009-11-01

We study the self-assembly behavior of patchy particles with "proteinlike" interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.

Lifelong disturbance of serotonin transporter functioning results in fear learning deficits: Reversal by blockade of CRF1 receptors.

PubMed

Bijlsma, Elisabeth Y; Hendriksen, Hendrikus; Baas, Johanna M P; Millan, Mark J; Groenink, Lucianne

2015-10-01

The inability to associate aversive events with relevant cues (i.e. fear learning) may lead to maladaptive anxiety. To further study the role of the serotonin transporter (SERT) in fear learning, classical fear conditioning was studied in SERT knockout rats (SERT(-/-)) using fear potentiation of the startle reflex. Next, fear acquisition and concomitant development of contextual conditioned fear were monitored during training. To differentiate between developmental and direct effects of reduced SERT functioning, effects of acute and chronic SSRI treatment were studied in adult rats. Considering the known interactions between serotonin and corticotropin-releasing factor (CRF), we studied the effect of the CRFR1 antagonist CP154,526 on behavioral changes observed and determined CRF1 receptor levels in SERT(-/-) rats. SERT(-/-) showed blunted fear potentiation and enhanced contextual fear, which resulted from a deficit in fear acquisition. Paroxetine treatment did not affect acquisition or expression of fear-potentiated startle, suggesting that disturbed fear learning in SERT(-/-) results from developmental changes and not from reduced SERT functioning. Although CRF1 receptor levels did not differ significantly between genotypes, CP154,526 treatment normalized both cue- and contextual fear in SERT(-/-) during acquisition, but not expression of fear-potentiated startle. The disrupted fear acquisition and concomitant increase in contextual conditioned fear-potentiated startle fear in SERT(-/-) resembles the associative learning deficit seen in patients with panic disorder and suggests that normal SERT functioning is crucial for the development of an adequate fear neuro-circuitry. Moreover, the normalization of fear acquisition by CP154,526 suggests a role for central CRF signaling in the generalization of fear. Copyright © 2015 Elsevier B.V. and ECNP. All rights reserved.

Alter spontaneous activity in amygdala and vmPFC during fear consolidation following 24 h sleep deprivation.

PubMed

Feng, Pan; Becker, Benjamin; Feng, Tingyong; Zheng, Yong

2018-05-15

Sleep deprivation (SD) has been associated with cognitive and emotional disruptions, however its impact on the acquisition of fear and subsequent fear memory consolidation remain unknown. To address this question, we measured human brain activity before and after fear acquisition under conditions of 24 h sleep deprivation versus normal sleep using resting-state functional magnetic resonance imaging (rs-fMRI). Additionally, we explored whether the fear acquisition-induced change of brain activity during the fear memory consolidation window can be predicted by subjective fear ratings and autonomic fear response, assessed by skin conductance responses (SCR) during acquisition. Behaviorally, the SD group demonstrated increased subjective and autonomic fear responses compared to controls at the stage of fear acquisition. During the stage of fear consolidation, the SD group displayed decreased ventromedial prefrontal cortex (vmPFC) activity and concomitantly increased amygdala activity. Moreover, in the SD group fear acquisition-induced brain activity changes in amygdala were positively correlated with both, subjective and autonomic fear indices during acquisition, whereas in controls changes vmPFC activity were positively correlated with fear indices during acquisition. Together, the present findings suggested that SD may weaken the top-down ability of the vmPFC to regulate amygdala activity during fear memory consolidation. Moreover, subjective and objective fear at fear acquisition stage can predict the change of brain activity in amygdala in fear memory consolidation following SD. Copyright © 2018 Elsevier Inc. All rights reserved.

Extinction during reconsolidation eliminates recovery of fear conditioned to fear-irrelevant and fear-relevant stimuli.

PubMed

Thompson, Alina; Lipp, Ottmar V

2017-05-01

Extant literature suggests that extinction training delivered during the memory reconsolidation period is superior to traditional extinction training in the reduction of fear recovery, as it targets the original fear memory trace. At present it is debated whether different types of fear memories are differentially sensitive to behavioral manipulations of reconsolidation. Here, we examined post-reconsolidation recovery of fear as a function of conditioned stimulus (CS) fear-relevance, using the unconditioned stimulus (US) to reactivate and destabilize conditioned fear memories. Participants (N = 56; 25 male; M = 24.39 years, SD = 7.71) in the US-reactivation and control group underwent differential fear conditioning to fear-relevant (spiders/snakes) and fear-irrelevant (geometric shapes) CSs on Day 1. On Day 2, participants received either reminded (US-reactivation) or non-reminded extinction training. Tests of fear recovery, conducted 24 h later, revealed recovery of differential electrodermal responding to both classes of CSs in the control group, but not in the US-reactivation group. These findings indicate that the US reactivation-extinction procedure eliminated recovery of extinguished responding not only to fear-irrelevant, but also to fear-relevant CSs. Contrasting previous reports, our findings show that post-reconsolidation recovery of conditioned responding is not a function of CS fear-relevance and that persistent reduction of fear, conditioned to fear-relevant CSs, can be achieved through behavioral manipulations of reconsolidation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nothing to Fear but Fear Itself? Fear of Fear, Fear of Greed and Gender Effects in Two-Person Asymmetric Social Dilemmas

ERIC Educational Resources Information Center

Kuwabara, Ko

2005-01-01

This article extends Simpson's (2003) research on sex differences in social dilemmas. To test the hypotheses that men defect in response to greed and women to fear, Simpson created Fear and Greed Dilemmas, but experiments using these games supported the greed hypothesis only. In this article I focus on why the fear hypothesis failed and suggest…

SAPNEW: Parallel finite element code for thin shell structures on the Alliant FX-80

NASA Astrophysics Data System (ADS)

Kamat, Manohar P.; Watson, Brian C.

1992-11-01

The finite element method has proven to be an invaluable tool for analysis and design of complex, high performance systems, such as bladed-disk assemblies in aircraft turbofan engines. However, as the problem size increase, the computation time required by conventional computers can be prohibitively high. Parallel processing computers provide the means to overcome these computation time limits. This report summarizes the results of a research activity aimed at providing a finite element capability for analyzing turbomachinery bladed-disk assemblies in a vector/parallel processing environment. A special purpose code, named with the acronym SAPNEW, has been developed to perform static and eigen analysis of multi-degree-of-freedom blade models built-up from flat thin shell elements. SAPNEW provides a stand alone capability for static and eigen analysis on the Alliant FX/80, a parallel processing computer. A preprocessor, named with the acronym NTOS, has been developed to accept NASTRAN input decks and convert them to the SAPNEW format to make SAPNEW more readily used by researchers at NASA Lewis Research Center.

Conditioned Fear Acquisition and Generalization in Generalized Anxiety Disorder.

PubMed

Tinoco-González, Daniella; Fullana, Miquel Angel; Torrents-Rodas, David; Bonillo, Albert; Vervliet, Bram; Blasco, María Jesús; Farré, Magí; Torrubia, Rafael

2015-09-01

Abnormal fear conditioning processes (including fear acquisition and conditioned fear-generalization) have been implicated in the pathogenesis of anxiety disorders. Previous research has shown that individuals with panic disorder present enhanced conditioned fear-generalization in comparison to healthy controls. Enhanced conditioned fear-generalization could also characterize generalized anxiety disorder (GAD), but research so far is inconclusive. An important confounding factor in previous research is comorbidity. The present study examined conditioned fear-acquisition and fear-generalization in 28 patients with GAD and 30 healthy controls using a recently developed fear acquisition and generalization paradigm assessing fear-potentiated startle and online expectancies of the unconditioned stimulus. Analyses focused on GAD patients without comorbidity but included also patients with comorbid anxiety disorders. Patients and controls did not differ as regards fear acquisition. However, contrary to our hypothesis, both groups did not differ either in most indexes of conditioned fear-generalization. Moreover, dimensional measures of GAD symptoms were not correlated with conditioned fear-generalization indexes. Comorbidity did not have a significant impact on the results. Our data suggest that conditioned fear-generalization is not enhanced in GAD. Results are discussed with special attention to the possible effects of comorbidity on fear learning abnormalities. Copyright © 2014. Published by Elsevier Ltd.

New image-stabilizing system

NASA Astrophysics Data System (ADS)

Zhao, Yuejin

1996-06-01

In this paper, a new method for image stabilization with a three-axis image- stabilizing reflecting prism assembly is presented, and the principle of image stabilization in this prism assembly, formulae for image stabilization and working formulae with an approximation up to the third power are given in detail. In this image-stabilizing system, a single chip microcomputer is used to calculate value of compensating angles and thus to control the prism assembly. Two gyroscopes act as sensors from which information of angular perturbation is obtained, three stepping motors drive the prism assembly to compensate for the movement of image produced by angular perturbation. The image-stabilizing device so established is a multifold system which involves optics, mechanics, electronics and computer.

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

The mathematics of virus shell assembly. Progress report 1995--1996

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

Berger, B.

1996-08-01

This research focuses on applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding. Significant progress has been made in the following areas relating to virus shell assembly: the local rules theory has been further developed; development has begun on a second-generation simulator which provides a more physically realistic model of assembly, collaborative efforts have continued with an experimental biologist to verify and inspire the local rules theory; an investigation has been initiated into the mechanics of virus shell assembly; laboratory experiments have been conducted on bacteriophage T4 which verify that the previouslymore » believed structure for the core may be incorrect.« less

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.

Learning to fear a second-order stimulus following vicarious learning.

PubMed

Reynolds, Gemma; Field, Andy P; Askew, Chris

2017-04-01

Vicarious fear learning refers to the acquisition of fear via observation of the fearful responses of others. The present study aims to extend current knowledge by exploring whether second-order vicarious fear learning can be demonstrated in children. That is, whether vicariously learnt fear responses for one stimulus can be elicited in a second stimulus associated with that initial stimulus. Results demonstrated that children's (5-11 years) fear responses for marsupials and caterpillars increased when they were seen with fearful faces compared to no faces. Additionally, the results indicated a second-order effect in which fear-related learning occurred for other animals seen together with the fear-paired animal, even though the animals were never observed with fearful faces themselves. Overall, the findings indicate that for children in this age group vicariously learnt fear-related responses for one stimulus can subsequently be observed for a second stimulus without it being experienced in a fear-related vicarious learning event. These findings may help to explain why some individuals do not recall involvement of a traumatic learning episode in the development of their fear of a specific stimulus.

Comparison of children's fears of medical experiences across two cultures.

PubMed

Mahat, Ganga; Scoloveno, Mary Ann; Cannella, Barbara

2004-01-01

This study examined the self-reported fears of school-age children living in the United States and in Nepal. Thirty school-age children from each country, matched by sex and age, participated in this study. The revised version of the Child Medical Fear Scale was used to identify medical fears of children. Among 17 feared items, the result showed getting a shot to be the most feared item reported by both groups. Nepalese children reported higher fear scores than did American children. It also was found that there was a significant difference in fear scores between Nepalese boys and girls, with girls reporting higher fear scores than boys. There was no difference in fear scores between American boys and girls. The findings of this study are important to nurse practitioners in understanding children's fears of medical experiences across different cultures. Nurses can support children in dealing with their fears of medical experiences by recognizing these fears and taking into consideration the child's family, sex, and culture when planning care. Nursing implications are discussed.

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

DOE PAGES

Wang, Qiong; Fish, Jordan A.; Gilman, Mariah; ...

2015-08-05

Here, metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility ofmore » this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. In conclusion, xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines.« less

Effectiveness of Various Computer-Based Instructional Strategies in Language Teaching. Final Report, November 1, 1969-August 31, 1970.

ERIC Educational Resources Information Center

Van Campen, Joseph A.

Computer software for programed language instruction, developed in the second quarter of 1970 at Stanford's Institute for Mathematical Studies in the Social Sciences is described in this report. The software includes: (1) a PDP-10 computer assembly language for generating drill sentences; (2) a coding system allowing a large number of sentences to…

A MAP fixed-point, packing-unpacking routine for the IBM 7094 computer

Treesearch

Robert S. Helfman

1966-01-01

Two MAP (Macro Assembly Program) computer routines for packing and unpacking fixed point data are described. Use of these routines with Fortran IV Programs provides speedy access to quantities of data which far exceed the normal storage capacity of IBM 7000-series computers. Many problems that could not be attempted because of the slow access-speed of tape...

Childhood dental fear in relation to parental child-rearing attitudes.

PubMed

ten Berge, M; Veerkamp, J S J; Hoogstraten, J; Prins, P J M

2003-02-01

The aim of this study was to assess the relation between parental self-reported child-rearing attitudes and dental fear in children. The parents of 51 children with high dental fear and of 56 children with low dental fear, of different age groups, completed the Amsterdam version of the Parental Attitude Research Instrument. In addition, parents were asked to rate their own dental fear. Multivariate analysis of variance (child fear x parental fear x child age) showed a significant main effect only of child dental fear on parental self-complaints (p = .03). For parental dental fear, main effects were found on overprotection and on promotion of autonomy (p < or = .01). No age effects were found. Also, no relation between children's dental fear and parental dental fear was found. Based on the present findings, it was concluded that parents may play a more secondary, mediating role in the etiological process of dental fear in children.

Evoked fear and effects of appeals on attitudes to performing breast self-examination: an information-processing perspective.

PubMed

Ruiter, R A; Kok, G; Verplanken, B; Brug, J

2001-06-01

The effect of fear arousal on attitude toward participating in early detection activities [i.e. breast self-examination (BSE)] was studied from an information-processing perspective. It was hypothesized that fear arousal motivates respondents to more argument-based processing of fear-relevant persuasive information. Respondents first read information about breast cancer in which fear was manipulated. After measuring fear arousal, respondents read a persuasive message about performing BSE. Analyses with reported fear, but not manipulated fear, found support for the hypothesis. Respondents who reported mild fear of breast cancer based their attitude toward BSE more on the arguments provided than respondents who reported low fear of breast cancer. This finding suggests that the use of fear arousal may be an efficient tool in health education practice. However, alternative interpretations are provided, in addition to the suggestion to be careful with using fear arousal in health education messages.

Fears about antiretroviral therapy among users of the internet forum for people living with HIV/AIDS in Russia.

PubMed

Dudina, Victoria I; Judina, Darja I; King, Elizabeth J

2017-02-01

The purpose of this research was to identify different types of fear related to starting and adhering to antiretroviral therapy (ART) among people living with HIV (PLHIV) in Russia. Data were collected from the Russian-language internet forum for PLHIV (hivlife.info). Qualitative data analysis focused on the sections of the forum where users discussed health-related issues in order to identify fears related to HIV treatment. The following types of fear were revealed: fear of the illness, fear to learn negative information about one's health, fear of side effects, fear of therapy to be ineffective, fear that the appropriate medications will become unavailable, fear of lifestyle changes, and fear for the well-being of significant others. Efforts to increase the uptake of and adherence to ART should take into account the fears of PLHIV.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

PubMed

Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai

2017-08-07

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation. © The Author 2017. Published by Oxford University Press.

Recognizing Student Fear: The Elephant in the Classroom

ERIC Educational Resources Information Center

Bledsoe, T. Scott; Baskin, Janice J.

2014-01-01

Understanding fear, its causes, and its impact on students can be important for educators who seek ways to help students manage their fears. This paper explores common types of student fears such as performance-based anxiety, fear of failure, fear of being laughed at, and cultural components of fear that impact learning. The cognitive, emotional,…

Computationally efficient multibody simulations

NASA Technical Reports Server (NTRS)

Ramakrishnan, Jayant; Kumar, Manoj

1994-01-01

Computationally efficient approaches to the solution of the dynamics of multibody systems are presented in this work. The computational efficiency is derived from both the algorithmic and implementational standpoint. Order(n) approaches provide a new formulation of the equations of motion eliminating the assembly and numerical inversion of a system mass matrix as required by conventional algorithms. Computational efficiency is also gained in the implementation phase by the symbolic processing and parallel implementation of these equations. Comparison of this algorithm with existing multibody simulation programs illustrates the increased computational efficiency.

High fear of intra-oral injections: prevalence and relationship to dental fear and dental avoidance among 10- to 16-yr-old children.

PubMed

Berge, Karin G; Agdal, Maren L; Vika, Margrethe; Skeie, Marit S

2016-12-01

The present study aimed to: (i) estimate the prevalence of self-reported high fear of intra-oral injections, high blood-injury fear, and injection fear; (ii) explore the overlap between high fear of intra-oral injections and high fear of dental treatment; and (iii) evaluate the possible consequence of high fear of intra-oral injections in terms of avoidance of dental care. The sample included 1,441 subjects, 10- to 16-yr of age, attending elementary schools in a county of Norway. Data were collected using questionnaires that were completed in classrooms. The survey instruments used were the Intra-Oral Injection Fear-scale, the Children's Fear Survey Schedule-Dental Subscale, the Injection Phobia scale for children, and the Mutilation Questionnaire for children. In total, 13.9% of the children reported high intra-oral injection fear. A strong association was found between fear of intra-oral injections and dental fear. When an intra-oral injection was needed, 10.6% would avoid dental treatment. In multiple regression analysis, high intra-oral injection fear was found to be associated with avoidance of dental treatment (OR = 6.52; 95% CI: 3.99-10.67). It was concluded that high fear of intra-oral injections was prevalent and might lead to avoidance of necessary dental treatment. Hence, intra-oral injection fear should be addressed before treatment of dental fear. © 2016 Eur J Oral Sci.

A latent growth examination of fear development in infancy: contributions of maternal depression and the risk for toddler anxiety.

PubMed

Gartstein, Maria A; Bridgett, David J; Rothbart, Mary K; Robertson, Christopher; Iddins, Erin; Ramsay, Kristin; Schlect, Sarah

2010-05-01

Growth modeling was used to examine the developmental trajectory of infant temperamental fear with maternal fear and depressive symptoms as predictors of infant fearfulness and change in infant fear predicting toddler anxiety symptoms. In Study 1, a sample of 158 mothers reported their own depressive symptoms and fear when their children were 4 months of age and infant fearfulness at 4, 6, 8, 10, and 12 months. Maternal symptoms of depression predicted steeper increases in infant fearfulness over time (z = 2.06, p < .05), with high initial infant fear and steeper increases in fear (intercept, z = 2.32, p < .05, and slope, z = 1.88, p < .05) predicting more severe toddler anxiety symptoms. In Study 2, an independent sample of 134 mothers completed measures of maternal depression and fear when the infants were 4 months old, and standardized laboratory observations of infant fear were made at 8, 10, and 12 months. Consistent with Study 1, maternal depression accounted for change in fearfulness (z = 2.30, p < .05), with more frequent and more severe maternal symptoms leading to greater increases in infant fear and increases in fearfulness z = 2.08, p < .05) leading to more problematic toddler anxiety. The implications and contributions of these findings are discussed in terms of methodology, fear development, and developmental psychopathology. 2010 APA, all rights reserved

Resting-state functional connectivity between amygdala and the ventromedial prefrontal cortex following fear reminder predicts fear extinction

PubMed Central

Feng, Pan; Zheng, Yong

2016-01-01

Investigations of fear conditioning have elucidated the neural mechanisms of fear acquisition, consolidation and extinction, but it is not clear how the neural activation following fear reminder influence the following extinction. To address this question, we measured human brain activity following fear reminder using resting-state functional magnetic resonance imaging, and investigated whether the extinction effect can be predicted by resting-state functional connectivity (RSFC). Behaviorally, we found no significant differences of fear ratings between the reminder group and the no reminder group at the fear acquisition and extinction stages, but spontaneous recovery during re-extinction stage appeared only in the no reminder group. Imaging data showed that functional connectivity between ventromedial prefrontal cortex (vmPFC) and amygdala in the reminder group was greater than that in the no reminder group after fear memory reactivation. More importantly, the functional connectivity between amygdala and vmPFC of the reminder group after fear memory reactivation was positively correlated with extinction effect. These results suggest RSFC between amygdala and the vmPFC following fear reminder can predict fear extinction, which provide important insight into the neural mechanisms of fear memory after fear memory reactivation. PMID:27013104

Computer technology forecast study for general aviation

NASA Technical Reports Server (NTRS)

Seacord, C. L.; Vaughn, D.

1976-01-01

A multi-year, multi-faceted program is underway to investigate and develop potential improvements in airframes, engines, and avionics for general aviation aircraft. The objective of this study was to assemble information that will allow the government to assess the trends in computer and computer/operator interface technology that may have application to general aviation in the 1980's and beyond. The current state of the art of computer hardware is assessed, technical developments in computer hardware are predicted, and nonaviation large volume users of computer hardware are identified.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Preliminary control/structure interaction study of coupled Space Station Freedom/Assembly Work Platform/orbiter

NASA Technical Reports Server (NTRS)

Singh, Sudeep K.; Lindenmoyer, Alan J.

1989-01-01

Results are presented from a preliminary control/structure interaction study of the Space Station, the Assembly Work Platform, and the STS orbiter dynamics coupled with the orbiter and station control systems. The first three Space Station assembly flight configurations and their finite element representations are illustrated. These configurations are compared in terms of control authority in each axis and propellant usage. The control systems design parameters during assembly are computed. Although the rigid body response was acceptable with the orbiter Primary Reaction Control System, the flexible body response showed large structural deflections and loads. It was found that severe control/structure interaction occurred if the stiffness of the Assembly Work Platform was equal to that of the station truss. Also, the response of the orbiter Vernier Reaction Control System to small changes in inertia properties is examined.

Component fears of claustrophobia associated with mock magnetic resonance imaging.

PubMed

McGlynn, F Dudley; Smitherman, Todd A; Hammel, Jacinda C; Lazarte, Alejandro A

2007-01-01

A conceptualization of claustrophobia [Rachman, S., & Taylor, S. (1993). Analyses of claustrophobia. Journal of Anxiety Disorders, 7, 281-291] was evaluated in the context of magnetic resonance imaging. One hundred eleven students responded to questionnaires that quantified fear of suffocation, fear of restriction, and sensitivity to anxiety symptoms. Sixty-four of them were then exposed to a mock magnetic resonance imaging assessment; maximum subjective fear during the mock assessment was self-reported, behavioral reactions to the mock assessment were characterized, and heart rates before and during the assessment were recorded. Scores for fear of suffocation, fear of restriction, and anxiety sensitivity were used to predict subjective, behavioral, and cardiac fear. Subjective fear during the mock assessment was predicted by fears of suffocation and public anxiousness. Behavioral fear (escape/avoidance) was predicted by fears of restriction and suffocation, and sensitivity to symptoms related to suffocation. Cardiac fear was predicted by fear of public anxiousness. The criterion variance predicted was impressive, clearly sufficient to legitimize both the research preparation and the conceptualization of claustrophobia that was evaluated.

Beyond the Syndemic: Condom Negotiation and Use among Women Experiencing Partner Violence

PubMed Central

Peasant, Courtney; Sullivan, Tami P.; Weiss, Nicole H.; Martinez, Isabel; Meyer, Jaimie P.

2016-01-01

Background HIV and sexually transmitted infections (STIs) disproportionately affect women who experience intimate partner violence (IPV). Objective The current study 1) applied a syndemic framework to study the collective effects of problematic drug use, hazardous drinking, depression, and posttraumatic stress disorder (PTSD) on fear of condom negotiation, condom negotiation, and condom use and 2) evaluated condom negotiation (controlling for fear of condom negotiation) as a mediator of the association between syndemic severity and condom use among low-income IPV-exposed women. Methods Participants were 158 women living in the community and experiencing ongoing IPV who completed face-to-face, computer-assisted interviews. Almost three-fourths of the participants reported problematic drug use, hazardous drinking, depression, and/or PTSD; many of these factors were significantly correlated, indicating a syndemic. Results Multivariate logistic and linear regression analyses revealed associations between syndemic severity and fear of condom negotiation (OR = 1.57, p = .02), condom negotiation (β = −8.51, p = .001) and condom use (β = −8.26, p = .01). Meditation analyses identified condom negotiation as a mediator of the association between syndemic severity and condom use (Effect = −6.57, SE = 2.01, [95% CI: − 10.66, − 2.77]). Conclusions Results fill a critical gap in previous research by identifying condom negotiation as a mechanism through which this syndemic affects condom use. Prevention and intervention programs should consider addressing condom negotiation to reduce sexual risk among this high-risk population. Further, because IPV-exposed women may experience fear related to condom negotiation, it is critical that prevention and intervention efforts for this population offer skills to safely negotiate condom use, increase condom use, and reduce STI and HIV risk. PMID:27590004

Beyond the syndemic: condom negotiation and use among women experiencing partner violence.

PubMed

Peasant, Courtney; Sullivan, Tami P; Weiss, Nicole H; Martinez, Isabel; Meyer, Jaimie P

2017-04-01

HIV and sexually transmitted infections (STIs) disproportionately affect women who experience intimate partner violence (IPV). The current study (1) applied a syndemic framework to study the collective effects of problematic drug use, hazardous drinking, depression, and posttraumatic stress disorder (PTSD) on fear of condom negotiation, condom negotiation, and condom use and (2) evaluated condom negotiation (controlling for fear of condom negotiation) as a mediator of the association between syndemic severity and condom use among low-income IPV-exposed women. Participants were 158 women living in the community and experiencing ongoing IPV who completed face-to-face, computer-assisted interviews. Almost three-fourths of the participants reported problematic drug use, hazardous drinking, depression, and/or PTSD; many of these factors were correlated, indicating a syndemic. Multivariate logistic and linear regression analyses revealed associations between syndemic severity and fear of condom negotiation (OR = 1.57, p = .02), condom negotiation (β = -8.51, p = .001), and condom use (β = -8.26, p = .01). Meditation analyses identified condom negotiation as a mediator of the association between syndemic severity and condom use (effect = -6.57, SE = 2.01, [95% CI: -10.66, -2.77]). Results fill a critical gap in previous research by identifying condom negotiation as a mechanism through which this syndemic affects condom use. Prevention and intervention programs should consider addressing condom negotiation to reduce sexual risk among this high-risk population. Further, because IPV-exposed women may experience fear related to condom negotiation, it is critical that prevention and intervention efforts for this population offer skills to safely negotiate condom use, increase condom use, and reduce STI and HIV risk.

The opinion of Turkish cardiologists on current malpractice system and an alternative patient compensation system proposal: PCS study group.

PubMed

Olcay, Ayhan; Emren, Sadık Volkan; Babür Güler, Gamze; Güler, Ekrem; Ertunç, Vedat; Berilgen, Rida; Aslan, Abdullah; Şimşek, Ersin Çağrı; Gölcük, Şükriye Ebru; Yalın, Kıvanç

2017-10-01

Cardiologists participate in the diagnosis and interventional treatment of numerous high-risk patients. The goal of this study was to investigate how the current malpractice system in Turkey influences cardiologists' diagnostic and interventional behavior and to obtain their opinions about an alternative patient compensation system. The present cross-sectional study assessed the practice of defensive medicine among cardiologists who are actively working in various types of workplace within the Turkish healthcare system. A 24-item questionnaire was distributed to cardiology residents, specialists, and academics in Turkey in print format, by electronic mail, or via cell phone message. A total of 253 cardiologists responded to the survey. Among them, 29 (11.6%) had been sued for malpractice claims in the past. Of the cardiologists who had been sued, 2 (6.9%) had been ordered to pay financial compensation, and 1 (3.4%) was given a sentence of imprisonment due to negligence. In all, 132 (52.8%) of the surveyed cardiologists reported that they had changed their practices due to fear of litigation, and 232 (92.8%) reported that they would prefer the new proposed patient compensation system to the current malpractice system. Among the cardiologists surveyed, 78.8% indicated that malpractice fear had affected their decision-making with regard to requesting computed tomography angiography or thallium scintigraphy, 71.6% for coronary angiography, 20% for stent implantation, and 83.2% for avoiding treating high-risk patients. The results of this survey demonstrated that cardiologists may request unnecessary tests and perform unneeded interventions due to the fear of malpractice litigation fear. Many also avoid high-risk patients and interventions. The majority indicated that they would prefer the proposed alternative patient compensation system to the current malpractice system.

Temporal and spatial neural dynamics in the perception of basic emotions from complex scenes

PubMed Central

Costa, Tommaso; Cauda, Franco; Crini, Manuella; Tatu, Mona-Karina; Celeghin, Alessia; de Gelder, Beatrice

2014-01-01

The different temporal dynamics of emotions are critical to understand their evolutionary role in the regulation of interactions with the surrounding environment. Here, we investigated the temporal dynamics underlying the perception of four basic emotions from complex scenes varying in valence and arousal (fear, disgust, happiness and sadness) with the millisecond time resolution of Electroencephalography (EEG). Event-related potentials were computed and each emotion showed a specific temporal profile, as revealed by distinct time segments of significant differences from the neutral scenes. Fear perception elicited significant activity at the earliest time segments, followed by disgust, happiness and sadness. Moreover, fear, disgust and happiness were characterized by two time segments of significant activity, whereas sadness showed only one long-latency time segment of activity. Multidimensional scaling was used to assess the correspondence between neural temporal dynamics and the subjective experience elicited by the four emotions in a subsequent behavioral task. We found a high coherence between these two classes of data, indicating that psychological categories defining emotions have a close correspondence at the brain level in terms of neural temporal dynamics. Finally, we localized the brain regions of time-dependent activity for each emotion and time segment with the low-resolution brain electromagnetic tomography. Fear and disgust showed widely distributed activations, predominantly in the right hemisphere. Happiness activated a number of areas mostly in the left hemisphere, whereas sadness showed a limited number of active areas at late latency. The present findings indicate that the neural signature of basic emotions can emerge as the byproduct of dynamic spatiotemporal brain networks as investigated with millisecond-range resolution, rather than in time-independent areas involved uniquely in the processing one specific emotion. PMID:24214921

Opioid receptors regulate blocking and overexpectation of fear learning in conditioned suppression.

PubMed

Arico, Carolyn; McNally, Gavan P

2014-04-01

Endogenous opioids play an important role in prediction error during fear learning. However, the evidence for this role has been obtained almost exclusively using the species-specific defense response of freezing as the measure of learned fear. It is unknown whether opioid receptors regulate predictive fear learning when other measures of learned fear are used. Here, we used conditioned suppression as the measure of learned fear to assess the role of opioid receptors in fear learning. Experiment 1a studied associative blocking of fear learning. Rats in an experimental group received conditioned stimulus A (CSA) + training in Stage I and conditioned stimulus A and B (CSAB) + training in Stage II, whereas rats in a control group received only CSAB + training in Stage II. The prior fear conditioning of CSA blocked fear learning to conditioned stimulus B (CSB) in the experimental group. In Experiment 1b, naloxone (4 mg/kg) administered before Stage II prevented this blocking, thereby enabling normal fear learning to CSB. Experiment 2a studied overexpectation of fear. Rats received CSA + training and CSB + training in Stage I, and then rats in the experimental group received CSAB + training in Stage II whereas control rats did not. The Stage II compound training of CSAB reduced fear to CSA and CSB on test. In Experiment 2b, naloxone (4 mg/kg) administered before Stage II prevented this overexpectation. These results show that opioid receptors regulate Pavlovian fear learning, augmenting learning in response to positive prediction error and impairing learning in response to negative prediction error, when fear is assessed via conditioned suppression. These effects are identical to those observed when freezing is used as the measure of learned fear. These findings show that the role for opioid receptors in regulating fear learning extends across multiple measures of learned fear.

Cultural aspects of morbid fears in Qatari women.

PubMed

el-Islam, M F

1994-05-01

The contents of morbid fears are patterned by cultural factors that decide the nature of the objects of the fears. Common factors in Western cultures do not obtain in local culture, which provides other objects for morbid fears in predisposed individuals. In the muslim community in Qatar, after-death fears dominated panic attacks, agoraphobia was rare, social phobias mirrored shame rather than guilt about failure to fulfil socially accepted norms of social behaviour, and obsessional fears revolved around fears of failure to control devil-induced impulses to harm self or others. Hypochondriacal fears of disease thrived because somatically oriented physicians colluded with somatizing patients in an endless search for presumed organic aetiology. Generalized anxiety fears were not encountered independently of other morbid fears.

Automated ensemble assembly and validation of microbial genomes.

PubMed

Koren, Sergey; Treangen, Todd J; Hill, Christopher M; Pop, Mihai; Phillippy, Adam M

2014-05-03

The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.

Xander: employing a novel method for efficient gene-targeted metagenomic assembly.

PubMed

Wang, Qiong; Fish, Jordan A; Gilman, Mariah; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2015-01-01

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.

Incubation of conditioned fear in the conditioned suppression model in rats: role of food-restriction conditions, length of conditioned stimulus, and generality to conditioned freezing

PubMed Central

Pickens, Charles L.; Navarre, Brittany M.; Nair, Sunila G.

2010-01-01

We recently adapted the conditioned suppression of operant responding method to study fear incubation. We found that food-restricted rats show low fear 2 days after extended (10 d; 100 30-sec tone-shock pairings) fear training and high fear after 1–2 months. Here, we studied a potential mechanism of fear incubation: extended food-restriction stress. We also studied whether fear incubation is observed after fear training with a prolonged-duration (6-min) tone conditioned stimulus (CS), and whether conditioned freezing incubates after extended training in rats with or without a concurrent operant task. Conditioned fear was assessed 2 days and 1 month after training. In the conditioned suppression method, fear incubation was reliably observed in rats under moderate food-restriction conditions (18–20 g food/day) that allowed for weight gain, and after extended (10 d), but not limited (1 d), fear training with the 6-min CS. Incubation of conditioned freezing was observed after extended fear training in rats lever-pressing for food and, to a lesser degree, in rats not performing an operant task. Results indicate that prolonged hunger-related stress does not account for fear incubation in the conditioned suppression method, and that fear incubation occurs to a longer-duration (6-min) fear CS. Extended training also leads to robust fear incubation of conditioned freezing in rats performing an operant task and weaker fear incubation in rats not performing an operant task. PMID:20600654

Incubation of conditioned fear in the conditioned suppression model in rats: role of food-restriction conditions, length of conditioned stimulus, and generality to conditioned freezing.

PubMed

Pickens, C L; Navarre, B M; Nair, S G

2010-09-15

We recently adapted the conditioned suppression of operant responding method to study fear incubation. We found that food-restricted rats show low fear 2 days after extended (10 d; 100 30-s tone-shock pairings) fear training and high fear after 1-2 months. Here, we studied a potential mechanism of fear incubation: extended food-restriction stress. We also studied whether fear incubation is observed after fear training with a prolonged-duration (6-min) tone conditioned stimulus (CS), and whether conditioned freezing incubates after extended training in rats with or without a concurrent operant task. Conditioned fear was assessed 2 days and 1 month after training. In the conditioned suppression method, fear incubation was reliably observed in rats under moderate food-restriction conditions (18-20 g food/day) that allowed for weight gain, and after extended (10 d), but not limited (1 d), fear training with the 6-min CS. Incubation of conditioned freezing was observed after extended fear training in rats lever-pressing for food and, to a lesser degree, in rats not performing an operant task. Results indicate that prolonged hunger-related stress does not account for fear incubation in the conditioned suppression method, and that fear incubation occurs to a longer-duration (6-min) fear CS. Extended training also leads to robust fear incubation of conditioned freezing in rats performing an operant task and weaker fear incubation in rats not performing an operant task. (c) 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

Spontaneous brain activity following fear reminder of fear conditioning by using resting-state functional MRI

PubMed Central

Feng, Pan; Zheng, Yong; Feng, Tingyong

2015-01-01

Although disrupting reconsolidation may be a promising approach to attenuate or erase the expression of fear memory, it is not clear how the neural state following fear reminder contribute to the following fear extinction. To address this question, we used resting-state functional magnetic resonance imaging (rs-fMRI) to measure spontaneous neuronal activity and functional connectivity (RSFC) following fear reminder. Some brain regions such as dorsal anterior cingulate (dACC) and ventromedial prefrontal cortex (vmPFC) showed increased amplitude of LFF (ALFF) in the fear reminder group than the no reminder group following fear reminder. More importantly, there was much stronger functional connectivity between the amygdala and vmPFC in the fear reminder group than those in the no reminder group. These findings suggest that the strong functional connectivity between vmPFC and amygdala following a fear reminder could serve as a key role in the followed-up fear extinction stages, which may contribute to the erasing of fear memory. PMID:26576733

Unraveling the Determinants of Fear of Crime Among Men and Women in Istanbul: Examining the Impact of Perceived Risk and Fear of Sexual Assault.

PubMed

Özaşçılar, Mine; Ziyalar, Neylan

2017-07-01

Studies have examined university students' fear of crime focusing on the relationship between the fear of sexual assault and fear of other crimes, termed the shadow of sexual assault hypothesis; however, no study to date has examined the shadow thesis in a Turkish context. Drawing on the shadow thesis, using a sample of 723 university students in Istanbul, this study focuses on the effect of fear of sexual assault and perceived risk of crime to general fear of crime among university students in Istanbul. Also, the predictors of fear of crime are explored to examine the relationship between lifestyle characteristics, constrained behaviors, and fear. The findings of the study supported the shadow thesis, indicating that fear of sexual assault shaped the nonsexual crimes, especially crimes involving face-to-face confrontations between the victim and offender. Furthermore, lifestyle characteristics are correlated with the men's fear of nonsexual crimes, particularly fear of robbery, aggravated assault, and burglary home.

Spontaneous brain activity following fear reminder of fear conditioning by using resting-state functional MRI.

PubMed

Feng, Pan; Zheng, Yong; Feng, Tingyong

2015-11-18

Although disrupting reconsolidation may be a promising approach to attenuate or erase the expression of fear memory, it is not clear how the neural state following fear reminder contribute to the following fear extinction. To address this question, we used resting-state functional magnetic resonance imaging (rs-fMRI) to measure spontaneous neuronal activity and functional connectivity (RSFC) following fear reminder. Some brain regions such as dorsal anterior cingulate (dACC) and ventromedial prefrontal cortex (vmPFC) showed increased amplitude of LFF (ALFF) in the fear reminder group than the no reminder group following fear reminder. More importantly, there was much stronger functional connectivity between the amygdala and vmPFC in the fear reminder group than those in the no reminder group. These findings suggest that the strong functional connectivity between vmPFC and amygdala following a fear reminder could serve as a key role in the followed-up fear extinction stages, which may contribute to the erasing of fear memory.

Bilateral Alternating Auditory Stimulations Facilitate Fear Extinction and Retrieval.

PubMed

Boukezzi, Sarah; Silva, Catarina; Nazarian, Bruno; Rousseau, Pierre-François; Guedj, Eric; Valenzuela-Moguillansky, Camila; Khalfa, Stéphanie

2017-01-01

Disruption of fear conditioning, its extinction and its retrieval are at the core of posttraumatic stress disorder (PTSD). Such deficits, especially fear extinction delay, disappear after alternating bilateral stimulations (BLS) during eye movement desensitization and reprocessing (EMDR) therapy. An animal model of fear recovery, based on auditory cued fear conditioning and extinction learning, recently showed that BLS facilitate fear extinction and fear extinction retrieval. Our goal was to determine if these previous results found in animals can be reproduced in humans. Twenty-two healthy participants took part in a classical fear conditioning, extinction, and extinction recall paradigm. Behavioral responses (fear expectations) as well as psychophysiological measures (skin conductance responses, SCRs) were recorded. The results showed a significant fear expectation decrease during fear extinction with BLS. Additionally, SCR for fear extinction retrieval were significantly lower with BLS. Our results demonstrate the importance of BLS to reduce negative emotions, and provide a successful model to further explore the neural mechanisms underlying the sole BLS effect in the EMDR.

Bilateral Alternating Auditory Stimulations Facilitate Fear Extinction and Retrieval

PubMed Central

Boukezzi, Sarah; Silva, Catarina; Nazarian, Bruno; Rousseau, Pierre-François; Guedj, Eric; Valenzuela-Moguillansky, Camila; Khalfa, Stéphanie

2017-01-01

Disruption of fear conditioning, its extinction and its retrieval are at the core of posttraumatic stress disorder (PTSD). Such deficits, especially fear extinction delay, disappear after alternating bilateral stimulations (BLS) during eye movement desensitization and reprocessing (EMDR) therapy. An animal model of fear recovery, based on auditory cued fear conditioning and extinction learning, recently showed that BLS facilitate fear extinction and fear extinction retrieval. Our goal was to determine if these previous results found in animals can be reproduced in humans. Twenty-two healthy participants took part in a classical fear conditioning, extinction, and extinction recall paradigm. Behavioral responses (fear expectations) as well as psychophysiological measures (skin conductance responses, SCRs) were recorded. The results showed a significant fear expectation decrease during fear extinction with BLS. Additionally, SCR for fear extinction retrieval were significantly lower with BLS. Our results demonstrate the importance of BLS to reduce negative emotions, and provide a successful model to further explore the neural mechanisms underlying the sole BLS effect in the EMDR. PMID:28659851

A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly

NASA Astrophysics Data System (ADS)

Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

2016-04-01

In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation. Electronic supplementary information (ESI) available: Additional figures (Tables S1-S3 and Fig. S1-S6). See DOI: 10.1039/c6nr01072e

Inhibiting corticosterone synthesis during fear memory formation exacerbates cued fear extinction memory deficits within the single prolonged stress model.

PubMed

Keller, Samantha M; Schreiber, William B; Stanfield, Briana R; Knox, Dayan

2015-01-01

Using the single prolonged stress (SPS) animal model of post-traumatic stress disorder (PTSD), previous studies suggest that enhanced glucocorticoid receptor (GR) expression leads to cued fear extinction retention deficits. However, it is unknown how the endogenous ligand of GRs, corticosterone (CORT), may contribute to extinction retention deficits in the SPS model. Given that CORT synthesis during fear learning is critical for fear memory consolidation and SPS enhances GR expression, CORT synthesis during fear memory formation could strengthen fear memory in SPS rats by enhancing GR activation during fear learning. In turn, this could lead to cued fear extinction retention deficits. We tested the hypothesis that CORT synthesis during fear learning leads to cued fear extinction retention deficits in SPS rats by administering the CORT synthesis inhibitor metyrapone to SPS and control rats prior to fear conditioning, and observed the effect this had on extinction memory. Inhibiting CORT synthesis during fear memory formation in control rats tended to decrease cued freezing, though this effect never reached statistical significance. Contrary to our hypothesis, inhibiting CORT synthesis during fear memory formation disrupted extinction retention in SPS rats. This finding suggests that even though SPS exposure leads to cued fear extinction memory deficits, CORT synthesis during fear memory formation enhances extinction retention in SPS rats. This suggests that stress-induced CORT synthesis in previously stressed rats can be beneficial. Copyright © 2015 Elsevier B.V. All rights reserved.

Living in the nuclear age: An Australian study of children's and adolescent's fears

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

Slee, P.T.; Cross, D.G.

Developmental changes in children's fears with a particular focus on fears of nuclear war were studied in a sample of 1243 Australian children and adolescents aged between 4-19 years. The average number of fears reported per child was 9.3. Females reported significantly more fears than males. Developmental changes also were apparent with animal and supernatural fears in the youngest age group giving way to social fears and fear of war in the older age brackets. An average of 67.4% of the sample expressed a fear of nuclear war. The implications of this finding for parents and educators are discussed.

Erasing fear memories with extinction training

PubMed Central

Quirk, Gregory J.; Paré, Denis; Richardson, Rick; Herry, Cyril; Monfils, Marie H.; Schiller, Daniela; Vicentic, Aleksandra

2012-01-01

Decades of behavioral studies have confirmed that extinction does not erase classically-conditioned fear memories. For this reason, research efforts have focused on the mechanisms underlying the development of extinction-induced inhibition within fear circuits. However, recent studies in rodents have uncovered mechanisms that stabilize and destabilize fear memories, opening the possibility that extinction might be used to erase fear memories. This symposium focuses on several of these new developments, which involve the timing of extinction training. Extinction-induced erasure of fear occurs in very young rats, but is lost with the development of perineuronal nets in the amygdala that render fear memories impervious to extinction. Moreover, extinction administered during the reconsolidation phase, when fear memory is destabilized, updates the fear association as safe, thereby preventing the return of fear, in both rats and humans. The use of modified extinction protocols to eliminate fear memories complements existing pharmacological strategies for strengthening extinction. PMID:21068303

In the face of fear: Anxiety sensitizes defensive responses to fearful faces

PubMed Central

Grillon, Christian; Charney, Danielle R.

2011-01-01

Fearful faces readily activate the amygdala. Yet, whether fearful faces evoke fear is unclear. Startle studies show no potentiation of startle by fearful faces, suggesting that such stimuli do not activate defense mechanisms. However, the response to biologically relevant stimuli may be sensitized by anxiety. The present study tested the hypothesis that startle would not be potentiated by fearful faces in a safe context, but that startle would be larger during fearful faces compared to neutral faces in a threat-of-shock context. Subjects viewed fearful and neutral faces in alternating periods of safety and threat of shock. Acoustic startle stimuli were presented in the presence and absence of the faces. Startle was transiently potentiated by fearful faces compared to neutral faces in the threat periods. This suggests that although fearful faces do not prompt behavioral mobilization in an innocuous context, they can do so in an anxiogenic one. PMID:21824155

Fear conditioning to subliminal fear relevant and non fear relevant stimuli.

PubMed

Lipp, Ottmar V; Kempnich, Clare; Jee, Sang Hoon; Arnold, Derek H

2014-01-01

A growing body of evidence suggests that conscious visual awareness is not a prerequisite for human fear learning. For instance, humans can learn to be fearful of subliminal fear relevant images--images depicting stimuli thought to have been fear relevant in our evolutionary context, such as snakes, spiders, and angry human faces. Such stimuli could have a privileged status in relation to manipulations used to suppress usually salient images from awareness, possibly due to the existence of a designated sub-cortical 'fear module'. Here we assess this proposition, and find it wanting. We use binocular masking to suppress awareness of images of snakes and wallabies (particularly cute, non-threatening marsupials). We find that subliminal presentations of both classes of image can induce differential fear conditioning. These data show that learning, as indexed by fear conditioning, is neither contingent on conscious visual awareness nor on subliminal conditional stimuli being fear relevant.

Better safe than sorry: simplistic fear-relevant stimuli capture attention.

PubMed

Forbes, Sarah J; Purkis, Helena M; Lipp, Ottmar V

2011-08-01

It has been consistently demonstrated that fear-relevant images capture attention preferentially over fear-irrelevant images. Current theory suggests that this faster processing could be mediated by an evolved module that allows certain stimulus features to attract attention automatically, prior to the detailed processing of the image. The present research investigated whether simplified images of fear-relevant stimuli would produce interference with target detection in a visual search task. In Experiment 1, silhouettes and degraded silhouettes of fear-relevant animals produced more interference than did the fear-irrelevant images. Experiment 2, compared the effects of fear-relevant and fear-irrelevant distracters and confirmed that the interference produced by fear-relevant distracters was not an effect of novelty. Experiment 3 suggested that fear-relevant stimuli produced interference regardless of whether participants were instructed as to the content of the images. The three experiments indicate that even very simplistic images of fear-relevant animals can divert attention.

Uplifting Fear Appeals: Considering the Role of Hope in Fear-Based Persuasive Messages.

PubMed

Nabi, Robin L; Myrick, Jessica Gall

2018-01-09

Fear appeal research has focused, understandably, on fear as the primary emotion motivating attitude and behavior change. However, while the threat component of fear appeals associates with fear responses, a fear appeals' efficacy component likely associates with a different emotional experience: hope. Drawing from appraisal theories of emotion in particular, this article theorizes about the role of hope in fear appeals, testing hypotheses with two existing data sets collected within the context of sun safety messages. In both studies, significant interactions between hope and self-efficacy emerged to predict behavioral intentions. Notable main effects for hope also emerged, though with less consistency. Further, these effects persisted despite controlling for the four cognitions typically considered central to fear appeal effectiveness. These results, consistent across two samples, support the claim that feelings of hope in response to fear appeals contribute to their persuasive success. Implications for developing a recursive model of fear appeal processing are discussed.

8 CFR 1208.6 - Disclosure to third parties.

Code of Federal Regulations, 2010 CFR

2010-01-01

... application, records pertaining to any credible fear determination conducted pursuant to § 1208.30, and records pertaining to any reasonable fear determination conducted pursuant to § 1208.31, shall not be... a credible fear or reasonable fear interview, or received a credible fear or reasonable fear review...

Acute exercise enhances the consolidation of fear extinction memory and reduces conditioned fear relapse in a sex-dependent manner.

PubMed

Bouchet, Courtney A; Lloyd, Brian A; Loetz, Esteban C; Farmer, Caroline E; Ostrovskyy, Mykola; Haddad, Natalie; Foright, Rebecca M; Greenwood, Benjamin N

2017-08-01

Fear extinction-based exposure therapy is the most common behavioral therapy for anxiety and trauma-related disorders, but fear extinction memories are labile and fear tends to return even after successful extinction. The relapse of fear contributes to the poor long-term efficacy of exposure therapy. A single session of voluntary exercise can enhance the acquisition and consolidation of fear extinction in male rats, but the effects of exercise on relapse of fear after extinction are not well understood. Here, we characterized the effects of 2 h of voluntary exercise during the consolidation phase of contextual or auditory fear extinction learning on long-term fear extinction memory and renewal in adult, male and female, Long-Evans rats. Results indicate that exercise enhances consolidation of fear extinction memory and reduces fear relapse after extinction in a sex-dependent manner. These data suggest that brief bouts of exercise could be used as an augmentation strategy for exposure therapy, even in previously sedentary subjects. Fear memories of discrete cues, rather than of contextual ones, may be most susceptible to exercise-augmented extinction, especially in males. Additionally, exercise seems to have the biggest impact on fear relapse phenomena, even if fear extinction memories themselves are only minimally enhanced. © 2017 Bouchet et al.; Published by Cold Spring Harbor Laboratory Press.

The Genetic Covariation between Fear Conditioning and Self-Report Fears

PubMed Central

Hettema, John M.; Annas, Peter; Neale, Michael C.; Fredrikson, Mats; Sci, Dr Med; Kendler, Kenneth S.

2008-01-01

Background Fear conditioning is a traditional model for the acquisition of phobias, while behavioral therapies utilize processes underlying extinction to treat phobic and other anxiety disorders. Furthermore, fear conditioning has been proposed as an endophenotype for genetic studies of anxiety disorders. While prior studies have demonstrated that fear conditioning and self-report fears are heritable, no studies have determined whether they share a common genetic basis. Methods We obtained fear conditioning data from 173 twin pairs from the Swedish Twin Registry who also provided self-report ratings of 16 common fears. Using multivariate structural equation modeling, we analyzed factor-derived scores for the subjective fear ratings together with the electrophysiologic skin conductance responses during habituation, acquisition, and extinction to determine the extent of their genetic covariation. Results Phenotypic correlations between experimental and self-report fear measures were modest and, and counter-intuitively, negative; that is, subjects who reported themselves as more fearful had smaller electrophysiologic responses. Best-fit models estimated a significant (negative) genetic correlation between them, although genetic factors underlying fear conditioning accounted for only 9% of individual differences in self-report fears. Conclusions Experimentally-derived fear conditioning measures share only a small portion of the genetic factors underlying individual differences in subjective fears, cautioning against relying too heavily on the former as an endophenotype for genetic studies of phobic disorders. PMID:17698042

Shaded-Color Picture Generation of Computer-Defined Arbitrary Shapes

NASA Technical Reports Server (NTRS)

Cozzolongo, J. V.; Hermstad, D. L.; Mccoy, D. S.; Clark, J.

1986-01-01

SHADE computer program generates realistic color-shaded pictures from computer-defined arbitrary shapes. Objects defined for computer representation displayed as smooth, color-shaded surfaces, including varying degrees of transparency. Results also used for presentation of computational results. By performing color mapping, SHADE colors model surface to display analysis results as pressures, stresses, and temperatures. NASA has used SHADE extensively in sign and analysis of high-performance aircraft. Industry should find applications for SHADE in computer-aided design and computer-aided manufacturing. SHADE written in VAX FORTRAN and MACRO Assembler for either interactive or batch execution.

Study to define an approach for developing a computer-based system capable of automatic, unattended assembly/disassembly of spacecraft, phase 1

NASA Technical Reports Server (NTRS)

Nevins, J. L.; Defazio, T. L.; Seltzer, D. S.; Whitney, D. E.

1981-01-01

The initial set of requirements for additional studies necessary to implement a space-borne, computer-based work system capable of achieving assembly, disassembly, repair, or maintenance in space were developed. The specific functions required of a work system to perform repair and maintenance were discussed. Tasks and relevant technologies were identified and delineated. The interaction of spacecraft design and technology options, including a consideration of the strategic issues of repair versus retrieval-replacement or destruction by removal were considered along with the design tradeoffs for accomplishing each of the options. A concept system design and its accompanying experiment or test plan were discussed.

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

NASA Astrophysics Data System (ADS)

He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.

2010-02-01

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.

Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications.

PubMed

Kuang, Hua; Ma, Wei; Xu, Liguang; Wang, Libing; Xu, Chuanlai

2013-11-19

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

Repressor logic modules assembled by rolling circle amplification platform to construct a set of logic gates

PubMed Central

Wei, Hua; Hu, Bo; Tang, Suming; Zhao, Guojie; Guan, Yifu

2016-01-01

Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully. To achieve various logic computations based on these basic modules, we designed series and parallel strategies of circular templates, which can further assemble these repressor modules in an RCA platform to realize twelve two-input Boolean logic gates and a three-input logic gate. The RCA-output and RCA-assembled platform was proved to be easy and flexible for complex logic processes and might have application potential in molecular computing and synthetic biology. PMID:27869177

Cylindrical surface profile and diameter measuring tool and method

NASA Technical Reports Server (NTRS)

Currie, James R. (Inventor); Kissel, Ralph R. (Inventor); Smith, Earnest C. (Inventor); Oliver, Charles E. (Inventor); Redmon, John W., Sr. (Inventor); Wallace, Charles C. (Inventor); Swanson, Charles P. (Inventor)

1987-01-01

A tool is shown having a cross beam assembly made of beams joined by a center box structure. The assembly is adapted to be mounted by brackets to the outer end of a cylindrical case. The center box structure has a vertical shaft rotatably mounted therein and extending beneath the assembly. Secured to the vertical shaft is a radius arm which is adapted to rotate with the shaft. On the longer end of the radius arm is a measuring tip which contacts the cylindrical surface to be measured and which provides an electric signal representing the radius of the cylindrical surface from the center of rotation of the radius arm. An electric servomotor rotates the vertical shaft and an electronic resolver provides an electric signal representing the angle of rotation of the shaft. The electric signals are provided to a computer station which has software for its computer to calculate and print out the continuous circumference profile of the cylindrical surface, and give its true diameter and the deviations from the ideal circle.

8 CFR 208.6 - Disclosure to third parties.

Code of Federal Regulations, 2010 CFR

2010-01-01

... credible fear determination conducted pursuant to § 208.30, and records pertaining to any reasonable fear... that a specific alien has applied for asylum, received a credible fear or reasonable fear interview, or received a credible fear or reasonable fear review shall also be protected from disclosure. The Service...

Resting-state functional connectivity between amygdala and the ventromedial prefrontal cortex following fear reminder predicts fear extinction.

PubMed

Feng, Pan; Zheng, Yong; Feng, Tingyong

2016-06-01

Investigations of fear conditioning have elucidated the neural mechanisms of fear acquisition, consolidation and extinction, but it is not clear how the neural activation following fear reminder influence the following extinction. To address this question, we measured human brain activity following fear reminder using resting-state functional magnetic resonance imaging, and investigated whether the extinction effect can be predicted by resting-state functional connectivity (RSFC). Behaviorally, we found no significant differences of fear ratings between the reminder group and the no reminder group at the fear acquisition and extinction stages, but spontaneous recovery during re-extinction stage appeared only in the no reminder group. Imaging data showed that functional connectivity between ventromedial prefrontal cortex (vmPFC) and amygdala in the reminder group was greater than that in the no reminder group after fear memory reactivation. More importantly, the functional connectivity between amygdala and vmPFC of the reminder group after fear memory reactivation was positively correlated with extinction effect. These results suggest RSFC between amygdala and the vmPFC following fear reminder can predict fear extinction, which provide important insight into the neural mechanisms of fear memory after fear memory reactivation. © The Author (2016). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Behavioral mechanisms of context fear generalization in mice

PubMed Central

Huckleberry, Kylie A.; Ferguson, Laura B.

2016-01-01

There is growing interest in generalization of learned contextual fear, driven in part by the hypothesis that mood and anxiety disorders stem from impaired hippocampal mechanisms of fear generalization and discrimination. However, there has been relatively little investigation of the behavioral and procedural mechanisms that might control generalization of contextual fear. We assessed the relative contribution of different contextual features to context fear generalization and characterized how two common conditioning protocols—foreground (uncued) and background (cued) contextual fear conditioning—affected context fear generalization. In one experiment, mice were fear conditioned in context A, and then tested for contextual fear both in A and in an alternate context created by changing a subset of A's elements. The results suggest that floor configuration and odor are more salient features than chamber shape. A second experiment compared context fear generalization in background and foreground context conditioning. Although foreground conditioning produced more context fear than background conditioning, the two procedures produced equal amounts of generalized fear. Finally, results indicated that the order of context tests (original first versus alternate first) significantly modulates context fear generalization, perhaps because the original and alternate contexts are differentially sensitive to extinction. Overall, results demonstrate that context fear generalization is sensitive to procedural variations and likely reflects the operation of multiple interacting psychological and neural mechanisms. PMID:27918275

Implications of newborn amygdala connectivity for fear and cognitive development at 6-months-of-age

PubMed Central

Graham, Alice M.; Buss, Claudia; Rasmussen, Jerod M.; Rudolph, Marc D.; Demeter, Damion V.; Gilmore, John H.; Styner, Martin; Entringer, Sonja; Wadhwa, Pathik D.; Fair, Damien A.

2015-01-01

The first year of life is an important period for emergence of fear in humans. While animal models have revealed developmental changes in amygdala circuitry accompanying emerging fear, human neural systems involved in early fear development remain poorly understood. To increase understanding of the neural foundations of human fear, it is important to consider parallel cognitive development, which may modulate associations between typical development of early fear and subsequent risk for fear-related psychopathology. We, therefore, examined amygdala functional connectivity with rs-fcMRI in 48 neonates (M=3.65 weeks, SD=1.72), and measured fear and cognitive development at 6-months-of-age. Stronger, positive neonatal amygdala connectivity to several regions, including bilateral anterior insula and ventral striatum, was prospectively associated with higher fear at 6-months. Stronger amygdala connectivity to ventral anterior cingulate/anterior medial prefrontal cortex predicted a specific phenotype of higher fear combined with more advanced cognitive development. Overall, findings demonstrate unique profiles of neonatal amygdala functional connectivity related to emerging fear and cognitive development, which may have implications for normative and pathological fear in later years. Consideration of infant fear in the context of cognitive development will likely contribute to a more nuanced understanding of fear, its neural bases, and its implications for future mental health. PMID:26499255

Neural-like computing with populations of superparamagnetic basis functions.

PubMed

Mizrahi, Alice; Hirtzlin, Tifenn; Fukushima, Akio; Kubota, Hitoshi; Yuasa, Shinji; Grollier, Julie; Querlioz, Damien

2018-04-18

In neuroscience, population coding theory demonstrates that neural assemblies can achieve fault-tolerant information processing. Mapped to nanoelectronics, this strategy could allow for reliable computing with scaled-down, noisy, imperfect devices. Doing so requires that the population components form a set of basis functions in terms of their response functions to inputs, offering a physical substrate for computing. Such a population can be implemented with CMOS technology, but the corresponding circuits have high area or energy requirements. Here, we show that nanoscale magnetic tunnel junctions can instead be assembled to meet these requirements. We demonstrate experimentally that a population of nine junctions can implement a basis set of functions, providing the data to achieve, for example, the generation of cursive letters. We design hybrid magnetic-CMOS systems based on interlinked populations of junctions and show that they can learn to realize non-linear variability-resilient transformations with a low imprint area and low power.

Robust Optimization Design for Turbine Blade-Tip Radial Running Clearance using Hierarchically Response Surface Method

NASA Astrophysics Data System (ADS)

Zhiying, Chen; Ping, Zhou

2017-11-01

Considering the robust optimization computational precision and efficiency for complex mechanical assembly relationship like turbine blade-tip radial running clearance, a hierarchically response surface robust optimization algorithm is proposed. The distribute collaborative response surface method is used to generate assembly system level approximation model of overall parameters and blade-tip clearance, and then a set samples of design parameters and objective response mean and/or standard deviation is generated by using system approximation model and design of experiment method. Finally, a new response surface approximation model is constructed by using those samples, and this approximation model is used for robust optimization process. The analyses results demonstrate the proposed method can dramatic reduce the computational cost and ensure the computational precision. The presented research offers an effective way for the robust optimization design of turbine blade-tip radial running clearance.

A Computer Model for Analyzing Volatile Removal Assembly

NASA Technical Reports Server (NTRS)

Guo, Boyun

2010-01-01

A computer model simulates reactional gas/liquid two-phase flow processes in porous media. A typical process is the oxygen/wastewater flow in the Volatile Removal Assembly (VRA) in the Closed Environment Life Support System (CELSS) installed in the International Space Station (ISS). The volatile organics in the wastewater are combusted by oxygen gas to form clean water and carbon dioxide, which is solved in the water phase. The model predicts the oxygen gas concentration profile in the reactor, which is an indicator of reactor performance. In this innovation, a mathematical model is included in the computer model for calculating the mass transfer from the gas phase to the liquid phase. The amount of mass transfer depends on several factors, including gas-phase concentration, distribution, and reaction rate. For a given reactor dimension, these factors depend on pressure and temperature in the reactor and composition and flow rate of the influent.

Space shuttle main engine computed tomography applications

NASA Technical Reports Server (NTRS)

Sporny, Richard F.

1990-01-01

For the past two years the potential applications of computed tomography to the fabrication and overhaul of the Space Shuttle Main Engine were evaluated. Application tests were performed at various government and manufacturer facilities with equipment produced by four different manufacturers. The hardware scanned varied in size and complexity from a small temperature sensor and turbine blades to an assembled heat exchanger and main injector oxidizer inlet manifold. The evaluation of capabilities included the ability to identify and locate internal flaws, measure the depth of surface cracks, measure wall thickness, compare manifold design contours to actual part contours, perform automatic dimensional inspections, generate 3D computer models of actual parts, and image the relationship of the details in a complex assembly. The capabilities evaluated, with the exception of measuring the depth of surface flaws, demonstrated the existing and potential ability to perform many beneficial Space Shuttle Main Engine applications.

USGS Digital Spectral Library splib05a

USGS Publications Warehouse

Clark, Roger N.; Swayze, Gregg A.; Wise, Richard K.; Livo, Eric; Hoefen, Todd M.; Kokaly, Raymond F.; Sutley, Steve J.

2003-01-01

We have assembled a digital reflectance spectral library of spectra that covers wavelengths from the ultraviolet to near-infrared along with sample documentation. The library includes samples of minerals, rocks, soils, physically constructed as well as mathematically computed mixtures, vegetation, microorganisms, and man-made materials. The samples and spectra collected were assembled for the purpose of using spectral features for the remote detection of these and similar materials.

The CAN Microcluster: Parallel Processing over the Controller Area Network

ERIC Educational Resources Information Center

Kuban, Paul A.; Ragade, Rammohan K.

2005-01-01

Most electrical engineering and computer science undergraduate programs include at least one course on microcontrollers and assembly language programming. Some departments offer legacy courses in C programming, but few include C programming from an embedded systems perspective, where it is still regularly used. Distributed computing and parallel…

The V1.0 ’Pushpin’ Nixel 2-D Self-Assembling Display Array

DTIC Science & Technology

2004-08-01

H. Abelson, D. Allen, D. Coore, C. Hanson, G. Homsy, T. Knight, R. Nagpal , E. Rauch, G. J. Sussntan, and R. Weiss Amorphous Computing Communications...November 2003. [9] R. Nagpal , Organizing a Global Coordinate System from Local Information on an Amorphous Computer, Massachusetts Institute

Engineering Graphics Educational Outcomes for the Global Engineer: An Update

ERIC Educational Resources Information Center

Barr, R. E.

2012-01-01

This paper discusses the formulation of educational outcomes for engineering graphics that span the global enterprise. Results of two repeated faculty surveys indicate that new computer graphics tools and techniques are now the preferred mode of engineering graphical communication. Specifically, 3-D computer modeling, assembly modeling, and model…

Manifestations, acquisition and diagnostic categories of dental fear in a self-referred population.

PubMed

Moore, R; Brødsgaard, I; Birn, H

1991-01-01

This study aimed to clarify how manifestations and acquisition relate to diagnostic categories of dental fear in a population of self-referred dental fear patients, since diagnostic criteria specifically related to dental fear have not been validated. DSM III-R diagnostic criteria for phobias were used to compare with four existing dental fear diagnostic categories, referred to as the Seattle system. Subjects were 208 persons with dental fear who were telephone interviewed, of whom a subsample of 155 responded to a mailed Dental Anxiety Scale (DAS), State-Trait Anxiety Inventory and a modified FSS-II Geer Fear Scale (GFS). Personal interviews and a Dental Beliefs Scale of perceived trust and social interaction with dentists were also used to evaluate a subsample of 80 patients selected by sex and high dental fear. Results showed that the majority of the 80 patients (66%), suffered from social embarrassment about their dental fear problem and their inability to do something about it. The largest cause of their fear (84%) was reported to be traumatic dental experiences, especially in childhood (70%). A minority of patients (16%) could not isolate traumatic experiences and had a history of general fearfulness or anxiety. Analysis of GFS data for the 155 subjects showed that fear of snakes and injuries were highest among women; heights and injections among men. Fear of blood was rarely reported. Spearman correlations between GFS individual items and DAS scores indicated functional independence between dental fear and common fears such as blood, injections and enclosures in most cases. Only in specific types of dental fear did these results support Rachman and Lopatka's contention that fears are thought to summate.(ABSTRACT TRUNCATED AT 250 WORDS)

Plasticity of Fear and Safety Neurons of the Amygdala in Response to Fear Extinction

PubMed Central

Sangha, Susan

2015-01-01

Fear inhibition learning induces plasticity and remodeling of circuits within the amygdala. Most studies examine these changes in nondiscriminative fear conditioning paradigms. Using a discriminative fear, safety, and reward conditioning task, Sangha et al. (2013) have previously reported several neural microcircuits within the basal amygdala (BA) which discriminate among these cues, including a subpopulation of neurons responding selectively to a safety cue and not a fear cue. Here, the hypothesis that these “safety” neurons isolated during discriminative conditioning are biased to become fear cue responsive as a result of extinction, when fear behavior diminishes, was tested. Although 41% of “safety” neurons became fear cue responsive as a result of extinction, the data revealed that there was no bias for these neurons to become preferentially responsive during fear extinction compared to the other identified subgroups. In addition to the plasticity seen in the “safety” neurons, 44% of neurons unresponsive to either the fear cue or safety cue during discriminative conditioning became fear cue responsive during extinction. Together these emergent responses to the fear cue as a result of extinction support the hypothesis that new learning underlies extinction. In contrast, 47% of neurons responsive to the fear cue during discriminative conditioning became unresponsive to the fear cue during extinction. These findings are consistent with a suppression of neural responding mediated by inhibitory learning, or, potentially, by direct unlearning. Together, the data support extinction as an active process involving both gains and losses of responses to the fear cue and suggests the final output of the integrated BA circuit in influencing fear behavior is a balance of excitation and inhibition, and perhaps reversal of learning-induced changes. PMID:26733838

Excitatory strength of expressive faces: effects of happy and fear expressions and context on the extinction of a conditioned fear response.

PubMed

Lanzetta, J T; Orr, S P

1986-01-01

In a recent study, Orr and Lanzetta (1984) showed that the excitatory properties of fear facial expressions previously described (Lanzetta & Orr, 1981; Orr & Lanzetta, 1980) do not depend on associative mechanisms; even in the absence of reinforcement, fear faces intensify the emotional reaction to a previously conditioned stimulus and disrupt extinction of an acquired fear response. In conjunction with the findings on acquisition, the failure to obtain extinction suggests that fear faces have some of the functional properties of "prepared" (fear-relevant) stimuli. In the present study we compared the magnitude of conditioned fear responses to happy and fear faces when a potent danger signal, the shock electrodes, are attached or unattached. If fear faces are functionally analogous to prepared stimuli, then, even in the absence of veridical support for an expectation of shock, they should retain excitatory strength, whereas happy faces should not. The results are consistent with this view of fear expressions. In the absence of reinforcement, and with shock electrodes removed, conditioned fear responses and basal levels of arousal were of greater magnitude for the fear-face condition than for the happy-face condition.

The advanced receiver 2: Telemetry test results in CTA 21

NASA Technical Reports Server (NTRS)

Hinedi, S.; Bevan, R.; Marina, M.

1991-01-01

Telemetry tests with the Advanced Receiver II (ARX II) in Compatibility Test Area 21 are described. The ARX II was operated in parallel with a Block-III Receiver/baseband processor assembly combination (BLK-III/BPA) and a Block III Receiver/subcarrier demodulation assembly/symbol synchronization assembly combination (BLK-III/SDA/SSA). The telemetry simulator assembly provided the test signal for all three configurations, and the symbol signal to noise ratio as well as the symbol error rates were measured and compared. Furthermore, bit error rates were also measured by the system performance test computer for all three systems. Results indicate that the ARX-II telemetry performance is comparable and sometimes superior to the BLK-III/BPA and BLK-III/SDA/SSA combinations.

Optofluidic encapsulation and manipulation of silicon microchips using image processing based optofluidic maskless lithography and railed microfluidics.

PubMed

Chung, Su Eun; Lee, Seung Ah; Kim, Jiyun; Kwon, Sunghoon

2009-10-07

We demonstrate optofluidic encapsulation of silicon microchips using image processing based optofluidic maskless lithography and manipulation using railed microfluidics. Optofluidic maskless lithography is a dynamic photopolymerization technique of free-floating microstructures within a fluidic channel using spatial light modulator. Using optofluidic maskless lithography via computer-vision aided image processing, polymer encapsulants are fabricated for chip protection and guiding-fins for efficient chip conveying within a fluidic channel. Encapsulated silicon chips with guiding-fins are assembled using railed microfluidics, which is an efficient guiding and heterogeneous self-assembly system of microcomponents. With our technology, externally fabricated silicon microchips are encapsulated, fluidically guided and self-assembled potentially enabling low cost fluidic manipulation and assembly of integrated circuits.

A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly.

PubMed

Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

2016-04-28

In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.

Fear of property crime: examining the effects of victimization, vicarious victimization, and perceived risk.

PubMed

Cook, Carrie L; Fox, Kathleen A

2011-01-01

Fear of crime research has primarily focused on fear of crime in general or on fear of specific types of violent crimes. This study builds from this line of research by focusing exclusively on the night fear of six types of property crimes, including fear of burglary while away from home, vehicle theft, bicycle theft, property theft, vandalism, and vehicle burglary. This study examines the effects of victimization, vicarious victimization, and perceived risk on fear of property crime. Survey data from college students reveal that victimization and vicarious victimization were not significant predictors of fear of property crime, whereas perceived risk was a consistent and significant predictor of fear of all property crimes.

Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.

PubMed

Malan-Müller, Stefanie; Fairbairn, Lorren; Daniels, Willie M U; Dashti, Mahjoubeh Jalali Sefid; Oakeley, Edward J; Altorfer, Marc; Kidd, Martin; Seedat, Soraya; Gamieldien, Junaid; Hemmings, Sîan Megan Joanna

2016-02-01

D-cycloserine (DCS) has been shown to be effective in facilitating fear extinction in animal and human studies, however the precise mechanisms whereby the co-administration of DCS and behavioural fear extinction reduce fear are still unclear. This study investigated the molecular mechanisms of intrahippocampally administered D-cycloserine in facilitating fear extinction in a contextual fear conditioning animal model. Male Sprague Dawley rats (n = 120) were grouped into four experimental groups (n = 30) based on fear conditioning and intrahippocampal administration of either DCS or saline. The light/dark avoidance test was used to differentiate maladapted (MA) (anxious) from well-adapted (WA) (not anxious) subgroups. RNA extracted from the left dorsal hippocampus was used for RNA sequencing and gene expression data was compared between six fear-conditioned + saline MA (FEAR + SALINE MA) and six fear-conditioned + DCS WA (FEAR + DCS WA) animals. Of the 424 significantly downregulated and 25 significantly upregulated genes identified in the FEAR + DCS WA group compared to the FEAR + SALINE MA group, 121 downregulated and nine upregulated genes were predicted to be relevant to fear conditioning and anxiety and stress-related disorders. The majority of downregulated genes transcribed immune, proinflammatory and oxidative stress systems molecules. These molecules mediate neuroinflammation and cause neuronal damage. DCS also regulated genes involved in learning and memory processes, and genes associated with anxiety, stress-related disorders and co-occurring diseases (e.g., cardiovascular diseases, digestive system diseases and nervous system diseases). Identifying the molecular underpinnings of DCS-mediated fear extinction brings us closer to understanding the process of fear extinction.

A shuttle and space station manipulator system for assembly, docking, maintenance, cargo handling and spacecraft retrieval (preliminary design). Volume 3: Concept analysis. Part 1: Technical

NASA Technical Reports Server (NTRS)

1972-01-01

Information backing up the key features of the manipulator system concept and detailed technical information on the subsystems are presented. Space station assembly and shuttle cargo handling tasks are emphasized in the concept analysis because they involve shuttle berthing, transferring the manipulator boom between shuttle and station, station assembly, and cargo handling. Emphasis is also placed on maximizing commonality in the system areas of manipulator booms, general purpose end effectors, control and display, data processing, telemetry, dedicated computers, and control station design.

Fear during labor: the impact of sexual abuse in adult life.

PubMed

Eberhard-Gran, Malin; Slinning, Kari; Eskild, Anne

2008-12-01

Our aim was to study the occurrence of extreme fear during labor and its association with previous sexual abuse in adult life. All postpartum women (n = 414) in two municipalities in Norway participated in a questionnaire study. Self-reported fear during labor was categorized as "no fear/some fear/extreme fear". Sexual abuse was measured by the Abuse Assessment Screen (AAS). Three percent of the women reported extreme fear during labor, 13% some fear and 84% no fear. In total, 12% had been sexually abused as an adult. Among the women with extreme fear during labor, however, one third had a history of sexual abuse in adult life (crude odds ratio 3.7; 95% CI: 1.0-3.7). When controlling for depression in pregnancy, duration of labor and mode of delivery, the adjusted odds ratio for extreme fear during labor was 4.9 (95% CI: 1.2-19.1). The results suggest that women with a history of sexual abuse in adult life have an increased risk of extreme fear during labor.

Passive avoidance is linked to impaired fear extinction in humans

PubMed Central

Cornwell, Brian R.; Overstreet, Cassie; Krimsky, Marissa; Grillon, Christian

2013-01-01

Conventional wisdom dictates we must face our fears to conquer them. This idea is embodied in exposure-based treatments for anxiety disorders, where the intent of exposure is to reverse a history of avoidant behavior that is thought to fuel a patient’s irrational fears. We tested in humans the relationship between fear and avoidance by combining Pavlovian differential fear conditioning with a novel task for quantifying spontaneous passive avoidant behavior. During self-guided navigation in virtual reality following de novo fear conditioning, we observed participants keeping their distance from the feared object. At the individual level, passive avoidant behavior was highly associated with maladaptive fear expression (fear-potentiated startle) during late extinction training, indicating that extinction learning was impaired following a brief episode of avoidance. Avoidant behavior, however, was not related to initial acquired fear, raising doubt about a straightforward link between physiological fear and behavioral avoidance. We conclude that a deeper understanding of what motivates avoidance may offer a target for early intervention, before fears transition from the rational to the irrational. PMID:23427168

Effective and ineffective use of fear in health promotion campaigns.

PubMed Central

Soames Job, R F

1988-01-01

Health promotion campaigns are typically designed to elicit fear, yet the use of fear is often ineffective in achieving the desired behavior change. Campaigns which attempt to use fear as part of a punishment procedure are unlikely to succeed. Consistent with established principles of learning, fear is most likely to be effective if the campaign allows for the desired behavior to be reinforced by a reduction in the level of fear. This entails five requirements: 1) fear onset should occur before the desired behavior is offered; 2) the event upon which the fear is based should appear to be likely; 3) a specific desired behavior should be offered as part of the campaign; 4) the level of fear elicited should only be such that the desired behavior offered is sufficient to substantially reduce the fear; 5) fear offset should occur as a reinforcer for the desired behavior, confirming its effectiveness. Under some circumstances it may be difficult to ensure that these requirements are met. In general, a positive reinforcement approach may prove to be more effective than the use of fear. PMID:3276236

Fear of progression.

PubMed

Herschbach, Peter; Dinkel, Andreas

2014-01-01

Fear of progression (or fear of recurrence) is an appropriate, rational response to the real threat of cancer and cancer treatments. However, elevated levels of fear of progression can become dysfunctional, affecting well-being, quality of life, and social functioning. Research has shown that fear of progression is one of the most frequent distress symptoms of patients with cancer and with other chronic diseases. As a clear consensus concerning clinically relevant states of fear of progression is currently lacking, it is difficult to provide a valid estimate of the rate of cancer patients who clearly suffer from fear of progression. However, recent systematic reviews suggest that probably 50 % of cancer patients experience moderate to severe fear of progression. Furthermore, many patients express unmet needs in dealing with the fear of cancer spreading. These results underline the necessity to provide effective psychological treatments for clinical levels of fear of progression. A few psychosocial interventions for treating fear of progression have been developed so far. Our own, targeted intervention study showed that dysfunctional fear of progression can be effectively treated with a brief group therapy.

Fear of Death in a Sample of Physicians

PubMed Central

Wood, Keith; Robinson, Paul J.

1984-01-01

Recently, reliable and valid methods of assessing fear of death have been developed. In this study, three well established questionnaires (the Threat Index, the Death Anxiety Scale and the Collett-Lester Fear of Death Scale) were used to assess and compare fear of death in a group of physicians (n = 30) with a group of non-physicians (n = 30). T-tests and hierarchical multiple regression analyses revealed no significant differences between physicians' and non-physicians' fear of death as measured by the Threat Index and Templer's Death Anxiety Scale. The Collett-Lester Fear of Death Scale revealed that physicians were less fearful of death. More specifically, physicians demonstrated less fear on the Collett-Lester subscales, `fear of dying of self' and `fear of dying of others', than did non-physicians. These findings and those of earlier, contradictory research, are discussed. PMID:21279021

Living in Fear of Your Child's Pain: The Parent Fear of Pain Questionnaire

PubMed Central

Simons, Laura E.; Smith, Allison; Kaczynski, Karen; Basch, Molly

2015-01-01

Fear and avoidance have been consistently associated with poor pain-related outcomes in children. In the context of the pediatric pain experience, parent distress and behaviors can be highly influential. The current study validated the Parent Fear of Pain Questionnaire (PFOPQ) to assess a parent's fears and avoidance behaviors associated with their child's pain. Using the PFOPQ in conjunction with measures of parent and child pain-related variables, we tested the Interpersonal Fear Avoidance Model (IFAM). The sample comprised of 321 parents and their child with chronic or new-onset pain who presented to a multidisciplinary outpatient pain clinic. An exploratory factor analysis yielded a 4-factor structure for the PFOPQ consisting of Fear of Pain, Fear of Movement, Fear of School, and Avoidance. As hypothesized, Fear of Pain was most closely related to parent pain catastrophizing and child fear of pain, while Avoidance was most closely related to parent protective behaviors and child avoidance of activities. In testing the IFAM, parent behavior contributed directly and indirectly to child avoidance while parent fear and catastrophizing contributed indirectly to child avoidance through parent behavior and child fear and catastrophizing, in turn, influencing child functional disability levels. The current study provides the first measure of parent pain-related fears and avoidance behaviors and evaluates the theorized IFAM. These results underscore the important influence of parents on child pain-related outcomes and puts forth a psychometrically sound measure to assess parent fear and avoidance in the context of their child's pain. PMID:25630026

A role for midline and intralaminar thalamus in the associative blocking of Pavlovian fear conditioning.

PubMed

Sengupta, Auntora; McNally, Gavan P

2014-01-01

Fear learning occurs in response to positive prediction error, when the expected outcome of a conditioning trial exceeds that predicted by the conditioned stimuli present. This role for error in Pavlovian association formation is best exemplified by the phenomenon of associative blocking, whereby prior fear conditioning of conditioned stimulus (CS) A is able to prevent learning to CSB when they are conditioned in compound. The midline and intralaminar thalamic nuclei (MIT) are well-placed to contribute to fear prediction error because they receive extensive projections from the midbrain periaqueductal gray-which has a key role in fear prediction error-and project extensively to prefrontal cortex and amygdala. Here we used an associative blocking design to study the role of MIT in fear learning. In Stage I rats were trained to fear CSA via pairings with shock. In Stage II rats received compound fear conditioning of CSAB paired with shock. On test, rats that received Stage I training expressed less fear to CSB relative to control rats that did not receive this training. Microinjection of bupivacaine into MIT prior to Stage II training had no effect on the expression of fear during Stage II and had no effect on fear learning in controls, but prevented associative blocking and so enabled fear learning to CSB. These results show an important role for MIT in predictive fear learning and are discussed with reference to previous findings implicating the midline and posterior intralaminar thalamus in fear learning and fear responding.

Living in fear of your child's pain: the Parent Fear of Pain Questionnaire.

PubMed

Simons, Laura E; Smith, Allison; Kaczynski, Karen; Basch, Molly

2015-04-01

Fear and avoidance have been consistently associated with poor pain-related outcomes in children. In the context of the pediatric pain experience, parent distress and behaviors can be highly influential. This study validated the Parent Fear of Pain Questionnaire (PFOPQ) to assess a parent's fears and avoidance behaviors associated with their child's pain. Using the PFOPQ in conjunction with measures of parent and child pain-related variables, we tested the interpersonal fear-avoidance model (IFAM). The sample comprised 321 parents and their child with chronic or new-onset pain who presented to a multidisciplinary outpatient pain clinic. An exploratory factor analysis yielded a 4-factor structure for the PFOPQ consisting of Fear of Pain, Fear of Movement, Fear of School, and Avoidance. As hypothesized, Fear of Pain was most closely related to parent pain catastrophizing and child fear of pain, whereas Avoidance was most closely related to parent protective behaviors and child avoidance of activities. In testing the IFAM, parent behavior contributed directly and indirectly to child avoidance, whereas parent fear and catastrophizing contributed indirectly to child avoidance through parent behavior and child fear and catastrophizing, in turn, influencing child functional disability levels. This study provides the first measure of parent pain-related fears and avoidance behaviors and evaluates the theorized IFAM. These results underscore the important influence of parents on child pain-related outcomes and put forth a psychometrically sound measure to assess parent fear and avoidance in the context of their child's pain.

Fine tuning fear of childbirth: the relationship between Childbirth Fear Questionnaire subscales and demographic and reproductive variables.

PubMed

Fairbrother, Nichole; Thordarson, Dana S; Stoll, Kathrin

2018-02-01

The objective of the current study was to investigate the relationship between the newly developed Childbirth Fear Questionnaire (CFQ) and demographic and reproductive variables. The CFQ was developed in an effort to improve measurement and understanding of women's childbirth fears. To our knowledge the CFQ is the only multidimensional measure of childbirth fears in which (a) multiple domains of childbirth fear are assessed and (b) individual subscales have been psychometrically developed. Participants were 643 pregnant women residing in English-speaking countries, recruited via online forums. Participants completed a set of questionnaires, including the multidimensional CFQ, via an online survey. Given the differences in childbirth fear between nulliparous and multiparous women, findings are stratified by parity. Gestational age was largely unrelated to fear of childbirth. Age, income and education were negatively related to fear of childbirth. Assisted vaginal delivery and episiotomy in a previous pregnancy were positively associated with a fear of pain. Self-reported history of traumatic vaginal birth was associated with higher scores on all aspects of fear of childbirth. History of caesarean birth was not generally associated with increased childbirth fears, but women with a prior, self-reported traumatic caesarean birth reported more fear of future caesarean births. Findings are consistent with previous reports of fear of childbirth. However, the CFQ provides increased specificity with respect to women's childbirth fears. This information is relevant to both education and treatment planning for pregnant women and women wishing to reproduce.

Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers

PubMed Central

Wajid, Bilal; Serpedin, Erchin

2012-01-01

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity. PMID:22768980

Water ordering controls the dynamic equilibrium of micelle-fibre formation in self-assembly of peptide amphiphiles.

PubMed

Deshmukh, Sanket A; Solomon, Lee A; Kamath, Ganesh; Fry, H Christopher; Sankaranarayanan, Subramanian K R S

2016-08-24

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides remains elusive. Here, we use a multistage atomistic-coarse-grained approach, complemented by circular dichroism/infrared spectroscopy and dynamic light scattering experiments to highlight the dual nature of water in driving the self-assembly of peptide amphiphiles (PAs). We show computationally that water cage formation and breakage near the hydrophobic groups control the fusion dynamics and aggregation of PAs in the micellar stage. Simulations also suggest that enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards the fibre phase and stimulates structure and order during the PA assembly into nanofibres. Experiments validate our simulation findings; the measured infrared O-H bond stretching frequency is reminiscent of an ice-like bond which suggests that the solvated water becomes increasingly ordered with time in the assembled peptide network, thus shedding light on the role of water in a self-assembly process.

Automatic Assembly of Combined Checkingfixture for Auto-Body Components Based Onfixture Elements Libraries

NASA Astrophysics Data System (ADS)

Jiang, Jingtao; Sui, Rendong; Shi, Yan; Li, Furong; Hu, Caiqi

In this paper 3-D models of combined fixture elements are designed, classified by their functions, and saved in computer as supporting elements library, jointing elements library, basic elements library, localization elements library, clamping elements library, and adjusting elements library etc. Then automatic assembly of 3-D combined checking fixture for auto-body part is presented based on modularization theory. And in virtual auto-body assembly space, Locating constraint mapping technique and assembly rule-based reasoning technique are used to calculate the position of modular elements according to localization points and clamp points of auto-body part. Auto-body part model is transformed from itself coordinate system space to virtual assembly space by homogeneous transformation matrix. Automatic assembly of different functional fixture elements and auto-body part is implemented with API function based on the second development of UG. It is proven in practice that the method in this paper is feasible and high efficiency.

Computational protein design: a review

NASA Astrophysics Data System (ADS)

Coluzza, Ivan

2017-04-01

Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future.

A new strategy for genome assembly using short sequence reads and reduced representation libraries.

PubMed

Young, Andrew L; Abaan, Hatice Ozel; Zerbino, Daniel; Mullikin, James C; Birney, Ewan; Margulies, Elliott H

2010-02-01

We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.

Simulations of polymorphic icosahedral shells assembling around many cargo molecules

NASA Astrophysics Data System (ADS)

Mohajerani, Farzaneh; Perlmutter, Jason; Hagan, Michael

Bacterial microcompartments (BMCs) are large icosahedral shells that sequester the enzymes and reactants responsible for particular metabolic pathways in bacteria. Although different BMCs vary in size and encapsulate different cargoes, they are constructed from similar pentameric and hexameric shell proteins. Despite recent groundbreaking experiments which visualized the formation of individual BMCs, the detailed assembly pathways and the factors which control shell size remain unclear. In this talk, we describe theoretical and computational models that describe the dynamical encapsulation of hundreds of cargo molecules by self-assembling icosahedral shells. We present phase diagrams and analysis of dynamical simulation trajectories showing how the thermodynamics, assembly pathways, and emergent structures depend on the interactions among shell proteins and cargo molecules. Our model suggests a mechanism for controlling insertion of the 12 pentamers required for a closed shell topology, and the relationship between assembly pathway and BMC size polydispersity. In addition to elucidating how native BMCs assemble,our results establish principles for reengineering BMCs or viral capsids as customizable nanoreactors that can assemble around a programmable set of enzymes and reactants. Supported by NIH R01GM108021 and Brandeis MRSEC DMR-1420382.

Experience-dependent modification of a central amygdala fear circuit

PubMed Central

Li, Haohong; Penzo, Mario A.; Taniguchi, Hiroki; Kopec, Charles D.; Huang, Z. Josh; Li, Bo

2013-01-01

The amygdala is essential for fear learning and expression. The central amygdala (CeA), once viewed as a passive relay between the amygdala complex and downstream fear effectors, has emerged as an active participant in fear conditioning. However, how CeA contributes to the learning and expression of fear is unclear. Here we show in mice that fear conditioning induces robust plasticity of excitatory synapses onto inhibitory neurons in the lateral subdivision of CeA (CeL). This experience-dependent plasticity is cell-specific, bidirectional, and expressed presynaptically by inputs from the lateral amygdala. In particular, preventing synaptic potentiation onto somatostatin-positive neurons impairs fear memory formation. Furthermore, activation of these neurons is necessary for fear memory recall and sufficient to drive fear responses. Our findings support a model in which the fear conditioning-induced synaptic modifications in CeL favor the activation of somatostatin-positive neurons, which inhibit CeL output thereby disinhibiting the medial subdivision of CeA and releasing fear expression. PMID:23354330

Fears of institutionalized mentally retarded adults.

PubMed

Sternlicht, M

1979-01-01

The patterns of fears of institutionalized mentally retarded adults were studied in a sample of i2 moderately retarded men and women between the ages of 21-49. The direct questioning method was employed. Two interviews were held, two weeks apart; the first interview elicited the Ss' fears, while the second concerned the fears of their friends. A total of 146 responses were obtained, and these were categorized according to the types of fears: supernatural-natural events, animals, physical injury, psychological stress, egocentric responses, and no fears. The Ss displayed a higher percentage of fears in the preoperational stage than in the concrete operational stage. In a comparison of male to female fears, only one category, that of fears of animals, reached significance. The study suggested that the same developmental trend of fears that appears in normal children appears in the retarded as well, and these fears follow Piaget's level of cognitive development, proceeding from egocentric perceptions of causality to realistic cause and effect thinking.

Fears and Phobias

MedlinePlus

... a strong swimmer might have a fear of deep water. In this case, the fear is helpful because it cautions the person to stay safe. Someone could overcome this fear by learning how to swim safely. A fear can be ...

33 CFR 165.530 - Safety Zone: Cape Fear and Northeast Cape Fear Rivers, NC.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Northeast Cape Fear Rivers, NC. 165.530 Section 165.530 Navigation and Navigable Waters COAST GUARD... § 165.530 Safety Zone: Cape Fear and Northeast Cape Fear Rivers, NC. (a) Location. The following area is a moving safety zone during the specified conditions: The waters of the Cape Fear and Northeast Cape...

What Can Ethobehavioral Studies Tell Us About The Brain’s Fear System?

PubMed Central

Pellman, Blake A.; Kim, Jeansok J.

2016-01-01

Foraging-associated predation risk is a natural problem all prey must face. Fear evolved due to its protective functions, guiding and shaping behaviors that help animals adapt to various ecological challenges. Despite the breadth of risky situations in nature that demand diversity in fear behaviors, contemporary neurobiological models of fear stem largely from Pavlovian fear conditioning studies that focus on how a particular cue becomes capable of eliciting learned fear responses, thus oversimplifying the brain’s fear system. Here we review fear from functional, mechanistic, and phylogenetic perspectives where environmental threats cause animals to alter their foraging strategies in terms of spatial and temporal navigation, and discuss whether the inferences we draw from fear conditioning studies operate in the natural world. PMID:27130660

Guided and magnetic self-assembly of tunable magnetoceptive gels

NASA Astrophysics Data System (ADS)

Tasoglu, S.; Yu, C. H.; Gungordu, H. I.; Guven, S.; Vural, T.; Demirci, U.

2014-09-01

Self-assembly of components into complex functional patterns at microscale is common in nature, and used increasingly in numerous disciplines such as optoelectronics, microfabrication, sensors, tissue engineering and computation. Here, we describe the use of stable radicals to guide the self-assembly of magnetically tunable gels, which we call ‘magnetoceptive’ materials at the scale of hundreds of microns to a millimeter, each can be programmed by shape and composition, into heterogeneous complex structures. Using paramagnetism of free radicals as a driving mechanism, complex heterogeneous structures are built in the magnetic field generated by permanent magnets. The overall magnetic signature of final structure is erased via an antioxidant vitamin E, subsequent to guided self-assembly. We demonstrate unique capabilities of radicals and antioxidants in fabrication of soft systems with heterogeneity in material properties, such as porosity, elastic modulus and mass density; then in bottom-up tissue engineering and finally, levitational and selective assembly of microcomponents.

Guided and magnetic self-assembly of tunable magnetoceptive gels

PubMed Central

Tasoglu, S.; Yu, C.H.; Gungordu, H.I.; Guven, S.; Vural, T.; Demirci, U.

2014-01-01

Self-assembly of components into complex functional patterns at microscale is common in nature, and used increasingly in numerous disciplines such as optoelectronics, microfabrication, sensors, tissue engineering and computation. Here, we describe the use of stable radicals to guide the self-assembly of magnetically tunable gels, which we call ‘magnetoceptive’ materials at the scale of hundreds of microns to a millimeter, each can be programmed by shape and composition, into heterogeneous complex structures. Using paramagnetism of free radicals as a driving mechanism, complex heterogeneous structures are built in the magnetic field generated by permanent magnets. The overall magnetic signature of final structure is erased via an antioxidant vitamin E, subsequent to guided self-assembly. We demonstrate unique capabilities of radicals and antioxidants in fabrication of soft systems with heterogeneity in material properties, such as porosity, elastic modulus and mass density; then in bottom-up tissue engineering and finally, levitational and selective assembly of microcomponents. PMID:25175148

Where There is Smoke There is Fear-Impaired Contextual Inhibition of Conditioned Fear in Smokers.

PubMed

Haaker, Jan; Lonsdorf, Tina B; Schümann, Dirk; Bunzeck, Nico; Peters, Jan; Sommer, Tobias; Kalisch, Raffael

2017-07-01

The odds-ratio of smoking is elevated in populations with neuropsychiatric diseases, in particular in the highly prevalent diagnoses of post-traumatic stress and anxiety disorders. Yet, the association between smoking and a key dimensional phenotype of these disorders-maladaptive deficits in fear learning and fear inhibition-is unclear. We therefore investigated acquisition and memory of fear and fear inhibition in healthy smoking and non-smoking participants (N=349, 22% smokers). We employed a well validated paradigm of context-dependent fear and safety learning (day 1) including a memory retrieval on day 2. During fear learning, a geometrical shape was associated with an aversive electrical stimulation (classical fear conditioning, in danger context) and fear responses were extinguished within another context (extinction learning, in safe context). On day 2, the conditioned stimuli were presented again in both contexts, without any aversive stimulation. Autonomic physiological measurements of skin conductance responses as well as subjective evaluations of fear and expectancy of the aversive stimulation were acquired. We found that impairment of fear inhibition (extinction) in the safe context during learning (day 1) was associated with the amount of pack-years in smokers. During retrieval of fear memories (day 2), smokers showed an impairment of contextual (safety context-related) fear inhibition as compared with non-smokers. These effects were found in physiological as well as subjective measures of fear. We provide initial evidence that smokers as compared with non-smokers show an impairment of fear inhibition. We propose that smokers have a deficit in integrating contextual signs of safety, which is a hallmark of post-traumatic stress and anxiety disorders.

Prevalence of childbirth fear in an Australian sample of pregnant women.

PubMed

Toohill, Jocelyn; Fenwick, Jennifer; Gamble, Jenny; Creedy, Debra K

2014-08-14

Childbirth fear is reported to affect around 20% of women. However reporting on levels of symptom severity vary. Unlike Scandinavian countries, there has been limited focus on childbirth fear in Australia. The aim of this paper is to determine the prevalence of low, moderate, high and severe levels of childbirth fear in a large representative sample of pregnant women drawn from a large randomised controlled trial and identify demographic and obstetric characteristics associated with childbirth fear. Using a descriptive cross-sectional design, 1,410 women in their second trimester were recruited from one of three public hospitals in south-east Queensland. Participants were screened for childbirth fear using the Wijma Delivery Expectancy/Experience Questionnaire Version A (WDEQ-A). Associations of demographic and obstetric factors and levels of childbirth fear between nulliparous and multiparous women were investigated. Prevalence of childbirth fear was 24% overall, with 31.5% of nulliparous women reporting high levels of fear (score ≥ 66 on the WDEQ-A) compared to 18% of multiparous women. Childbirth fear was associated with paid employment, parity, and mode of last birth, with higher levels of fear in first time mothers (p < 0.001) and in women who had previously had an operative birth (p < 0.001). Prevalence of childbirth fear in Australian women was comparable to international rates. Significant factors associated with childbirth fear were being in paid employment, and obstetric characteristics such as parity and birth mode in the previous pregnancy. First time mothers had higher levels of fear than women who had birthed before. A previous operative birth was fear provoking. Experiencing a previous normal birth was protective of childbirth fear.

Interference effects of transcranial direct current stimulation over the right frontal cortex and adrenergic system on conditioned fear.

PubMed

Nasehi, Mohammad; Soltanpour, Reyhaneh; Ebrahimi-Ghiri, Mohaddeseh; Zarrabian, Shahram; Zarrindast, Mohammad-Reza

2017-11-01

The effects of pharmacological interventions on fear memory have widely been studied, but there are very few studies about the effects of brain electrical stimulation on fear memory function. Therefore, our aim was to determine whether anodal/cathodal transcranial direct current stimulation (tDCS) over the right frontal cortex would modify propranolol-induced contextual and auditory fear memory deficits, before or after training. The adult NMRI male mice were randomly assigned into three groups: the sham group, the anodal tDCS group, and the cathodal tDCS group. Fear memories were evaluated using a classical fear conditioning apparatus. While the anodal stimulation did not affect fear retrieval, post-training cathodal stimulation improved fear memory retrieval. Regardless of when propranolol (0.1 mg/kg) was administered, it impaired fear memory retrieval. However, when anodal stimulation and propranolol were applied prior to the training, contextual fear memory retrieval was increased and auditory fear memory was reversed. An enhanced contextual retrieval was also observed when propranolol was administered prior to the training and stimulation occurred after the training. Only when the stimulation occurred prior to the training and propranolol was administered after the training was there a selective improvement in contextual fear memory retrieval, leaving the auditory fear memory retrieval impaired. Interestingly, cathodal stimulation improved the effects of propranolol on auditory fear memory only when it occurred prior to the training. The results highlight possible improving effects for anodal/cathodal tDCS on propranolol-induced deficits on fear memories. The timing of the interventions related to the specific phases of memory formation is important in modulating fear behaviors.

Cross-frequency power coupling between hierarchically organized face-selective areas.

PubMed

Furl, Nicholas; Coppola, Richard; Averbeck, Bruno B; Weinberger, Daniel R

2014-09-01

Neural oscillations are linked to perception and behavior and may reflect mechanisms for long-range communication between brain areas. We developed a causal model of oscillatory dynamics in the face perception network using magnetoencephalographic data from 51 normal volunteers. This model predicted induced responses to faces by estimating oscillatory power coupling between source locations corresponding to bilateral occipital and fusiform face areas (OFA and FFA) and the right superior temporal sulcus (STS). These sources showed increased alpha and theta and decreased beta power as well as selective responses to fearful facial expressions. We then used Bayesian model comparison to compare hypothetical models, which were motivated by previous connectivity data and a well-known theory of temporal lobe function. We confirmed this theory in detail by showing that the OFA bifurcated into 2 independent, hierarchical, feedforward pathways, with fearful expressions modulating power coupling only in the more dorsal (STS) pathway. The power coupling parameters showed a common pattern over connections. Low-frequency bands showed same-frequency power coupling, which, in the dorsal pathway, was modulated by fearful faces. Also, theta power showed a cross-frequency suppression of beta power. This combination of linear and nonlinear mechanisms could reflect computational mechanisms in hierarchical feedforward networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Stimulus fear relevance and the speed, magnitude, and robustness of vicariously learned fear.

PubMed

Dunne, Güler; Reynolds, Gemma; Askew, Chris

2017-08-01

Superior learning for fear-relevant stimuli is typically indicated in the laboratory by faster acquisition of fear responses, greater learned fear, and enhanced resistance to extinction. Three experiments investigated the speed, magnitude, and robustness of UK children's (6-10 years; N = 290; 122 boys, 168 girls) vicariously learned fear responses for three types of stimuli. In two experiments, children were presented with pictures of novel animals (Australian marsupials) and flowers (fear-irrelevant stimuli) alone (control) or together with faces expressing fear or happiness. To determine learning speed the number of stimulus-face pairings seen by children was varied (1, 10, or 30 trials). Robustness of learning was examined via repeated extinction procedures over 3 weeks. A third experiment compared the magnitude and robustness of vicarious fear learning for snakes and marsupials. Significant increases in fear responses were found for snakes, marsupials and flowers. There was no indication that vicarious learning for marsupials was faster than for flowers. Moreover, vicariously learned fear was neither greater nor more robust for snakes compared to marsupials, or for marsupials compared to flowers. These findings suggest that for this age group stimulus fear relevance may have little influence on vicarious fear learning. Copyright © 2017 Elsevier Ltd. All rights reserved.

An inquiry about clinical death--considering spiritual pain.

PubMed

Deeken, Alfons

2009-06-01

According to a paper published by the International Work Group on Death, Dying and Bereavement, "Each person has a spiritual dimension." That means each person has spiritual energy and spiritual needs. In facing death, a patient suffers spiritual pain and needs spiritual care. This paper describes what spirituality and spiritual pain mean. It identifies nine types of fears and anxieties about death which become a source of spiritual pain: 1. Fear of pain; 2. Fear of loneliness; 3. Fear of unpleasant experiences; 4. Fear of becoming a burden to the family and to society; 5. Anxiety towards the unknown; 6. Fear of death resulting from fear of life; 7. Fear of death as a feeling that one's life task is still incomplete; 8. Fear of death as fear of personal extinction; 9. Fear of death as fear of judgment and punishment after death. Five types of spiritual pain that seem to be frequent among patients facing death are discussed: 1. Loss of self-determination; 2. Loss of meaning; 3. Guilt feelings; 4. Loneliness and isolation; 5. Loss of hope. Three ways of preventing or reducing excessive fear of death and of lowering the various types of spiritual pain are suggested: 1. Death education; 2. Presence at the bedside; 3. Humor as an expression of love.

Phasic vs Sustained Fear in Rats and Humans: Role of the Extended Amygdala in Fear vs Anxiety

PubMed Central

Davis, Michael; Walker, David L; Miles, Leigh; Grillon, Christian

2010-01-01

Data will be reviewed using the acoustic startle reflex in rats and humans based on our attempts to operationally define fear vs anxiety. Although the symptoms of fear and anxiety are very similar, they also differ. Fear is a generally adaptive state of apprehension that begins rapidly and dissipates quickly once the threat is removed (phasic fear). Anxiety is elicited by less specific and less predictable threats, or by those that are physically or psychologically more distant. Thus, anxiety is a more long-lasting state of apprehension (sustained fear). Rodent studies suggest that phasic fear is mediated by the amygdala, which sends outputs to the hypothalamus and brainstem to produce symptoms of fear. Sustained fear is also mediated by the amygdala, which releases corticotropin-releasing factor, a stress hormone that acts on receptors in the bed nucleus of the stria terminalis (BNST), a part of the so-called ‘extended amygdala.' The amygdala and BNST send outputs to the same hypothalamic and brainstem targets to produce phasic and sustained fear, respectively. In rats, sustained fear is more sensitive to anxiolytic drugs. In humans, symptoms of clinical anxiety are better detected in sustained rather than phasic fear paradigms. PMID:19693004

Fear, pain and stress hormones during childbirth.

PubMed

Alehagen, Siw; Wijma, Barbro; Lundberg, Ulf; Wijma, Klaas

2005-09-01

To investigate the course of fear, pain and stress hormones during labor, and the associations between fear, pain, stress hormones and duration of labor in nulliparous women with and without epidural analgesia (EDA). One day during gestation weeks 37-39, urinary and salivary samples were collected to measure catecholamines and cortisol. Hourly during labor, the participants answered the Delivery Fear Scale and a pain intensity scale, and urinary and salivary samples were collected to measure stress hormones. The course of fear, pain and stress hormones differed throughout labor in women with and without EDA. Pain and cortisol increased throughout labor in women without EDA. Women who received EDA had more fear, but not more pain, before the administration of the EDA than women who did not receive EDA. Pain, fear and catecholamines decreased when women received EDA, but fear and pain increased again later in labor. Fear and pain correlated, as well as levels of fear in the different phases of labor. During phase one of labor epinephrine and duration of the phase were negatively correlated. The course of fear, pain and concentrations of stress hormones differed, highly influenced by the administration of EDA. Fear and pain correlated more pronounced than stress hormones and fear, pain and duration of labor.

Presence and process of fear of birth during pregnancy-Findings from a longitudinal cohort study.

PubMed

Hildingsson, Ingegerd; Haines, Helen; Karlström, Annika; Nystedt, Astrid

2017-10-01

The prevalence of fear of birth has been estimated between 8-30%, but there is considerable heterogeneity in research design, definitions, measurement tools used and populations. There are some inconclusive findings about the stability of childbirth fear. to assess the prevalence and characteristics of women presenting with scores ≥60 on FOBS-The Fear of Birth Scale, in mid and late pregnancy, and to study change in fear of birth and associated factors. A prospective longitudinal cohort study of a one-year cohort of 1212 pregnant women from a northern part of Sweden, recruited in mid pregnancy and followed up in late pregnancy. Fear of birth was assessed using FOBS-The fear of birth scale, with the cut off at ≥60. The prevalence of fear of birth was 22% in mid pregnancy and 19% in late pregnancy, a statistically significant decrease. Different patterns were found where some women presented with increased fear and some with decreased fear. The women who experienced more fear or less fear later in pregnancy could not be differentiated by background factors. More research is needed to explore factors important to reduce fear of childbirth and the optimal time to measure it. Copyright © 2017 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

Posterior insular cortex is necessary for conditioned inhibition of fear

PubMed Central

Foilb, Allison R.; Flyer-Adams, Johanna G.; Maier, Steven F.; Christianson, John P.

2016-01-01

Veridical detection of safety versus danger is critical to survival. Learned signals for safety inhibit fear, and so when presented, reduce fear responses produced by danger signals. This phenomenon is termed conditioned inhibition of fear. Here, we report that CS+/CS− fear discrimination conditioning over 5 days in rats leads the CS− to become a conditioned inhibitor of fear, as measured by the classic tests of conditioned inhibition: summation and retardation of subsequent fear acquisition. We then show that NMDA-receptor antagonist AP5 injected to posterior insular cortex (IC) before training completely prevented the acquisition of a conditioned fear inhibitor, while intra-AP5 to anterior and medial IC had no effect. To determine if the IC contributes to the recall of learned fear inhibition, injections of the GABAA agonist muscimol were made to posterior IC before a summation test. This resulted in fear inhibition per se, which obscured inference to the effect of IC inactivation with recall of the safety cue. Control experiments sought to determine if the role of the IC in conditioned inhibition learning could be reduced to simpler fear discrimination function, but fear discrimination and recall were unaffected by AP5 or muscmiol, respectively, in the posterior IC. These data implicate a role of posterior IC in the learning of conditioned fear inhibitors. PMID:27523750

From normal fear to pathological anxiety.

PubMed

Rosen, J B; Schulkin, J

1998-04-01

In this article the authors address how pathological anxiety may develop from adaptive fear states. Fear responses (e.g., freezing, startle, heart rate and blood pressure changes, and increased vigilance) are functionally adaptive behavioral and perceptual responses elicited during danger to facilitate appropriate defensive responses that can reduce danger or injury (e.g., escape and avoidance). Fear is a central motive state of action tendencies subserved by fear circuits, with the amygdala playing a central role. Pathological anxiety is conceptualized as an exaggerated fear state in which hyperexcitability of fear circuits that include the amygdala and extended amygdala (i.e., bed nucleus of the stria terminalis) is expressed as hypervigilance and increased behavioral responsivity to fearful stimuli. Reduced thresholds for activation and hyperexcitability in fear circuits develop through sensitization- or kindling-like processes that involve neuropeptides, hormones, and other proteins. Hyperexcitability in fear circuits is expressed as pathological anxiety that is manifested in the various anxiety disorders.

[Relationship between early maladaptive schemas, attachment quality and fear of darkness].

PubMed

Kopcsó, Krisztina; Láng, András

2014-12-07

Although fear of darkness is most common in childhood, it is also a remarkable phenomenon in young adulthood. To examine the relationship between fear of darkness, early maladaptive schemas and attachment quality in young adults and assess fear related sex differences. A self-developed scale was used to measure fear of darkness' intensity and frequency. Young Schema Questionnaire - Short Form and two scales that measure attachment dimensions were also applied. 120 university students (68 women, 52 men) filled in the tests. Fear of darkness' frequency correlated with avoidant attachment, and intensity with independent and anxious attachment. Fear of darkness variables correlated with several early maladaptive schemas. Women reported more frequent and intensive fear of darkness than men. These results indicated that the elevated level of fear of darkness is related to specific cognitive style and attachment quality. This highlights the potential clinical relevance of fear of darkness.

[How to properly use the fear in AIDS intervention-the history and further of fear appeal development].

PubMed

Zhang, Ke; Du, Xiufang; Tao, Xiaorun; Zhang, Yuanyuan; Kang, Dianmin

2015-08-01

The AIDS epidemic in men who have sex wlth men (MSM) in recent years showed a sharp upward trend, looking for behavioral intervention strategies should be imperative. Fear appeals by fear prompted intervention received intervention information, provide a new breakthrough to achieve better effect of propaganda and intervention. After over 70 years development, the Fear Appeal generated from the driver model that proposed the fear decided the effectiveness of behavior intervention, to the extended parallel process model theory which integrated protection motivation theory and parallel process theory, both of which believed the fear is just one of the estimators, suggested fear is the key factor. The fear appeal theory is turning to be even more comprehensive and accurate. As an important theoretical basement, the fear appeal is still developing, and need more work to make it perfection.

Hippocampal Processing of Ambiguity Enhances Fear Memory

PubMed Central

Amadi, Ugwechi; Lim, Seh Hong; Liu, Elizabeth; Baratta, Michael V.; Goosens, Ki Ann

2016-01-01

Despite the ubiquitous use of Pavlovian fear conditioning as a model for fear learning, the highly predictable conditions used in the laboratory do not resemble real-world conditions, where dangerous situations can lead to unpleasant outcomes in unpredictable ways. Here we varied the timing of aversive events following predictive cues in rodents and discovered that temporal ambiguity of aversive events greatly enhances fear. During fear conditioning with unpredictably timed aversive events, pharmacological inactivation of the dorsal hippocampus or optogenetic silencing of CA1 cells during aversive negative prediction errors prevented this enhancement of fear without impacting fear learning for predictable events. Dorsal hippocampal inactivation also prevented ambiguity-related enhancement of fear during auditory fear conditioning under a partial reinforcement schedule. These results reveal that information about the timing and occurrence of aversive events is rapidly acquired and that unexpectedly timed or omitted aversive events generate hippocampal signals to enhance fear learning. PMID:28182526

Gender role orientation and fearfulness in children with anxiety disorders.

PubMed

Ginsburg, G S; Silverman, W K

2000-01-01

Research on gender differences in children's fears has generally shown that girls are more fearful than boys. A common hypothesis offered for this finding is that gender role orientations or expectations may be operating. However, this hypothesis has not been directly investigated in child samples. The present study examined the relation between a self-report measure of gender role orientation (i.e., masculinity/femininity) and the intensity of self-reported fears in a clinic sample of children (N = 66; ages 6-11; 41 boys and 25 girls) with anxiety disorders. Results revealed that masculinity was negatively related to overall levels of fearfulness as well as specific fears of failure and criticism, medical fears, and fears of the unknown. In contrast, no relation was found between femininity and fearfulness. These findings suggest that gender role orientation, especially masculinity, may play a role in the development and/or maintenance of fearfulness in children.

Fear-relevant illusory correlations in different fears and anxiety disorders: A review of the literature.

PubMed

Wiemer, Julian; Pauli, Paul

2016-08-01

Fearful individuals often overestimate the relationship between fear-relevant stimuli and aversive consequences. Such fear-relevant illusory correlations (ICs) might be involved in the maintenance of anxiety disorders. In this literature review, we found clear evidence that ICs are present and enhanced in fear of animals. We also revealed some evidence for ICs related to fear of flying, social anxiety, contamination fear, panic disorder, and post-traumatic stress disorder, but with considerably less clarity. Fear-relevant ICs seem to be best explained by both a priori expectancies and biased encoding of the experienced associations. Studies to date suggest that one important biased encoding process is the enhanced aversiveness/salience of fear-relevant outcomes. Future studies may improve insight by developing more reliable IC measures and testing the effect of encoding processes on treatment outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Toddlers’ dysregulated fear predicts delta-beta coupling during preschool

PubMed Central

Phelps, Randi A.; Brooker, Rebecca J.; Buss, Kristin A.

2015-01-01

Dysregulated fear, or the persistence of high levels of fear in low-threat contexts, is an early risk factor for the development of anxiety symptoms. Previous work has suggested both propensities for over-control and under-control of fearfulness as risk factors for anxiety problems, each of which may be relevant to observations of dysregulated fear. Given difficulty disentangling over-control and under-control through traditional behavioral measures, we used delta-beta coupling to begin to understand the degree to which dysregulated fear may reflect propensities for over- or under-control. We found that toddlers who showed high levels of dysregulated fear evidenced greater delta-beta coupling at frontal and central electrode sites as preschoolers relative to children who were low in dysregulated fear. Importantly, these differences were not observed when comparisons were made based on fear levels in high threat contexts. Results suggest dysregulated fear may involve tendencies toward over-control at the neural level. PMID:26624221

Hippocampal Processing of Ambiguity Enhances Fear Memory.

PubMed

Amadi, Ugwechi; Lim, Seh Hong; Liu, Elizabeth; Baratta, Michael V; Goosens, Ki A

2017-02-01

Despite the ubiquitous use of Pavlovian fear conditioning as a model for fear learning, the highly predictable conditions used in the laboratory do not resemble real-world conditions, in which dangerous situations can lead to unpleasant outcomes in unpredictable ways. In the current experiments, we varied the timing of aversive events after predictive cues in rodents and discovered that temporal ambiguity of aversive events greatly enhances fear. During fear conditioning with unpredictably timed aversive events, pharmacological inactivation of the dorsal hippocampus or optogenetic silencing of cornu ammonis 1 cells during aversive negative prediction errors prevented this enhancement of fear without affecting fear learning for predictable events. Dorsal hippocampal inactivation also prevented ambiguity-related enhancement of fear during auditory fear conditioning under a partial-reinforcement schedule. These results reveal that information about the timing and occurrence of aversive events is rapidly acquired and that unexpectedly timed or omitted aversive events generate hippocampal signals to enhance fear learning.

Implications of memory modulation for post-traumatic stress and fear disorders

PubMed Central

Parsons, Ryan G; Ressler, Kerry J

2013-01-01

Post-traumatic stress disorder, panic disorder and phobia manifest in ways that are consistent with an uncontrollable state of fear. Their development involves heredity, previous sensitizing experiences, association of aversive events with previous neutral stimuli, and inability to inhibit or extinguish fear after it is chronic and disabling. We highlight recent progress in fear learning and memory, differential susceptibility to disorders of fear, and how these findings are being applied to the understanding, treatment and possible prevention of fear disorders. Promising advances are being translated from basic science to the clinic, including approaches to distinguish risk versus resilience before trauma exposure, methods to interfere with fear development during memory consolidation after a trauma, and techniques to inhibit fear reconsolidation and to enhance extinction of chronic fear. It is hoped that this new knowledge will translate to more successful, neuroscientifically informed and rationally designed approaches to disorders of fear regulation. PMID:23354388

Instructed fear learning, extinction, and recall: additive effects of cognitive information on emotional learning of fear.

PubMed

Javanbakht, Arash; Duval, Elizabeth R; Cisneros, Maria E; Taylor, Stephan F; Kessler, Daniel; Liberzon, Israel

2017-08-01

The effects of instruction on learning of fear and safety are rarely studied. We aimed to examine the effects of cognitive information and experience on fear learning. Fourty healthy participants, randomly assigned to three groups, went through fear conditioning, extinction learning, and extinction recall with two conditioned stimuli (CS+). Information was presented about the presence or absence of conditioned stimulus-unconditioned stimulus (CS-US) contingency at different stages of the experiment. Information about the CS-US contingency prior to fear conditioning enhanced fear response and reduced extinction recall. Information about the absence of CS-US contingency promoted extinction learning and recall, while omission of this information prior to recall resulted in fear renewal. These findings indicate that contingency information can facilitate fear expression during fear learning, and can facilitate extinction learning and recall. Information seems to function as an element of the larger context in which conditioning occurs.

Oxytocin and Social Support as Synergistic Inhibitors of Aversive Fear Conditioning and Fear-Potentiated Startle in Male Rats

DTIC Science & Technology

2009-09-01

startle amplitude. They then received Pavlovian fear conditioning of five pairings of a 3 s light co-terminating with a 500 ms, 0.6mA footshock. Four...Synergistic Inhibitors of Aversive Fear Conditioning and Fear-Potentiated Startle in Male Rats PRINCIPAL INVESTIGATOR: Jeffrey B. Rosen, Ph.D...NUMBER Oxytocin and Social Support as Synergistic Inhibitors of Aversive Fear Conditioning and Fear-Potentiated Startle in Male Rats 5b. GRANT

National Computer Security Conference (15th) held in Baltimore, Maryland on October 13-16, 1992. Volume 2: Proceedings

DTIC Science & Technology

1992-10-16

the DNA Fingerprint Laboratory. The Los Angeles Police Department and its former Chief, Daryl Gates for permitting a secret unit, the ...authorized to change information in. Conclusions Where angels fear .... Of all the reasons for compartmentation for which the level of evaluation...database, and a security label attribute is associated with data in each tuple in a relation. The range and distribution of security levels may

Early Social Fear Predicts Kindergarteners' Socially Anxious Behaviors: Direct Associations, Moderation by Inhibitory Control, and Differences from Nonsocial Fear

PubMed Central

Brooker, Rebecca J.; Kiel, Elizabeth J.; Buss, Kristin A.

2015-01-01

Although social and nonsocial fear are discernable as early as preschool, little is known about their distinct associations with developmental outcomes. For example, fear has been identified as a predictor of social anxiety problems, but no work has examined whether social and nonsocial fear make independent contributions to risk. We investigated the extent to which early social and non-social fear were associated with socially anxious behaviors during kindergarten. To do this, we identified distinct trajectories of social and nonsocial fear across toddlerhood and preschool. Only social fear was associated with socially anxious behaviors at ages 2 and 5. Because the ability to regulate fear contributes to the degree to which fearful children are at risk for anxiety problems, we also tested whether an early-developing aspect of self-regulation modulated associations between early fear and kindergarten socially anxious behaviors. Specifically, we tested whether inhibitory control differentially modulated associations between early levels of social and nonsocial fear and socially anxious behaviors during kindergarten. Associations between trajectories of early social fear and age 5 socially anxious behaviors were moderated by individual differences in inhibitory control. Consistent with previous research showing associations between overcontrol and anxiety symptoms, more negative outcomes were observed when stable, high levels of social fear across childhood were coupled with high levels of inhibitory control. Results suggest that the combination of social fear and overcontrol reflect a profile of early risk for the development of social inhibition and social anxiety problems. PMID:27213729

Fear-avoidance beliefs and parental responses to pain in adolescents with chronic pain.

PubMed

Wilson, Anna C; Lewandowski, Amy S; Palermo, Tonya M

2011-01-01

The fear-avoidance model of chronic pain posits that fear of pain is associated with fear and avoidance of activity, which can lead to deconditioning and persistence of pain and disability. Despite being well supported in adults, little is known about the role of fear-avoidance beliefs regarding physical activity in children. Research has shown that parental protectiveness contributes to activity limitations in children; however, no studies have examined relationships between protectiveness, and fear and avoidance. To conduct a cross-sectional study to provide additional information regarding the reliability and validity of the Fear-Avoidance Beliefs Questionnaire physical activity subscale among adolescents with chronic pain; examine fear-avoidance beliefs and depressive symptoms as concurrent predictors of physical activity limitations; and test competing models using fear-avoidance beliefs as mediators and moderators of the association between parental protectiveness and activity limitations. Adolescents (n=42) 11 to 17 years of age with chronic pain completed questionnaires assessing pain intensity, fear-avoidance beliefs, depressive symptoms and physical activity limitations. Their parents completed questionnaires regarding protectiveness and adolescent activity limitations. The Fear-Avoidance Beliefs Questionnaire physical activity subscale was useful for assessing fear-avoidance beliefs in the present population. In support of hypotheses, greater fear-avoidance beliefs were associated with greater activity limitations, above pain intensity and depressive symptoms. Support was found for fear-avoidance beliefs as mediators of the association between parental protectiveness and activity limitations. Tests of moderation were not significant. Fear-avoidance beliefs may be an important target for interventions focused on decreasing activity limitations in youth with chronic pain. Future research should investigate these associations longitudinally.

Amygdala upregulation of NCAM polysialylation induced by auditory fear conditioning is not required for memory formation, but plays a role in fear extinction.

PubMed

Markram, Kamila; Lopez Fernandez, Miguel Angel; Abrous, Djoher Nora; Sandi, Carmen

2007-05-01

There is much interest to understand the mechanisms leading to the establishment, maintenance, and extinction of fear memories. The amygdala has been critically involved in the processing of fear memories and a number of molecular changes have been implicated in this brain region in relation to fear learning. Although neural cell adhesion molecules (NCAMs) have been hypothesized to play a role, information available about their contribution to fear memories is scarce. We investigate here whether polysialylated NCAM (PSA-NCAM) contributes to auditory fear conditioning in the amygdala. First, PSA-NCAM expression was evaluated in different amygdala nuclei after auditory fear conditioning at two different shock intensities. Results showed that PSA-NCAM expression was increased 24 h post-training only in animals subjected to the highest shock intensity (1mA). Second, PSA-NCAM was cleaved in the basolateral amygdaloid complex through micro-infusions of the enzyme endoneuraminidase N, and the consequences of such treatment were investigated on the acquisition, consolidation, remote memory expression, and extinction of conditioned fear memories. Intra-amygdaloid cleavage of PSA-NCAM did not affect acquisition, consolidation or expression of remote fear memories. However, intra-amygdaloid PSA-NCAM cleavage enhanced fear extinction processes. These results suggest that upregulation of PSA-NCAM is a correlate of fear conditioning that is not necessary for the establishment of fear memory in the amygdala, but participates in mechanisms precluding fear extinction. These findings point out PSA-NCAM as a potential target for the treatment of psychopathologies that involve impairment in fear extinction.

NPY controls fear conditioning and fear extinction by combined action on Y₁ and Y₂ receptors.

PubMed

Verma, D; Tasan, R O; Herzog, H; Sperk, G

2012-06-01

Neuropeptide Y (NPY) and its receptors have been implicated in the control of emotional-affective processing, but the mechanism is unclear. While it is increasingly evident that stimulation of Y₁ and inhibition of Y₂ receptors produce prominent anxiolytic and antidepressant effects, the contribution of the individual NPY receptor subtypes in the acquisition and extinction of learned fear are unknown. Here we performed Pavlovian fear conditioning and extinction in NPY knockout (KO) and in NPY receptor KO mice. NPY KO mice display a dramatically accelerated acquisition of conditioned fear. Deletion of Y₁ receptors revealed only a moderately accelerated acquisition of conditioned fear, while lack of Y₂ receptors was without any effect on fear learning. However, the strong phenotype seen in NPY KO mice was reproduced in mice lacking both Y₁ and Y₂ receptors. In addition, NPY KO mice showed excessive recall of conditioned fear and impaired fear extinction. This behaviour was replicated only after deletion of both Y₁ and Y₂ receptors. In Y₁ receptor single KO mice, fear extinction was delayed and was unchanged in Y₂ receptor KO mice. Deletion of NPY and particularly Y₂ receptors resulted in a generalization of conditioned fear. Our data demonstrate that NPY delays the acquisition, reduces the expression of conditioned fear while promoting fear extinction. Although these effects appear to be primarily mediated by Y₁ receptors, the pronounced phenotype of Y₁Y₂ receptor double KO mice suggests a synergistic role of Y₂ receptors in fear acquisition and in fear extinction. © 2012 The Authors. British Journal of Pharmacology © 2012 The British Pharmacological Society.

Compensated Crystal Assemblies for Type-II Entangled Photon Generation in Quantum Cluster States

DTIC Science & Technology

2010-03-01

in quantum computational architectures that operate by principles entirely distinct from any based on classical physics. In contrast with other...of the SPDC spectral function, to enable applications in regions that have not been accessible with other methods. Quantum Information and Computation ...Eliminating frequency and space-time correlations in multi-photon states, PRA 64, 063815, 2001 [2]A. Zeilinger et.al. Experimental One-way computing

Investigation, Development, and Evaluation of Performance Proving for Fault-tolerant Computers

NASA Technical Reports Server (NTRS)

Levitt, K. N.; Schwartz, R.; Hare, D.; Moore, J. S.; Melliar-Smith, P. M.; Shostak, R. E.; Boyer, R. S.; Green, M. W.; Elliott, W. D.

1983-01-01

A number of methodologies for verifying systems and computer based tools that assist users in verifying their systems were developed. These tools were applied to verify in part the SIFT ultrareliable aircraft computer. Topics covered included: STP theorem prover; design verification of SIFT; high level language code verification; assembly language level verification; numerical algorithm verification; verification of flight control programs; and verification of hardware logic.

Surface Modification Engineered Assembly of Novel Quantum Dot Architectures for Advanced Applications

DTIC Science & Technology

2008-02-09

Campbell, S. Ogata, and F. Shimojo, “ Multimillion atom simulations of nanosystems on parallel computers,” in Proceedings of the International...nanomesas: multimillion -atom molecular dynamics simulations on parallel computers,” J. Appl. Phys. 94, 6762 (2003). 21. P. Vashishta, R. K. Kalia...and A. Nakano, “ Multimillion atom molecular dynamics simulations of nanoparticles on parallel computers,” Journal of Nanoparticle Research 5, 119-135

75 FR 54770 - Drawbridge Operation Regulations; Cape Fear River and Northeast Cape Fear River, in Wilmington, NC

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-09

... Regulations; Cape Fear River and Northeast Cape Fear River, in Wilmington, NC AGENCY: Coast Guard, DHS. ACTION..., mile 26.8, and the Isabel S. Holmes Bridge, across Northeast Cape Fear River, mile 1.0, both in... Isabel S. Holmes Bridge, across Northeast Cape Fear River, mile 1.0, a bascule lift bridge, has a...

76 FR 39298 - Drawbridge Operation Regulation; Cape Fear River, and Northeast Cape Fear River, in Wilmington, NC

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-06

... Operation Regulation; Cape Fear River, and Northeast Cape Fear River, in Wilmington, NC AGENCY: Coast Guard... Northeast Cape Fear River, at mile 1.0, both in Wilmington, NC. The deviation restricts the operation of the... across Northeast Cape Fear River, at mile 1.0, both in Wilmington, NC, requested a temporary deviation...

A meta-analysis of fear appeals: implications for effective public health campaigns.

PubMed

Witte, K; Allen, M

2000-10-01

The fear appeal literature is examined in a comprehensive synthesis using meta-analytical techniques. The meta-analysis suggests that strong fear appeals produce high levels of perceived severity and susceptibility, and are more persuasive than low or weak fear appeals. The results also indicate that fear appeals motivate adaptive danger control actions such as message acceptance and maladaptive fear control actions such as defensive avoidance or reactance. It appears that strong fear appeals and high-efficacy messages produce the greatest behavior change, whereas strong fear appeals with low-efficacy messages produce the greatest levels of defensive responses. Future directions and practical implications are provided.

Young and old Pavlovian fear memories can be modified with extinction training during reconsolidation in humans

PubMed Central

Steinfurth, Elisa C.K.; Kanen, Jonathan W.; Raio, Candace M.; Clem, Roger L.; Huganir, Richard L.; Phelps, Elizabeth A.

2014-01-01

Extinction training during reconsolidation has been shown to persistently diminish conditioned fear responses across species. We investigated in humans if older fear memories can benefit similarly. Using a Pavlovian fear conditioning paradigm we compared standard extinction and extinction after memory reactivation 1 d or 7 d following acquisition. Participants who underwent extinction during reconsolidation showed no evidence of fear recovery, whereas fear responses returned in participants who underwent standard extinction. We observed this effect in young and old fear memories. Extending the beneficial use of reconsolidation to older fear memories in humans is promising for therapeutic applications. PMID:24934333

Dental Fear among Medical and Dental Undergraduates

PubMed Central

Hakim, H.; Razak, I. A.

2014-01-01

Objective. To assess the prevalence and level of dental fear among health related undergraduates and to identify factors causing such fear using Kleinknecht's Dental Fear Survey (DFS) questionnaire. Methods. Kleinknecht's DFS questionnaire was used to assess dental fear and anxiety among the entire enrollment of the medical and dental undergraduates' of the University of Malaya. Results. Overall response rate was 82.2%. Dental students reported higher prevalence of dental fear (96.0% versus 90.4%). However, most of the fear encountered among dental students was in the low fear category as compared to their medical counterpart (69.2 versus 51.2%). Significantly more medical students cancelled dental appointment due to fear compared to dental students (P = 0.004). “Heart beats faster” and “muscle being tensed” were the top two physiological responses experienced by the respondents. “Drill” and “anesthetic needle” were the most fear provoking objects among respondents of both faculties. Conclusion. Dental fear and anxiety are a common problem encountered among medical and dental undergraduates who represent future health care professionals. Also, high level of dental fear and anxiety leads to the avoidance of the dental services. PMID:25386615

Enabling Graph Appliance for Genome Assembly

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

Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun

2015-01-01

In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to storemore » and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.« less

Does fear extinction in the laboratory predict outcomes of exposure therapy? A treatment analog study.

PubMed

Forcadell, Eduard; Torrents-Rodas, David; Vervliet, Bram; Leiva, David; Tortella-Feliu, Miquel; Fullana, Miquel A

2017-11-01

Fear extinction models have a key role in our understanding of anxiety disorders and their treatment with exposure therapy. Here, we tested whether individual differences in fear extinction learning and fear extinction recall in the laboratory were associated with the outcomes of an exposure therapy analog (ETA). Fifty adults with fear of spiders participated in a two-day fear-learning paradigm assessing fear extinction learning and fear extinction recall, and then underwent a brief ETA. Correlational analyses indicated that enhanced extinction learning was associated with better ETA outcome. Our results partially support the idea that individual differences in fear extinction learning may be associated with exposure therapy outcome, but suggest that further research in this area is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

A User Modelling Approach for Computer-Based Critiquing

DTIC Science & Technology

1990-01-01

example a CAD/CAM system). Com- puters are good for simulating in circumstances where training on the actual equip- 13 ment (for example a power plant or...system. It is an environment in which simulated devices, such as steam plant controllers, can be assembled and operated. Students can assemble a...Con- cordia hypermedia system, graphics can be integrated easily. Concordia is a hy- permedia development and presentation system available on the

Atomistic Design and Simulations of Nanoscale Machines and Assembly

NASA Technical Reports Server (NTRS)

Goddard, William A., III; Cagin, Tahir; Walch, Stephen P.

2000-01-01

Over the three years of this project, we made significant progress on critical theoretical and computational issues in nanoscale science and technology, particularly in:(1) Fullerenes and nanotubes, (2) Characterization of surfaces of diamond and silicon for NEMS applications, (3) Nanoscale machine and assemblies, (4) Organic nanostructures and dendrimers, (5) Nanoscale confinement and nanotribology, (6) Dynamic response of nanoscale structures nanowires (metals, tubes, fullerenes), (7) Thermal transport in nanostructures.

Dynamic self-assembly and self-organized transport of magnetic micro-swimmers

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

Kokot, Gasper; Kolmakov, German V.; Aranson, Igor S.

We demonstrate experimentally and in computer simulations that magnetic microfloaters can self-organize into various functional structures while energized by an external alternating (ac) magnetic field. The structures exhibit self-propelled motion and an ability to carry a cargo along a pre-defined path. As a result, the morphology of the self-assembled swimmers is controlled by the frequency and amplitude of the magnetic field.

Dynamic self-assembly and self-organized transport of magnetic micro-swimmers

DOE PAGES

Kokot, Gasper; Kolmakov, German V.; Aranson, Igor S.; ...

2017-11-07

We demonstrate experimentally and in computer simulations that magnetic microfloaters can self-organize into various functional structures while energized by an external alternating (ac) magnetic field. The structures exhibit self-propelled motion and an ability to carry a cargo along a pre-defined path. As a result, the morphology of the self-assembled swimmers is controlled by the frequency and amplitude of the magnetic field.

Advanced Extravehicular Mobility Unit Informatics Software Design

NASA Technical Reports Server (NTRS)

Wright, Theodore

2014-01-01

This is a description of the software design for the 2013 edition of the Advanced Extravehicular Mobility Unit (AEMU) Informatics computer assembly. The Informatics system is an optional part of the space suit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and caution and warning information. In the future it will display maps with GPS position data, and video and still images captured by the astronaut.

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

PubMed Central

Polles, Guido; Indelicato, Giuliana; Potestio, Raffaello; Cermelli, Paolo; Twarock, Reidun; Micheletti, Cristian

2013-01-01

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available. PMID:24244139

SvABA: genome-wide detection of structural variants and indels by local assembly.

PubMed

Wala, Jeremiah A; Bandopadhayay, Pratiti; Greenwald, Noah F; O'Rourke, Ryan; Sharpe, Ted; Stewart, Chip; Schumacher, Steve; Li, Yilong; Weischenfeldt, Joachim; Yao, Xiaotong; Nusbaum, Chad; Campbell, Peter; Getz, Gad; Meyerson, Matthew; Zhang, Cheng-Zhong; Imielinski, Marcin; Beroukhim, Rameen

2018-04-01

Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA's performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs and substantially improves detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (<1000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types and found that short templated-sequence insertions occur in ∼4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized (50-300 bp) SVs. © 2018 Wala et al.; Published by Cold Spring Harbor Laboratory Press.

Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters

PubMed Central

Singharoy, Abhishek; Sereda, Yuriy

2012-01-01

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure. PMID:22661911

Origins of common fears in South African children.

PubMed

Muris, Peter; du Plessis, Michelle; Loxton, Helene

2008-12-01

The present study examined the origins of common childhood fears within a South African context. Six-hundred-and-fifty-five 10- to 14-year-old children were given a brief fear list that helped them to identify their most intense fear and then completed a brief questionnaire for assessing the origins of fears that was based on Rachman's [Rachman, S. (1977). The conditioning theory of fear acquisition: A critical examination. Behaviour Research and Therapy, 15, 375-387; Rachman, S. (1991). Neoconditioning and the classical theory of fear acquisition. Clinical Psychology Review, 17, 47-67] three-pathways theory. More precisely, children were asked to report whether they had experienced conditioning, modeling, and negative information experiences in relation to their most feared stimulus or situation, and also had to indicate to what extent such experiences had actually played a role in the onset and/or intensification of their fears. Results showed that children most frequently reported indirect learning experiences (i.e., modeling and negative information) in relation to their fears, whereas conditioning was clearly less often mentioned. The majority of the children had no precise idea of how their fear had actually begun, but a substantial proportion of them reported various learning experiences in relation to the onset and intensification of fears. Significant cultural differences were not only observed in the prevalence of common fears, but also in the pathways reported for the origins of fears. The results are briefly discussed in terms of the living conditions of South African children from various cultural backgrounds.

A twin study of the genetics of fear conditioning.

PubMed

Hettema, John M; Annas, Peter; Neale, Michael C; Kendler, Kenneth S; Fredrikson, Mats

2003-07-01

Fear conditioning is a traditional model for the acquisition of fears and phobias. Studies of the genetic architecture of fear conditioning may inform gene-finding strategies for anxiety disorders. The objective of this study was to determine the genetic and environmental sources of individual differences in fear conditioning by means of a twin sample. Classic fear conditioning data were experimentally obtained from 173 same-sex twin pairs (90 monozygotic and 83 dizygotic). Sequences of evolutionary fear-relevant (snakes and spiders) and fear-irrelevant (circles and triangles) pictorial stimuli served as conditioned stimuli paired with a mild electric shock serving as the unconditioned stimulus. The outcome measure was the electrodermal skin conductance response. We applied structural equation modeling methods to the 3 conditioning phases of habituation, acquisition, and extinction to determine the extent to which genetic and environmental factors underlie individual variation in associative and nonassociative learning. All components of the fear conditioning process in humans demonstrated moderate heritability, in the range of 35% to 45%. Best-fitting multivariate models suggest that 2 sets of genes may underlie the trait of fear conditioning: one that most strongly affects nonassociative processes of habituation that also is shared with acquisition and extinction, and a second that appears related to associative fear conditioning processes. In addition, these data provide tentative evidence of differences in heritability based on the fear relevance of the stimuli. Genes represent a significant source of individual variation in the habituation, acquisition, and extinction of fears, and genetic effects specific to fear conditioning are involved.

Glucocorticoids reduce phobic fear in humans

PubMed Central

Soravia, Leila M.; Heinrichs, Markus; Aerni, Amanda; Maroni, Caroline; Schelling, Gustav; Ehlert, Ulrike; Roozendaal, Benno; de Quervain, Dominique J.-F.

2006-01-01

Phobias are characterized by excessive fear, cued by the presence or anticipation of a fearful situation. Whereas it is well established that glucocorticoids are released in fearful situations, it is not known whether these hormones, in turn, modulate perceived fear. As extensive evidence indicates that elevated glucocorticoid levels impair the retrieval of emotionally arousing information, they might also inhibit retrieval of fear memory associated with phobia and, thereby, reduce phobic fear. Here, we investigated whether acutely administrated glucocorticoids reduced phobic fear in two double-blind, placebo-controlled studies in 40 subjects with social phobia and 20 subjects with spider phobia. In the social phobia study, cortisone (25 mg) administered orally 1 h before a socio-evaluative stressor significantly reduced self-reported fear during the anticipation, exposure, and recovery phase of the stressor. Moreover, the stress-induced release of cortisol in placebo-treated subjects correlated negatively with fear ratings, suggesting that endogenously released cortisol in the context of a phobic situation buffers fear symptoms. In the spider phobia study, repeated oral administration of cortisol (10 mg), but not placebo, 1 h before exposure to a spider photograph induced a progressive reduction of stimulus-induced fear. This effect was maintained when subjects were exposed to the stimulus again 2 days after the last cortisol administration, suggesting that cortisol may also have facilitated the extinction of phobic fear. Cortisol treatment did not reduce general, phobia-unrelated anxiety. In conclusion, the present findings in two distinct types of phobias indicate that glucocorticoid administration reduces phobic fear. PMID:16567641

A reinforcement learning model of joy, distress, hope and fear

NASA Astrophysics Data System (ADS)

Broekens, Joost; Jacobs, Elmer; Jonker, Catholijn M.

2015-07-01

In this paper we computationally study the relation between adaptive behaviour and emotion. Using the reinforcement learning framework, we propose that learned state utility, ?, models fear (negative) and hope (positive) based on the fact that both signals are about anticipation of loss or gain. Further, we propose that joy/distress is a signal similar to the error signal. We present agent-based simulation experiments that show that this model replicates psychological and behavioural dynamics of emotion. This work distinguishes itself by assessing the dynamics of emotion in an adaptive agent framework - coupling it to the literature on habituation, development, extinction and hope theory. Our results support the idea that the function of emotion is to provide a complex feedback signal for an organism to adapt its behaviour. Our work is relevant for understanding the relation between emotion and adaptation in animals, as well as for human-robot interaction, in particular how emotional signals can be used to communicate between adaptive agents and humans.

Cruel to Be Kind: Factors Underlying Altruistic Efforts to Worsen Another Person's Mood.

PubMed

López-Pérez, Belén; Howells, Laura; Gummerum, Michaela

2017-07-01

When aiming to improve another person's long-term well-being, people may choose to induce a negative emotion in that person in the short term. We labeled this form of agent-target interpersonal emotion regulation altruistic affect worsening and hypothesized that it may happen when three conditions are met: (a) The agent experiences empathic concern for the target of the affect-worsening process, (b) the negative emotion to be induced helps the target achieve a goal (e.g., anger for confrontation or fear for avoidance), and (c) there is no benefit for the agent. This hypothesis was tested by manipulating perspective-taking instructions and the goal to be achieved while participants ( N = 140) played a computer-based video game. Participants following other-oriented perspective-taking instructions, compared with those following objective perspective-taking instructions, decided to induce more anger in a supposed fellow participant who was working to achieve a confrontation goal and to induce more fear in a supposed fellow participant who was working to achieve an avoidance goal.

Inexpensive Miniature Programmable Magnetic Stirrer from Reconfigured Computer Parts

ERIC Educational Resources Information Center

Mercer, Conan; Leech, Donal

2017-01-01

This technology report outlines a robust and easy to assemble magnetic stirrer that is programmable. All of the parts are recycled from obsolete computer hardware except the Arduino microcontroller and motor driver, at a total cost of around $40. This multidisciplinary approach introduces microcontrollers to students and grants the opportunity to…

USSR Report, Cybernetics, Computers and Automation Technology

DTIC Science & Technology

1987-03-31

version of the system was tested by adapting PAL-11 and MACRO-11 assembly code for the "Elektronika=60" and "Elektronika-60M" computers; ASM -86 for the...GS, "On the Results of Evaluation of Insurance Payments in Collective and State Farms and Private Households," the actuarial analysis tables based

Inhibition of Rac1 activity in the hippocampus impaired extinction of contextual fear.

PubMed

Jiang, Lizhu; Mao, Rongrong; Tong, Jianbin; Li, Jinnan; Chai, Anping; Zhou, Qixin; Yang, Yuexiong; Wang, Liping; Li, Lingjiang; Xu, Lin

2016-10-01

Promoting extinction of fear memory is the main treatment of fear disorders, especially post-traumatic stress disorder (PTSD). However, fear extinction is often incomplete in these patients. Our previous study had shown that Rac1 activity in hippocampus plays a crucial role in the learning of contextual fear memory in rats. Here, we further investigated whether Rac1 activity also modulated the extinction of contextual fear memory. We found that massed extinction obviously upregulated hippocampal Rac1 activity and induced long-term extinction of contextual fear in rats. Intrahippocampal injection of the Rac1 inhibitor NSC23766 prevents extinction of contextual fear in massed extinction training rats. In contrast, long-spaced extinction downregulated Rac1 activity and caused less extinction. And Rac1 activator CN04-A promotes extinction of contextual fear in long-spaced extinction rats. Our study demonstrates that inhibition of Rac1 activity in the hippocampus impaired extinction of contextual fear, suggesting that modulating Rac1 activity of the hippocampus may be promising therapy of fear disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contextual and Auditory Fear Conditioning Continue to Emerge during the Periweaning Period in Rats

PubMed Central

Burman, Michael A.; Erickson, Kristen J.; Deal, Alex L.; Jacobson, Rose E.

2014-01-01

Anxiety disorders often emerge during childhood. Rodent models using classical fear conditioning have shown that different types of fear depend upon different neural structures and may emerge at different stages of development. For example, some work has suggested that contextual fear conditioning generally emerges later in development (postnatal day 23–24) than explicitly cued fear conditioning (postnatal day 15–17) in rats. This has been attributed to an inability of younger subjects to form a representation of the context due to an immature hippocampus. However, evidence that contextual fear can be observed in postnatal day 17 subjects and that cued fear conditioning continues to emerge past this age raises questions about the nature of this deficit. The current studies examine this question using both the context pre-exposure facilitation effect for immediate single-shock contextual fear conditioning and traditional cued fear conditioning using Sprague-Dawley rats. The data suggest that both cued and contextual fear conditioning are continuing to develop between PD 17 and 24, consistent with development occurring the in essential fear conditioning circuit. PMID:24977415

The fears, phobias and anxieties of children with autism spectrum disorders and Down syndrome: comparisons with developmentally and chronologically age matched children.

PubMed

Evans, David W; Canavera, Kristin; Kleinpeter, F Lee; Maccubbin, Elise; Taga, Ken

2005-01-01

This study compared the fears and behavior problems of 25 children with an autism spectrum disorder (ASD), 43 children with Down syndrome (DS), 45 mental age (MA) matched children, and 37 chronologically age (CA) matched children. Children's fears, phobias, anxieties and behavioral problems were assessed using parent reports. Significant differences emerged across the diagnostic groups on a variety of fears. Children with ASD were reported to have more situation phobias and medical fears, but fewer fears of harm/injury compared to all other groups. The groups also differed in terms of the pattern of correlations between fears, phobias, anxieties and behavior problems. For children with ASD, fears, phobias and anxieties were closely related to problem behaviors, whereas fears, phobias, and anxieties were less related to behavioral symptoms for the other groups of subjects. Such findings suggest that children with ASD exhibit a distinct profile of fear and anxiety compared to other mental age and chronologically age-matched children, and these fears are related to the symptoms associated with ASD.

Comparing de novo assemblers for 454 transcriptome data

PubMed Central

2010-01-01

Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended. PMID:20950480

Benchmarking undedicated cloud computing providers for analysis of genomic datasets.

PubMed

Yazar, Seyhan; Gooden, George E C; Mackey, David A; Hewitt, Alex W

2014-01-01

A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coli CC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95% CI: 27.5-78.2) for E.coli and 53.5% (95% CI: 34.4-72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95% CI: 211.5-303.1) and 173.9% (95% CI: 134.6-213.1) more expensive for E.coli and human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE.

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets

PubMed Central

Yazar, Seyhan; Gooden, George E. C.; Mackey, David A.; Hewitt, Alex W.

2014-01-01

A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coli CC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95% CI: 27.5–78.2) for E.coli and 53.5% (95% CI: 34.4–72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95% CI: 211.5–303.1) and 173.9% (95% CI: 134.6–213.1) more expensive for E.coli and human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE. PMID:25247298

Acute Exercise Enhances the Consolidation of Fear Extinction Memory and Reduces Conditioned Fear Relapse in a Sex-Dependent Manner

ERIC Educational Resources Information Center

Bouchet, Courtney A.; Lloyd, Brian A.; Loetz, Esteban C.; Farmer, Caroline E.; Ostrovskyy, Mykola; Haddad, Natalie; Foright, Rebecca M.; Greenwood, Benjamin N.

2017-01-01

Fear extinction-based exposure therapy is the most common behavioral therapy for anxiety and trauma-related disorders, but fear extinction memories are labile and fear tends to return even after successful extinction. The relapse of fear contributes to the poor long-term efficacy of exposure therapy. A single session of voluntary exercise can…

A Latent Growth Examination of Fear Development in Infancy: Contributions of Maternal Depression and the Risk for Toddler Anxiety

ERIC Educational Resources Information Center

Gartstein, Maria A.; Bridgett, David J.; Rothbart, Mary K.; Robertson, Christopher; Iddins, Erin; Ramsay, Kristin; Schlect, Sarah

2010-01-01

Growth modeling was used to examine the developmental trajectory of infant temperamental fear with maternal fear and depressive symptoms as predictors of infant fearfulness and change in infant fear predicting toddler anxiety symptoms. In Study 1, a sample of 158 mothers reported their own depressive symptoms and fear when their children were 4…

Maternal Modeling and the Acquisition of Fear and Avoidance in Toddlers: Influence of Stimulus Preparedness and Child Temperament

ERIC Educational Resources Information Center

Dubi, Kathrin; Rapee, Ronald M.; Emerton, Jane L.; Schniering, Carolyn A.

2008-01-01

The aim of the present study was to investigate the influence of maternal modeling on the acquisition of fear and avoidance towards fear-relevant and fear-irrelevant, novel stimuli in a sample of 71 toddlers. Children were shown a rubber snake or spider (fear-relevant objects) and a rubber mushroom or flower (fear-irrelevant objects), which were…

Differences in the Fears of Elementary School Children in North and South America: A Cross-Cultural Comparison

ERIC Educational Resources Information Center

Burnham, Joy J.; Hooper, Lisa M.; Ogorchock, Heather N.

2011-01-01

This study compared the fears of North American and South American children in Grades 2-5. Fears were assessed with English and Spanish versions of the American Fear Survey Schedule (FSSC-AM; Burnham 2005). Specific fears and several most common fears differed across the two countries. Overall, the South American children and the girls from both…

Remembering the object you fear: brain potentials during recognition of spiders in spider-fearful individuals.

PubMed

Michalowski, Jaroslaw M; Weymar, Mathias; Hamm, Alfons O

2014-01-01

In the present study we investigated long-term memory for unpleasant, neutral and spider pictures in 15 spider-fearful and 15 non-fearful control individuals using behavioral and electrophysiological measures. During the initial (incidental) encoding, pictures were passively viewed in three separate blocks and were subsequently rated for valence and arousal. A recognition memory task was performed one week later in which old and new unpleasant, neutral and spider pictures were presented. Replicating previous results, we found enhanced memory performance and higher confidence ratings for unpleasant when compared to neutral materials in both animal fearful individuals and controls. When compared to controls high animal fearful individuals also showed a tendency towards better memory accuracy and significantly higher confidence during recognition of spider pictures, suggesting that memory of objects prompting specific fear is also facilitated in fearful individuals. In line, spider-fearful but not control participants responded with larger ERP positivity for correctly recognized old when compared to correctly rejected new spider pictures, thus showing the same effects in the neural signature of emotional memory for feared objects that were already discovered for other emotional materials. The increased fear memory for phobic materials observed in the present study in spider-fearful individuals might result in an enhanced fear response and reinforce negative beliefs aggravating anxiety symptomatology and hindering recovery.

Effects of chemogenetic excitation or inhibition of the ventrolateral periaqueductal gray on the acquisition and extinction of Pavlovian fear conditioning.

PubMed

Arico, Carolyn; Bagley, Elena E; Carrive, Pascal; Assareh, Neda; McNally, Gavan P

2017-10-01

The midbrain periaqueductal gray (PAG) has been implicated in the generation and transmission of a prediction error signal that instructs amygdala-based fear and extinction learning. However, the PAG also plays a key role in the expression of conditioned fear responses. The evidence for a role of the PAG in fear learning and extinction learning has been obtained almost exclusively using PAG-dependent fear responses. It is less clear whether the PAG regulates fear learning when other measures of learned fear are used. Here we combined a chemogenetic approach, permitting excitation or inhibition of neurons in the ventrolateral PAG (VLPAG), with conditioned suppression as the measure of learned fear to assess the role of VLPAG in the acquisition and extinction of fear learning. We show that chemogenetic excitation of VLPAG (with some encroachment on lateral PAG [LPAG]) impairs acquisition of fear and, conversely, chemogenetic inhibition impairs extinction of fear. These effects on fear and extinction learning were specific to the combination of DREADD expression and injection of CNO because they were observed relative to both eYFP controls injected with CNO as well as DREADD expressing controls injected with vehicle. Taken together, these results show that activity of L/VLPAG neurons regulates both the acquisition and extinction of Pavlovian fear learning. Copyright © 2017 Elsevier Inc. All rights reserved.

Predicting the fear of assault at school and while going to and from school in an adolescent population.

PubMed

Alvarez, A; Bachman, R

1997-01-01

Recent research investigating the fear of crime has shown that when crime and behavior-specific measures of fear are utilized, the young are more likely than the elderly to be the most fearful. Research investigating the etiology of fear within adolescent populations, however, remains very limited. Using a sample of over 10,000 junior high and high school students from a supplement to the National Crime Victimization Survey, this paper examines the factors contributing to students' fear of assault both at school and while going to and from school. Results indicate that recent victimization experiences, the presence of a violent subculture at the school (e.g., gang presence and attacks on teachers) and availability of drugs/alcohol were related to fear in both contexts. The predictability of fear from individual characteristics, however, was context specific. Contrary to findings from earlier research, it was found that young females were not more fearful than their male counterparts in all contexts. While they were more fearful of an attack while going to and from school, there were no differences in fear levels while at school between males and females after controlling for other environmental and experiential factors. Conclusions largely support the contention that fear is a rational calculation based on objective criteria. Moreover, results underscore the need for more specificity when operationalizing the context and content of fearfulness.

Individual changes in dental fear among children and parents: a longitudinal study.

PubMed

Luoto, Anni; Tolvanen, Mimmi; Rantavuori, Kari; Pohjola, Vesa; Karlsson, Linnea; Lahti, Satu

2014-11-01

The aim was to study longitudinal changes in dental fear among children and one of their parents separately for girls, boys, mothers and fathers over a 3.5-year period. 11-12-year-old children in Pori, Finland (n = 1691) and one of their parents were invited to participate in this longitudinal study. Dental fear was measured in 2001, 2003 and 2005 when the children were 11-12, 13-14 and 15-16-years-old, respectively. The participants were asked if they were afraid of dental care (1 = 'not afraid', 2 = 'slightly afraid', 3 = 'afraid to some degree', 4 = 'quite afraid', 5 = 'very afraid' and 6 = 'I don't know'). The participants' gender was also registered. Mean values of the change scores were studied. Prevalence and incidence of dental fear and changes in dichotomized dental fear (responses 4-5 = high dental fear and responses 1-3 = low dental fear) were studied using cross-tabulations and Cochran's Q test. Overall, the prevalence of dental fear slightly increased and female preponderance in dental fear became more evident during the follow-up. Of the mothers and children with high dental fear at the baseline, 24% and 56%, respectively, reported not to be fearful at the end of the follow-up. Dental fear seems to be more stable in adulthood than in childhood. Thus, it might be better to intervene in dental fear during childhood rather than during adulthood.

Emotional contagion of dental fear to children: the fathers' mediating role in parental transfer of fear.

PubMed

Lara, America; Crego, Antonio; Romero-Maroto, Martin

2012-09-01

Dental fear is considered to be one of the most frequent problems in paediatric dentistry. According to literature, parents' levels of dental fear play a key role in the development of child's dental anxiety. HYPOTHESIS OR AIM: We have tried to identify the presence of emotional transmission of dental fear among family members and to analyse the different roles that mothers and fathers might play concerning the contagion of dental fear to children. We have hypothesized a key role of the father in the transfer of dental fear from mother to child. A questionnaire-based survey (Children's Fear Survey Schedule-Dental Subscale) has been distributed among 183 schoolchildren and their parents in Madrid (Spain). Inferential statistical analyses, i.e. correlation and hierarchical multiple regression, were carried out and possible mediating effects between variables have been tested. Our results support the hypothesis that family members' levels of dental fear are significantly correlated, and they also allow us to affirm that fathers' dental fear is a mediating variable in the relationship between mothers and children's fear scores. Together with the presence of emotional transmission of dental fear among family members, we identified the relevant role that fathers play as regards the transfer of dental fear from parents to children. © 2011 The Authors. International Journal of Paediatric Dentistry © 2011 BSPD, IAPD and Blackwell Publishing Ltd.

Posterior insular cortex is necessary for conditioned inhibition of fear.

PubMed

Foilb, Allison R; Flyer-Adams, Johanna G; Maier, Steven F; Christianson, John P

2016-10-01

Veridical detection of safety versus danger is critical to survival. Learned signals for safety inhibit fear, and so when presented, reduce fear responses produced by danger signals. This phenomenon is termed conditioned inhibition of fear. Here, we report that CS+/CS- fear discrimination conditioning over 5 days in rats leads the CS- to become a conditioned inhibitor of fear, as measured by the classic tests of conditioned inhibition: summation and retardation of subsequent fear acquisition. We then show that NMDA-receptor antagonist AP5 injected to posterior insular cortex (IC) before training completely prevented the acquisition of a conditioned fear inhibitor, while intra-AP5 to anterior and medial IC had no effect. To determine if the IC contributes to the recall of learned fear inhibition, injections of the GABAA agonist muscimol were made to posterior IC before a summation test. This resulted in fear inhibition per se, which obscured inference to the effect of IC inactivation with recall of the safety cue. Control experiments sought to determine if the role of the IC in conditioned inhibition learning could be reduced to simpler fear discrimination function, but fear discrimination and recall were unaffected by AP5 or muscimol, respectively, in the posterior IC. These data implicate a role of posterior IC in the learning of conditioned fear inhibitors. Copyright © 2016 Elsevier Inc. All rights reserved.

The Set of Fear Inducing Pictures (SFIP): Development and validation in fearful and nonfearful individuals.

PubMed

Michałowski, Jarosław M; Droździel, Dawid; Matuszewski, Jacek; Koziejowski, Wojtek; Jednoróg, Katarzyna; Marchewka, Artur

2017-08-01

Emotionally charged pictorial materials are frequently used in phobia research, but no existing standardized picture database is dedicated to the study of different phobias. The present work describes the results of two independent studies through which we sought to develop and validate this type of database-a Set of Fear Inducing Pictures (SFIP). In Study 1, 270 fear-relevant and 130 neutral stimuli were rated for fear, arousal, and valence by four groups of participants; small-animal (N = 34), blood/injection (N = 26), social-fearful (N = 35), and nonfearful participants (N = 22). The results from Study 1 were employed to develop the final version of the SFIP, which includes fear-relevant images of social exposure (N = 40), blood/injection (N = 80), spiders/bugs (N = 80), and angry faces (N = 30), as well as 726 neutral photographs. In Study 2, we aimed to validate the SFIP in a sample of spider, blood/injection, social-fearful, and control individuals (N = 66). The fear-relevant images were rated as being more unpleasant and led to greater fear and arousal in fearful than in nonfearful individuals. The fear images differentiated between the three fear groups in the expected directions. Overall, the present findings provide evidence for the high validity of the SFIP and confirm that the set may be successfully used in phobia research.

The Topological Properties of Stimuli Influence Fear Generalization and Extinction in Humans

PubMed Central

Xu, Liang; Su, Hongyu; Xie, Xiaoyuan; Yan, Pei; Li, Junjiao; Zheng, Xifu

2018-01-01

Fear generalization is an etiologically significant indicator of anxiety disorders, and understanding how to inhibit it is important in their treatment. Prior studies have found that reducing fear generalization using a generalization stimulus (GS) is ineffective in removing a conditioned fear that incorporates local features, and that topological properties appear to play a comparatively more significant role in the processes of perception and categorization. Our study utilized a conditioned-fear generalization design to examine whether the topological properties of stimuli influence the generalization and return of fear. Fear was indexed using online expectancy ratings and skin conductance responses (SCRs). The study’s 52 participants were divided into three groups: Group 1, conditioned danger cue (CS+) extinction; Group 2, extinction of one GS; Group 3, extinction of three GSs. We found that the three groups acquired conditioned fear at the same level. In the generalization and extinction phase, fear was transferred to the GS with the same topological properties as CS+, and gradual decreases in both shock expectancy and SCRs over non-reinforced extinction trials were observed. In the test phase, participants’ online expectancy ratings indicated that fear did not return in Group 1, but did return in Groups 2 and 3. All three groups demonstrated successful GS fear extinction, but only Group 1 did not show a return of fear for CS+. Regarding SCRs results, none of the groups demonstrated a return of fear, suggesting that utilization of topological properties successfully reduced the return of conditioned fear. Our results indicate that, in clinical settings, using GS with topological equivalence to CS+ might offer a potential method with which to extinct conditioned fear. PMID:29643824

A model of the generation of ataque de nervios: the role of fear of negative affect and fear of arousal symptoms.

PubMed

Hinton, Devon E; Lewis-Fernández, Roberto; Pollack, Mark H

2009-01-01

This article examines a model of the generation of ataque de nervios, according to which both fear of negative affectivity and fear of arousal symptoms are associated with the emergence of ataques. We examine the relationship of fear of negative affectivity and fear of arousal to the severity of ataque de nervios during the last month and the last 6 months among Caribbean Latinos residing in the United States. The measures include a Fear of Anger Scale and the Anxiety Sensitivity Index (ASI), the ASI augmented with two items that assess fear of arousal symptoms common in ataques: chest tightness and a sense of inner heat. In keeping with the model of ataque generation, one-way analysis of variances (ANOVAs) and discriminant function analyses illustrated that items assessing "fear of negative affect" and "fear of somatic and psychological symptoms of arousal" both differentiated well among the levels of ataque severity. In addition, key ataque symptoms-mental incapacitation fears, shakiness, chest tightness, palpitations, and a sense of inner heat-were the best discriminators among levels of ataque severity. In patients with severe ataques, the scores of "fear of negative affect" and "fear of ataque-de-nervios-type somatic and psychological symptoms" were extremely elevated. This further suggests that both these types of fears are associated with this idiom of distress and that the specific content of the fears is linked to the symptom picture of the idiom. This suggests specific therapeutic targets for the treatment of ataque, namely, the reduction of anxiety sensitivity (and more generally negative-emotion and arousal sensitivity) using cognitive behavioral therapy (CBT), relaxation, and mindfulness techniques.

An Additional Prior Retrieval Alters the Effects of a Retrieval-Extinction Procedure on Recent and Remote Fear Memory

PubMed Central

An, Xianli; Yang, Ping; Chen, Siguang; Zhang, Fenfen; Yu, Duonan

2018-01-01

Several studies have shown that the isolated retrieval of a consolidated fear memory can induce a labile phase, during which extinction training can prevent the reinstatement, a form of relapse in which fear response to a fear-provoking context returns when a mild shock is presented. However, fear memory retrieval may also have another opposing result: the enhancement of fear memory. This implies that the fear memory trace can be modified by a brief retrieval. Unclear is whether the fear-impairing effect of retrieval-extinction (RE) is altered by a prior brief retrieval. The present study investigated the responses of recent and remote fear memories to the RE procedure after the presentation of an additional prior retrieval (priRet). We found that a single RE procedure effectively blocked the reinstatement of 2-day recent contextual fear memory. The memory-impairing effect of the RE procedure on recent fear was not observed when priRet was presented 6 or 24 h before the RE procedure. In contrast to the 2-day recent memory, the RE procedure failed to block the reinstatement of 36-day remote fear memory but successfully disrupted the return of remote fear memory after priRet. This memory-disruptive effect on remote memory did not occur when priRet was performed in a novel context. Nimodipine administration revealed that the blockade of priRet-induced processes recovered the effects of the RE procedure on both recent and remote fear memories. Our findings suggest that the susceptibility of recent and remote fear memories to RE procedures can be altered by an additional retrieval. PMID:29358910

Work-related fear and the threats of fear among emergency department nursing staff and physicians in Finland.

PubMed

Mikkola, Riitta; Huhtala, Heini; Paavilainen, Eija

2017-10-01

To describe fear, the threats causing fear and the occurrence of fear among emergency department nursing staff and physicians. The emergency department is a challenging workplace where the staff is often confronted by factors that cause fear. A cross-sectional study. A survey was conducted in 16 hospitals (n = 544). Nurses, practical nurses, orderlies and physicians from those hospitals participated in the survey. The survey questionnaire was based on the analysis of interviews of 30 nurses from one university hospital and one central hospital. The results of the interviews were analysed using the inductive content analysis method. The analysis of the survey was performed using statistical methods, such as frequencies, cross-tabulation and principal component analysis. The results showed that nearly all of the emergency department personnel had experienced work-related fear. Generally, the fear had been momentary. According to the survey results, fear was most often caused by medication errors, the resuscitation of a child, a catastrophic accident, urgent or violent situations or patients armed with weapons. Threats that caused fear included insecurity, danger in the work environment, threat of loss of one's health and threat of the consequences of one's mistakes and actions. The staff of emergency departments often encountered factors or situations that caused fear. The main threats causing fear that were raised by the respondents were insecurity and danger in the work environment. The data obtained from this study can be utilised in identifying and describing work-related fear and threats of fear among emergency department nursing staff and physicians. Based on the information herein, it will be possible to develop methods to prevent situations that cause fear in emergency departments. © 2016 John Wiley & Sons Ltd.

Oxytocin receptor neurotransmission in the dorsolateral bed nucleus of the stria terminalis facilitates the acquisition of cued fear in the fear-potentiated startle paradigm in rats.

PubMed

Moaddab, Mahsa; Dabrowska, Joanna

2017-07-15

Oxytocin (OT) is a hypothalamic neuropeptide that modulates fear and anxiety-like behaviors. Dorsolateral bed nucleus of the stria terminalis (BNST dl ) plays a critical role in the regulation of fear and anxiety, and expresses high levels of OT receptor (OTR). However, the role of OTR neurotransmission within the BNST dl in mediating these behaviors is unknown. Here, we used adult male Sprague-Dawley rats to investigate the role of OTR neurotransmission in the BNST dl in the modulation of the acoustic startle response, as well as in the acquisition and consolidation of conditioned fear using fear potentiated startle (FPS) paradigm. Bilateral intra-BNST dl administration of OT (100 ng) did not affect the acquisition of conditioned fear response. However, intra-BNST dl administration of specific OTR antagonist (OTA), (d(CH 2 ) 5 1 , Tyr(Me) 2 , Thr 4 , Orn 8 , des-Gly-NH 2 9 )-vasotocin, (200 ng), prior to the fear conditioning session, impaired the acquisition of cued fear, without affecting a non-cued fear component of FPS. Neither OTA, nor OT affected baseline startle or shock reactivity during fear conditioning. Therefore, the observed impairment of cued fear after OTA infusion resulted from the specific effect on the formation of cued fear. In contrast to the acquisition, neither OTA nor OT affected the consolidation of FPS, when administered after the completion of fear conditioning session. Taken together, these results reveal the important role of OTR neurotransmission in the BNST dl in the formation of conditioned fear to a discrete cue. This study also highlights the role of the BNST dl in learning to discriminate between threatening and safe stimuli. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dissociating response systems: erasing fear from memory.

PubMed

Soeter, Marieke; Kindt, Merel

2010-07-01

In addition to the extensive evidence in animals, we previously showed that disrupting reconsolidation by noradrenergic blockade produced amnesia for the original fear response in humans. Interestingly, the declarative memory for the fear association remained intact. These results asked for a solid replication. Moreover, given the constructive nature of memories, the intact recollection of the fear association could eventually 'rebuild' the fear memory, resulting in the spontaneous recovery of the fear response. Yet, perseverance of the amnesic effects would have substantial clinical implications, as even the most effective treatments for psychiatric disorders display high percentages of relapse. Using a differential fear conditioning procedure in humans, we replicated our previous findings by showing that administering propranolol (40mg) prior to memory reactivation eliminated the startle fear response 24h later. But most importantly, this effect persisted at one month follow-up. Notably, the propranolol manipulation not only left the declarative memory for the acquired contingency untouched, but also skin conductance discrimination. In addition, a close association between declarative knowledge and skin conductance responses was found. These findings are in line with the supposed double dissociation of fear conditioning and declarative knowledge relative to the amygdala and hippocampus in humans. They support the view that skin conductance conditioning primarily reflects contingency learning, whereas the startle response is a rather specific measure of fear. Furthermore, the results indicate the absence of a causal link between the actual knowledge of a fear association and its fear response, even though they often operate in parallel. Interventions targeting the amygdalar fear memory may be essential in specifically and persistently dampening the emotional impact of fear. From a clinical and ethical perspective, disrupting reconsolidation points to promising interventions persistently erasing fear responses from trauma memory without affecting the actual recollection.

An Additional Prior Retrieval Alters the Effects of a Retrieval-Extinction Procedure on Recent and Remote Fear Memory.

PubMed

An, Xianli; Yang, Ping; Chen, Siguang; Zhang, Fenfen; Yu, Duonan

2017-01-01

Several studies have shown that the isolated retrieval of a consolidated fear memory can induce a labile phase, during which extinction training can prevent the reinstatement, a form of relapse in which fear response to a fear-provoking context returns when a mild shock is presented. However, fear memory retrieval may also have another opposing result: the enhancement of fear memory. This implies that the fear memory trace can be modified by a brief retrieval. Unclear is whether the fear-impairing effect of retrieval-extinction (RE) is altered by a prior brief retrieval. The present study investigated the responses of recent and remote fear memories to the RE procedure after the presentation of an additional prior retrieval (priRet). We found that a single RE procedure effectively blocked the reinstatement of 2-day recent contextual fear memory. The memory-impairing effect of the RE procedure on recent fear was not observed when priRet was presented 6 or 24 h before the RE procedure. In contrast to the 2-day recent memory, the RE procedure failed to block the reinstatement of 36-day remote fear memory but successfully disrupted the return of remote fear memory after priRet. This memory-disruptive effect on remote memory did not occur when priRet was performed in a novel context. Nimodipine administration revealed that the blockade of priRet-induced processes recovered the effects of the RE procedure on both recent and remote fear memories. Our findings suggest that the susceptibility of recent and remote fear memories to RE procedures can be altered by an additional retrieval.

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.

PubMed

Lu, Fu-Hao; McKenzie, Neil; Kettleborough, George; Heavens, Darren; Clark, Matthew D; Bevan, Michael W

2018-05-01

The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Here we use a Fosill 38-kb jumping library to assess medium and longer-range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.

Dynamic simulations of many-body electrostatic self-assembly

NASA Astrophysics Data System (ADS)

Lindgren, Eric B.; Stamm, Benjamin; Maday, Yvon; Besley, Elena; Stace, A. J.

2018-03-01

Two experimental studies relating to electrostatic self-assembly have been the subject of dynamic computer simulations, where the consequences of changing the charge and the dielectric constant of the materials concerned have been explored. One series of calculations relates to experiments on the assembly of polymer particles that have been subjected to tribocharging and the simulations successfully reproduce many of the observed patterns of behaviour. A second study explores events observed following collisions between single particles and small clusters composed of charged particles derived from a metal oxide composite. As before, observations recorded during the course of the experiments are reproduced by the calculations. One study in particular reveals how particle polarizability can influence the assembly process. This article is part of the theme issue `Modern theoretical chemistry'.

Dynamic Simulation of 1D Cellular Automata in the Active aTAM.

PubMed

Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

2015-07-01

The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location.

Communication: Microphase equilibrium and assembly dynamics.

PubMed

Zhuang, Yuan; Charbonneau, Patrick

2017-09-07

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

Using Markov state models to study self-assembly

NASA Astrophysics Data System (ADS)

Perkett, Matthew R.; Hagan, Michael F.

2014-06-01

Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.

Dynamic Simulation of 1D Cellular Automata in the Active aTAM

PubMed Central

Jonoska, Nataša; Karpenko, Daria; Seki, Shinnosuke

2016-01-01

The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location. PMID:27789918

"It was pretty scary": the theme of fear in young adult women's descriptions of a history of adolescent dating abuse.

PubMed

Burton, Candace W; Halpern-Felsher, Bonnie; Rehm, Roberta S; Rankin, Sally; Humphreys, Janice C

2013-11-01

The mental health impact of abusive adolescent dating relationships has not been well described, but fear related to abuse has been reported. We elaborate the theme of fear in women's descriptions of a history of adolescent dating abuse. A sample of community-based women, ages 19-34, who experienced an abusive dating relationship during adolescence (ages 11-20) was used. Data were analyzed via thematic analysis. Fear was a consistent and resonant theme. Three types of fear were identified: fear for self, fear for other relationships, and fearful expectation. These results offer important insights into the impact of abusive adolescent relationships on women's mental health.

Fear of Crime in the Sanctuary: Comparing American and Ghanaian University Students' Fearfulness.

PubMed

Boateng, Francis D

2018-02-01

While much is known about fear of crime in the West, little is known about how fearfulness of crime develops in non-Western societies, especially among university students. Representing the first attempt to empirically compare levels of fear of crime between Ghanaian and U.S. college students, this article examined students' levels of fear of crime on campus, and tested the applicability of two evolving models of fear of crime-the vulnerability and reassurance models-using comparative data. The general finding is that Ghanaian and U.S. college students differ in terms of their rates of fearfulness on campus. This significant difference adds to the already existing differences between the two countries.

Infralimbic EphB2 Modulates Fear Extinction in Adolescent Rats

PubMed Central

Cruz, Emmanuel; Soler-Cedeño, Omar; Negrón, Geovanny; Criado-Marrero, Marangelie; Chompré, Gladys

2015-01-01

Adolescent rats are prone to impaired fear extinction, suggesting that mechanistic differences in extinction could exist in adolescent and adult rats. Since the infralimbic cortex (IL) is critical for fear extinction, we used PCR array technology to identify gene expression changes in IL induced by fear extinction in adolescent rats. Interestingly, the ephrin type B receptor 2 (EphB2), a tyrosine kinase receptor associated with synaptic development, was downregulated in IL after fear extinction. Consistent with the PCR array results, EphB2 levels of mRNA and protein were reduced in IL after fear extinction compared with fear conditioning, suggesting that EphB2 signaling in IL regulates fear extinction memory in adolescents. Finally, reducing EphB2 synthesis in IL with shRNA accelerated fear extinction learning in adolescent rats, but not in adult rats. These findings identify EphB2 in IL as a key regulator of fear extinction during adolescence, perhaps due to the increase in synaptic remodeling occurring during this developmental phase. PMID:26354908

Social anxiety and eating disorder comorbidity: The role of negative social evaluation fears

PubMed Central

Levinson, Cheri A.; Rodebaugh, Thomas L.

2011-01-01

Social anxiety and eating disorders are highly comorbid. However, it is unknown how specific domains of social anxiety relate to disordered eating. We provide data on these relationships and investigate social appearance anxiety and fear of negative evaluation as potential vulnerabilities linking social anxiety with eating disorders. Specifically, we examined five domains of social anxiety: Social interaction anxiety, fear of scrutiny, fear of positive evaluation, fear of negative evaluation, and social appearance anxiety. Results indicated that social appearance anxiety predicted body dissatisfaction, bulimia symptoms, shape concern, weight concern, and eating concern over and above fear of scrutiny, social interaction anxiety, and fear of positive evaluation. Fear of negative evaluation uniquely predicted drive for thinness and restraint. Structural equation modeling supported a model in which social appearance anxiety and fear of negative evaluation are vulnerabilities for both social anxiety and eating disorder symptoms. Interventions that target these negative social evaluation fears may help prevent development of eating disorders. PMID:22177392

Fear conditioned responses and PTSD symptoms in children: Sex differences in fear-related symptoms.

PubMed

Gamwell, Kaitlyn; Nylocks, Maria; Cross, Dorthie; Bradley, Bekh; Norrholm, Seth D; Jovanovic, Tanja

2015-11-01

Fear conditioning studies in adults have found that posttraumatic stress disorder (PTSD) is associated with heightened fear responses and impaired discrimination. The objective of the current study was to examine the association between PTSD symptoms and fear conditioned responses in children from a highly traumatized urban population. Children between 8 and 13 years old participated in a fear conditioning study in addition to providing information about their trauma history and PTSD symptoms. Results showed that females showed less discrimination between danger and safety signals during conditioning compared to age-matched males. In boys, intrusive symptoms were predictive of fear responses, even after controlling for trauma exposure. However, in girls, conditioned fear to the danger cue was predictive of self-blame and fear of repeated trauma. This study suggests there are early sex differences in the patterns of fear conditioning and that these sex differences may translate to differential risk for trauma-related psychopathology. © 2015 Wiley Periodicals, Inc.

Vicarious Learning and Reduction of Fear in Children via Adult and Child Models.

PubMed

Dunne, Güler; Askew, Chris

2017-06-01

Children can learn to fear stimuli vicariously, by observing adults' or peers' responses to them. Given that much of school-age children's time is typically spent with their peers, it is important to establish whether fear learning from peers is as effective or robust as learning from adults, and also whether peers can be successful positive models for reducing fear. During a vicarious fear learning procedure, children (6 to 10 years; N = 60) were shown images of novel animals together with images of adult or peer faces expressing fear. Later they saw their fear-paired animal again together with positive emotional adult or peer faces. Children's fear beliefs and avoidance for the animals increased following vicarious fear learning and decreased following positive vicarious counterconditioning. There was little evidence of differences in learning from adults and peers, demonstrating that for this age group peer models are effective models for both fear acquisition and reduction. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Cellular and oscillatory substrates of fear extinction learning.

PubMed

Davis, Patrick; Zaki, Yosif; Maguire, Jamie; Reijmers, Leon G

2017-11-01

The mammalian brain contains dedicated circuits for both the learned expression and suppression of fear. These circuits require precise coordination to facilitate the appropriate expression of fear behavior, but the mechanisms underlying this coordination remain unclear. Using a combination of chemogenetics, activity-based neuronal-ensemble labeling and in vivo electrophysiology, we found that fear extinction learning confers on parvalbumin-expressing (PV) interneurons in the basolateral amygdala (BLA) a dedicated role in the selective suppression of a previously encoded fear memory and BLA fear-encoding neurons. In addition, following extinction learning, PV interneurons enable a competing interaction between a 6-12 Hz oscillation and a fear-associated 3-6 Hz oscillation within the BLA. Loss of this competition increases a 3-6 Hz oscillatory signature, with BLA→medial prefrontal cortex directionality signaling the recurrence of fear expression. The discovery of cellular and oscillatory substrates of fear extinction learning that critically depend on BLA PV interneurons could inform therapies aimed at preventing the pathological recurrence of fear following extinction learning.

Encoding of Discriminative Fear Memory by Input-Specific LTP in the Amygdala.

PubMed

Kim, Woong Bin; Cho, Jun-Hyeong

2017-08-30

In auditory fear conditioning, experimental subjects learn to associate an auditory conditioned stimulus (CS) with an aversive unconditioned stimulus. With sufficient training, animals fear conditioned to an auditory CS show fear response to the CS, but not to irrelevant auditory stimuli. Although long-term potentiation (LTP) in the lateral amygdala (LA) plays an essential role in auditory fear conditioning, it is unknown whether LTP is induced selectively in the neural pathways conveying specific CS information to the LA in discriminative fear learning. Here, we show that postsynaptically expressed LTP is induced selectively in the CS-specific auditory pathways to the LA in a mouse model of auditory discriminative fear conditioning. Moreover, optogenetically induced depotentiation of the CS-specific auditory pathways to the LA suppressed conditioned fear responses to the CS. Our results suggest that input-specific LTP in the LA contributes to fear memory specificity, enabling adaptive fear responses only to the relevant sensory cue. VIDEO ABSTRACT. Copyright © 2017 Elsevier Inc. All rights reserved.

Negative Social Evaluative Fears Produce Social Anxiety, Food Intake, and Body Dissatisfaction: Evidence of Similar Mechanisms through Different Pathways

PubMed Central

Levinson, Cheri A.; Rodebaugh, Thomas L.

2014-01-01

Social anxiety and eating disorders are highly comorbid, suggesting there are shared vulnerabilities that underlie the development of these disorders. Two proposed vulnerabilities are fear of negative evaluation and social appearance anxiety (i.e., fear of negative evaluation regarding one's appearance). In the current experimental study (N=160 women) we measured these fears: (a) through a manipulation comparing fear conditions, (b) with trait fears, and (c) state fears. Results indicated that participants in the fear of negative evaluation condition increased food consumption, whereas participants in the social appearance anxiety condition and high in trait social appearance anxiety experienced the highest amounts of body dissatisfaction. Participants in the fear of evaluation and social appearance anxiety conditions experienced elevated social anxiety. These results support the idea that negative evaluation fears are shared vulnerabilities for eating and social anxiety disorders, but that the way these variables exert their effects may lead to disorder specific behaviors. PMID:26504674

Social anxiety and eating disorder comorbidity: the role of negative social evaluation fears.

PubMed

Levinson, Cheri A; Rodebaugh, Thomas L

2012-01-01

Social anxiety and eating disorders are highly comorbid. However, it is unknown how specific domains of social anxiety relate to disordered eating. We provide data on these relationships and investigate social appearance anxiety and fear of negative evaluation as potential vulnerabilities linking social anxiety with disordered eating. Specifically, we examined five domains of social anxiety: Social interaction anxiety, fear of scrutiny, fear of positive evaluation, fear of negative evaluation, and social appearance anxiety. Results indicated that social appearance anxiety predicted body dissatisfaction, bulimic symptoms, shape concern, weight concern, and eating concern over and above fear of scrutiny, social interaction anxiety, and fear of positive evaluation. Fear of negative evaluation uniquely predicted drive for thinness and restraint. Structural equation modeling supported a model in which social appearance anxiety and fear of negative evaluation are vulnerabilities for both social anxiety and eating disorder symptoms. Interventions that target these negative social evaluation fears may help prevent development of eating disorders. Copyright © 2011 Elsevier Ltd. All rights reserved.