Telemedicine with mobile devices and augmented reality for early postoperative care.

PubMed

Ponce, Brent A; Brabston, Eugene W; Shin Zu; Watson, Shawna L; Baker, Dustin; Winn, Dennis; Guthrie, Barton L; Shenai, Mahesh B

2016-08-01

Advanced features are being added to telemedicine paradigms to enhance usability and usefulness. Virtual Interactive Presence (VIP) is a technology that allows a surgeon and patient to interact in a "merged reality" space, to facilitate both verbal, visual, and manual interaction. In this clinical study, a mobile VIP iOS application was introduced into routine post-operative orthopedic and neurosurgical care. Survey responses endorse the usefulness of this tool, as it relates to The virtual interaction provides needed virtual follow-up in instances where in-person follow-up may be limited, and enhances the subjective patient experience.

The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.

PubMed

Zhao, Huaying; Balbo, Andrea; Brown, Patrick H; Schuck, Peter

2011-05-01

Sedimentation velocity (SV) experiments of heterogeneous interacting systems exhibit characteristic boundary structures that can usually be very easily recognized and quantified. For slowly interacting systems, the boundaries represent concentrations of macromolecular species sedimenting at different rates, and they can be interpreted directly with population models based solely on the mass action law. For fast reactions, migration and chemical reactions are coupled, and different, but equally easily discernable boundary structures appear. However, these features have not been commonly utilized for data analysis, for the lack of an intuitive and computationally simple model. The recently introduced effective particle theory (EPT) provides a suitable framework. Here, we review the motivation and theoretical basis of EPT, and explore practical aspects for its application. We introduce an EPT-based design tool for SV experiments of heterogeneous interactions in the software SEDPHAT. As a practical tool for the first step of data analysis, we describe how the boundary resolution of the sedimentation coefficient distribution c(s) can be further improved with a Bayesian adjustment of maximum entropy regularization to the case of heterogeneous interactions between molecules that have been previously studied separately. This can facilitate extracting the characteristic boundary features by integration of c(s). In a second step, these are assembled into isotherms as a function of total loading concentrations and fitted with EPT. Methods for addressing concentration errors in isotherms are discussed. Finally, in an experimental model system of alpha-chymotrypsin interacting with soybean trypsin inhibitor, we show that EPT provides an excellent description of the experimental sedimentation boundary structure of fast interacting systems. Published by Elsevier Inc.

QA4, a language for artificial intelligence.

NASA Technical Reports Server (NTRS)

Derksen, J. A. C.

1973-01-01

Introduction of a language for problem solving and specifically robot planning, program verification, and synthesis and theorem proving. This language, called question-answerer 4 (QA4), embodies many features that have been found useful for constructing problem solvers but have to be programmed explicitly by the user of a conventional language. The most important features of QA4 are described, and examples are provided for most of the material introduced. Language features include backtracking, parallel processing, pattern matching, set manipulation, and pattern-triggered function activation. The language is most convenient for use in an interactive way and has extensive trace and edit facilities.

An interactive method based on the live wire for segmentation of the breast in mammography images.

PubMed

Zewei, Zhang; Tianyue, Wang; Li, Guo; Tingting, Wang; Lu, Xu

2014-01-01

In order to improve accuracy of computer-aided diagnosis of breast lumps, the authors introduce an improved interactive segmentation method based on Live Wire. This paper presents the Gabor filters and FCM clustering algorithm is introduced to the Live Wire cost function definition. According to the image FCM analysis for image edge enhancement, we eliminate the interference of weak edge and access external features clear segmentation results of breast lumps through improving Live Wire on two cases of breast segmentation data. Compared with the traditional method of image segmentation, experimental results show that the method achieves more accurate segmentation of breast lumps and provides more accurate objective basis on quantitative and qualitative analysis of breast lumps.

Atomic Structure

NASA Astrophysics Data System (ADS)

Whelan, Colm T.

2018-04-01

A knowledge of atomic theory should be an essential part of every physicist's and chemist's toolkit. This book provides an introduction to the basic ideas that govern our understanding of microscopic matter, and the essential features of atomic structure and spectra are presented in a direct and easily accessible manner. Semi-classical ideas are reviewed and an introduction to the quantum mechanics of one and two electron systems and their interaction with external electromagnetic fields is featured. Multielectron atoms are also introduced, and the key methods for calculating their properties reviewed.

Tuning the hybridization bandgap by meta-molecules with in-unit interaction

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

Chen, Yongqiang; Li, Yunhui, E-mail: liyunhui@tongji.edu.cn; Wu, Qian

2015-09-07

In this paper, we demonstrate that the hybridization bandgap (HBG) can be tuned conveniently by deep subwavelength meta-molecules with in-unit interaction. Spontaneous-emission-cancellation-like (SEC-like) effect is realized in a meta-molecule by introducing the destructive interference of two detuned meta-atoms. The meta-atoms consisting of subwavelength zero-index-metamaterial-based resonators are side-coupled to a microstrip. Compared to conventional HBG configurations, the presence of in-unit interaction between meta-atoms provides more flexibility in tuning the bandgap properties, keeping the device volume almost unchanged. Both numerical simulations and microwave experiments confirm that the width, depth, and spectrum shape of HBG can be tuned by simply introducing SEC-like interactionmore » into the meta-molecule. Due to these features, our design may be promising to be applied in microwave or optics communications systems with strict limitation of device volume and flexible bandgap properties.« less

Facilitating Learnscape Development, Maintenance and Use: Teachers' Perceptions and Self-Reported Practices.

ERIC Educational Resources Information Center

Skamp, Keith; Bergmann, Iris

2001-01-01

Introduces two pilot schools participating in the project Learnscapes, a learning program in which users interact with the environment on school grounds with features such as an edible garden, a poetry corner, or a wildlife corridor. Presents teachers' ideas on the relationship of learnscapes to environmental education and discusses pedagogical…

Measuring Reciprocity in High Functioning Children and Adolescents with Autism Spectrum Disorders

ERIC Educational Resources Information Center

van Ommeren, Tineke Backer; Begeer, Sander; Scheeren, Anke M.; Koot, Hans M.

2012-01-01

Few instruments have been developed that measure impairments in reciprocity, a defining feature of autism. We introduce a new test assessing the quality of reciprocal behaviour: the interactive drawing test (IDT). Children and adolescents (n = 49) with and without high functioning autism spectrum disorders (HFASD) were invited to collaborate with…

Triple Helix Systems: An Analytical Framework for Innovation Policy and Practice in the Knowledge Society

ERIC Educational Resources Information Center

Ranga, Marina; Etzkowitz, Henry

2013-01-01

This paper introduces the concept of Triple Helix systems as an analytical construct that synthesizes the key features of university--industry--government (Triple Helix) interactions into an "innovation system" format, defined according to systems theory as a set of components, relationships and functions. Among the components of Triple…

Success for All and Comprehensive School Reform: Evidence-Based Policies for Urban Education.

ERIC Educational Resources Information Center

Slavin, Robert E.; Madden, Nancy A.

This paper discusses comprehensive school reform (CSR), which accepts the importance of standards and accountability but adds to these strategies for introducing innovations in curriculum, instruction, school organization, governance, parent interactions, and other core features of practice. The paper reviews research on the nature and quality of…

"Et Pis Bon, Ben Alors Voilà Quoi!" Teaching Those Pesky Discourse Markers

ERIC Educational Resources Information Center

Mullan, Kerry

2016-01-01

Discourse markers have been described as "nervous tics, fillers, or signs of hesitation", and are frequently dismissed as features of lazy or inarticulate speech. Yet in fact they have a number of crucial functions in spoken interaction, such as buying time, managing turn taking, linking utterances, introducing a new topic and indicating…

Designing perturbative metamaterials from discrete models.

PubMed

Matlack, Kathryn H; Serra-Garcia, Marc; Palermo, Antonio; Huber, Sebastian D; Daraio, Chiara

2018-04-01

Identifying material geometries that lead to metamaterials with desired functionalities presents a challenge for the field. Discrete, or reduced-order, models provide a concise description of complex phenomena, such as negative refraction, or topological surface states; therefore, the combination of geometric building blocks to replicate discrete models presenting the desired features represents a promising approach. However, there is no reliable way to solve such an inverse problem. Here, we introduce 'perturbative metamaterials', a class of metamaterials consisting of weakly interacting unit cells. The weak interaction allows us to associate each element of the discrete model with individual geometric features of the metamaterial, thereby enabling a systematic design process. We demonstrate our approach by designing two-dimensional elastic metamaterials that realize Veselago lenses, zero-dispersion bands and topological surface phonons. While our selected examples are within the mechanical domain, the same design principle can be applied to acoustic, thermal and photonic metamaterials composed of weakly interacting unit cells.

Automatic recognition of emotions from facial expressions

NASA Astrophysics Data System (ADS)

Xue, Henry; Gertner, Izidor

2014-06-01

In the human-computer interaction (HCI) process it is desirable to have an artificial intelligent (AI) system that can identify and categorize human emotions from facial expressions. Such systems can be used in security, in entertainment industries, and also to study visual perception, social interactions and disorders (e.g. schizophrenia and autism). In this work we survey and compare the performance of different feature extraction algorithms and classification schemes. We introduce a faster feature extraction method that resizes and applies a set of filters to the data images without sacrificing the accuracy. In addition, we have enhanced SVM to multiple dimensions while retaining the high accuracy rate of SVM. The algorithms were tested using the Japanese Female Facial Expression (JAFFE) Database and the Database of Faces (AT&T Faces).

Coupled Brownian motors: Anomalous hysteresis and zero-bias negative conductance

NASA Astrophysics Data System (ADS)

Reimann, P.; Kawai, R.; Van den Broeck, C.; Hänggi, P.

1999-03-01

We introduce a model of interacting Brownian particles in a symmetric, periodic potential that undergoes a noise-induced non-equilibrium phase transition. The associated spontaneous symmetry breaking entails a ratchet-like transport mechanism. In response to an external force we identify several novel features; among the most prominent being a zero-bias negative conductance and a prima facie counterintuitive, anomalous hysteresis.

A Framework for Spatial Interaction Analysis Based on Large-Scale Mobile Phone Data

PubMed Central

Li, Weifeng; Cheng, Xiaoyun; Guo, Gaohua

2014-01-01

The overall understanding of spatial interaction and the exact knowledge of its dynamic evolution are required in the urban planning and transportation planning. This study aimed to analyze the spatial interaction based on the large-scale mobile phone data. The newly arisen mass dataset required a new methodology which was compatible with its peculiar characteristics. A three-stage framework was proposed in this paper, including data preprocessing, critical activity identification, and spatial interaction measurement. The proposed framework introduced the frequent pattern mining and measured the spatial interaction by the obtained association. A case study of three communities in Shanghai was carried out as verification of proposed method and demonstration of its practical application. The spatial interaction patterns and the representative features proved the rationality of the proposed framework. PMID:25435865

Process migration in UNIX environments

NASA Technical Reports Server (NTRS)

Lu, Chin; Liu, J. W. S.

1988-01-01

To support process migration in UNIX environments, the main problem is how to encapsulate the location dependent features of the system in such a way that a host independent virtual environment is maintained by the migration handlers on the behalf of each migrated process. An object-oriented approach is used to describe the interaction between a process and its environment. More specifically, environmental objects were introduced in UNIX systems to carry out the user-environment interaction. The implementation of the migration handlers is based on both the state consistency criterion and the property consistency criterion.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

PubMed Central

Alhroub, Younes; Anyango, Stephen; Armstrong, David R; Berrisford, John M; Clark, Alice R; Conroy, Matthew J; Dana, Jose M; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver S; Varadi, Mihaly; Kleywegt, Gerard J

2018-01-01

Abstract The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API. PMID:29126160

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

The mass media destabilizes the cultural homogenous regime in Axelrod's model

NASA Astrophysics Data System (ADS)

Peres, Lucas R.; Fontanari, José F.

2010-02-01

An important feature of Axelrod's model for culture dissemination or social influence is the emergence of many multicultural absorbing states, despite the fact that the local rules that specify the agents interactions are explicitly designed to decrease the cultural differences between agents. Here we re-examine the problem of introducing an external, global interaction—the mass media—in the rules of Axelrod's model: in addition to their nearest neighbors, each agent has a certain probability p to interact with a virtual neighbor whose cultural features are fixed from the outset. Most surprisingly, this apparently homogenizing effect actually increases the cultural diversity of the population. We show that, contrary to previous claims in the literature, even a vanishingly small value of p is sufficient to destabilize the homogeneous regime for very large lattice sizes.

Freeform object design and simultaneous manufacturing

NASA Astrophysics Data System (ADS)

Zhang, Wei; Zhang, Weihan; Lin, Heng; Leu, Ming C.

2003-04-01

Today's product design, especially the consuming product design, focuses more and more on individuation, originality, and the time to market. One way to meet these challenges is using the interactive and creationary product design methods and rapid prototyping/rapid tooling. This paper presents a novel Freeform Object Design and Simultaneous Manufacturing (FODSM) method that combines the natural interaction feature in the design phase and simultaneous manufacturing feature in the prototyping phase. The natural interactive three-dimensional design environment is achieved by adopting virtual reality technology. The geometry of the designed object is defined through the process of "virtual sculpting" during which the designer can touch and visualize the designed object and can hear the virtual manufacturing environment noise. During the designing process, the computer records the sculpting trajectories and automatically translates them into NC codes so as to simultaneously machine the designed part. The paper introduced the principle, implementation process, and key techniques of the new method, and compared it with other popular rapid prototyping methods.

GENIE Production Release 2.10.0

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

Alam, M.; Andreopoulos, C.; Athar, M.

2015-12-25

GENIE is a neutrino Monte Carlo event generator that simulates the primary interaction of a neutrino with a nuclear target, along with the subsequent propagation of the reaction products through the nuclear medium. It additionally contains libraries for fully-featured detector geometries and for managing various types of neutrino flux. This note details recent updates to GENIE, in particular, changes introduced into the newest production release, version 2.10.0.

A 3D isodose manipulation tool for interactive dose shaping

NASA Astrophysics Data System (ADS)

Kamerling, C. P.; Ziegenhein, P.; Heinrich, H.; Oelfke, U.

2014-03-01

The interactive dose shaping (IDS) planning paradigm aims to perform interactive local dose adaptations of an IMRT plan without compromising already established valuable dose features in real-time. In this work we introduce an interactive 3D isodose manipulation tool which enables local modifications of a dose distribution intuitively by direct manipulation of an isodose surface. We developed an in-house IMRT TPS framework employing an IDS engine as well as a 3D GUI for dose manipulation and visualization. In our software an initial dose distribution can be interactively modified through an isodose surface manipulation tool by intuitively clicking on an isodose surface. To guide the user interaction, the position of the modification is indicated by a sphere while the mouse cursor hovers the isodose surface. The sphere's radius controls the locality of the modification. The tool induces a dose modification as a direct change of dose in one or more voxels, which is incrementally obtained by fluence adjustments. A subsequent recovery step identifies voxels with violated dose features and aims to recover their original dose. We showed a proof of concept study for the proposed tool by adapting the dose distribution of a prostate case (9 beams, coplanar). Single dose modifications take less than 2 seconds on an actual desktop PC.

Emergence of clustering in an acquaintance model without homophily

NASA Astrophysics Data System (ADS)

Bhat, Uttam; Krapivsky, P. L.; Redner, S.

2014-11-01

We introduce an agent-based acquaintance model in which social links are created by processes in which there is no explicit homophily. In spite of the homogeneous nature of the social interactions, highly-clustered social networks can arise. The crucial feature of our model is that of variable transitive interactions. Namely, when an agent introduces two unconnected friends, the rate at which a connection actually occurs between them depends on the number of their mutual acquaintances. As this transitive interaction rate is varied, the social network undergoes a dramatic clustering transition. Close to the transition, the network consists of a collection of well-defined communities. As a function of time, the network can also undergo an incomplete gelation transition, in which the gel, or giant cluster, does not constitute the entire network, even at infinite time. Some of the clustering properties of our model also arise, but in a more gradual manner, in Facebook networks. Finally, we discuss a more realistic variant of our original model in which network realizations can be constructed that quantitatively match Facebook networks.

Wave reflection and transmission in multiply stented blood vessels

NASA Astrophysics Data System (ADS)

Papathanasiou, T. K.; Movchan, A. B.; Bigoni, D.

2017-06-01

Closed circulatory systems display an exquisite balance between vascular elasticity and viscous fluid effects, to induce pulse-smoothing and avoid resonance during the cardiac cycle. Stents in the arterial tree alter this balance through stiffening and because a periodic structure is introduced, capable of interacting with the fluid in a complex way. While the former feature has been investigated, the latter received no attention so far. But periodic structures are the building blocks of metamaterials, known for their `non-natural' behaviour. Thus, the investigation of a stent's periodic microstructure dynamical interactions is crucial to assess possible pathological responses. A one-dimensional fluid-structure interaction model, simple enough to allow an analytical solution for situations of interest involving one or two interacting stents, is introduced. It is determined: (i) whether or not frequency bands exist in which reflected blood pulses are highly increased and (ii) if these bands are close to the characteristic frequencies of arteries and finally, (iii) if the internal structure of the stent can sensibly affect arterial blood dynamics. It is shown that, while the periodic structure of an isolated stent can induce anomalous reflection only in pathological conditions, the presence of two interacting stents is more critical, and high reflection can occur at frequencies not far from the physiological values.

Wave reflection and transmission in multiply stented blood vessels

PubMed Central

Movchan, A. B.

2017-01-01

Closed circulatory systems display an exquisite balance between vascular elasticity and viscous fluid effects, to induce pulse-smoothing and avoid resonance during the cardiac cycle. Stents in the arterial tree alter this balance through stiffening and because a periodic structure is introduced, capable of interacting with the fluid in a complex way. While the former feature has been investigated, the latter received no attention so far. But periodic structures are the building blocks of metamaterials, known for their ‘non-natural’ behaviour. Thus, the investigation of a stent's periodic microstructure dynamical interactions is crucial to assess possible pathological responses. A one-dimensional fluid–structure interaction model, simple enough to allow an analytical solution for situations of interest involving one or two interacting stents, is introduced. It is determined: (i) whether or not frequency bands exist in which reflected blood pulses are highly increased and (ii) if these bands are close to the characteristic frequencies of arteries and finally, (iii) if the internal structure of the stent can sensibly affect arterial blood dynamics. It is shown that, while the periodic structure of an isolated stent can induce anomalous reflection only in pathological conditions, the presence of two interacting stents is more critical, and high reflection can occur at frequencies not far from the physiological values. PMID:28690408

Gesture Recognition Based on the Probability Distribution of Arm Trajectories

NASA Astrophysics Data System (ADS)

Wan, Khairunizam; Sawada, Hideyuki

The use of human motions for the interaction between humans and computers is becoming an attractive alternative to verbal media, especially through the visual interpretation of the human body motion. In particular, hand gestures are used as non-verbal media for the humans to communicate with machines that pertain to the use of the human gestures to interact with them. This paper introduces a 3D motion measurement of the human upper body for the purpose of the gesture recognition, which is based on the probability distribution of arm trajectories. In this study, by examining the characteristics of the arm trajectories given by a signer, motion features are selected and classified by using a fuzzy technique. Experimental results show that the use of the features extracted from arm trajectories effectively works on the recognition of dynamic gestures of a human, and gives a good performance to classify various gesture patterns.

The oblique impingement of an axisymmetric jet. [flow characteristics of jet flow over flat plates

NASA Technical Reports Server (NTRS)

Foss, J. F.; Kleis, S. J.

1976-01-01

The mechanics of the oblique impingement of an axisymmetric jet on a plane surface are examined in detail. The stagnation point is discussed. A schematic drawing of the problem and coordinate system used to describe the flow field are given. The kinematic features of the flow above the plate are examined in the context of the conservation of mass, the vorticity of the jet, and the vorticity introduced by the jetplate interaction. The dynamic features of the flow are examined in terms of the surface pressure distribution and the cause-effect relationships which exist between the pressure and velocity/vorticity distributions. Flow calculations performed are given. The investigation is relevant to the flow resulting from the interaction of the propulsion jet with the main airfoil (STOL aircraft), and is appropriate to an over- or under- wing configuration.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

PubMed

Mir, Saqib; Alhroub, Younes; Anyango, Stephen; Armstrong, David R; Berrisford, John M; Clark, Alice R; Conroy, Matthew J; Dana, Jose M; Deshpande, Mandar; Gupta, Deepti; Gutmanas, Aleksandras; Haslam, Pauline; Mak, Lora; Mukhopadhyay, Abhik; Nadzirin, Nurul; Paysan-Lafosse, Typhaine; Sehnal, David; Sen, Sanchayita; Smart, Oliver S; Varadi, Mihaly; Kleywegt, Gerard J; Velankar, Sameer

2018-01-04

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Transition of the blind acupuncture and massage industry and its impacts in Japan].

PubMed

Wu, Yan

2016-01-01

After being introduced to Japan, the Chinese acupuncture and massage therapy has changed a lot, in which the influence aroused by the blind practitioners cannot be ignored. Through analyzing the development and the transition of the blind acupuncture and massage industry in Japan, it is found that the tube needle technique, changeable acupoints concept, technical deviation and the importance on acupoints rather than meridians are still existed commonly today, which are introduced by the blind acupuncture and massage practitioners, the special group in Japan. In the process of development, the interaction with the governmental strategy has played the essential role in the consolidation of the above features.

CognitionMaster: an object-based image analysis framework

PubMed Central

2013-01-01

Background Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired. Results In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept. Conclusions We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis. PMID:23445542

Analysis and application of opinion model with multiple topic interactions.

PubMed

Xiong, Fei; Liu, Yun; Wang, Liang; Wang, Ximeng

2017-08-01

To reveal heterogeneous behaviors of opinion evolution in different scenarios, we propose an opinion model with topic interactions. Individual opinions and topic features are represented by a multidimensional vector. We measure an agent's action towards a specific topic by the product of opinion and topic feature. When pairs of agents interact for a topic, their actions are introduced to opinion updates with bounded confidence. Simulation results show that a transition from a disordered state to a consensus state occurs at a critical point of the tolerance threshold, which depends on the opinion dimension. The critical point increases as the dimension of opinions increases. Multiple topics promote opinion interactions and lead to the formation of macroscopic opinion clusters. In addition, more topics accelerate the evolutionary process and weaken the effect of network topology. We use two sets of large-scale real data to evaluate the model, and the results prove its effectiveness in characterizing a real evolutionary process. Our model achieves high performance in individual action prediction and even outperforms state-of-the-art methods. Meanwhile, our model has much smaller computational complexity. This paper provides a demonstration for possible practical applications of theoretical opinion dynamics.

Attention and memory protection: Interactions between retrospective attention cueing and interference.

PubMed

Makovski, Tal; Pertzov, Yoni

2015-01-01

Visual working memory (VWM) and attention have a number of features in common, but despite extensive research it is still unclear how the two interact. Can focused attention improve VWM precision? Can it protect VWM from interference? Here we used a partial-report, continuous-response orientation memory task to examine how attention and interference affect different aspects of VWM and how they interact with one another. Both attention and interference were orthogonally manipulated during the retention interval. Attention was manipulated by presenting informative retro-cues, whereas interference was manipulated by introducing a secondary interfering task. Mixture-model analyses revealed that retro-cues, compared to uninformative cues, improved all aspects of performance: Attention increased recall precision and decreased guessing rate and swap-errors (reporting a wrong item in memory). Similarly, performing a secondary task impaired all aspects of the VWM task. In particular, an interaction between retro-cue and secondary task interference was found primarily for swap-errors. Together these results suggest that both the quantity and quality of VWM representations are sensitive to attention cueing and interference modulations, and they highlight the role of attention in protecting the feature-location associations needed to access the correct items in memory.

The media effect in Axelrod's model explained

NASA Astrophysics Data System (ADS)

Peres, L. R.; Fontanari, J. F.

2011-11-01

We revisit the problem of introducing an external global field —the mass media— in Axelrod's model of social dynamics, where in addition to their nearest neighbors, the agents can interact with a virtual neighbor whose cultural features are fixed from the outset. The finding that this apparently homogenizing field actually increases the cultural diversity has been considered a puzzle since the phenomenon was first reported more than a decade ago. Here we offer a simple explanation for it, which is based on the pedestrian observation that Axelrod's model exhibits more cultural diversity, i.e., more distinct cultural domains, when the agents are allowed to interact solely with the media field than when they can interact with their neighbors as well. In this perspective, it is the local homogenizing interactions that work towards making the absorbing configurations less fragmented as compared with the extreme situation in which the agents interact with the media only.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

PubMed

Letunic, Ivica; Bork, Peer

2016-07-08

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Topological crystalline magnets: Symmetry-protected topological phases of fermions

DOE PAGES

Watanabe, Haruki; Fu, Liang

2017-02-27

Here, we introduce a novel class of interaction-enabled topological crystalline insulators in two- and three-dimensional electronic systems, which we call “topological crystalline magnet.” It is protected by the product of the time-reversal symmetry T and a mirror symmetry or a rotation symmetry R. A topological crystalline magnet exhibits two intriguing features: (i) it cannot be adiabatically connected to any Slater insulator and (ii) the edge state is robust against coupling electrons to the edge. These features are protected by the anomalous symmetry transformation property ( RT) 2 = -1 of the edge state. Finally, an anisotropic response to the externalmore » magnetic field can be an experimental signature.« less

Topological crystalline magnets: Symmetry-protected topological phases of fermions

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

Watanabe, Haruki; Fu, Liang

Here, we introduce a novel class of interaction-enabled topological crystalline insulators in two- and three-dimensional electronic systems, which we call “topological crystalline magnet.” It is protected by the product of the time-reversal symmetry T and a mirror symmetry or a rotation symmetry R. A topological crystalline magnet exhibits two intriguing features: (i) it cannot be adiabatically connected to any Slater insulator and (ii) the edge state is robust against coupling electrons to the edge. These features are protected by the anomalous symmetry transformation property ( RT) 2 = -1 of the edge state. Finally, an anisotropic response to the externalmore » magnetic field can be an experimental signature.« less

Axions and dark matter

NASA Astrophysics Data System (ADS)

Yang, Qiaoli

2017-05-01

Dark matter constitutes about 23% of the total energy density of the universe, but its properties are still little known besides that it should be composed by cold and weakly interacting particles. Many beyond Standard Model theories can provide proper candidates to serve as dark matter and the axion introduced to solve the strong CP problem turns out to be an attractive one. In this paper, we briefly review several important features of the axion and the axion dark matter.

Negligible Electronic Interaction between Photoexcited Electron–Hole Pairs and Free Electrons in Phosphorus–Boron Co-Doped Silicon Nanocrystals

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

Limpens, Rens; Fujii, Minoru; Neale, Nathan R.

Phosphorus (P) and boron (B) co-doped Si nanocrystals (NCs) have raised interest in the optoelectronic industry due to their electronic tunability, optimal carrier multiplication properties, and straightforward dispersibility in polar solvents. Yet a basic understanding of the interaction of photoexcited electron-hole (e-h) pairs with new physical features that are introduced by the co-doping process (free carriers, defect states, and surface chemistry) is missing. Here, we present the first study of the ultrafast carrier dynamics in SiO2-embedded P-B co-doped Si NC ensembles using induced absorption spectroscopy through a two-step approach. First, the induced absorption data show that the large fraction ofmore » the dopants residing on the NC surface slows down carrier relaxation dynamics within the first 20 ps relative to intrinsic (undoped) Si NCs, which we interpret as enhanced surface passivation. On longer time-scales (picosecond to nanosecond regime), we observe a speeding up of the carrier relaxation dynamics and ascribe it to doping-induced trap states. This argument is deduced from the second part of the study, where we investigate multiexciton interactions. From a stochastic modeling approach we show that localized carriers, which are introduced by the P or B dopants, have minor electronic interactions with the photoexcited e-h pairs. This is understood in light of the strong localization of the introduced carriers on their original P- or B-dopant atoms, due to the strong quantum confinement regime in these relatively small NCs (<6 nm).« less

Negligible Electronic Interaction between Photoexcited Electron-Hole Pairs and Free Electrons in Phosphorus-Boron Co-Doped Silicon Nanocrystals

DOE PAGES

Limpens, Rens; Neale, Nathan R; Fujii, Minoru; ...

2018-03-05

Phosphorus (P) and boron (B) co-doped Si nanocrystals (NCs) have raised interest in the optoelectronic industry due to their electronic tunability, optimal carrier multiplication properties, and straightforward dispersibility in polar solvents. Yet a basic understanding of the interaction of photoexcited electron-hole (e-h) pairs with new physical features that are introduced by the co-doping process (free carriers, defect states, and surface chemistry) is missing. Here, we present the first study of the ultrafast carrier dynamics in SiO2-embedded P-B co-doped Si NC ensembles using induced absorption spectroscopy through a two-step approach. First, the induced absorption data show that the large fraction ofmore » the dopants residing on the NC surface slows down carrier relaxation dynamics within the first 20 ps relative to intrinsic (undoped) Si NCs, which we interpret as enhanced surface passivation. On longer time-scales (picosecond to nanosecond regime), we observe a speeding up of the carrier relaxation dynamics and ascribe it to doping-induced trap states. This argument is deduced from the second part of the study, where we investigate multiexciton interactions. From a stochastic modeling approach we show that localized carriers, which are introduced by the P or B dopants, have minor electronic interactions with the photoexcited e-h pairs. This is understood in light of the strong localization of the introduced carriers on their original P- or B-dopant atoms, due to the strong quantum confinement regime in these relatively small NCs (<6 nm).« less

Negligible Electronic Interaction between Photoexcited Electron–Hole Pairs and Free Electrons in Phosphorus–Boron Co-Doped Silicon Nanocrystals

DOE PAGES

Limpens, Rens; Fujii, Minoru; Neale, Nathan R.; ...

2018-02-28

Phosphorus (P) and boron (B) co-doped Si nanocrystals (NCs) have raised interest in the optoelectronic industry due to their electronic tunability, optimal carrier multiplication properties, and straightforward dispersibility in polar solvents. Yet a basic understanding of the interaction of photoexcited electron-hole (e-h) pairs with new physical features that are introduced by the co-doping process (free carriers, defect states, and surface chemistry) is missing. Here, we present the first study of the ultrafast carrier dynamics in SiO2-embedded P-B co-doped Si NC ensembles using induced absorption spectroscopy through a two-step approach. First, the induced absorption data show that the large fraction ofmore » the dopants residing on the NC surface slows down carrier relaxation dynamics within the first 20 ps relative to intrinsic (undoped) Si NCs, which we interpret as enhanced surface passivation. On longer time-scales (picosecond to nanosecond regime), we observe a speeding up of the carrier relaxation dynamics and ascribe it to doping-induced trap states. This argument is deduced from the second part of the study, where we investigate multiexciton interactions. From a stochastic modeling approach we show that localized carriers, which are introduced by the P or B dopants, have minor electronic interactions with the photoexcited e-h pairs. This is understood in light of the strong localization of the introduced carriers on their original P- or B-dopant atoms, due to the strong quantum confinement regime in these relatively small NCs (<6 nm).« less

Modeling of fatigue crack induced nonlinear ultrasonics using a highly parallelized explicit local interaction simulation approach

NASA Astrophysics Data System (ADS)

Shen, Yanfeng; Cesnik, Carlos E. S.

2016-04-01

This paper presents a parallelized modeling technique for the efficient simulation of nonlinear ultrasonics introduced by the wave interaction with fatigue cracks. The elastodynamic wave equations with contact effects are formulated using an explicit Local Interaction Simulation Approach (LISA). The LISA formulation is extended to capture the contact-impact phenomena during the wave damage interaction based on the penalty method. A Coulomb friction model is integrated into the computation procedure to capture the stick-slip contact shear motion. The LISA procedure is coded using the Compute Unified Device Architecture (CUDA), which enables the highly parallelized supercomputing on powerful graphic cards. Both the explicit contact formulation and the parallel feature facilitates LISA's superb computational efficiency over the conventional finite element method (FEM). The theoretical formulations based on the penalty method is introduced and a guideline for the proper choice of the contact stiffness is given. The convergence behavior of the solution under various contact stiffness values is examined. A numerical benchmark problem is used to investigate the new LISA formulation and results are compared with a conventional contact finite element solution. Various nonlinear ultrasonic phenomena are successfully captured using this contact LISA formulation, including the generation of nonlinear higher harmonic responses. Nonlinear mode conversion of guided waves at fatigue cracks is also studied.

Discriminative latent models for recognizing contextual group activities.

PubMed

Lan, Tian; Wang, Yang; Yang, Weilong; Robinovitch, Stephen N; Mori, Greg

2012-08-01

In this paper, we go beyond recognizing the actions of individuals and focus on group activities. This is motivated from the observation that human actions are rarely performed in isolation; the contextual information of what other people in the scene are doing provides a useful cue for understanding high-level activities. We propose a novel framework for recognizing group activities which jointly captures the group activity, the individual person actions, and the interactions among them. Two types of contextual information, group-person interaction and person-person interaction, are explored in a latent variable framework. In particular, we propose three different approaches to model the person-person interaction. One approach is to explore the structures of person-person interaction. Differently from most of the previous latent structured models, which assume a predefined structure for the hidden layer, e.g., a tree structure, we treat the structure of the hidden layer as a latent variable and implicitly infer it during learning and inference. The second approach explores person-person interaction in the feature level. We introduce a new feature representation called the action context (AC) descriptor. The AC descriptor encodes information about not only the action of an individual person in the video, but also the behavior of other people nearby. The third approach combines the above two. Our experimental results demonstrate the benefit of using contextual information for disambiguating group activities.

Discriminative Latent Models for Recognizing Contextual Group Activities

PubMed Central

Lan, Tian; Wang, Yang; Yang, Weilong; Robinovitch, Stephen N.; Mori, Greg

2012-01-01

In this paper, we go beyond recognizing the actions of individuals and focus on group activities. This is motivated from the observation that human actions are rarely performed in isolation; the contextual information of what other people in the scene are doing provides a useful cue for understanding high-level activities. We propose a novel framework for recognizing group activities which jointly captures the group activity, the individual person actions, and the interactions among them. Two types of contextual information, group-person interaction and person-person interaction, are explored in a latent variable framework. In particular, we propose three different approaches to model the person-person interaction. One approach is to explore the structures of person-person interaction. Differently from most of the previous latent structured models, which assume a predefined structure for the hidden layer, e.g., a tree structure, we treat the structure of the hidden layer as a latent variable and implicitly infer it during learning and inference. The second approach explores person-person interaction in the feature level. We introduce a new feature representation called the action context (AC) descriptor. The AC descriptor encodes information about not only the action of an individual person in the video, but also the behavior of other people nearby. The third approach combines the above two. Our experimental results demonstrate the benefit of using contextual information for disambiguating group activities. PMID:22144516

Using the Concept of Transient Complex for Affinity Predictions in CAPRI Rounds 20–27 and Beyond

PubMed Central

Qin, Sanbo; Zhou, Huan-Xiang

2013-01-01

Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targets (T43–45, 55, and 56) of CAPRI rounds 20–27. For T43, we ranked the single crystallographic complex as number 1 and were one of only two groups that clearly identified that complex as a true binder; for T44, we ranked the only design with measurable binding affinity as number 4. For the nine docking targets, continuing on our success in previous CAPRI rounds, we produced 10 medium-quality models for T47 and acceptable models for T48 and T49. We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities. PMID:23873496

mapview - Interactive viewing of spatial data in R

NASA Astrophysics Data System (ADS)

Appelhans, Tim; Detsch, Florian; Reudenbach, Cristoph; Woellauer, Stefan

2016-04-01

In this talk we would like to introduce mapview, an R package designed to aid researchers during their work-flow of spatial data analysis. The package was initially developed within the framework of the DFG funded research group "KiLi - Kilimanjaro ecosystems under global change: Linking biodiversity, biotic interactions and biogeochemical ecosystem processes" but has quickly developed into a general purpose spatial data viewer. mapview provides some powerful tools for interactive visualization of standard spatial data in R. It has support for all Spatial*(DataFrame) objects as well as all Raster* objects. It is designed so that one function call - mapview(x) - is all you need to view the data interactively. Adding layers to existing views is very easy and we have taken great care in providing suitable defaults for features such as background maps or coloring but things can be customized flexibly (and permanently) to suit different needs. Even though mapview is for most parts based on the leaflet package, it is far more than just a convenience wrapper around leaflet functionality. mapview provides additional features for handling big data sets (up to several million points) as well as some specialized functionality to view and compare rasters of any size with arbitrary coordinate reference systems. Given that mapview is merely a bridge between R and the underlying leaflet.js javascript library, mapview can be used to produce web-maps by simply providing the path to a designated folder. This talk will be a live demonstration of some of the key features of mapview.

BlobContours: adapting Blobworld for supervised color- and texture-based image segmentation

NASA Astrophysics Data System (ADS)

Vogel, Thomas; Nguyen, Dinh Quyen; Dittmann, Jana

2006-01-01

Extracting features is the first and one of the most crucial steps in recent image retrieval process. While the color features and the texture features of digital images can be extracted rather easily, the shape features and the layout features depend on reliable image segmentation. Unsupervised image segmentation, often used in image analysis, works on merely syntactical basis. That is, what an unsupervised segmentation algorithm can segment is only regions, but not objects. To obtain high-level objects, which is desirable in image retrieval, human assistance is needed. Supervised image segmentations schemes can improve the reliability of segmentation and segmentation refinement. In this paper we propose a novel interactive image segmentation technique that combines the reliability of a human expert with the precision of automated image segmentation. The iterative procedure can be considered a variation on the Blobworld algorithm introduced by Carson et al. from EECS Department, University of California, Berkeley. Starting with an initial segmentation as provided by the Blobworld framework, our algorithm, namely BlobContours, gradually updates it by recalculating every blob, based on the original features and the updated number of Gaussians. Since the original algorithm has hardly been designed for interactive processing we had to consider additional requirements for realizing a supervised segmentation scheme on the basis of Blobworld. Increasing transparency of the algorithm by applying usercontrolled iterative segmentation, providing different types of visualization for displaying the segmented image and decreasing computational time of segmentation are three major requirements which are discussed in detail.

The forward rainbow scattering of low energy protons by a graphene sheet

NASA Astrophysics Data System (ADS)

Ćosić, M.; Petrović, S.; Nešković, N.

2018-05-01

This article studies the rainbow scattering of 5-keV protons by the single sheet of free-standing graphene and its possible use as a tool for investigation of the ion-graphene interaction. The proton-graphene interaction potential was constructed by using the Doyle-Turner, ZBL, and Molière proton-carbon interaction potentials. The thermal motion of carbon atoms was included by averaging the potentials according to the Debye model. Proton trajectories were obtained by numerical solution of the corresponding Newton equations of motion. They were used to obtain the mapping of the proton initial positions to their scattering angles. Morphological properties of the introduced mapping including its multiplicity and the rainbow singularities were used to explain important features of the obtained angular distributions of transmitted protons.

Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.

PubMed

Conlin, Peter L; Chandler, Josephine R; Kerr, Benjamin

2014-10-01

In this review, we demonstrate how game theory can be a useful first step in modeling and understanding interactions among bacteria that produce and resist antibiotics. We introduce the basic features of evolutionary game theory and explore model microbial systems that correspond to some classical games. Each game discussed defines a different category of social interaction with different resulting population dynamics (exclusion, coexistence, bistability, cycling). We then explore how the framework can be extended to incorporate some of the complexity of natural microbial communities. Overall, the game theoretical perspective helps to guide our expectations about the evolution of some forms of antibiotic resistance and production because it makes clear the precise nature of social interaction in this context. Copyright © 2014 Elsevier Ltd. All rights reserved.

The human dynamic clamp as a paradigm for social interaction.

PubMed

Dumas, Guillaume; de Guzman, Gonzalo C; Tognoli, Emmanuelle; Kelso, J A Scott

2014-09-02

Social neuroscience has called for new experimental paradigms aimed toward real-time interactions. A distinctive feature of interactions is mutual information exchange: One member of a pair changes in response to the other while simultaneously producing actions that alter the other. Combining mathematical and neurophysiological methods, we introduce a paradigm called the human dynamic clamp (HDC), to directly manipulate the interaction or coupling between a human and a surrogate constructed to behave like a human. Inspired by the dynamic clamp used so productively in cellular neuroscience, the HDC allows a person to interact in real time with a virtual partner itself driven by well-established models of coordination dynamics. People coordinate hand movements with the visually observed movements of a virtual hand, the parameters of which depend on input from the subject's own movements. We demonstrate that HDC can be extended to cover a broad repertoire of human behavior, including rhythmic and discrete movements, adaptation to changes of pacing, and behavioral skill learning as specified by a virtual "teacher." We propose HDC as a general paradigm, best implemented when empirically verified theoretical or mathematical models have been developed in a particular scientific field. The HDC paradigm is powerful because it provides an opportunity to explore parameter ranges and perturbations that are not easily accessible in ordinary human interactions. The HDC not only enables to test the veracity of theoretical models, it also illuminates features that are not always apparent in real-time human social interactions and the brain correlates thereof.

Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests.

PubMed

Le, Trang T; Simmons, W Kyle; Misaki, Masaya; Bodurka, Jerzy; White, Bill C; Savitz, Jonathan; McKinney, Brett A

2017-09-15

Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n , these differential privacy methods are susceptible to overfitting. We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection. On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder. Code available at http://insilico.utulsa.edu/software/privateEC . brett-mckinney@utulsa.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Modelling robot construction systems

NASA Technical Reports Server (NTRS)

Grasso, Chris

1990-01-01

TROTER's are small, inexpensive robots that can work together to accomplish sophisticated construction tasks. To understand the issues involved in designing and operating a team of TROTER's, the robots and their components are being modeled. A TROTER system that features standardized component behavior is introduced. An object-oriented model implemented in the Smalltalk programming language is described and the advantages of the object-oriented approach for simulating robot and component interactions are discussed. The presentation includes preliminary results and a discussion of outstanding issues.

Identity method-a new tool for studying chemical fluctuations

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

Mackowiak, M., E-mail: majam@if.pw.edu.pl

Event-by-event fluctuations of the chemical composition of the hadronic system produced in nuclear collisions are believed to be sensitive to properties of the transition between confined and deconfined strongly interacting matter. In this paper a new technique for the study of chemical fluctuation, the identity method, is introduced and its features are discussed. The method is tested using data on central PbPb collisions at 40 A GeV registered by the NA49 experiment at the CERN SPS.

Fast-response underwater TSP investigation of subcritical instabilities of a cylinder in crossflow

NASA Astrophysics Data System (ADS)

Capone, Alessandro; Klein, Christian; Di Felice, Fabio; Beifuss, Uwe; Miozzi, Massimo

2015-10-01

We investigate the classic cylinder in crossflow case to test the effectiveness of a fast-response underwater temperature-sensitive paint coating (TSP) in providing highly resolved spatial and time observations of the action of a flow over a bluff body surface. The flow is investigated at Reynolds number <190 k, before the onset of the drag-crisis state. The obtained TSP image sequences convey an accurate description of the evolution of the main features in the fluid-cylinder interaction, like the separation line position, the pattern of the large coherent structures acting on the cylinder's surface and the small-scale intermittent streamwise arrays of vortices. Ad hoc data management and features extraction techniques are proposed which allow extraction of quantitative data, such as separation line position and vortex-shedding frequency, and results are compared to the literature. Use of TSP for water applications introduces an interesting point of view about the fluid-body interactions by focusing directly on the effect of the flow on the model surface.

Modeling strategic behavior in human-automation interaction - Why an 'aid' can (and should) go unused

NASA Technical Reports Server (NTRS)

Kirlik, Alex

1993-01-01

Task-offload aids (e.g., an autopilot, an 'intelligent' assistant) can be selectively engaged by the human operator to dynamically delegate tasks to automation. Introducing such aids eliminates some task demands but creates new ones associated with programming, engaging, and disengaging the aiding device via an interface. The burdens associated with managing automation can sometimes outweigh the potential benefits of automation to improved system performance. Aid design parameters and features of the overall multitask context combine to determine whether or not a task-offload aid will effectively support the operator. A modeling and sensitivity analysis approach is presented that identifies effective strategies for human-automation interaction as a function of three task-context parameters and three aid design parameters. The analysis and modeling approaches provide resources for predicting how a well-adapted operator will use a given task-offload aid, and for specifying aid design features that ensure that automation will provide effective operator support in a multitask environment.

Exploring biological interaction networks with tailored weighted quasi-bicliques

PubMed Central

2012-01-01

Background Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms, and other biological tasks. Due to the experimental and biological complexity, their computational exploitation faces many algorithmic challenges. Results We introduce novel weighted quasi-biclique problems to identify functional modules in biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also describe IP formulations to compute exact solutions for moderately sized networks. Conclusions We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from biological networks. PMID:22759421

In silico modeling of the yeast protein and protein family interaction network

NASA Astrophysics Data System (ADS)

Goh, K.-I.; Kahng, B.; Kim, D.

2004-03-01

Understanding of how protein interaction networks of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce an in silico ``coevolutionary'' model for the protein interaction network and the protein family network. The essential ingredient of the model includes the protein family identity and its robustness under evolution, as well as the three previously proposed: gene duplication, divergence, and mutation. This model produces a prototypical feature of complex networks in a wide range of parameter space, following the generalized Pareto distribution in connectivity. Moreover, we investigate other structural properties of our model in detail with some specific values of parameters relevant to the yeast Saccharomyces cerevisiae, showing excellent agreement with the empirical data. Our model indicates that the physical constraints encoded via the domain structure of proteins play a crucial role in protein interactions.

Anselm's Discovery of the Gross-Neveu Model in 1958

NASA Astrophysics Data System (ADS)

Shifman, M.

2013-06-01

The Gross-Neveu model comprises quantum field theory of N Dirac fermions interacting via four-fermion interaction in one spatial and one time dimension. It was introduced in 1974 (shortly after quantum chromodynamics was discovered) by David Gross and André Neveu [1] as a toy model which mimics two crucial features of quantum chromodynamics: asymptotic freedom and spontaneous breaking of a chiral symmetry. The model is based on N Dirac (i.e. complex two-component) fermions, ψ1, ψ2, ..., ψN. The Lagrangian of the Gross-Neveau model is [ {L} = bar{psi}ipartial_{mu}gamma^{mu}psi + frac{g^{2}}{2}(sumlimits_{k = 1}^{N}bar{psi}_{k}psi^{k})^{2}.

Intuitive representation of surface properties of biomolecules using BioBlender.

PubMed

Andrei, Raluca Mihaela; Callieri, Marco; Zini, Maria Francesca; Loni, Tiziana; Maraziti, Giuseppe; Pan, Mike Chen; Zoppè, Monica

2012-03-28

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties. Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work. On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features. Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface. A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein. Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu.

Intuitive representation of surface properties of biomolecules using BioBlender

PubMed Central

2012-01-01

Background In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties. Methods Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work. On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features. Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface. Results A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein. Conclusions Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu PMID:22536962

A Higher-Order Neural Network Design for Improving Segmentation Performance in Medical Image Series

NASA Astrophysics Data System (ADS)

Selvi, Eşref; Selver, M. Alper; Güzeliş, Cüneyt; Dicle, Oǧuz

2014-03-01

Segmentation of anatomical structures from medical image series is an ongoing field of research. Although, organs of interest are three-dimensional in nature, slice-by-slice approaches are widely used in clinical applications because of their ease of integration with the current manual segmentation scheme. To be able to use slice-by-slice techniques effectively, adjacent slice information, which represents likelihood of a region to be the structure of interest, plays critical role. Recent studies focus on using distance transform directly as a feature or to increase the feature values at the vicinity of the search area. This study presents a novel approach by constructing a higher order neural network, the input layer of which receives features together with their multiplications with the distance transform. This allows higher-order interactions between features through the non-linearity introduced by the multiplication. The application of the proposed method to 9 CT datasets for segmentation of the liver shows higher performance than well-known higher order classification neural networks.

Multiscale wavelet representations for mammographic feature analysis

NASA Astrophysics Data System (ADS)

Laine, Andrew F.; Song, Shuwu

1992-12-01

This paper introduces a novel approach for accomplishing mammographic feature analysis through multiresolution representations. We show that efficient (nonredundant) representations may be identified from digital mammography and used to enhance specific mammographic features within a continuum of scale space. The multiresolution decomposition of wavelet transforms provides a natural hierarchy in which to embed an interactive paradigm for accomplishing scale space feature analysis. Choosing wavelets (or analyzing functions) that are simultaneously localized in both space and frequency, results in a powerful methodology for image analysis. Multiresolution and orientation selectivity, known biological mechanisms in primate vision, are ingrained in wavelet representations and inspire the techniques presented in this paper. Our approach includes local analysis of complete multiscale representations. Mammograms are reconstructed from wavelet coefficients, enhanced by linear, exponential and constant weight functions localized in scale space. By improving the visualization of breast pathology we can improve the changes of early detection of breast cancers (improve quality) while requiring less time to evaluate mammograms for most patients (lower costs).

Effects of chirp on two-dimensional Fourier transform electronic spectra.

PubMed

Tekavec, Patrick F; Myers, Jeffrey A; Lewis, Kristin L M; Fuller, Franklin D; Ogilvie, Jennifer P

2010-05-24

We examine the effect that pulse chirp has on the shape of two- dimensional electronic spectra through calculations and experiments. For the calculations we use a model two electronic level system with a solvent interaction represented by a simple Gaussian correlation function and compare the resulting spectra to experiments carried out on an organic dye molecule (Rhodamine 800). Both calculations and experiments show that distortions due to chirp are most significant when the pulses used in the experiment have different amounts of chirp, introducing peak shape asymmetry that could be interpreted as spectrally dependent relaxation. When all pulses have similar chirp the distortions are reduced but still affect the anti-diagonal symmetry of the peak shapes and introduce negative features that could be interpreted as excited state absorption.

Genome complexity, robustness and genetic interactions in digital organisms

NASA Astrophysics Data System (ADS)

Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

1999-08-01

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Genome complexity, robustness and genetic interactions in digital organisms.

PubMed

Lenski, R E; Ofria, C; Collier, T C; Adami, C

1999-08-12

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Multi-Axis Force Sensor for Human-Robot Interaction Sensing in a Rehabilitation Robotic Device.

PubMed

Grosu, Victor; Grosu, Svetlana; Vanderborght, Bram; Lefeber, Dirk; Rodriguez-Guerrero, Carlos

2017-06-05

Human-robot interaction sensing is a compulsory feature in modern robotic systems where direct contact or close collaboration is desired. Rehabilitation and assistive robotics are fields where interaction forces are required for both safety and increased control performance of the device with a more comfortable experience for the user. In order to provide an efficient interaction feedback between the user and rehabilitation device, high performance sensing units are demanded. This work introduces a novel design of a multi-axis force sensor dedicated for measuring pelvis interaction forces in a rehabilitation exoskeleton device. The sensor is conceived such that it has different sensitivity characteristics for the three axes of interest having also movable parts in order to allow free rotations and limit crosstalk errors. Integrated sensor electronics make it easy to acquire and process data for a real-time distributed system architecture. Two of the developed sensors are integrated and tested in a complex gait rehabilitation device for safe and compliant control.

Predicting a small molecule-kinase interaction map: A machine learning approach

PubMed Central

2011-01-01

Background We present a machine learning approach to the problem of protein ligand interaction prediction. We focus on a set of binding data obtained from 113 different protein kinases and 20 inhibitors. It was attained through ATP site-dependent binding competition assays and constitutes the first available dataset of this kind. We extract information about the investigated molecules from various data sources to obtain an informative set of features. Results A Support Vector Machine (SVM) as well as a decision tree algorithm (C5/See5) is used to learn models based on the available features which in turn can be used for the classification of new kinase-inhibitor pair test instances. We evaluate our approach using different feature sets and parameter settings for the employed classifiers. Moreover, the paper introduces a new way of evaluating predictions in such a setting, where different amounts of information about the binding partners can be assumed to be available for training. Results on an external test set are also provided. Conclusions In most of the cases, the presented approach clearly outperforms the baseline methods used for comparison. Experimental results indicate that the applied machine learning methods are able to detect a signal in the data and predict binding affinity to some extent. For SVMs, the binding prediction can be improved significantly by using features that describe the active site of a kinase. For C5, besides diversity in the feature set, alignment scores of conserved regions turned out to be very useful. PMID:21708012

Constraining OCT with Knowledge of Device Design Enables High Accuracy Hemodynamic Assessment of Endovascular Implants.

PubMed

O'Brien, Caroline C; Kolandaivelu, Kumaran; Brown, Jonathan; Lopes, Augusto C; Kunio, Mie; Kolachalama, Vijaya B; Edelman, Elazer R

2016-01-01

Stacking cross-sectional intravascular images permits three-dimensional rendering of endovascular implants, yet introduces between-frame uncertainties that limit characterization of device placement and the hemodynamic microenvironment. In a porcine coronary stent model, we demonstrate enhanced OCT reconstruction with preservation of between-frame features through fusion with angiography and a priori knowledge of stent design. Strut positions were extracted from sequential OCT frames. Reconstruction with standard interpolation generated discontinuous stent structures. By computationally constraining interpolation to known stent skeletons fitted to 3D 'clouds' of OCT-Angio-derived struts, implant anatomy was resolved, accurately rendering features from implant diameter and curvature (n = 1 vessels, r2 = 0.91, 0.90, respectively) to individual strut-wall configurations (average displacement error ~15 μm). This framework facilitated hemodynamic simulation (n = 1 vessel), showing the critical importance of accurate anatomic rendering in characterizing both quantitative and basic qualitative flow patterns. Discontinuities with standard approaches systematically introduced noise and bias, poorly capturing regional flow effects. In contrast, the enhanced method preserved multi-scale (local strut to regional stent) flow interactions, demonstrating the impact of regional contexts in defining the hemodynamic consequence of local deployment errors. Fusion of planar angiography and knowledge of device design permits enhanced OCT image analysis of in situ tissue-device interactions. Given emerging interests in simulation-derived hemodynamic assessment as surrogate measures of biological risk, such fused modalities offer a new window into patient-specific implant environments.

The human dynamic clamp as a paradigm for social interaction

PubMed Central

Dumas, Guillaume; de Guzman, Gonzalo C.; Tognoli, Emmanuelle; Kelso, J. A. Scott

2014-01-01

Social neuroscience has called for new experimental paradigms aimed toward real-time interactions. A distinctive feature of interactions is mutual information exchange: One member of a pair changes in response to the other while simultaneously producing actions that alter the other. Combining mathematical and neurophysiological methods, we introduce a paradigm called the human dynamic clamp (HDC), to directly manipulate the interaction or coupling between a human and a surrogate constructed to behave like a human. Inspired by the dynamic clamp used so productively in cellular neuroscience, the HDC allows a person to interact in real time with a virtual partner itself driven by well-established models of coordination dynamics. People coordinate hand movements with the visually observed movements of a virtual hand, the parameters of which depend on input from the subject’s own movements. We demonstrate that HDC can be extended to cover a broad repertoire of human behavior, including rhythmic and discrete movements, adaptation to changes of pacing, and behavioral skill learning as specified by a virtual “teacher.” We propose HDC as a general paradigm, best implemented when empirically verified theoretical or mathematical models have been developed in a particular scientific field. The HDC paradigm is powerful because it provides an opportunity to explore parameter ranges and perturbations that are not easily accessible in ordinary human interactions. The HDC not only enables to test the veracity of theoretical models, it also illuminates features that are not always apparent in real-time human social interactions and the brain correlates thereof. PMID:25114256

Analysis on vertical directional couplers with long range surface plasmons for multilayer optical routing

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

Alam, B., E-mail: badrul.alam@uniroma1.it; Veroli, A.; Benedetti, A.

2016-08-28

A structure featuring vertical directional coupling of long-range surface plasmon polaritons between strip waveguides at λ = 1.55 μm is investigated with the aim of producing efficient elements that enable optical multilayer routing for 3D photonics. We have introduced a practical computational method to calculate the interaction on the bent part. This method allows us both to assess the importance of the interaction in the bent part and to control it by a suitable choice of the fabrication parameters that helps also to restrain effects due to fabrication issues. The scheme adopted here allows to reduce the insertion losses compared with othermore » planar and multilayer devices.« less

Exploring social structure effect on language evolution based on a computational model

NASA Astrophysics Data System (ADS)

Gong, Tao; Minett, James; Wang, William

2008-06-01

A compositionality-regularity coevolution model is adopted to explore the effect of social structure on language emergence and maintenance. Based on this model, we explore language evolution in three experiments, and discuss the role of a popular agent in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of inter-community communications and that of simple linguistic features on convergence of communal languages in two communities. This work embodies several important interactions during social learning, and introduces a new approach that manipulates individuals' probabilities to participate in social interactions to study the effect of social structure. We hope it will stimulate further theoretical and empirical explorations on language evolution in a social environment.

Model-Driven Approach for Body Area Network Application Development.

PubMed

Venčkauskas, Algimantas; Štuikys, Vytautas; Jusas, Nerijus; Burbaitė, Renata

2016-05-12

This paper introduces the sensor-networked IoT model as a prototype to support the design of Body Area Network (BAN) applications for healthcare. Using the model, we analyze the synergistic effect of the functional requirements (data collection from the human body and transferring it to the top level) and non-functional requirements (trade-offs between energy-security-environmental factors, treated as Quality-of-Service (QoS)). We use feature models to represent the requirements at the earliest stage for the analysis and describe a model-driven methodology to design the possible BAN applications. Firstly, we specify the requirements as the problem domain (PD) variability model for the BAN applications. Next, we introduce the generative technology (meta-programming as the solution domain (SD)) and the mapping procedure to map the PD feature-based variability model onto the SD feature model. Finally, we create an executable meta-specification that represents the BAN functionality to describe the variability of the problem domain though transformations. The meta-specification (along with the meta-language processor) is a software generator for multiple BAN-oriented applications. We validate the methodology with experiments and a case study to generate a family of programs for the BAN sensor controllers. This enables to obtain the adequate measure of QoS efficiently through the interactive adjustment of the meta-parameter values and re-generation process for the concrete BAN application.

Model-Driven Approach for Body Area Network Application Development

PubMed Central

Venčkauskas, Algimantas; Štuikys, Vytautas; Jusas, Nerijus; Burbaitė, Renata

2016-01-01

This paper introduces the sensor-networked IoT model as a prototype to support the design of Body Area Network (BAN) applications for healthcare. Using the model, we analyze the synergistic effect of the functional requirements (data collection from the human body and transferring it to the top level) and non-functional requirements (trade-offs between energy-security-environmental factors, treated as Quality-of-Service (QoS)). We use feature models to represent the requirements at the earliest stage for the analysis and describe a model-driven methodology to design the possible BAN applications. Firstly, we specify the requirements as the problem domain (PD) variability model for the BAN applications. Next, we introduce the generative technology (meta-programming as the solution domain (SD)) and the mapping procedure to map the PD feature-based variability model onto the SD feature model. Finally, we create an executable meta-specification that represents the BAN functionality to describe the variability of the problem domain though transformations. The meta-specification (along with the meta-language processor) is a software generator for multiple BAN-oriented applications. We validate the methodology with experiments and a case study to generate a family of programs for the BAN sensor controllers. This enables to obtain the adequate measure of QoS efficiently through the interactive adjustment of the meta-parameter values and re-generation process for the concrete BAN application. PMID:27187394

Automated global structure extraction for effective local building block processing in XCS.

PubMed

Butz, Martin V; Pelikan, Martin; Llorà, Xavier; Goldberg, David E

2006-01-01

Learning Classifier Systems (LCSs), such as the accuracy-based XCS, evolve distributed problem solutions represented by a population of rules. During evolution, features are specialized, propagated, and recombined to provide increasingly accurate subsolutions. Recently, it was shown that, as in conventional genetic algorithms (GAs), some problems require efficient processing of subsets of features to find problem solutions efficiently. In such problems, standard variation operators of genetic and evolutionary algorithms used in LCSs suffer from potential disruption of groups of interacting features, resulting in poor performance. This paper introduces efficient crossover operators to XCS by incorporating techniques derived from competent GAs: the extended compact GA (ECGA) and the Bayesian optimization algorithm (BOA). Instead of simple crossover operators such as uniform crossover or one-point crossover, ECGA or BOA-derived mechanisms are used to build a probabilistic model of the global population and to generate offspring classifiers locally using the model. Several offspring generation variations are introduced and evaluated. The results show that it is possible to achieve performance similar to runs with an informed crossover operator that is specifically designed to yield ideal problem-dependent exploration, exploiting provided problem structure information. Thus, we create the first competent LCSs, XCS/ECGA and XCS/BOA, that detect dependency structures online and propagate corresponding lower-level dependency structures effectively without any information about these structures given in advance.

A study on the application of voice interaction in automotive human machine interface experience design

NASA Astrophysics Data System (ADS)

Huang, Zhaohui; Huang, Xiemin

2018-04-01

This paper, firstly, introduces the application trend of the integration of multi-channel interactions in automotive HMI ((Human Machine Interface) from complex information models faced by existing automotive HMI and describes various interaction modes. By comparing voice interaction and touch screen, gestures and other interaction modes, the potential and feasibility of voice interaction in automotive HMI experience design are concluded. Then, the related theories of voice interaction, identification technologies, human beings' cognitive models of voices and voice design methods are further explored. And the research priority of this paper is proposed, i.e. how to design voice interaction to create more humane task-oriented dialogue scenarios to enhance interactive experiences of automotive HMI. The specific scenarios in driving behaviors suitable for the use of voice interaction are studied and classified, and the usability principles and key elements for automotive HMI voice design are proposed according to the scenario features. Then, through the user participatory usability testing experiment, the dialogue processes of voice interaction in automotive HMI are defined. The logics and grammars in voice interaction are classified according to the experimental results, and the mental models in the interaction processes are analyzed. At last, the voice interaction design method to create the humane task-oriented dialogue scenarios in the driving environment is proposed.

An elementary model of money circulation

NASA Astrophysics Data System (ADS)

Pokrovskii, Vladimir N.; Schinckus, Christophe

2016-12-01

This paper investigates money circulation for a system, consisting of a production system, the government, a central bank, commercial banks and many customers of the commercial banks. A set of equations for the system is written; the theory determines the main features of interaction between production and money circulation. Investigation of the equations in a steady-state situation reveals some relationship among output of the production system and monetary variables. The relation of quantity theory of money is confirmed, whereas a new concept of the efficiency of the system is introduced.

User clustering in smartphone applications.

PubMed

Schaefers, Klaus; Ribeiro, David

2012-01-01

In the context of mobile health applications usability is a crucial factor to achieve user acceptance. The successful user interface (UI) design requires a deep understanding of the needs and requirements of the targeted audience. This paper explores the application of the K-Means algorithm on smartphone usage data in order to offer Human Computer Interaction (HCI) specialists a better insight into their user group. Two different feature space representations are introduced and used to identify persona like stereotypes in a real world data set, which was obtained from a public available smartphone application.

Couplings

NASA Astrophysics Data System (ADS)

Stošić, Dušan; Auroux, Aline

Basic principles of calorimetry coupled with other techniques are introduced. These methods are used in heterogeneous catalysis for characterization of acidic, basic and red-ox properties of solid catalysts. Estimation of these features is achieved by monitoring the interaction of various probe molecules with the surface of such materials. Overview of gas phase, as well as liquid phase techniques is given. Special attention is devoted to coupled calorimetry-volumetry method. Furthermore, the influence of different experimental parameters on the results of these techniques is discussed, since it is known that they can significantly influence the evaluation of catalytic properties of investigated materials.

Exploring excited eigenstates of many-body systems using the functional renormalization group

NASA Astrophysics Data System (ADS)

Klöckner, Christian; Kennes, Dante Marvin; Karrasch, Christoph

2018-05-01

We introduce approximate, functional renormalization group based schemes to obtain correlation functions in pure excited eigenstates of large fermionic many-body systems at arbitrary energies. The algorithms are thoroughly benchmarked and their strengths and shortcomings are documented using a one-dimensional interacting tight-binding chain as a prototypical testbed. We study two "toy applications" from the world of Luttinger liquid physics: the survival of power laws in lowly excited states as well as the spectral function of high-energy "block" excitations, which feature several single-particle Fermi edges.

Technique to measure wavenumber mismatch between quadratically interacting modes

NASA Astrophysics Data System (ADS)

Hajj, M. R.; Davila, J. B.; Miksad, R. W.; Powers, E. J.

1995-02-01

Nonlinear energy cascade by means of three-wave resonant interactions is a characteristic feature of transitioning and turbulent flows. Resonant wavenumber mismatch between these interacting modes can arise from the dispersive characteristics of the interacting waves and from spectral broadening due to random effects. In this paper, a general technique is presented to estimate the average level of instantaneous wavenumber mismatch, (Delta k) = (k(sub m) - k(sub i) - k(sub j)), between components whose frequencies obey the resonant selection condition, f(sub m) - f(sub i) - f(sub j) = 0. Cross-correlation of the auto-bispectrum is used to quantify the level of mismatch. The concept of bispectrum coupling coherency is introduced to determine the confidence level in the wavenumber mismatch estimates. These techniques are then applied to measure wavenumber mismatch in the transitioning field of a plane wake. The results show that the average of the instantaneous mismatch between the actual interacting modes (k(sub m) - k(sub i) - k(sub j)) is in general not equal to the mismatch between the average wavenumbers of each interacting mode (k(sub m) - (k(sub i)) - (k(sub j)).

Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers

NASA Astrophysics Data System (ADS)

Richa, Tambi; Ide, Soichiro; Suzuki, Ryosuke; Ebina, Teppei; Kuroda, Yutaka

2017-02-01

Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol. We reduced the computational time from 8.5 min per sequence in H-DROP to 14 s per sequence in Fast H-DROP on an 8 Xeon processor Linux server by using SWISS-PROT instead of Genbank non-redundant (nr) database for generating the PSSMs. The sensitivity and precision of Fast H-DROP assessed by cross-validation were 33.7 and 36.2%, which were merely 2% lower than that of H-DROP. The reduced computational time of Fast H-DROP, without affecting prediction performances, makes it more interactive and user-friendly. Fast H-DROP and H-DROP are freely available from http://domserv.lab.tuat.ac.jp/.

Nonlinear theory of shocked sound propagation in a nearly choked duct flow

NASA Technical Reports Server (NTRS)

Myers, M. K.; Callegari, A. J.

1982-01-01

The development of shocks in the sound field propagating through a nearly choked duct flow is analyzed by extending a quasi-one dimensional theory. The theory is applied to the case in which sound is introduced into the flow by an acoustic source located in the vicinity of a near-sonic throat. Analytical solutions for the field are obtained which illustrate the essential features of the nonlinear interaction between sound and flow. Numerical results are presented covering ranges of variation of source strength, throat Mach number, and frequency. It is found that the development of shocks leads to appreciable attenuation of acoustic power transmitted upstream through the near-sonic flow. It is possible, for example, that the power loss in the fundamental harmonic can be as much as 90% of that introduced at the source.

Dark Skies, Bright Kids Year 7

NASA Astrophysics Data System (ADS)

Bittle, Lauren E.; Johnson, Kelsey E.; Borish, H. Jacob; Burkhardt, Andrew; Firebaugh, Ariel; Hancock, Danielle; Rochford Hayes, Christian; Linden, Sean; Liss, Sandra; Matthews, Allison; Prager, Brian; Pryal, Matthew; Sokal, Kimberly R.; Troup, Nicholas William; Wenger, Trey

2016-01-01

We present updates from our seventh year of operation including new club content, continued assessments, and our fifth annual Star Party. Dark Skies, Bright Kids (DSBK) is an entirely volunteer-run outreach organization based out of the Department of Astronomy at the University of Virginia. Our core mission is to enhance elementary science education and literacy in Central Virginia through fun, hands-on activities that introduce basic Astronomy concepts. Our primary focus is hosting an 8-10 week after-school astronomy club at underserved elementary and middle schools. Each week, DSBK volunteers take the role of coaches to introduce astronomy-related concepts ranging from the Solar System to galaxies to astrobiology, and to lead students in interactive learning activities. Another hallmark of DSBK is hosting our Annual Central Virginia Star Party, a free event open to the community featuring star-gazing and planetarium shows.

Free stream turbulence and density ratio effects on the interaction region of a jet in a cross flow

NASA Technical Reports Server (NTRS)

Wark, C. E.; Foss, J. F.

1984-01-01

Jets of low temperature air are introduced into the aft sections of gas turbine combustors for the purpose of cooling the high temperature gases and quenching the combustion reactions. Research studies, motivated by this complex flow field, have been executed by introducing a heated jet into the cross stream of a wind tunnel. The investigation by Kamotani and Greber stands as a prime example of such investigations and it serves as the principal reference for the present study. The low disturbance level of the cross stream, in their study and in similar research investigations, is compatible with an interest in identifying the basic features of this flow field. The influence of the prototypes' strongly disturbed cross flow is not, however, made apparent in these prior investigations.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

NASA Astrophysics Data System (ADS)

Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

2015-06-01

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

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

Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.

2015-06-21

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including thosemore » corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.« less

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

PubMed Central

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C.; Noble, William Stafford; Yue, Feng; Li, Qunhua

2017-01-01

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach. PMID:28855260

A statistical mechanics approach to Granovetter theory

NASA Astrophysics Data System (ADS)

Barra, Adriano; Agliari, Elena

2012-05-01

In this paper we try to bridge breakthroughs in quantitative sociology/econometrics, pioneered during the last decades by Mac Fadden, Brock-Durlauf, Granovetter and Watts-Strogatz, by introducing a minimal model able to reproduce essentially all the features of social behavior highlighted by these authors. Our model relies on a pairwise Hamiltonian for decision-maker interactions which naturally extends the multi-populations approaches by shifting and biasing the pattern definitions of a Hopfield model of neural networks. Once introduced, the model is investigated through graph theory (to recover Granovetter and Watts-Strogatz results) and statistical mechanics (to recover Mac-Fadden and Brock-Durlauf results). Due to the internal symmetries of our model, the latter is obtained as the relaxation of a proper Markov process, allowing even to study its out-of-equilibrium properties. The method used to solve its equilibrium is an adaptation of the Hamilton-Jacobi technique recently introduced by Guerra in the spin-glass scenario and the picture obtained is the following: shifting the patterns from [-1,+1]→[0.+1] implies that the larger the amount of similarities among decision makers, the stronger their relative influence, and this is enough to explain both the different role of strong and weak ties in the social network as well as its small-world properties. As a result, imitative interaction strengths seem essentially a robust request (enough to break the gauge symmetry in the couplings), furthermore, this naturally leads to a discrete choice modelization when dealing with the external influences and to imitative behavior à la Curie-Weiss as the one introduced by Brock and Durlauf.

Boosting compound-protein interaction prediction by deep learning.

PubMed

Tian, Kai; Shao, Mingyu; Wang, Yang; Guan, Jihong; Zhou, Shuigeng

2016-11-01

The identification of interactions between compounds and proteins plays an important role in network pharmacology and drug discovery. However, experimentally identifying compound-protein interactions (CPIs) is generally expensive and time-consuming, computational approaches are thus introduced. Among these, machine-learning based methods have achieved a considerable success. However, due to the nonlinear and imbalanced nature of biological data, many machine learning approaches have their own limitations. Recently, deep learning techniques show advantages over many state-of-the-art machine learning methods in some applications. In this study, we aim at improving the performance of CPI prediction based on deep learning, and propose a method called DL-CPI (the abbreviation of Deep Learning for Compound-Protein Interactions prediction), which employs deep neural network (DNN) to effectively learn the representations of compound-protein pairs. Extensive experiments show that DL-CPI can learn useful features of compound-protein pairs by a layerwise abstraction, and thus achieves better prediction performance than existing methods on both balanced and imbalanced datasets. Copyright © 2016 Elsevier Inc. All rights reserved.

Mechanism Responsible for Intercalation of Dimethyl Sulfoxide in Kaolinite: Molecular Dynamics Simulations.

PubMed

Zhang, Shuai; Liu, Qinfu; Cheng, Hongfei; Gao, Feng; Liu, Cun; Teppen, Brian J

2018-01-01

Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space. The results showed that the favorable interaction of DMSO with both kaolinite interlayer octahedral surface and tetrahedral surface can help in introducing DMSO enter kaolinite interlayer. The hydroxyl groups on octahedral surface functioned as H-donors attracting the S=O groups of DMSO through hydrogen bonding interaction. The tetrahedral surface featuring hydrophobic property attracted the methyl groups of DMSO through hydrophobic interaction. The results provided a detailed picture of the energetics and interlayer structure of kaolinite-DMSO intercalate.

Computer simulation of a cellular automata model for the immune response in a retrovirus system

NASA Astrophysics Data System (ADS)

Pandey, R. B.

1989-02-01

Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B ca ( B cq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B ca ( B cq).

Dependency-based long short term memory network for drug-drug interaction extraction.

PubMed

Wang, Wei; Yang, Xi; Yang, Canqun; Guo, Xiaowei; Zhang, Xiang; Wu, Chengkun

2017-12-28

Drug-drug interaction extraction (DDI) needs assistance from automated methods to address the explosively increasing biomedical texts. In recent years, deep neural network based models have been developed to address such needs and they have made significant progress in relation identification. We propose a dependency-based deep neural network model for DDI extraction. By introducing the dependency-based technique to a bi-directional long short term memory network (Bi-LSTM), we build three channels, namely, Linear channel, DFS channel and BFS channel. All of these channels are constructed with three network layers, including embedding layer, LSTM layer and max pooling layer from bottom up. In the embedding layer, we extract two types of features, one is distance-based feature and another is dependency-based feature. In the LSTM layer, a Bi-LSTM is instituted in each channel to better capture relation information. Then max pooling is used to get optimal features from the entire encoding sequential data. At last, we concatenate the outputs of all channels and then link it to the softmax layer for relation identification. To the best of our knowledge, our model achieves new state-of-the-art performance with the F-score of 72.0% on the DDIExtraction 2013 corpus. Moreover, our approach obtains much higher Recall value compared to the existing methods. The dependency-based Bi-LSTM model can learn effective relation information with less feature engineering in the task of DDI extraction. Besides, the experimental results show that our model excels at balancing the Precision and Recall values.

A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences.

PubMed

Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

2013-11-07

Protein-Protein interaction (PPI) is one of the most important data in understanding the cellular processes. Many interesting methods have been proposed in order to predict PPIs. However, the methods which are based on the sequence of proteins as a prior knowledge are more universal. In this paper, a sequence-based, fast, and adaptive PPI prediction method is introduced to assign two proteins to an interaction class (yes, no). First, in order to improve the presentation of the sequences, twelve physicochemical properties of amino acid have been used by different representation methods to transform the sequence of protein pairs into different feature vectors. Then, for speeding up the learning process and reducing the effect of noise PPI data, principal component analysis (PCA) is carried out as a proper feature extraction algorithm. Finally, a new and adaptive Learning Vector Quantization (LVQ) predictor is designed to deal with different models of datasets that are classified into balanced and imbalanced datasets. The accuracy of 93.88%, 90.03%, and 89.72% has been found on S. cerevisiae, H. pylori, and independent datasets, respectively. The results of various experiments indicate the efficiency and validity of the method. © 2013 Published by Elsevier Ltd.

minepath.org: a free interactive pathway analysis web server.

PubMed

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Introducing and Evaluating the Behavior of Non-Verbal Features in the Virtual Learning

ERIC Educational Resources Information Center

Dharmawansa, Asanka D.; Fukumura, Yoshimi; Marasinghe, Ashu; Madhuwanthi, R. A. M.

2015-01-01

The objective of this research is to introduce the behavior of non-verbal features of e-Learners in the virtual learning environment to establish a fair representation of the real user by an avatar who represents the e-Learner in the virtual environment and to distinguish the deportment of the non-verbal features during the virtual learning…

Quantum Interactive Dualism: An Alternative to Materialism

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

Stapp, Henry P

2005-06-01

Materialism rest implicitly upon the general conception of nature promoted by Galileo and Newton during the seventeenth century. It features the causal closure of the physical: The course of physically described events for all time is fixed by laws that refer exclusively to the physically describeable features of nature, and initial conditions on these feature. No reference to subjective thoughts or feeling of human beings enter. That simple conception of nature was found during the first quarter of the twentieth century to be apparently incompatible with the empirical facts. The founders of quantum theory created a new fundamental physical theory,more » quantum theory, which introduced crucially into the causal structure certain conscious choices made by human agents about how they will act. These conscious human choices are ''free'' in the sense that they are not fixed by the known laws. But they can influence the course of physically described events. Thus the principle of the causal closure of the physical fails. Applications in psycho-neuro-dynamics are described.« less

Synchronization and Collective Dynamics of Flagella and Cilia as Hydrodynamically Coupled Oscillators

NASA Astrophysics Data System (ADS)

Uchida, Nariya; Golestanian, Ramin; Bennett, Rachel R.

2017-10-01

Cooperative motion of flagella and cilia faciliates swimming of microorganisms and material transport in the body of multicellular organisms. Using minimal models, we address the roles of hydrodynamic interaction in synchronization and collective dynamics of flagella and cilia. Collective synchronization of bacterial flagella is studied with a model of bacterial carpets. Cilia and eukaryotic flagella are characterized by periodic modulation of their driving forces, which produces various patterns of two-body synchronization and metachronal waves. Long-range nature of the interaction introduces novel features in the dynamics of these model systems. The flagella of a swimmer synchronize also by a viscous drag force mediated through the swimmer's body. Recent advance in experimental studies of the collective dynamics of flagella, cilia and related artificial systems are summarized.

Fourier decomposition of payoff matrix for symmetric three-strategy games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2014-10-01

In spatial evolutionary games the payoff matrices are used to describe pair interactions among neighboring players located on a lattice. Now we introduce a way how the payoff matrices can be built up as a sum of payoff components reflecting basic symmetries. For the two-strategy games this decomposition reproduces interactions characteristic to the Ising model. For the three-strategy symmetric games the Fourier components can be classified into four types representing games with self-dependent and cross-dependent payoffs, variants of three-strategy coordinations, and the rock-scissors-paper (RSP) game. In the absence of the RSP component the game is a potential game. The resultant potential matrix has been evaluated. The general features of these systems are analyzed when the game is expressed by the linear combinations of these components.

Interaction with a field: a simple integrable model with backreaction

NASA Astrophysics Data System (ADS)

Mouchet, Amaury

2008-09-01

The classical model of an oscillator linearly coupled to a string captures, for a low price in technique, many general features of more realistic models for describing a particle interacting with a field or an atom in an electromagnetic cavity. The scattering matrix and the asymptotic in and out-waves on the string can be computed exactly and the phenomenon of resonant scattering can be introduced in the simplest way. The dissipation induced by the coupling of the oscillator to the string can be studied completely. In the case of a d'Alembert string, the backreaction leads to an Abraham-Lorentz-Dirac-like equation. In the case of a Klein-Gordon string, one can see explicitly how radiation governs the (meta)stability of the (quasi)bounded mode.

Topological invariant and cotranslational symmetry in strongly interacting multi-magnon systems

NASA Astrophysics Data System (ADS)

Qin, Xizhou; Mei, Feng; Ke, Yongguan; Zhang, Li; Lee, Chaohong

2018-01-01

It is still an outstanding challenge to characterize and understand the topological features of strongly interacting states such as bound states in interacting quantum systems. Here, by introducing a cotranslational symmetry in an interacting multi-particle quantum system, we systematically develop a method to define a Chern invariant, which is a generalization of the well-known Thouless-Kohmoto-Nightingale-den Nijs invariant, for identifying strongly interacting topological states. As an example, we study the topological multi-magnon states in a generalized Heisenberg XXZ model, which can be realized by the currently available experiment techniques of cold atoms (Aidelsburger et al 2013 Phys. Rev. Lett. 111, 185301; Miyake et al 2013 Phys. Rev. Lett. 111, 185302). Through calculating the two-magnon excitation spectrum and the defined Chern number, we explore the emergence of topological edge bound states and give their topological phase diagram. We also analytically derive an effective single-particle Hofstadter superlattice model for a better understanding of the topological bound states. Our results not only provide a new approach to defining a topological invariant for interacting multi-particle systems, but also give insights into the characterization and understanding of strongly interacting topological states.

Effect of auditory presentation of words on color naming: the intermodal Stroop effect.

PubMed

Shimada, H

1990-06-01

To verify two hypotheses (the automatic parallel-processing model vs the feature integration theory) using the Stroop effect, an intermodal presentation method was introduced. The intermodal presentation (auditory presentation of the distractor word and visual presentation of color patch) separates completely the color and word information. Subjects were required to name the color patch on the CRT and to ignore the auditory color-word in the present experiment. A 5 (stimulus onset asynchronies) x 4 (levels of congruency) analysis of variance with repeated measures was performed on the response times. Two main effects and an interactive effect were significant. The findings indicate that without the presentation of color and word component in the same spatial location the Stroop effect occurs. These results suggest that the feature-integration theory cannot explain the mechanisms underlying the Stroop effect.

Wavelet processing techniques for digital mammography

NASA Astrophysics Data System (ADS)

Laine, Andrew F.; Song, Shuwu

1992-09-01

This paper introduces a novel approach for accomplishing mammographic feature analysis through multiresolution representations. We show that efficient (nonredundant) representations may be identified from digital mammography and used to enhance specific mammographic features within a continuum of scale space. The multiresolution decomposition of wavelet transforms provides a natural hierarchy in which to embed an interactive paradigm for accomplishing scale space feature analysis. Similar to traditional coarse to fine matching strategies, the radiologist may first choose to look for coarse features (e.g., dominant mass) within low frequency levels of a wavelet transform and later examine finer features (e.g., microcalcifications) at higher frequency levels. In addition, features may be extracted by applying geometric constraints within each level of the transform. Choosing wavelets (or analyzing functions) that are simultaneously localized in both space and frequency, results in a powerful methodology for image analysis. Multiresolution and orientation selectivity, known biological mechanisms in primate vision, are ingrained in wavelet representations and inspire the techniques presented in this paper. Our approach includes local analysis of complete multiscale representations. Mammograms are reconstructed from wavelet representations, enhanced by linear, exponential and constant weight functions through scale space. By improving the visualization of breast pathology we can improve the chances of early detection of breast cancers (improve quality) while requiring less time to evaluate mammograms for most patients (lower costs).

Computer-Aided Breast Cancer Diagnosis with Optimal Feature Sets: Reduction Rules and Optimization Techniques.

PubMed

Mathieson, Luke; Mendes, Alexandre; Marsden, John; Pond, Jeffrey; Moscato, Pablo

2017-01-01

This chapter introduces a new method for knowledge extraction from databases for the purpose of finding a discriminative set of features that is also a robust set for within-class classification. Our method is generic and we introduce it here in the field of breast cancer diagnosis from digital mammography data. The mathematical formalism is based on a generalization of the k-Feature Set problem called (α, β)-k-Feature Set problem, introduced by Cotta and Moscato (J Comput Syst Sci 67(4):686-690, 2003). This method proceeds in two steps: first, an optimal (α, β)-k-feature set of minimum cardinality is identified and then, a set of classification rules using these features is obtained. We obtain the (α, β)-k-feature set in two phases; first a series of extremely powerful reduction techniques, which do not lose the optimal solution, are employed; and second, a metaheuristic search to identify the remaining features to be considered or disregarded. Two algorithms were tested with a public domain digital mammography dataset composed of 71 malignant and 75 benign cases. Based on the results provided by the algorithms, we obtain classification rules that employ only a subset of these features.

Agent-Based Models in Social Physics

NASA Astrophysics Data System (ADS)

Quang, Le Anh; Jung, Nam; Cho, Eun Sung; Choi, Jae Han; Lee, Jae Woo

2018-06-01

We review the agent-based models (ABM) on social physics including econophysics. The ABM consists of agent, system space, and external environment. The agent is autonomous and decides his/her behavior by interacting with the neighbors or the external environment with the rules of behavior. Agents are irrational because they have only limited information when they make decisions. They adapt using learning from past memories. Agents have various attributes and are heterogeneous. ABM is a non-equilibrium complex system that exhibits various emergence phenomena. The social complexity ABM describes human behavioral characteristics. In ABMs of econophysics, we introduce the Sugarscape model and the artificial market models. We review minority games and majority games in ABMs of game theory. Social flow ABM introduces crowding, evacuation, traffic congestion, and pedestrian dynamics. We also review ABM for opinion dynamics and voter model. We discuss features and advantages and disadvantages of Netlogo, Repast, Swarm, and Mason, which are representative platforms for implementing ABM.

On-target diagnosing of few-cycle pulses by high-order-harmonic generation

NASA Astrophysics Data System (ADS)

Brambila, Danilo S.; Husakou, Anton; Ivanov, Misha; Zhavoronkov, Nickolai

2017-12-01

We propose an approach to determine the residual phase distortion directly in the interaction region of few-cycle laser radiation with a gaseous target. We describe how the spectra of the generated high harmonics measured as a function of externally introduced dispersion into the driving few-cycle laser pulse can be used to decode small amounts of second- and third-order spectral phase, including the sign. The diagnosis is based on the analysis of several key features in the high-harmonic spectrum: the depth of spectral modulation, the position of the cutoff, and the symmetry of the spectrum with respect to the introduced dispersion. The approach is applicable to pulses without carrier-envelope phase (CEP) stabilization. Surprisingly, we find that for nearly-single-cycle pulses with nonstabilized CEP, deep spectral modulations in the harmonic spectra emerge for positively rather than negatively chirped pulses, in contrast to the case of CEP-stabilized pulses.

Complex patterns of abnormal heartbeats

NASA Technical Reports Server (NTRS)

Schulte-Frohlinde, Verena; Ashkenazy, Yosef; Goldberger, Ary L.; Ivanov, Plamen Ch; Costa, Madalena; Morley-Davies, Adrian; Stanley, H. Eugene; Glass, Leon

2002-01-01

Individuals having frequent abnormal heartbeats interspersed with normal heartbeats may be at an increased risk of sudden cardiac death. However, mechanistic understanding of such cardiac arrhythmias is limited. We present a visual and qualitative method to display statistical properties of abnormal heartbeats. We introduce dynamical "heartprints" which reveal characteristic patterns in long clinical records encompassing approximately 10(5) heartbeats and may provide information about underlying mechanisms. We test if these dynamics can be reproduced by model simulations in which abnormal heartbeats are generated (i) randomly, (ii) at a fixed time interval following a preceding normal heartbeat, or (iii) by an independent oscillator that may or may not interact with the normal heartbeat. We compare the results of these three models and test their limitations to comprehensively simulate the statistical features of selected clinical records. This work introduces methods that can be used to test mathematical models of arrhythmogenesis and to develop a new understanding of underlying electrophysiologic mechanisms of cardiac arrhythmia.

Gravity, antigravity and gravitational shielding in (2+1) dimensions

NASA Astrophysics Data System (ADS)

Accioly, Antonio; Helayël-Neto, José; Lobo, Matheus

2009-07-01

Higher-derivative terms are introduced into three-dimensional gravity, thereby allowing for a dynamical theory. The resulting system, viewed as a classical field model, is endowed with a novel and peculiar feature: its nonrelativistic potential describes three gravitational regimes. Depending on the choice of the parameters in the action functional, one obtains gravity, antigravity or gravitational shielding. Interesting enough, this potential is very similar, mutatis mutandis, to the potential for the interaction of two superconducting vortices. Furthermore, the gravitational deflection angle of a light ray, unlike that of Einstein gravity in (2+1) dimensions, is dependent on the impact parameter.

Asymptotically Free Natural Supersymmetric Twin Higgs Model

NASA Astrophysics Data System (ADS)

Badziak, Marcin; Harigaya, Keisuke

2018-05-01

Twin Higgs (TH) models explain the absence of new colored particles responsible for natural electroweak symmetry breaking (EWSB). All known ultraviolet completions of TH models require some nonperturbative dynamics below the Planck scale. We propose a supersymmetric model in which the TH mechanism is introduced by a new asymptotically free gauge interaction. The model features natural EWSB for squarks and gluino heavier than 2 TeV even if supersymmetry breaking is mediated around the Planck scale, and has interesting flavor phenomenology including the top quark decay into the Higgs boson and the up quark which may be discovered at the LHC.

Asymptotically Free Natural Supersymmetric Twin Higgs Model.

PubMed

Badziak, Marcin; Harigaya, Keisuke

2018-05-25

Twin Higgs (TH) models explain the absence of new colored particles responsible for natural electroweak symmetry breaking (EWSB). All known ultraviolet completions of TH models require some nonperturbative dynamics below the Planck scale. We propose a supersymmetric model in which the TH mechanism is introduced by a new asymptotically free gauge interaction. The model features natural EWSB for squarks and gluino heavier than 2 TeV even if supersymmetry breaking is mediated around the Planck scale, and has interesting flavor phenomenology including the top quark decay into the Higgs boson and the up quark which may be discovered at the LHC.

Role of dimensionality in Axelrod's model for the dissemination of culture

NASA Astrophysics Data System (ADS)

Klemm, Konstantin; Eguíluz, Víctor M.; Toral, Raúl; Miguel, Maxi San

2003-09-01

We analyze a model of social interaction in one- and two-dimensional lattices for a moderate number of features. We introduce an order parameter as a function of the overlap between neighboring sites. In a one-dimensional chain, we observe that the dynamics is consistent with a second-order transition, where the order parameter changes continuously and the average domain diverges at the transition point. However, in a two-dimensional lattice the order parameter is discontinuous at the transition point characteristic of a first-order transition between an ordered and a disordered state.

Early stages of collapsing pentacene crystal by Au

NASA Astrophysics Data System (ADS)

Ihm, Kyuwook; Chung, Sukmin; Kang, Tai-Hee; Cheong, Sang-Wook

2008-10-01

The characteristic feature of metal contacts with gold on organics is deterioration of the organic crystals during the contact formation. The unveiled key challenge is to probe dynamic details of the microscopic evolution of the organic crystal when the atomic Au is introduced. Here, we report how the collapse of the pentacene crystal is initiated even by a few Au atoms. Our results indicate that the gentle decoupling of intra and intermolecular π-π interactions causes the localization of the lowest unoccupied molecular orbital as well as the removal of cohesive forces between molecules, leading to the subsequent crystal collapse.

Entangling mobility and interactions in social media.

PubMed

Grabowicz, Przemyslaw A; Ramasco, José J; Gonçalves, Bruno; Eguíluz, Víctor M

2014-01-01

Daily interactions naturally define social circles. Individuals tend to be friends with the people they spend time with and they choose to spend time with their friends, inextricably entangling physical location and social relationships. As a result, it is possible to predict not only someone's location from their friends' locations but also friendship from spatial and temporal co-occurrence. While several models have been developed to separately describe mobility and the evolution of social networks, there is a lack of studies coupling social interactions and mobility. In this work, we introduce a model that bridges this gap by explicitly considering the feedback of mobility on the formation of social ties. Data coming from three online social networks (Twitter, Gowalla and Brightkite) is used for validation. Our model reproduces various topological and physical properties of the networks not captured by models uncoupling mobility and social interactions such as: i) the total size of the connected components, ii) the distance distribution between connected users, iii) the dependence of the reciprocity on the distance, iv) the variation of the social overlap and the clustering with the distance. Besides numerical simulations, a mean-field approach is also used to study analytically the main statistical features of the networks generated by a simplified version of our model. The robustness of the results to changes in the model parameters is explored, finding that a balance between friend visits and long-range random connections is essential to reproduce the geographical features of the empirical networks.

Separable spectro-temporal Gabor filter bank features: Reducing the complexity of robust features for automatic speech recognition.

PubMed

Schädler, Marc René; Kollmeier, Birger

2015-04-01

To test if simultaneous spectral and temporal processing is required to extract robust features for automatic speech recognition (ASR), the robust spectro-temporal two-dimensional-Gabor filter bank (GBFB) front-end from Schädler, Meyer, and Kollmeier [J. Acoust. Soc. Am. 131, 4134-4151 (2012)] was de-composed into a spectral one-dimensional-Gabor filter bank and a temporal one-dimensional-Gabor filter bank. A feature set that is extracted with these separate spectral and temporal modulation filter banks was introduced, the separate Gabor filter bank (SGBFB) features, and evaluated on the CHiME (Computational Hearing in Multisource Environments) keywords-in-noise recognition task. From the perspective of robust ASR, the results showed that spectral and temporal processing can be performed independently and are not required to interact with each other. Using SGBFB features permitted the signal-to-noise ratio (SNR) to be lowered by 1.2 dB while still performing as well as the GBFB-based reference system, which corresponds to a relative improvement of the word error rate by 12.8%. Additionally, the real time factor of the spectro-temporal processing could be reduced by more than an order of magnitude. Compared to human listeners, the SNR needed to be 13 dB higher when using Mel-frequency cepstral coefficient features, 11 dB higher when using GBFB features, and 9 dB higher when using SGBFB features to achieve the same recognition performance.

Sleep electroencephalography and heart rate variability interdependence amongst healthy subjects and insomnia/schizophrenia patients.

PubMed

Chaparro-Vargas, Ramiro; Schilling, Claudia; Schredl, Michael; Cvetkovic, Dean

2016-01-01

The quantification of interdependencies within autonomic nervous system has gained increasing importance to characterise healthy and psychiatric disordered subjects. The present work introduces a biosignal processing approach, suggesting a computational resource to estimate coherent or synchronised interactions as an eventual supportive aid in the diagnosis of primary insomnia and schizophrenia pathologies. By deploying linear, nonlinear and statistical methods upon 25 electroencephalographic and electrocardiographic overnight sleep recordings, the assessment of cross-correlation, wavelet coherence and [Formula: see text]:[Formula: see text] phase synchronisation is focused on tracking discerning features amongst the clinical cohorts. Our results indicate that certain neuronal oscillations interact with cardiac power bands in distinctive ways responding to standardised sleep stages and patient groups, which promotes the hypothesis of subtle functional dynamics between neuronal assembles and (para)sympathetic activity subject to pathophysiological conditions.

Entanglement structures in qubit systems

NASA Astrophysics Data System (ADS)

Rangamani, Mukund; Rota, Massimiliano

2015-09-01

Using measures of entanglement such as negativity and tangles we provide a detailed analysis of entanglement structures in pure states of non-interacting qubits. The motivation for this exercise primarily comes from holographic considerations, where entanglement is inextricably linked with the emergence of geometry. We use the qubit systems as toy models to probe the internal structure, and introduce some useful measures involving entanglement negativity to quantify general features of entanglement. In particular, our analysis focuses on various constraints on the pattern of entanglement which are known to be satisfied by holographic sates, such as the saturation of Araki-Lieb inequality (in certain circumstances), and the monogamy of mutual information. We argue that even systems as simple as few non-interacting qubits can be useful laboratories to explore how the emergence of the bulk geometry may be related to quantum information principles.

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

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

Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov

2015-01-01

Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysicalmore » techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.« less

Epiviz: a view inside the design of an integrated visual analysis software for genomics

PubMed Central

2015-01-01

Background Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. In our previous work, we introduced Epiviz, which bridges the gap between the two types of tools, simplifying these workflows. Results In this paper we expand on the design decisions behind Epiviz, and introduce a series of new advanced features that further support the type of interactive exploratory workflow we have targeted. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a genome browser. In our discussion section, we present security implications of the current design, as well as a series of limitations and future research steps. Conclusions Since many of the design choices of Epiviz are novel in genomics data analysis, this paper serves both as a document of our own approaches with lessons learned, as well as a start point for future efforts in the same direction for the genomics community. PMID:26328750

Agent-based model with multi-level herding for complex financial systems

NASA Astrophysics Data System (ADS)

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-02-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level.

Heterogeneous resource allocation can change social hierarchy in public goods games.

PubMed

Meloni, Sandro; Xia, Cheng-Yi; Moreno, Yamir

2017-03-01

Public goods games (PGGs) represent one of the most useful tools to study group interactions. However, even if they could provide an explanation for the emergence and stability of cooperation in modern societies, they are not able to reproduce some key features observed in social and economical interactions. The typical shape of wealth distribution-known as Pareto Law-and the microscopic organization of wealth production are two of them. Here, we introduce a modification to the classical formulation of PGGs that allows for the emergence of both of these features from first principles. Unlike traditional PGGs, where players contribute equally to all the games in which they participate, we allow individuals to redistribute their contribution according to what they earned in previous rounds. Results from numerical simulations show that not only a Pareto distribution for the pay-offs naturally emerges but also that if players do not invest enough in one round they can act as defectors even if they are formally cooperators. Our results not only give an explanation for wealth heterogeneity observed in real data but also point to a conceptual change on cooperation in collective dilemmas.

Agent-based model with multi-level herding for complex financial systems

PubMed Central

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-01-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level. PMID:25669427

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

PubMed

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua

2017-11-01

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.

Heterogeneous resource allocation can change social hierarchy in public goods games

NASA Astrophysics Data System (ADS)

Meloni, Sandro; Xia, Cheng-Yi; Moreno, Yamir

2017-03-01

Public goods games (PGGs) represent one of the most useful tools to study group interactions. However, even if they could provide an explanation for the emergence and stability of cooperation in modern societies, they are not able to reproduce some key features observed in social and economical interactions. The typical shape of wealth distribution-known as Pareto Law-and the microscopic organization of wealth production are two of them. Here, we introduce a modification to the classical formulation of PGGs that allows for the emergence of both of these features from first principles. Unlike traditional PGGs, where players contribute equally to all the games in which they participate, we allow individuals to redistribute their contribution according to what they earned in previous rounds. Results from numerical simulations show that not only a Pareto distribution for the pay-offs naturally emerges but also that if players do not invest enough in one round they can act as defectors even if they are formally cooperators. Our results not only give an explanation for wealth heterogeneity observed in real data but also point to a conceptual change on cooperation in collective dilemmas.

Some remarks about simulation of cosmic ray phenomena with use of nuclear interaction models based on the current SPS proton-antiproton data

NASA Technical Reports Server (NTRS)

Wrotniak, J. A.; Yodh, G. B.

1985-01-01

The x-y controversy is studied by introducing models with as many features (except for x and y distributions) in common, as possible, to avoid an extrapolation problem, only primary energies of 500 TeV are considered. To prove the point, Monte Carlo simulations are performed of EAS generated by 500 TeV vertical primary protons. Four different nuclear interaction models were used. Two of them are described elsewhere. Two are: (1) Model M-Y00 - with inclusive x and y distributions behaving in a scaling way; and (2) Model M-F00 - at and below ISR energies (1 TeV in Lab) exactly equivalent to the above, then gradually changing to provide the distributions in rapidity at 155 TeV as given by SPS proton-antiproton. This was achieved by gradual decrease in the scale unit in x distributions of produced secondaries, as interaction energy increases. Other modifications to the M-Y00 model were made.

A Method for Predicting Protein Complexes from Dynamic Weighted Protein-Protein Interaction Networks.

PubMed

Liu, Lizhen; Sun, Xiaowu; Song, Wei; Du, Chao

2018-06-01

Predicting protein complexes from protein-protein interaction (PPI) network is of great significance to recognize the structure and function of cells. A protein may interact with different proteins under different time or conditions. Existing approaches only utilize static PPI network data that may lose much temporal biological information. First, this article proposed a novel method that combines gene expression data at different time points with traditional static PPI network to construct different dynamic subnetworks. Second, to further filter out the data noise, the semantic similarity based on gene ontology is regarded as the network weight together with the principal component analysis, which is introduced to deal with the weight computing by three traditional methods. Third, after building a dynamic PPI network, a predicting protein complexes algorithm based on "core-attachment" structural feature is applied to detect complexes from each dynamic subnetworks. Finally, it is revealed from the experimental results that our method proposed in this article performs well on detecting protein complexes from dynamic weighted PPI networks.

Highlighting the nuances behind interaction of picosecond pulses with human skin: Relating distinct laser-tissue interactions to their potential in cutaneous interventions

NASA Astrophysics Data System (ADS)

Uzunbajakava, Natallia E.; Varghese, Babu; Botchkareva, Natalia V.; Verhagen, Rieko; Vogel, Alfred

2018-02-01

In recent years, several commercial systems relying on picosecond pulses have been introduced into the field of cutaneous interventions. In parallel with this development, a somewhat distinct research prototype also operating in the picosecond regime was described in literature. Albeit both market-available products and the investigational device employ laser beams of nearly the same pulse duration and were reported to cause laser-induced optical breakdown (LIOB), they are different in terms of wavelength, applied fluence, laser beam quality, optical architecture and related focusing optics, resulting in different histomorphological features (such as e.g. lesion size, location, expression of collagen). Understanding the differences between these systems in relation to implications for clinical results raises a need in highlighting the nuances behind interaction of picosecond pulses with biological tissue. To achieve this, we accentuate the interplay of irradiance levels of picosecond pulses in W/cm2 , absorption properties of a target tissue at a wavelength of a light source and resulting interaction mechanisms with biological object. We also relate these nuances to potential consequences for cutaneous interventions.

Computer simulation of a cellular automata model for the immune response in a retrovirus system

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

Pandey, R.B.

1989-02-01

Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viralmore » cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B/sub ca/ (B/sub cq/). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B/sub ca/ (B/sub cq/).« less

Magnetic susceptibility and spin-lattice interactions in U1-xPuxO2 single crystals

NASA Astrophysics Data System (ADS)

Kolberg, D.; Wastin, F.; Rebizant, J.; Boulet, P.; Lander, G. H.; Schoenes, J.

2002-12-01

Single crystals of mixed uranium-plutonium dioxides have been grown by means of a chemical vapor transport reaction and characterized by x-ray diffraction on bulk and powdered single crystals. Magnetization and susceptibility data were taken using a commercial superconducting quantum interference device. Characteristic ordering temperatures have been determined as well as paramagnetic Curie temperatures and effective magnetic moments. Departures of the reciprocal susceptibility as a function of temperature from linearity have been treated in detail based on a model of vibronic interactions introduced to explain the gross features of susceptibility measurements on thorium-diluted UO2 [Sasaki and Obata, J. Phys. Soc. Jpn. 28, 1157 (1970)]. The influence of spin-lattice interactions causes a certain shape of the observed 1/χ vs T curves from which we are able to suggest different mechanisms for the interactions as a function of the constituent’s concentrations. From our susceptibility measurements characteristic parameters have been calculated using a model of tetragonal vibrational modes of the oxygen cage surrounding each uranium ion. These include specific coupling parameters G, mode characteristic temperatures Tω, and molecular-field constants λ.

Standardization of accelerator irradiation procedures for simulation of neutron induced damage in reactor structural materials

NASA Astrophysics Data System (ADS)

Shao, Lin; Gigax, Jonathan; Chen, Di; Kim, Hyosim; Garner, Frank A.; Wang, Jing; Toloczko, Mychailo B.

2017-10-01

Self-ion irradiation is widely used as a method to simulate neutron damage in reactor structural materials. Accelerator-based simulation of void swelling, however, introduces a number of neutron-atypical features which require careful data extraction and, in some cases, introduction of innovative irradiation techniques to alleviate these issues. We briefly summarize three such atypical features: defect imbalance effects, pulsed beam effects, and carbon contamination. The latter issue has just been recently recognized as being relevant to simulation of void swelling and is discussed here in greater detail. It is shown that carbon ions are entrained in the ion beam by Coulomb force drag and accelerated toward the target surface. Beam-contaminant interactions are modeled using molecular dynamics simulation. By applying a multiple beam deflection technique, carbon and other contaminants can be effectively filtered out, as demonstrated in an irradiation of HT-9 alloy by 3.5 MeV Fe ions.

Variational nonadiabatic dynamics in the moving crude adiabatic representation: Further merging of nuclear dynamics and electronic structure

NASA Astrophysics Data System (ADS)

Joubert-Doriol, Loïc; Izmaylov, Artur F.

2018-03-01

A new methodology of simulating nonadiabatic dynamics using frozen-width Gaussian wavepackets within the moving crude adiabatic representation with the on-the-fly evaluation of electronic structure is presented. The main feature of the new approach is the elimination of any global or local model representation of electronic potential energy surfaces; instead, the electron-nuclear interaction is treated explicitly using the Gaussian integration. As a result, the new scheme does not introduce any uncontrolled approximations. The employed variational principle ensures the energy conservation and leaves the number of electronic and nuclear basis functions as the only parameter determining the accuracy. To assess performance of the approach, a model with two electronic and two nuclear spacial degrees of freedom containing conical intersections between potential energy surfaces has been considered. Dynamical features associated with nonadiabatic transitions and nontrivial geometric (or Berry) phases were successfully reproduced within a limited basis expansion.

Predicting perceptual quality of images in realistic scenario using deep filter banks

NASA Astrophysics Data System (ADS)

Zhang, Weixia; Yan, Jia; Hu, Shiyong; Ma, Yang; Deng, Dexiang

2018-03-01

Classical image perceptual quality assessment models usually resort to natural scene statistic methods, which are based on an assumption that certain reliable statistical regularities hold on undistorted images and will be corrupted by introduced distortions. However, these models usually fail to accurately predict degradation severity of images in realistic scenarios since complex, multiple, and interactive authentic distortions usually appear on them. We propose a quality prediction model based on convolutional neural network. Quality-aware features extracted from filter banks of multiple convolutional layers are aggregated into the image representation. Furthermore, an easy-to-implement and effective feature selection strategy is used to further refine the image representation and finally a linear support vector regression model is trained to map image representation into images' subjective perceptual quality scores. The experimental results on benchmark databases present the effectiveness and generalizability of the proposed model.

miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis

PubMed Central

Fan, Yannan; Siklenka, Keith; Arora, Simran K.; Ribeiro, Paula; Kimmins, Sarah; Xia, Jianguo

2016-01-01

MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRNA target genes and their interactions with small molecules, long non-coding RNAs, epigenetic modifiers, disease associations, etc. These rich sets of information have enabled the creation of comprehensive networks linking miRNAs with various biologically important entities to shed light on their collective functions and regulatory mechanisms. Here, we introduce miRNet, an easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet include: (i) a comprehensive knowledge base integrating high-quality miRNA-target interaction data from 11 databases; (ii) support for differential expression analysis of data from microarray, RNA-seq and quantitative PCR; (iii) implementation of a flexible interface for data filtering, refinement and customization during network creation; (iv) a powerful fully featured network visualization system coupled with enrichment analysis. miRNet offers a comprehensive tool suite to enable statistical analysis and functional interpretation of various data generated from current miRNA studies. miRNet is freely available at http://www.mirnet.ca. PMID:27105848

A multiscale interaction model for the origin of the tropospheric QBO

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

Goswami, B.N.

1995-03-01

A conceptual model for the origin of the tropospheric quasi-biennial oscillation (QBO) is presented. It is argued that the tropospheric QBO may not be a fundamental mode of oscillation of the tropical coupled system. It is proposed that it may arise due to multiscale interactions between high-frequency synoptic and intraseasonal oscillations of the atmosphere and a low-frequency oscillation of the couple system in the presence of the annual cycle. This is demonstrated using a conceptual low-order system consisting of three variables representing the nonlinear atmospheric oscillations and a linear oscillator representing the low-frequency coupled mode. The annual cycle and couplingmore » to the low-frequency linear oscillator provide slowly varying forcings for the atmospheric high-frequency oscillations. The atmospheric oscillations go through a chaotic regime during a certain part of the slowly varying forcing. Such variable forcing introduces a low-frequency tail in the spectrum of the atmospheric high-frequency oscillations. The low-frequency tail resonantly interacts with the low-frequency oscillation and produces the QBO in addition to broadening the spectrum of the low-frequency oscillator. The conceptual model simulates features similar to many observed features of the tropospheric QBO but depends on the assumption that there is an inherent low-frequency El Nino-Southern Oscillation oscillation with a four-year period that occurs independently of the high-frequency forcing or the QBO.« less

Filter bank common spatial patterns in mental workload estimation.

PubMed

Arvaneh, Mahnaz; Umilta, Alberto; Robertson, Ian H

2015-01-01

EEG-based workload estimation technology provides a real time means of assessing mental workload. Such technology can effectively enhance the performance of the human-machine interaction and the learning process. When designing workload estimation algorithms, a crucial signal processing component is the feature extraction step. Despite several studies on this field, the spatial properties of the EEG signals were mostly neglected. Since EEG inherently has a poor spacial resolution, features extracted individually from each EEG channel may not be sufficiently efficient. This problem becomes more pronounced when we use low-cost but convenient EEG sensors with limited stability which is the case in practical scenarios. To address this issue, in this paper, we introduce a filter bank common spatial patterns algorithm combined with a feature selection method to extract spatio-spectral features discriminating different mental workload levels. To evaluate the proposed algorithm, we carry out a comparative analysis between two representative types of working memory tasks using data recorded from an Emotiv EPOC headset which is a mobile low-cost EEG recording device. The experimental results showed that the proposed spatial filtering algorithm outperformed the state-of-the algorithms in terms of the classification accuracy.

A Spatial-frequency Method for Analyzing Antenna-to-Probe Interactions in Near-field Antenna Measurements.

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

Brock, Billy C.

The measurement of the radiation characteristics of an antenna on a near-field range requires that the antenna under test be located very close to the near-field probe. Although the direct coupling is utilized for characterizing the near field, this close proximity also presents the opportunity for significant undesired interactions (for example, reflections) to occur between the antenna and the near-field probe. When uncompensated, these additional interactions will introduce error into the measurement, increasing the uncertainty in the final gain pattern obtained through the near-field-to-far-field transformation. Quantifying this gain-uncertainty contribution requires quantifying the various additional interactions. A method incorporating spatial-frequency analysismore » is described which allows the dominant interaction contributions to be easily identified and quantified. In addition to identifying the additional antenna-to-probe interactions, the method also allows identification and quantification of interactions with other nearby objects within the measurement room. Because the method is a spatial-frequency method, wide-bandwidth data is not required, and it can be applied even when data is available at only a single temporal frequency. This feature ensures that the method can be applied to narrow-band antennas, where a similar time-domain analysis would not be possible. - 3 - - 4 -« less

Counter-intuitive features of the dynamic topography unveiled by tectonically realistic 3D numerical models of mantle-lithosphere interactions

NASA Astrophysics Data System (ADS)

Burov, Evgueni; Gerya, Taras

2013-04-01

It has been long assumed that the dynamic topography associated with mantle-lithosphere interactions should be characterized by long-wavelength features (> 1000 km) correlating with morphology of mantle flow and expanding beyond the scale of tectonic processes. For example, debates on the existence of mantle plumes largely originate from interpretations of expected signatures of plume-induced topography that are compared to the predictions of analytical and numerical models of plume- or mantle-lithosphere interactions (MLI). Yet, most of the large-scale models treat the lithosphere as a homogeneous stagnant layer. We show that in continents, the dynamic topography is strongly affected by rheological properties and layered structure of the lithosphere. For that we reconcile mantle- and tectonic-scale models by introducing a tectonically realistic continental plate model in 3D large-scale plume-mantle-lithosphere interaction context. This model accounts for stratified structure of continental lithosphere, ductile and frictional (Mohr-Coulomb) plastic properties and thermodynamically consistent density variations. The experiments reveal a number of important differences from the predictions of the conventional models. In particular, plate bending, mechanical decoupling of crustal and mantle layers and intra-plate tension-compression instabilities result in transient topographic signatures such as alternating small-scale surface features that could be misinterpreted in terms of regional tectonics. Actually thick ductile lower crustal layer absorbs most of the "direct" dynamic topography and the features produced at surface are mostly controlled by the mechanical instabilities in the upper and intermediate crustal layers produced by MLI-induced shear and bending at Moho and LAB. Moreover, the 3D models predict anisotropic response of the lithosphere even in case of isotropic solicitations by axisymmetric mantle upwellings such as plumes. In particular, in presence of small (i.e. insufficient to produce solely any significant deformation) uniaxial extensional tectonic stress field, the plume-produced surface and LAB features have anisotropic linear shapes perpendicular to the far-field tectonic forces, typical for continental rifts. Compressional field results in singular sub-linear folds above the plume head, perpendicular to the direction of compression. Small bi-axial tectonic stress fields (compression in one direction and extension in the orthogonal direction) result in oblique, almost linear segmented normal or inverse faults with strike-slip components (or visa verse , strike-slip faults with normal or inverse components)

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P. E.; Geerke, Daan P.

2018-01-01

Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network.

PubMed

Katzman, Jared L; Shaham, Uri; Cloninger, Alexander; Bates, Jonathan; Jiang, Tingting; Kluger, Yuval

2018-02-26

Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations. We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients. The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.

What Can We Learn from a Simple Physics-Based Earthquake Simulator?

NASA Astrophysics Data System (ADS)

Artale Harris, Pietro; Marzocchi, Warner; Melini, Daniele

2018-03-01

Physics-based earthquake simulators are becoming a popular tool to investigate on the earthquake occurrence process. So far, the development of earthquake simulators is commonly led by the approach "the more physics, the better". However, this approach may hamper the comprehension of the outcomes of the simulator; in fact, within complex models, it may be difficult to understand which physical parameters are the most relevant to the features of the seismic catalog at which we are interested. For this reason, here, we take an opposite approach and analyze the behavior of a purposely simple earthquake simulator applied to a set of California faults. The idea is that a simple simulator may be more informative than a complex one for some specific scientific objectives, because it is more understandable. Our earthquake simulator has three main components: the first one is a realistic tectonic setting, i.e., a fault data set of California; the second is the application of quantitative laws for earthquake generation on each single fault, and the last is the fault interaction modeling through the Coulomb Failure Function. The analysis of this simple simulator shows that: (1) the short-term clustering can be reproduced by a set of faults with an almost periodic behavior, which interact according to a Coulomb failure function model; (2) a long-term behavior showing supercycles of the seismic activity exists only in a markedly deterministic framework, and quickly disappears introducing a small degree of stochasticity on the recurrence of earthquakes on a fault; (3) faults that are strongly coupled in terms of Coulomb failure function model are synchronized in time only in a marked deterministic framework, and as before, such a synchronization disappears introducing a small degree of stochasticity on the recurrence of earthquakes on a fault. Overall, the results show that even in a simple and perfectly known earthquake occurrence world, introducing a small degree of stochasticity may blur most of the deterministic time features, such as long-term trend and synchronization among nearby coupled faults.

V-ELMpiRNAPred: Identification of human piRNAs by the voting-based extreme learning machine (V-ELM) with a new hybrid feature.

PubMed

Pian, Cong; Chen, Yuan-Yuan; Zhang, Jin; Chen, Zhi; Zhang, Guang-Le; Li, Qiang; Yang, Tao; Zhang, Liang-Yun

2017-02-01

Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this paper, we introduce a series of new features with 80 dimension called short sequence motifs (SSM). A hybrid feature vector with 1444 dimension can be formed by combining 1364 features of [Formula: see text]-mer strings and 80 features of SSM features. We optimize the 1444 dimension features using the feature score criterion (FSC) and list them in descending order according to the scores. The first 462 are selected as the input feature vector in the classifier. Moreover, eight of 80 SSM features appear in the top 20. This indicates that these eight SSM features play an important part in the identification of piRNAs. Since five of the above eight SSM features are associated with nucleotide A and G ('A*G', 'A**G', 'A***G', 'A****G', 'A*****G'). So, we guess there may exist some biological significance. We also use a neural network algorithm called voting-based extreme learning machine (V-ELM) to identify real piRNAs. The Specificity (Sp) and Sensitivity (Sn) of our method are 95.48% and 94.61%, respectively in human species. This result shows that our method is more effective compared with those of the piRPred, piRNApredictor, Asym-Pibomd, Piano and McRUMs. The web service of V-ELMpiRNAPred is available for free at http://mm20132014.wicp.net:38601/velmprepiRNA/Main.jsp .

User-oriented summary extraction for soccer video based on multimodal analysis

NASA Astrophysics Data System (ADS)

Liu, Huayong; Jiang, Shanshan; He, Tingting

2011-11-01

An advanced user-oriented summary extraction method for soccer video is proposed in this work. Firstly, an algorithm of user-oriented summary extraction for soccer video is introduced. A novel approach that integrates multimodal analysis, such as extraction and analysis of the stadium features, moving object features, audio features and text features is introduced. By these features the semantic of the soccer video and the highlight mode are obtained. Then we can find the highlight position and put them together by highlight degrees to obtain the video summary. The experimental results for sports video of world cup soccer games indicate that multimodal analysis is effective for soccer video browsing and retrieval.

Blended particle filters for large-dimensional chaotic dynamical systems

PubMed Central

Majda, Andrew J.; Qi, Di; Sapsis, Themistoklis P.

2014-01-01

A major challenge in contemporary data science is the development of statistically accurate particle filters to capture non-Gaussian features in large-dimensional chaotic dynamical systems. Blended particle filters that capture non-Gaussian features in an adaptively evolving low-dimensional subspace through particles interacting with evolving Gaussian statistics on the remaining portion of phase space are introduced here. These blended particle filters are constructed in this paper through a mathematical formalism involving conditional Gaussian mixtures combined with statistically nonlinear forecast models compatible with this structure developed recently with high skill for uncertainty quantification. Stringent test cases for filtering involving the 40-dimensional Lorenz 96 model with a 5-dimensional adaptive subspace for nonlinear blended filtering in various turbulent regimes with at least nine positive Lyapunov exponents are used here. These cases demonstrate the high skill of the blended particle filter algorithms in capturing both highly non-Gaussian dynamical features as well as crucial nonlinear statistics for accurate filtering in extreme filtering regimes with sparse infrequent high-quality observations. The formalism developed here is also useful for multiscale filtering of turbulent systems and a simple application is sketched below. PMID:24825886

Field-controllable second harmonic generation at a graphene oxide heterointerface

NASA Astrophysics Data System (ADS)

Fernandes, Gustavo E.; Kim, Jin Ho; Osgood, Richard, III; Xu, Jimmy

2018-03-01

We report on the voltage-dependent SHG signal obtained in a reduced-graphene oxide (rGO)/p-type Si heterointerface. A simple qualitative model considering the interaction between the heterointerface depletion region potential and the naturally occurring surface dipole layer on the rGO is introduced to account for the characteristics of the SHG signal, specifically, a minimum point at ≈ -3 V bias on the rGO side of the interface. This feature-rich system has the potential to provide field-controllable surface-dipole moments and second-order nonlinearities, which may find applications in tunable nonlinear photonic devices for realizing second-harmonic generation and optical-rectification.

Toward a computational psycholinguistics of reference production.

PubMed

van Deemter, Kees; Gatt, Albert; van Gompel, Roger P G; Krahmer, Emiel

2012-04-01

This article introduces the topic ''Production of Referring Expressions: Bridging the Gap between Computational and Empirical Approaches to Reference'' of the journal Topics in Cognitive Science. We argue that computational and psycholinguistic approaches to reference production can benefit from closer interaction, and that this is likely to result in the construction of algorithms that differ markedly from the ones currently known in the computational literature. We focus particularly on determinism, the feature of existing algorithms that is perhaps most clearly at odds with psycholinguistic results, discussing how future algorithms might include non-determinism, and how new psycholinguistic experiments could inform the development of such algorithms. Copyright © 2012 Cognitive Science Society, Inc.

The FRUITY database on AGB stars: past, present and future

NASA Astrophysics Data System (ADS)

Cristallo, S.; Piersanti, L.; Straniero, O.

2016-01-01

We present and show the features of the FRUITY database, an interactive web- based interface devoted to the nucleosynthesis in AGB stars. We describe the current available set of AGB models (largely expanded with respect to the original one) with masses in the range 1.3≤M/M⊙≤3.0 and metallicities -2.15 ≤[Fe/H]≤+0.15. We illustrate the details of our s-process surface distributions and we compare our results to observations. Moreover, we introduce a new set of models where the effects of rotation are taken into account. Finally, we shortly describe next planned upgrades.

Single realization stochastic FDTD for weak scattering waves in biological random media.

PubMed

Tan, Tengmeng; Taflove, Allen; Backman, Vadim

2013-02-01

This paper introduces an iterative scheme to overcome the unresolved issues presented in S-FDTD (stochastic finite-difference time-domain) for obtaining ensemble average field values recently reported by Smith and Furse in an attempt to replace the brute force multiple-realization also known as Monte-Carlo approach with a single-realization scheme. Our formulation is particularly useful for studying light interactions with biological cells and tissues having sub-wavelength scale features. Numerical results demonstrate that such a small scale variation can be effectively modeled with a random medium problem which when simulated with the proposed S-FDTD indeed produces a very accurate result.

Single realization stochastic FDTD for weak scattering waves in biological random media

PubMed Central

Tan, Tengmeng; Taflove, Allen; Backman, Vadim

2015-01-01

This paper introduces an iterative scheme to overcome the unresolved issues presented in S-FDTD (stochastic finite-difference time-domain) for obtaining ensemble average field values recently reported by Smith and Furse in an attempt to replace the brute force multiple-realization also known as Monte-Carlo approach with a single-realization scheme. Our formulation is particularly useful for studying light interactions with biological cells and tissues having sub-wavelength scale features. Numerical results demonstrate that such a small scale variation can be effectively modeled with a random medium problem which when simulated with the proposed S-FDTD indeed produces a very accurate result. PMID:27158153

Exploratory visualization of astronomical data on ultra-high-resolution wall displays

NASA Astrophysics Data System (ADS)

Pietriga, Emmanuel; del Campo, Fernando; Ibsen, Amanda; Primet, Romain; Appert, Caroline; Chapuis, Olivier; Hempel, Maren; Muñoz, Roberto; Eyheramendy, Susana; Jordan, Andres; Dole, Hervé

2016-07-01

Ultra-high-resolution wall displays feature a very high pixel density over a large physical surface, which makes them well-suited to the collaborative, exploratory visualization of large datasets. We introduce FITS-OW, an application designed for such wall displays, that enables astronomers to navigate in large collections of FITS images, query astronomical databases, and display detailed, complementary data and documents about multiple sources simultaneously. We describe how astronomers interact with their data using both the wall's touchsensitive surface and handheld devices. We also report on the technical challenges we addressed in terms of distributed graphics rendering and data sharing over the computer clusters that drive wall displays.

General three-state model with biased population replacement: Analytical solution and application to language dynamics

NASA Astrophysics Data System (ADS)

Colaiori, Francesca; Castellano, Claudio; Cuskley, Christine F.; Loreto, Vittorio; Pugliese, Martina; Tria, Francesca

2015-01-01

Empirical evidence shows that the rate of irregular usage of English verbs exhibits discontinuity as a function of their frequency: the most frequent verbs tend to be totally irregular. We aim to qualitatively understand the origin of this feature by studying simple agent-based models of language dynamics, where each agent adopts an inflectional state for a verb and may change it upon interaction with other agents. At the same time, agents are replaced at some rate by new agents adopting the regular form. In models with only two inflectional states (regular and irregular), we observe that either all verbs regularize irrespective of their frequency, or a continuous transition occurs between a low-frequency state, where the lemma becomes fully regular, and a high-frequency one, where both forms coexist. Introducing a third (mixed) state, wherein agents may use either form, we find that a third, qualitatively different behavior may emerge, namely, a discontinuous transition in frequency. We introduce and solve analytically a very general class of three-state models that allows us to fully understand these behaviors in a unified framework. Realistic sets of interaction rules, including the well-known naming game (NG) model, result in a discontinuous transition, in agreement with recent empirical findings. We also point out that the distinction between speaker and hearer in the interaction has no effect on the collective behavior. The results for the general three-state model, although discussed in terms of language dynamics, are widely applicable.

Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions

NASA Astrophysics Data System (ADS)

Biswas, Rajib; Bagchi, Biman

2018-01-01

In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama

PubMed Central

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M. T.; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range. PMID:26863538

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama.

PubMed

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M T; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range.

Visualization of molecular structures using HoloLens-based augmented reality

PubMed Central

Hoffman, MA; Provance, JB

2017-01-01

Biological molecules and biologically active small molecules are complex three dimensional structures. Current flat screen monitors are limited in their ability to convey the full three dimensional characteristics of these molecules. Augmented reality devices, including the Microsoft HoloLens, offer an immersive platform to change how we interact with molecular visualizations. We describe a process to incorporate the three dimensional structures of small molecules and complex proteins into the Microsoft HoloLens using aspirin and the human leukocyte antigen (HLA) as examples. Small molecular structures can be introduced into the HoloStudio application, which provides native support for rotating, resizing and performing other interactions with these molecules. Larger molecules can be imported through the Unity gaming development platform and then Microsoft Visual Developer. The processes described here can be modified to import a wide variety of molecular structures into augmented reality systems and improve our comprehension of complex structural features. PMID:28815109

Post-Markovian dynamics of quantum correlations: entanglement versus discord

NASA Astrophysics Data System (ADS)

Mohammadi, Hamidreza

2017-02-01

Dynamics of an open two-qubit system is investigated in the post-Markovian regime, where the environments have a short-term memory. Each qubit is coupled to separate environment which is held in its own temperature. The inter-qubit interaction is modeled by XY-Heisenberg model in the presence of spin-orbit interaction and inhomogeneous magnetic field. The dynamical behavior of entanglement and discord has been considered. The results show that quantum discord is more robust than quantum entanglement, during the evolution. Also the asymmetric feature of quantum discord can be monitored by introducing the asymmetries due to inhomogeneity of magnetic field and temperature difference between the reservoirs. By employing proper parameters of the model, it is possible to maintain nonvanishing quantum correlation at high degree of temperature. The results can provide a useful recipe for studying dynamical behavior of two-qubit systems such as trapped spin electrons in coupled quantum dots.

Coupling Functions Enable Secure Communications

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; McClintock, Peter V. E.; Stefanovska, Aneta

2014-01-01

Secure encryption is an essential feature of modern communications, but rapid progress in illicit decryption brings a continuing need for new schemes that are harder and harder to break. Inspired by the time-varying nature of the cardiorespiratory interaction, here we introduce a new class of secure communications that is highly resistant to conventional attacks. Unlike all earlier encryption procedures, this cipher makes use of the coupling functions between interacting dynamical systems. It results in an unbounded number of encryption key possibilities, allows the transmission or reception of more than one signal simultaneously, and is robust against external noise. Thus, the information signals are encrypted as the time variations of linearly independent coupling functions. Using predetermined forms of coupling function, we apply Bayesian inference on the receiver side to detect and separate the information signals while simultaneously eliminating the effect of external noise. The scheme is highly modular and is readily extendable to support different communications applications within the same general framework.

Electronegative Guests in CoSb 3

DOE PAGES

Duan, Bo; Yang, Jiong; Salvador, James R.; ...

2016-04-19

Introducing guests into a host framework to form a so called inclusion compound can be used to design materials with new and fascinating functionalities. The vast majority of inclusion compounds have electropositive guests with neutral or negatively charged frameworks. Here, we show a series of electronegative guest filled skutterudites with inverse polarity. The strong covalent guest-host interactions observed for the electronegative group VIA guests, i.e., S and Se, feature a unique localized cluster vibration which significantly influences the lattice dynamics, together with the point-defect scattering caused by element substitutions, resulting in very low lattice thermal conductivity values. The findings ofmore » electronegative guests provide a new perspective for guest-filling in skutterudites, and the covalent filler/lattice interactions lead to an unusual lattice dynamics phenomenon which can be used for designing high-efficiency thermoelectric materials and novel functional inclusion compounds with open structures.« less

Data visualization, bar naked: A free tool for creating interactive graphics.

PubMed

Weissgerber, Tracey L; Savic, Marko; Winham, Stacey J; Stanisavljevic, Dejana; Garovic, Vesna D; Milic, Natasa M

2017-12-15

Although bar graphs are designed for categorical data, they are routinely used to present continuous data in studies that have small sample sizes. This presentation is problematic, as many data distributions can lead to the same bar graph, and the actual data may suggest different conclusions from the summary statistics. To address this problem, many journals have implemented new policies that require authors to show the data distribution. This paper introduces a free, web-based tool for creating an interactive alternative to the bar graph (http://statistika.mfub.bg.ac.rs/interactive-dotplot/). This tool allows authors with no programming expertise to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of a continuous variable across different study groups. Individual data points may be overlaid on the graphs. Additional features facilitate visualization of subgroups or clusters of non-independent data. A second tool enables authors to create interactive graphics from data obtained with repeated independent experiments (http://statistika.mfub.bg.ac.rs/interactive-repeated-experiments-dotplot/). These tools are designed to encourage exploration and critical evaluation of the data behind the summary statistics and may be valuable for promoting transparency, reproducibility, and open science in basic biomedical research. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Plant microRNA-Target Interaction Identification Model Based on the Integration of Prediction Tools and Support Vector Machine

PubMed Central

Meng, Jun; Shi, Lin; Luan, Yushi

2014-01-01

Background Confident identification of microRNA-target interactions is significant for studying the function of microRNA (miRNA). Although some computational miRNA target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. To address these issues, we developed an integrated model for identifying plant miRNA–target interactions. Results Three online miRNA target prediction toolkits and machine learning algorithms were integrated to identify and analyze Arabidopsis thaliana miRNA-target interactions. Principle component analysis (PCA) feature extraction and self-training technology were introduced to improve the performance. Results showed that the proposed model outperformed the previously existing methods. The results were validated by using degradome sequencing supported Arabidopsis thaliana miRNA-target interactions. The proposed model constructed on Arabidopsis thaliana was run over Oryza sativa and Vitis vinifera to demonstrate that our model is effective for other plant species. Conclusions The integrated model of online predictors and local PCA-SVM classifier gained credible and high quality miRNA-target interactions. The supervised learning algorithm of PCA-SVM classifier was employed in plant miRNA target identification for the first time. Its performance can be substantially improved if more experimentally proved training samples are provided. PMID:25051153

RecceMan: an interactive recognition assistance for image-based reconnaissance: synergistic effects of human perception and computational methods for object recognition, identification, and infrastructure analysis

NASA Astrophysics Data System (ADS)

El Bekri, Nadia; Angele, Susanne; Ruckhäberle, Martin; Peinsipp-Byma, Elisabeth; Haelke, Bruno

2015-10-01

This paper introduces an interactive recognition assistance system for imaging reconnaissance. This system supports aerial image analysts on missions during two main tasks: Object recognition and infrastructure analysis. Object recognition concentrates on the classification of one single object. Infrastructure analysis deals with the description of the components of an infrastructure and the recognition of the infrastructure type (e.g. military airfield). Based on satellite or aerial images, aerial image analysts are able to extract single object features and thereby recognize different object types. It is one of the most challenging tasks in the imaging reconnaissance. Currently, there are no high potential ATR (automatic target recognition) applications available, as consequence the human observer cannot be replaced entirely. State-of-the-art ATR applications cannot assume in equal measure human perception and interpretation. Why is this still such a critical issue? First, cluttered and noisy images make it difficult to automatically extract, classify and identify object types. Second, due to the changed warfare and the rise of asymmetric threats it is nearly impossible to create an underlying data set containing all features, objects or infrastructure types. Many other reasons like environmental parameters or aspect angles compound the application of ATR supplementary. Due to the lack of suitable ATR procedures, the human factor is still important and so far irreplaceable. In order to use the potential benefits of the human perception and computational methods in a synergistic way, both are unified in an interactive assistance system. RecceMan® (Reconnaissance Manual) offers two different modes for aerial image analysts on missions: the object recognition mode and the infrastructure analysis mode. The aim of the object recognition mode is to recognize a certain object type based on the object features that originated from the image signatures. The infrastructure analysis mode pursues the goal to analyze the function of the infrastructure. The image analyst extracts visually certain target object signatures, assigns them to corresponding object features and is finally able to recognize the object type. The system offers him the possibility to assign the image signatures to features given by sample images. The underlying data set contains a wide range of objects features and object types for different domains like ships or land vehicles. Each domain has its own feature tree developed by aerial image analyst experts. By selecting the corresponding features, the possible solution set of objects is automatically reduced and matches only the objects that contain the selected features. Moreover, we give an outlook of current research in the field of ground target analysis in which we deal with partly automated methods to extract image signatures and assign them to the corresponding features. This research includes methods for automatically determining the orientation of an object and geometric features like width and length of the object. This step enables to reduce automatically the possible object types offered to the image analyst by the interactive recognition assistance system.

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

PubMed Central

Ravindranath, Pradeep Anand; Sanner, Michel F.

2016-01-01

Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

Child-Robot Interactions for Second Language Tutoring to Preschool Children

PubMed Central

Vogt, Paul; de Haas, Mirjam; de Jong, Chiara; Baxter, Peta; Krahmer, Emiel

2017-01-01

In this digital age social robots will increasingly be used for educational purposes, such as second language tutoring. In this perspective article, we propose a number of design features to develop a child-friendly social robot that can effectively support children in second language learning, and we discuss some technical challenges for developing these. The features we propose include choices to develop the robot such that it can act as a peer to motivate the child during second language learning and build trust at the same time, while still being more knowledgeable than the child and scaffolding that knowledge in adult-like manner. We also believe that the first impressions children have about robots are crucial for them to build trust and common ground, which would support child-robot interactions in the long term. We therefore propose a strategy to introduce the robot in a safe way to toddlers. Other features relate to the ability to adapt to individual children’s language proficiency, respond contingently, both temporally and semantically, establish joint attention, use meaningful gestures, provide effective feedback and monitor children’s learning progress. Technical challenges we observe include automatic speech recognition (ASR) for children, reliable object recognition to facilitate semantic contingency and establishing joint attention, and developing human-like gestures with a robot that does not have the same morphology humans have. We briefly discuss an experiment in which we investigate how children respond to different forms of feedback the robot can give. PMID:28303094

Child-Robot Interactions for Second Language Tutoring to Preschool Children.

PubMed

Vogt, Paul; de Haas, Mirjam; de Jong, Chiara; Baxter, Peta; Krahmer, Emiel

2017-01-01

In this digital age social robots will increasingly be used for educational purposes, such as second language tutoring. In this perspective article, we propose a number of design features to develop a child-friendly social robot that can effectively support children in second language learning, and we discuss some technical challenges for developing these. The features we propose include choices to develop the robot such that it can act as a peer to motivate the child during second language learning and build trust at the same time, while still being more knowledgeable than the child and scaffolding that knowledge in adult-like manner. We also believe that the first impressions children have about robots are crucial for them to build trust and common ground, which would support child-robot interactions in the long term. We therefore propose a strategy to introduce the robot in a safe way to toddlers. Other features relate to the ability to adapt to individual children's language proficiency, respond contingently, both temporally and semantically, establish joint attention, use meaningful gestures, provide effective feedback and monitor children's learning progress. Technical challenges we observe include automatic speech recognition (ASR) for children, reliable object recognition to facilitate semantic contingency and establishing joint attention, and developing human-like gestures with a robot that does not have the same morphology humans have. We briefly discuss an experiment in which we investigate how children respond to different forms of feedback the robot can give.

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

Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood modelmore » derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.« less

Computation of three-dimensional nozzle-exhaust flow fields with the GIM code

NASA Technical Reports Server (NTRS)

Spradley, L. W.; Anderson, P. G.

1978-01-01

A methodology is introduced for constructing numerical analogs of the partial differential equations of continuum mechanics. A general formulation is provided which permits classical finite element and many of the finite difference methods to be derived directly. The approach, termed the General Interpolants Method (GIM), can combined the best features of finite element and finite difference methods. A quasi-variational procedure is used to formulate the element equations, to introduce boundary conditions into the method and to provide a natural assembly sequence. A derivation is given in terms of general interpolation functions from this procedure. Example computations for transonic and supersonic flows in two and three dimensions are given to illustrate the utility of GIM. A three-dimensional nozzle-exhaust flow field is solved including interaction with the freestream and a coupled treatment of the shear layer. Potential applications of the GIM code to a variety of computational fluid dynamics problems is then discussed in terms of existing capability or by extension of the methodology.

Characterization of enzymatic micromachining for construction of variable cross-section microchannel topologies

PubMed Central

Ruggles, Molly E.; Jayaraman, Arul; Ugaz, Victor M.

2016-01-01

The ability to harness enzymatic activity as an etchant to precisely machine biodegradable substrates introduces new possibilities for microfabrication. This flow-based etching is straightforward to implement, enabling patterning of microchannels with topologies that incorporate variable depth along the cross-sectional dimension. Additionally, unlike conventional small-molecule formulations, the macromolecular nature of enzymatic etchants enables features to be precisely positioned. Here, we introduce a kinetic model to characterize the enzymatic machining process and its localization by co-injection of a macromolecular inhibitor species. Our model captures the interaction between enzyme, inhibitor, and substrate under laminar flow, enabling rational prediction of etched microchannel profiles so that cross-sectional topologies incorporating complex lateral variations in depth can be constructed. We also apply this approach to achieve simultaneous widening of an entire network of microchannels produced in the biodegradable polymeric substrate poly(lactic acid), laying a foundation to construct systems incorporating a broad range of internal cross-sectional dimensions by manipulating the process conditions. PMID:27190566

New insights into chromatin folding and dynamics from multi-scale modeling

NASA Astrophysics Data System (ADS)

Olson, Wilma

The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

Feature Selection for Ridge Regression with Provable Guarantees.

PubMed

Paul, Saurabh; Drineas, Petros

2016-04-01

We introduce single-set spectral sparsification as a deterministic sampling-based feature selection technique for regularized least-squares classification, which is the classification analog to ridge regression. The method is unsupervised and gives worst-case guarantees of the generalization power of the classification function after feature selection with respect to the classification function obtained using all features. We also introduce leverage-score sampling as an unsupervised randomized feature selection method for ridge regression. We provide risk bounds for both single-set spectral sparsification and leverage-score sampling on ridge regression in the fixed design setting and show that the risk in the sampled space is comparable to the risk in the full-feature space. We perform experiments on synthetic and real-world data sets; a subset of TechTC-300 data sets, to support our theory. Experimental results indicate that the proposed methods perform better than the existing feature selection methods.

Wearable Sensor-Based Human Activity Recognition Method with Multi-Features Extracted from Hilbert-Huang Transform.

PubMed

Xu, Huile; Liu, Jinyi; Hu, Haibo; Zhang, Yi

2016-12-02

Wearable sensors-based human activity recognition introduces many useful applications and services in health care, rehabilitation training, elderly monitoring and many other areas of human interaction. Existing works in this field mainly focus on recognizing activities by using traditional features extracted from Fourier transform (FT) or wavelet transform (WT). However, these signal processing approaches are suitable for a linear signal but not for a nonlinear signal. In this paper, we investigate the characteristics of the Hilbert-Huang transform (HHT) for dealing with activity data with properties such as nonlinearity and non-stationarity. A multi-features extraction method based on HHT is then proposed to improve the effect of activity recognition. The extracted multi-features include instantaneous amplitude (IA) and instantaneous frequency (IF) by means of empirical mode decomposition (EMD), as well as instantaneous energy density (IE) and marginal spectrum (MS) derived from Hilbert spectral analysis. Experimental studies are performed to verify the proposed approach by using the PAMAP2 dataset from the University of California, Irvine for wearable sensors-based activity recognition. Moreover, the effect of combining multi-features vs. a single-feature are investigated and discussed in the scenario of a dependent subject. The experimental results show that multi-features combination can further improve the performance measures. Finally, we test the effect of multi-features combination in the scenario of an independent subject. Our experimental results show that we achieve four performance indexes: recall, precision, F-measure, and accuracy to 0.9337, 0.9417, 0.9353, and 0.9377 respectively, which are all better than the achievements of related works.

Wearable Sensor-Based Human Activity Recognition Method with Multi-Features Extracted from Hilbert-Huang Transform

PubMed Central

Xu, Huile; Liu, Jinyi; Hu, Haibo; Zhang, Yi

2016-01-01

Wearable sensors-based human activity recognition introduces many useful applications and services in health care, rehabilitation training, elderly monitoring and many other areas of human interaction. Existing works in this field mainly focus on recognizing activities by using traditional features extracted from Fourier transform (FT) or wavelet transform (WT). However, these signal processing approaches are suitable for a linear signal but not for a nonlinear signal. In this paper, we investigate the characteristics of the Hilbert-Huang transform (HHT) for dealing with activity data with properties such as nonlinearity and non-stationarity. A multi-features extraction method based on HHT is then proposed to improve the effect of activity recognition. The extracted multi-features include instantaneous amplitude (IA) and instantaneous frequency (IF) by means of empirical mode decomposition (EMD), as well as instantaneous energy density (IE) and marginal spectrum (MS) derived from Hilbert spectral analysis. Experimental studies are performed to verify the proposed approach by using the PAMAP2 dataset from the University of California, Irvine for wearable sensors-based activity recognition. Moreover, the effect of combining multi-features vs. a single-feature are investigated and discussed in the scenario of a dependent subject. The experimental results show that multi-features combination can further improve the performance measures. Finally, we test the effect of multi-features combination in the scenario of an independent subject. Our experimental results show that we achieve four performance indexes: recall, precision, F-measure, and accuracy to 0.9337, 0.9417, 0.9353, and 0.9377 respectively, which are all better than the achievements of related works. PMID:27918414

Exactly Solvable Models for Topological Phases of Matter

NASA Astrophysics Data System (ADS)

Tarantino, Nicolas Alessandro

Topological systems are characterized by some collection of features which remain unchanged under deformations of the Hamiltonian which leave the band gap open. The earliest examples of these were free fermion systems, allowing us to study the band structure to determine if a candidate material supports topological features. However, we can also ask the reversed question, i.e. Given a band gap, what topological features can be engineered? This classification problem proved to have numerous answers depending on which extra assumptions we allow, producing many candidate phases. While free fermion topological features could be classified by their band structures (culminating in the 10-fold way), strongly interacting systems defied this approach, and so classification outstripped the construction of even the most elementary Hamiltonians, leaving us with a number of phases which could exist, but do not have a single strongly interacting representative. The purpose of this thesis is to resolve this in certain cases by constructing commuting projector models (CPM), a class of exactly solvable models, for two types of topological phases, known as symmetry enriched topological (SET) order and fermionic symmetry protected topological (SPT) phases respectively. After introducing the background and history of commuting projector models, we will move on to the details of how these Hamiltonians are built. In the first case, we construct a CPM for a SET, showing how to encode the necessary group cohomology data into a lattice model. In the second, we construct a CPM for a fermionic SPT, and find that we must include a combinatorial representation of a spin structure to make the model consistent. While these two projects were independent, they are linked thematically by a technique known as decoration, where extra data is encoded onto simple models to generate exotic phases.

Collective decision making in cohesive flocks

NASA Astrophysics Data System (ADS)

Bhattacharya, K.; Vicsek, Tamás

2010-09-01

Most of us must have been fascinated by the eye-catching displays of collectively moving animals. Schools of fish can move in a rather orderly fashion and then change direction amazingly abruptly. There are a large number of further examples both from the living and the non-living world for phenomena during which the many interacting, permanently moving units seem to arrive at a common behavioural pattern taking place in a short time. As a paradigm of this type of phenomena we consider the problem of how birds arrive at a decision resulting in their synchronized landing. We introduce a simple model to interpret this process. Collective motion prior to landing is modelled using a simple self-propelled particle (SPP) system with a new kind of boundary condition, while the tendency and the sudden propagation of the intention of landing are introduced through rules analogous to the random field Ising model in an external field. We show that our approach is capable of capturing the most relevant features of collective decision making in a system of units with variance of individual intentions and being under an increasing level of pressure to switch states. We find that as a function of the few parameters of our model the collective switching from the flying to the landing state is indeed much sharper than the distribution of individual landing intentions. The transition is accompanied by a number of interesting features discussed in this paper.

Fostering Organizational Sustainability through Dialogical Interaction

ERIC Educational Resources Information Center

Wals, Arjen E. J.; Schwarzin, Lisa

2012-01-01

Purpose: This paper aims to introduce and investigate dialogic interaction as a key element of achieving a transition towards sustainability in people, organizations and society as a whole. Furthermore "sustainability competence" as a potential outcome of such interaction is to be introduced, referring to the capacities and qualities…

Preferential binding of positive nanoparticles on cell membranes is due to electrostatic interactions: A too simplistic explanation that does not take into account the nanoparticle protein corona.

PubMed

Forest, Valérie; Pourchez, Jérémie

2017-01-01

The internalization of nanoparticles by cells (and more broadly the nanoparticle/cell interaction) is a crucial issue both for biomedical applications (for the design of nanocarriers with enhanced cellular uptake to reach their intracellular therapeutic targets) and in a nanosafety context (as the internalized dose is one of the key factors in cytotoxicity). Many parameters can influence the nanoparticle/cell interaction, among them, the nanoparticle physico-chemical features, and especially the surface charge. It is generally admitted that positive nanoparticles are more uptaken by cells than neutral or negative nanoparticles. It is supposedly due to favorable electrostatic interactions with negatively charged cell membrane. However, this theory seems too simplistic as it does not consider a fundamental element: the nanoparticle protein corona. Indeed, once introduced in a biological medium nanoparticles adsorb proteins at their surface, forming a new interface defining the nanoparticle "biological identity". This adds a new level of complexity in the interactions with biological systems that cannot be any more limited to electrostatic binding. These interactions will then influence cell behavior. Based on a literature review and on an example of our own experience the parameters involved in the nanoparticle protein corona formation as well as in the nanoparticle/cell interactions are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

A separate phase drag model and a surrogate approximation for simulation of the steam assisted gravity drainage (SAGD) process

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

Padrino-Inciarte, Juan Carlos; Ma, Xia; VanderHeyden, W. Brian

General ensemble phase averaged equations for multiphase flows have been specialized for the simulation of the steam assisted gravity drainage (SAGD) process. In the average momentum equation, fluid-solid and fluid-fluid viscous interactions are represented by separate force terms. This equation has a form similar to that of Darcy’s law for multiphase flow but augmented by the fluid-fluid viscous forces. Models for these fluid-fluid interactions are suggested and implemented into the numerical code CartaBlanca. Numerical results indicate that the model captures the main features of the multiphase flow in the SAGD process, but the detailed features, such as plumes are missed.more » We find that viscous coupling among the fluid phases is important. Advection time scales for the different fluids differ by several orders of magnitude because of vast viscosity differences. Numerically resolving all of these time scales is time consuming. To address this problem, we introduce a steam surrogate approximation to increase the steam advection time scale, while keeping the mass and energy fluxes well approximated. This approximation leads to about a 40-fold speed-up in execution speed of the numerical calculations at the cost of a few percent error in the relevant quantities.« less

Progress in EEG-Based Brain Robot Interaction Systems

PubMed Central

Li, Mengfan; Niu, Linwei; Xian, Bin; Zeng, Ming; Chen, Genshe

2017-01-01

The most popular noninvasive Brain Robot Interaction (BRI) technology uses the electroencephalogram- (EEG-) based Brain Computer Interface (BCI), to serve as an additional communication channel, for robot control via brainwaves. This technology is promising for elderly or disabled patient assistance with daily life. The key issue of a BRI system is to identify human mental activities, by decoding brainwaves, acquired with an EEG device. Compared with other BCI applications, such as word speller, the development of these applications may be more challenging since control of robot systems via brainwaves must consider surrounding environment feedback in real-time, robot mechanical kinematics, and dynamics, as well as robot control architecture and behavior. This article reviews the major techniques needed for developing BRI systems. In this review article, we first briefly introduce the background and development of mind-controlled robot technologies. Second, we discuss the EEG-based brain signal models with respect to generating principles, evoking mechanisms, and experimental paradigms. Subsequently, we review in detail commonly used methods for decoding brain signals, namely, preprocessing, feature extraction, and feature classification, and summarize several typical application examples. Next, we describe a few BRI applications, including wheelchairs, manipulators, drones, and humanoid robots with respect to synchronous and asynchronous BCI-based techniques. Finally, we address some existing problems and challenges with future BRI techniques. PMID:28484488

Figure-Ground Segmentation Using Factor Graphs

PubMed Central

Shen, Huiying; Coughlan, James; Ivanchenko, Volodymyr

2009-01-01

Foreground-background segmentation has recently been applied [26,12] to the detection and segmentation of specific objects or structures of interest from the background as an efficient alternative to techniques such as deformable templates [27]. We introduce a graphical model (i.e. Markov random field)-based formulation of structure-specific figure-ground segmentation based on simple geometric features extracted from an image, such as local configurations of linear features, that are characteristic of the desired figure structure. Our formulation is novel in that it is based on factor graphs, which are graphical models that encode interactions among arbitrary numbers of random variables. The ability of factor graphs to express interactions higher than pairwise order (the highest order encountered in most graphical models used in computer vision) is useful for modeling a variety of pattern recognition problems. In particular, we show how this property makes factor graphs a natural framework for performing grouping and segmentation, and demonstrate that the factor graph framework emerges naturally from a simple maximum entropy model of figure-ground segmentation. We cast our approach in a learning framework, in which the contributions of multiple grouping cues are learned from training data, and apply our framework to the problem of finding printed text in natural scenes. Experimental results are described, including a performance analysis that demonstrates the feasibility of the approach. PMID:20160994

A Transparent Window into Biology: A Primer on Caenorhabditis elegans.

PubMed

Corsi, Ann K; Wightman, Bruce; Chalfie, Martin

2015-06-01

A little over 50 years ago, Sydney Brenner had the foresight to develop the nematode (round worm) Caenorhabditis elegans as a genetic model for understanding questions of developmental biology and neurobiology. Over time, research on C. elegans has expanded to explore a wealth of diverse areas in modern biology including studies of the basic functions and interactions of eukaryotic cells, host-parasite interactions, and evolution. C. elegans has also become an important organism in which to study processes that go awry in human diseases. This primer introduces the organism and the many features that make it an outstanding experimental system, including its small size, rapid life cycle, transparency, and well-annotated genome. We survey the basic anatomical features, common technical approaches, and important discoveries in C. elegans research. Key to studying C. elegans has been the ability to address biological problems genetically, using both forward and reverse genetics, both at the level of the entire organism and at the level of the single, identified cell. These possibilities make C. elegans useful not only in research laboratories, but also in the classroom where it can be used to excite students who actually can see what is happening inside live cells and tissues. Copyright © 2015 Corsi, Wightman, and Chalfie.

A separate phase drag model and a surrogate approximation for simulation of the steam assisted gravity drainage (SAGD) process

DOE PAGES

Padrino-Inciarte, Juan Carlos; Ma, Xia; VanderHeyden, W. Brian; ...

2016-01-01

General ensemble phase averaged equations for multiphase flows have been specialized for the simulation of the steam assisted gravity drainage (SAGD) process. In the average momentum equation, fluid-solid and fluid-fluid viscous interactions are represented by separate force terms. This equation has a form similar to that of Darcy’s law for multiphase flow but augmented by the fluid-fluid viscous forces. Models for these fluid-fluid interactions are suggested and implemented into the numerical code CartaBlanca. Numerical results indicate that the model captures the main features of the multiphase flow in the SAGD process, but the detailed features, such as plumes are missed.more » We find that viscous coupling among the fluid phases is important. Advection time scales for the different fluids differ by several orders of magnitude because of vast viscosity differences. Numerically resolving all of these time scales is time consuming. To address this problem, we introduce a steam surrogate approximation to increase the steam advection time scale, while keeping the mass and energy fluxes well approximated. This approximation leads to about a 40-fold speed-up in execution speed of the numerical calculations at the cost of a few percent error in the relevant quantities.« less

Influences of Ru-doping on the magnetic properties of Ca0.85Pr0.15Mn1- x Ru x O3

NASA Astrophysics Data System (ADS)

Phan, T. L.; Zhang, Y. D.; Yu, S. C.; Thanh, P. Q.; Yen, P. D. H.

2012-11-01

CaMnO3 is an antiferromagnet, in which the super-exchange interaction taking place between Mn4+ ions plays an important role. The doping of a small amount of 15% Pr into the Ca site, Ca0.85Pr0.15MnO3, leads to the appearance of Mn3+ ions, and introduces the ferromagnetic (FM) double-exchange interaction between Mn3+ and Mn4+ ions, which is dominant in a narrow temperature range of 90 ˜ 115 K. The FM interaction becomes strong for Ca0.85Pr0.15MnO3 doped with 4 and 8% Ru into the Mn site ( i.e., Ca0.85Pr0.15Mn1- x Ru x O3 with x = 0.04 and 0.08). The Curie temperature obtained for x = 0.04 and 0.08 are about 135 and 180 K, respectively. While the FM interaction in the former is dominant due to Mn3+-Mn4+ exchange pairs, the latter has the contribution of Ru ions. This results in remarkable differences in the features of their FM-paramagnetic phase transitions and their coercive fields H c .

Interactive numerals

PubMed Central

2017-01-01

Although Arabic numerals (like ‘2016’ and ‘3.14’) are ubiquitous, we show that in interactive computer applications they are often misleading and surprisingly unreliable. We introduce interactive numerals as a new concept and show, like Roman numerals and Arabic numerals, interactive numerals introduce another way of using and thinking about numbers. Properly understanding interactive numerals is essential for all computer applications that involve numerical data entered by users, including finance, medicine, aviation and science. PMID:28484609

Relations between Automatically Extracted Motion Features and the Quality of Mother-Infant Interactions at 4 and 13 Months

PubMed Central

Egmose, Ida; Varni, Giovanna; Cordes, Katharina; Smith-Nielsen, Johanne; Væver, Mette S.; Køppe, Simo; Cohen, David; Chetouani, Mohamed

2017-01-01

Bodily movements are an essential component of social interactions. However, the role of movement in early mother-infant interaction has received little attention in the research literature. The aim of the present study was to investigate the relationship between automatically extracted motion features and interaction quality in mother-infant interactions at 4 and 13 months. The sample consisted of 19 mother-infant dyads at 4 months and 33 mother-infant dyads at 13 months. The coding system Coding Interactive Behavior (CIB) was used for rating the quality of the interactions. Kinetic energy of upper-body, arms and head motion was calculated and used as segmentation in order to extract coarse- and fine-grained motion features. Spearman correlations were conducted between the composites derived from the CIB and the coarse- and fine-grained motion features. At both 4 and 13 months, longer durations of maternal arm motion and infant upper-body motion were associated with more aversive interactions, i.e., more parent-led interactions and more infant negativity. Further, at 4 months, the amount of motion silence was related to more adaptive interactions, i.e., more sensitive and child-led interactions. Analyses of the fine-grained motion features showed that if the mother coordinates her head movements with her infant's head movements, the interaction is rated as more adaptive in terms of less infant negativity and less dyadic negative states. We found more and stronger correlations between the motion features and the interaction qualities at 4 compared to 13 months. These results highlight that motion features are related to the quality of mother-infant interactions. Factors such as infant age and interaction set-up are likely to modify the meaning and importance of different motion features. PMID:29326626

Relations between Automatically Extracted Motion Features and the Quality of Mother-Infant Interactions at 4 and 13 Months.

PubMed

Egmose, Ida; Varni, Giovanna; Cordes, Katharina; Smith-Nielsen, Johanne; Væver, Mette S; Køppe, Simo; Cohen, David; Chetouani, Mohamed

2017-01-01

Bodily movements are an essential component of social interactions. However, the role of movement in early mother-infant interaction has received little attention in the research literature. The aim of the present study was to investigate the relationship between automatically extracted motion features and interaction quality in mother-infant interactions at 4 and 13 months. The sample consisted of 19 mother-infant dyads at 4 months and 33 mother-infant dyads at 13 months. The coding system Coding Interactive Behavior (CIB) was used for rating the quality of the interactions. Kinetic energy of upper-body, arms and head motion was calculated and used as segmentation in order to extract coarse- and fine-grained motion features. Spearman correlations were conducted between the composites derived from the CIB and the coarse- and fine-grained motion features. At both 4 and 13 months, longer durations of maternal arm motion and infant upper-body motion were associated with more aversive interactions, i.e., more parent-led interactions and more infant negativity. Further, at 4 months, the amount of motion silence was related to more adaptive interactions, i.e., more sensitive and child-led interactions. Analyses of the fine-grained motion features showed that if the mother coordinates her head movements with her infant's head movements, the interaction is rated as more adaptive in terms of less infant negativity and less dyadic negative states. We found more and stronger correlations between the motion features and the interaction qualities at 4 compared to 13 months. These results highlight that motion features are related to the quality of mother-infant interactions. Factors such as infant age and interaction set-up are likely to modify the meaning and importance of different motion features.

Local cell metrics: a novel method for analysis of cell-cell interactions.

PubMed

Su, Jing; Zapata, Pedro J; Chen, Chien-Chiang; Meredith, J Carson

2009-10-23

The regulation of many cell functions is inherently linked to cell-cell contact interactions. However, effects of contact interactions among adherent cells can be difficult to detect with global summary statistics due to the localized nature and noise inherent to cell-cell interactions. The lack of informatics approaches specific for detecting cell-cell interactions is a limitation in the analysis of large sets of cell image data, including traditional and combinatorial or high-throughput studies. Here we introduce a novel histogram-based data analysis strategy, termed local cell metrics (LCMs), which addresses this shortcoming. The new LCM method is demonstrated via a study of contact inhibition of proliferation of MC3T3-E1 osteoblasts. We describe how LCMs can be used to quantify the local environment of cells and how LCMs are decomposed mathematically into metrics specific to each cell type in a culture, e.g., differently-labelled cells in fluorescence imaging. Using this approach, a quantitative, probabilistic description of the contact inhibition effects in MC3T3-E1 cultures has been achieved. We also show how LCMs are related to the naïve Bayes model. Namely, LCMs are Bayes class-conditional probability functions, suggesting their use for data mining and classification. LCMs are successful in robust detection of cell contact inhibition in situations where conventional global statistics fail to do so. The noise due to the random features of cell behavior was suppressed significantly as a result of the focus on local distances, providing sensitive detection of cell-cell contact effects. The methodology can be extended to any quantifiable feature that can be obtained from imaging of cell cultures or tissue samples, including optical, fluorescent, and confocal microscopy. This approach may prove useful in interpreting culture and histological data in fields where cell-cell interactions play a critical role in determining cell fate, e.g., cancer, developmental biology, and tissue regeneration.

Theory of Photoemission in Actinides

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

Svane, Axel

2008-07-01

A theory is presented which describes the photoemission spectra of actinide compounds starting from the atomic limit of isolated actinide ions. The multiplets of the ion are calculated and an additional term is introduced to describe the interaction with the sea of conduction electrons. This leads to complex mixed-valent ground states, which describes well the rich spectrum observed for PuSe. In particular, the three-peak feature, which is often seen in Pu and Pu compounds in the vicinity of the Fermi level originates from f{sup 6} {yields} f{sup 5} emission. The theory is further applied to PuSb, PuCoGa{sub 5} and Am.more » (author)« less

An interactive dynamic analysis and decision support software for MR mammography.

PubMed

Ertaş, Gökhan; Gülçür, H Ozcan; Tunaci, Mehtap

2008-06-01

A fully automated software is introduced to facilitate MR mammography (MRM) examinations and overcome subjectiveness in diagnosis using normalized maximum intensity-time ratio (nMITR) maps. These maps inherently suppress enhancements due to normal parenchyma and blood vessels that surround lesions and have natural tolerance to small field inhomogeneities and motion artifacts. The classifier embedded within the software is trained with normalized complexity and maximum nMITR of 22 lesions and tested with the features of remaining 22 lesions. Achieved diagnostic performances are 92% sensitivity, 90% specificity, 91% accuracy, 92% positive predictive value and 90% negative predictive value. DynaMammoAnalyst shortens evaluation time considerably and reduces inter and intra-observer variability by providing decision support.

Other satellite atmospheres: Their nature and planetary interactions

NASA Technical Reports Server (NTRS)

Smyth, W. H.

1982-01-01

The Io sodium cloud model was successfully generated to include the time and spatial dependent lifetime sink produced by electron impact ionization as the plasma torus oscillates about the satellite plane, while simultaneously including the additional time dependence introduced by the action of solar radiation pressure on the cloud. Very preliminary model results are discussed and continuing progress in analysis of the peculiar directional features of the sodium cloud is also reported. Significant progress was made in developing a model for the Io potassium cloud and differences anticipated between the potassium and sodium cloud are described. An effort to understand the hydrogen atmosphere associated with Saturn's rings was initiated and preliminary results of a very and study are summarized.

Effects of charge symmetry on heavy ion reaction mechanisms

NASA Astrophysics Data System (ADS)

Colonna, M.; di Toro, M.; Fabbri, G.; Maccarone, S.

1998-03-01

We suggest several possibilities to study the properties of the symmetry term in the nuclear equation of state from radioactive beam experiments. Collision simulations with a stochastic transport approach, where asymmetry effects are suitably introduced, are presented. The dynamical response of an interacting highly asymmetric nuclear matter can be studied, taking advantage of the neutron skin structure. The main reaction mechanisms, from fusion to deep inelastic and fragmentation, appear quite sensitive to the form of the symmetry term of the effective force used, opening some new appealing experimental perspectives. Finally new features of fragment production are presented, due to the onset of chemical plus mechanical instabilities in dilute asymmetric nuclear matter.

Shell Biorefinery: Dream or Reality?

PubMed

Chen, Xi; Yang, Huiying; Yan, Ning

2016-09-12

Shell biorefinery, referring to the fractionation of crustacean shells into their major components and the transformation of each component into value-added chemicals and materials, has attracted growing attention in recent years. Since the large quantities of waste shells remain underexploited, their valorization can potentially bring both ecological and economic benefits. This Review provides an overview of the current status of shell biorefinery. It first describes the structural features of crustacean shells, including their composition and their interactions. Then, various fractionation methods for the shells are introduced. The last section is dedicated to the valorization of chitin and its derivatives for chemicals, porous carbon materials and functional polymers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pteros: fast and easy to use open-source C++ library for molecular analysis.

PubMed

Yesylevskyy, Semen O

2012-07-15

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

Sirius PSB: a generic system for analysis of biological sequences.

PubMed

Koh, Chuan Hock; Lin, Sharene; Jedd, Gregory; Wong, Limsoon

2009-12-01

Computational tools are essential components of modern biological research. For example, BLAST searches can be used to identify related proteins based on sequence homology, or when a new genome is sequenced, prediction models can be used to annotate functional sites such as transcription start sites, translation initiation sites and polyadenylation sites and to predict protein localization. Here we present Sirius Prediction Systems Builder (PSB), a new computational tool for sequence analysis, classification and searching. Sirius PSB has four main operations: (1) Building a classifier, (2) Deploying a classifier, (3) Search for proteins similar to query proteins, (4) Preliminary and post-prediction analysis. Sirius PSB supports all these operations via a simple and interactive graphical user interface. Besides being a convenient tool, Sirius PSB has also introduced two novelties in sequence analysis. Firstly, genetic algorithm is used to identify interesting features in the feature space. Secondly, instead of the conventional method of searching for similar proteins via sequence similarity, we introduced searching via features' similarity. To demonstrate the capabilities of Sirius PSB, we have built two prediction models - one for the recognition of Arabidopsis polyadenylation sites and another for the subcellular localization of proteins. Both systems are competitive against current state-of-the-art models based on evaluation of public datasets. More notably, the time and effort required to build each model is greatly reduced with the assistance of Sirius PSB. Furthermore, we show that under certain conditions when BLAST is unable to find related proteins, Sirius PSB can identify functionally related proteins based on their biophysical similarities. Sirius PSB and its related supplements are available at: http://compbio.ddns.comp.nus.edu.sg/~sirius.

An artificial network model for estimating the network structure underlying partially observed neuronal signals.

PubMed

Komatsu, Misako; Namikawa, Jun; Chao, Zenas C; Nagasaka, Yasuo; Fujii, Naotaka; Nakamura, Kiyohiko; Tani, Jun

2014-01-01

Many previous studies have proposed methods for quantifying neuronal interactions. However, these methods evaluated the interactions between recorded signals in an isolated network. In this study, we present a novel approach for estimating interactions between observed neuronal signals by theorizing that those signals are observed from only a part of the network that also includes unobserved structures. We propose a variant of the recurrent network model that consists of both observable and unobservable units. The observable units represent recorded neuronal activity, and the unobservable units are introduced to represent activity from unobserved structures in the network. The network structures are characterized by connective weights, i.e., the interaction intensities between individual units, which are estimated from recorded signals. We applied this model to multi-channel brain signals recorded from monkeys, and obtained robust network structures with physiological relevance. Furthermore, the network exhibited common features that portrayed cortical dynamics as inversely correlated interactions between excitatory and inhibitory populations of neurons, which are consistent with the previous view of cortical local circuits. Our results suggest that the novel concept of incorporating an unobserved structure into network estimations has theoretical advantages and could provide insights into brain dynamics beyond what can be directly observed. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Improving deep convolutional neural networks with mixed maxout units.

PubMed

Zhao, Hui-Zhen; Liu, Fu-Xian; Li, Long-Yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that "non-maximal features are unable to deliver" and "feature mapping subspace pooling is insufficient," we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance.

Telescopic multi-resolution augmented reality

NASA Astrophysics Data System (ADS)

Jenkins, Jeffrey; Frenchi, Christopher; Szu, Harold

2014-05-01

To ensure a self-consistent scaling approximation, the underlying microscopic fluctuation components can naturally influence macroscopic means, which may give rise to emergent observable phenomena. In this paper, we describe a consistent macroscopic (cm-scale), mesoscopic (micron-scale), and microscopic (nano-scale) approach to introduce Telescopic Multi-Resolution (TMR) into current Augmented Reality (AR) visualization technology. We propose to couple TMR-AR by introducing an energy-matter interaction engine framework that is based on known Physics, Biology, Chemistry principles. An immediate payoff of TMR-AR is a self-consistent approximation of the interaction between microscopic observables and their direct effect on the macroscopic system that is driven by real-world measurements. Such an interdisciplinary approach enables us to achieve more than multiple scale, telescopic visualization of real and virtual information but also conducting thought experiments through AR. As a result of the consistency, this framework allows us to explore a large dimensionality parameter space of measured and unmeasured regions. Towards this direction, we explore how to build learnable libraries of biological, physical, and chemical mechanisms. Fusing analytical sensors with TMR-AR libraries provides a robust framework to optimize testing and evaluation through data-driven or virtual synthetic simulations. Visualizing mechanisms of interactions requires identification of observable image features that can indicate the presence of information in multiple spatial and temporal scales of analog data. The AR methodology was originally developed to enhance pilot-training as well as `make believe' entertainment industries in a user-friendly digital environment We believe TMR-AR can someday help us conduct thought experiments scientifically, to be pedagogically visualized in a zoom-in-and-out, consistent, multi-scale approximations.

Containerless protein crystal growth method

NASA Technical Reports Server (NTRS)

Rhim, Won-Kyu; Chung, Sang K.

1991-01-01

A method of growing protein crystals from levitated drops is introduced and unique features of containerless approach in 1-g and micro-G laboratories are discussed. Electrostatic multidrop levitation system which is capable of simultaneous four drop levitation is described. A method of controlling protein saturation level in a programmed way is introduced and discussed. Finally, some of the unique features of containerless approach of protein crystal growth in space are discussed and summarized.

Optical implementation of neocognitron and its applications to radar signature discrimination

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin; Stoner, William W.

1991-01-01

A feature-extraction-based optoelectronic neural network is introduced. The system implementation approach applies the principle of the neocognitron paradigm first introduced by Fukushima et al. (1983). A multichannel correlator is used as a building block of a generic single layer of the neocognitron for shift-invariant feature correlation. Multilayer processing is achieved by iteratively feeding back the output of the feature correlator to the input spatial light modulator. Successful pattern recognition with intraclass fault tolerance and interclass discrimination is achieved using this optoelectronic neocognitron. Detailed system analysis is described. Experimental demonstration of radar signature processing is also provided.

Extended behavioural device modelling and circuit simulation with Qucs-S

NASA Astrophysics Data System (ADS)

Brinson, M. E.; Kuznetsov, V.

2018-03-01

Current trends in circuit simulation suggest a growing interest in open source software that allows access to more than one simulation engine while simultaneously supporting schematic drawing tools, behavioural Verilog-A and XSPICE component modelling, and output data post-processing. This article introduces a number of new features recently implemented in the 'Quite universal circuit simulator - SPICE variant' (Qucs-S), including structure and fundamental schematic capture algorithms, at the same time highlighting their use in behavioural semiconductor device modelling. Particular importance is placed on the interaction between Qucs-S schematics, equation-defined devices, SPICE B behavioural sources and hardware description language (HDL) scripts. The multi-simulator version of Qucs is a freely available tool that offers extended modelling and simulation features compared to those provided by legacy circuit simulators. The performance of a number of Qucs-S modelling extensions are demonstrated with a GaN HEMT compact device model and data obtained from tests using the Qucs-S/Ngspice/Xyce ©/SPICE OPUS multi-engine circuit simulator.

Crossing the threshold

NASA Astrophysics Data System (ADS)

Bush, John; Tambasco, Lucas

2017-11-01

First, we summarize the circumstances in which chaotic pilot-wave dynamics gives rise to quantum-like statistical behavior. For ``closed'' systems, in which the droplet is confined to a finite domain either by boundaries or applied forces, quantum-like features arise when the persistence time of the waves exceeds the time required for the droplet to cross its domain. Second, motivated by the similarities between this hydrodynamic system and stochastic electrodynamics, we examine the behavior of a bouncing droplet above the Faraday threshold, where a stochastic element is introduced into the drop dynamics by virtue of its interaction with a background Faraday wave field. With a view to extending the dynamical range of pilot-wave systems to capture more quantum-like features, we consider a generalized theoretical framework for stochastic pilot-wave dynamics in which the relative magnitudes of the drop-generated pilot-wave field and a stochastic background field may be varied continuously. We gratefully acknowledge the financial support of the NSF through their CMMI and DMS divisions.

Networks of plants: how to measure similarity in vegetable species.

PubMed

Vivaldo, Gianna; Masi, Elisa; Pandolfi, Camilla; Mancuso, Stefano; Caldarelli, Guido

2016-06-07

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.

Standardization of accelerator irradiation procedures for simulation of neutron induced damage in reactor structural materials

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

Shao, Lin; Gigax, Jonathan; Chen, Di

Self-ion irradiation is widely used as a method to simulate neutron damage in reactor structural materials. Accelerator-based simulation of void swelling, however, introduces a number of neutron-atypical features which require careful data extraction and in some cases introduction of innovative irradiation techniques to alleviate these issues. We briefly summarize three such atypical features: defect imbalance effects, pulsed beam effects, and carbon contamination. The latter issue has just been recently recognized as being relevant to simulation of void swelling and is discussed here in greater detail. It is shown that carbon ions are entrained in the ion beam by Coulomb forcemore » drag and accelerated toward the target surface. Beam-contaminant interactions are modeled using molecular dynamics simulation. By applying a multiple beam deflection technique, carbon and other contaminants can be effectively filtered out, as demonstrated in an irradiation of HT-9 alloy by 3.5 MeV Fe ions.« less

Standardization of accelerator irradiation procedures for simulation of neutron induced damage in reactor structural materials

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

Shao, Lin; Gigax, Jonathan; Chen, Di

Self-ion irradiation is widely used as a method to simulate neutron damage in reactor structural materials. Accelerator-based simulation of void swelling, however, introduces a number of neutron-atypical features which require careful data extraction and, in some cases, introduction of innovative irradiation techniques to alleviate these issues. In this paper, we briefly summarize three such atypical features: defect imbalance effects, pulsed beam effects, and carbon contamination. The latter issue has just been recently recognized as being relevant to simulation of void swelling and is discussed here in greater detail. It is shown that carbon ions are entrained in the ion beammore » by Coulomb force drag and accelerated toward the target surface. Beam-contaminant interactions are modeled using molecular dynamics simulation. Finally, by applying a multiple beam deflection technique, carbon and other contaminants can be effectively filtered out, as demonstrated in an irradiation of HT-9 alloy by 3.5 MeV Fe ions.« less

Standardization of accelerator irradiation procedures for simulation of neutron induced damage in reactor structural materials

DOE PAGES

Shao, Lin; Gigax, Jonathan; Chen, Di; ...

2017-06-12

Self-ion irradiation is widely used as a method to simulate neutron damage in reactor structural materials. Accelerator-based simulation of void swelling, however, introduces a number of neutron-atypical features which require careful data extraction and, in some cases, introduction of innovative irradiation techniques to alleviate these issues. In this paper, we briefly summarize three such atypical features: defect imbalance effects, pulsed beam effects, and carbon contamination. The latter issue has just been recently recognized as being relevant to simulation of void swelling and is discussed here in greater detail. It is shown that carbon ions are entrained in the ion beammore » by Coulomb force drag and accelerated toward the target surface. Beam-contaminant interactions are modeled using molecular dynamics simulation. Finally, by applying a multiple beam deflection technique, carbon and other contaminants can be effectively filtered out, as demonstrated in an irradiation of HT-9 alloy by 3.5 MeV Fe ions.« less

Hybrid Ni/SiO2/Au dimer arrays for high-resolution refractive index sensing

NASA Astrophysics Data System (ADS)

Pourjamal, Sara; Kataja, Mikko; Maccaferri, Nicolò; Vavassori, Paolo; van Dijken, Sebastiaan

2018-05-01

We introduce a novel magnetoplasmonic sensor concept for sensitive detection of refractive index changes. The sensor consists of a periodic array of Ni/SiO2/Au dimer nanodisks. Combined effects of near-field interactions between the Ni and Au disks within the individual dimers and far-field diffractive coupling between the dimers of the array produce narrow linewidth features in the magneto-optical Faraday spectrum. We associate these features with the excitation of surface lattice resonances and show that they exhibit a spectral shift when the refractive index of the surrounding environment is varied. Because the resonances are sharp, refractive index changes are accurately detected by tracking the wavelength where the Faraday signal crosses 0. Compared to random distributions of pure Ni nanodisks or Ni/SiO2/Au dimers or periodic arrays of Ni nanodisks, the sensing figure of merit of the hybrid magnetoplasmonic array is more than one order of magnitude larger.

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

Acoustic and Lexical Representations for Affect Prediction in Spontaneous Conversations.

PubMed

Cao, Houwei; Savran, Arman; Verma, Ragini; Nenkova, Ani

2015-01-01

In this article we investigate what representations of acoustics and word usage are most suitable for predicting dimensions of affect|AROUSAL, VALANCE, POWER and EXPECTANCY|in spontaneous interactions. Our experiments are based on the AVEC 2012 challenge dataset. For lexical representations, we compare corpus-independent features based on psychological word norms of emotional dimensions, as well as corpus-dependent representations. We find that corpus-dependent bag of words approach with mutual information between word and emotion dimensions is by far the best representation. For the analysis of acoustics, we zero in on the question of granularity. We confirm on our corpus that utterance-level features are more predictive than word-level features. Further, we study more detailed representations in which the utterance is divided into regions of interest (ROI), each with separate representation. We introduce two ROI representations, which significantly outperform less informed approaches. In addition we show that acoustic models of emotion can be improved considerably by taking into account annotator agreement and training the model on smaller but reliable dataset. Finally we discuss the potential for improving prediction by combining the lexical and acoustic modalities. Simple fusion methods do not lead to consistent improvements over lexical classifiers alone but improve over acoustic models.

Semiempirical prediction of protein folds

NASA Astrophysics Data System (ADS)

Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

2001-08-01

We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

Visualizing Infrared (IR) Spectroscopy with Computer Animation

NASA Technical Reports Server (NTRS)

Abrams, Charles B.; Fine, Leonard W.

1996-01-01

IR Tutor, an interactive, animated infrared (IR) spectroscopy tutorial has been developed for Macintosh and IBM-compatible computers. Using unique color animation, complicated vibrational modes can be introduced to beginning students. Rules governing the appearance of IR absorption bands become obvious because the vibrational modes can be visualized. Each peak in the IR spectrum is highlighted, and the animation of the corresponding normal mode can be shown. Students can study each spectrum stepwise, or click on any individual peak to see its assignment. Important regions of each spectrum can be expanded and spectra can be overlaid for comparison. An introduction to the theory of IR spectroscopy is included, making the program a complete instructional package. Our own success in using this software for teaching and research in both academic and industrial environments will be described. IR Tutor consists of three sections: (1) The 'Introduction' is a review of basic principles of spectroscopy. (2) 'Theory' begins with the classical model of a simple diatomic molecule and is expanded to include larger molecules by introducing normal modes and group frequencies. (3) 'Interpretation' is the heart of the tutorial. Thirteen IR spectra are analyzed in detail, covering the most important functional groups. This section features color animation of each normal mode, full interactivity, overlay of related spectra, and expansion of important regions. This section can also be used as a reference.

The self-assembled behavior of DNA bases on the interface.

PubMed

Liu, Lei; Xia, Dan; Klausen, Lasse H; Dong, Mingdong

2014-01-27

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

The Self-Assembled Behavior of DNA Bases on the Interface

PubMed Central

Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

2014-01-01

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

Blood Glucose Meters That Are Accessible to Blind and Visually Impaired Persons

PubMed Central

Uslan, Mark M.; Burton, Darren M.; Clements, Charles W.

2008-01-01

Blood glucose meters (BGMs) that can be used nonvisually or with a visual limitation were introduced in the mid-1990s, but it was not until 2006 and 2007 that a new set of meters with accessibility features were introduced: Prodigy, Prodigy Autocode, and Prodigy Voice (Diagnostic Devices, Charlotte, NC), and Advocate and Advocate Redi-Code (TaiDoc, Taiwan). Accessibility attributes of the newly introduced BGMs were tabulated, and product design features were examined and documented. The Prodigy Voice was found to be the only one of these new BGMs that is fully usable by blind and visually impaired persons. PMID:19885356

Blood glucose meters that are accessible to blind and visually impaired persons.

PubMed

Uslan, Mark M; Burton, Darren M; Clements, Charles W

2008-03-01

Blood glucose meters (BGMs) that can be used nonvisually or with a visual limitation were introduced in the mid-1990s, but it was not until 2006 and 2007 that a new set of meters with accessibility features were introduced: Prodigy, Prodigy Autocode, and Prodigy Voice (Diagnostic Devices, Charlotte, NC), and Advocate and Advocate Redi-Code (TaiDoc, Taiwan). Accessibility attributes of the newly introduced BGMs were tabulated, and product design features were examined and documented. The Prodigy Voice was found to be the only one of these new BGMs that is fully usable by blind and visually impaired persons.

Discriminant Features and Temporal Structure of Nonmanuals in American Sign Language

PubMed Central

Benitez-Quiroz, C. Fabian; Gökgöz, Kadir; Wilbur, Ronnie B.; Martinez, Aleix M.

2014-01-01

To fully define the grammar of American Sign Language (ASL), a linguistic model of its nonmanuals needs to be constructed. While significant progress has been made to understand the features defining ASL manuals, after years of research, much still needs to be done to uncover the discriminant nonmanual components. The major barrier to achieving this goal is the difficulty in correlating facial features and linguistic features, especially since these correlations may be temporally defined. For example, a facial feature (e.g., head moves down) occurring at the end of the movement of another facial feature (e.g., brows moves up), may specify a Hypothetical conditional, but only if this time relationship is maintained. In other instances, the single occurrence of a movement (e.g., brows move up) can be indicative of the same grammatical construction. In the present paper, we introduce a linguistic–computational approach to efficiently carry out this analysis. First, a linguistic model of the face is used to manually annotate a very large set of 2,347 videos of ASL nonmanuals (including tens of thousands of frames). Second, a computational approach is used to determine which features of the linguistic model are more informative of the grammatical rules under study. We used the proposed approach to study five types of sentences – Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed, and Assertions – plus their polarities – positive and negative. Our results verify several components of the standard model of ASL nonmanuals and, most importantly, identify several previously unreported features and their temporal relationship. Notably, our results uncovered a complex interaction between head position and mouth shape. These findings define some temporal structures of ASL nonmanuals not previously detected by other approaches. PMID:24516528

Necessity of introducing postencounter note describing history and physical examination at clinical performance examination in Korea.

PubMed

Kim, Jonghoon

2014-06-01

Information gathering ability had been evaluated mainly via checklists in clinical performance examinations (CPX). But, it is not proved yet if students write the information correctly in postencounter note (PN), although they asked questions or performed physical examinations (PE) about the information when they interacted with standardized patients in CPX. This study addressed the necessity of introducing PN to evaluate the ability in CPX. After patient encounters, students were instructed to write the findings of history taking and physical examination that they considered as important information in approaching the patient's problems in PN. PNs were scored using answer keys selected from checklist items, which were considered to be recorded in PN by CPX experts. PNs of six CPX cases from 54 students were analyzed. Correlation coefficients between the key-checklist scores and PN scores of six cases were moderate to high (0.52 to 0.79). However, students frequently neglected some cardinal features of chief complains, pertinent findings of past/social history and PE, and pertinent negative findings of associated symptoms in PNs, which were checked as 'done' in the keys of checklists. It is necessary to introduce PN in CPX to evaluate the students' ability of synthesis and integration of patient information.

Smoke Ring Physics

ERIC Educational Resources Information Center

Huggins, Elisha

2011-01-01

The behavior of smoke rings, tornados, and quantized vortex rings in superfluid helium has many features in common. These features can be described by the same mathematics we use when introducing Ampere's law in an introductory physics course. We discuss these common features. (Contains 7 figures.)

A feature-based approach to modeling protein-protein interaction hot spots.

PubMed

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-05-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.

Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses

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

Zhang, Kai; Fan, Meng; Liu, Yanhui

When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate R{sub c}, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. R{sub c} (or the corresponding critical casting thickness d{sub c}) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small R{sub c} < 10{sup −2} K/s, pure metals and most alloys are typically poor glass-formers with large R{sub c} > 10{sup 10} K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with R{sub c} approachingmore » that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for designing BMGs with cm or greater casting thickness.« less

Research on gesture recognition of augmented reality maintenance guiding system based on improved SVM

NASA Astrophysics Data System (ADS)

Zhao, Shouwei; Zhang, Yong; Zhou, Bin; Ma, Dongxi

2014-09-01

Interaction is one of the key techniques of augmented reality (AR) maintenance guiding system. Because of the complexity of the maintenance guiding system's image background and the high dimensionality of gesture characteristics, the whole process of gesture recognition can be divided into three stages which are gesture segmentation, gesture characteristic feature modeling and trick recognition. In segmentation stage, for solving the misrecognition of skin-like region, a segmentation algorithm combing background mode and skin color to preclude some skin-like regions is adopted. In gesture characteristic feature modeling of image attributes stage, plenty of characteristic features are analyzed and acquired, such as structure characteristics, Hu invariant moments features and Fourier descriptor. In trick recognition stage, a classifier based on Support Vector Machine (SVM) is introduced into the augmented reality maintenance guiding process. SVM is a novel learning method based on statistical learning theory, processing academic foundation and excellent learning ability, having a lot of issues in machine learning area and special advantages in dealing with small samples, non-linear pattern recognition at high dimension. The gesture recognition of augmented reality maintenance guiding system is realized by SVM after the granulation of all the characteristic features. The experimental results of the simulation of number gesture recognition and its application in augmented reality maintenance guiding system show that the real-time performance and robustness of gesture recognition of AR maintenance guiding system can be greatly enhanced by improved SVM.

Fake/Bogus Conferences: Their Features and Some Subtle Ways to Differentiate Them from Real Ones.

PubMed

Asadi, Amin; Rahbar, Nader; Rezvani, Mohammad Javad; Asadi, Fahime

2018-04-01

The main objective of the present paper is to introduce some features of fake/bogus conferences and some viable approaches to differentiate them from the real ones. These fake/bogus conferences introduce themselves as international conferences, which are multidisciplinary and indexed in major scientific digital libraries. Furthermore, most of the fake/bogus conference holders offer publishing the accepted papers in ISI journals and use other techniques in their advertisement e-mails.

Feature selection and definition for contours classification of thermograms in breast cancer detection

NASA Astrophysics Data System (ADS)

Jagodziński, Dariusz; Matysiewicz, Mateusz; Neumann, Łukasz; Nowak, Robert M.; Okuniewski, Rafał; Oleszkiewicz, Witold; Cichosz, Paweł

2016-09-01

This contribution introduces the method of cancer pathologies detection on breast skin temperature distribution images. The use of thermosensitive foils applied to the breasts skin allows to create thermograms, which displays the amount of infrared energy emitted by all breast cells. The significant foci of hyperthermia or inflammation are typical for cancer cells. That foci can be recognized on thermograms as a contours, which are the areas of higher temperature. Every contour can be converted to a feature set that describe it, using the raw, central, Hu, outline, Fourier and colour moments of image pixels processing. This paper defines also the new way of describing a set of contours through theirs neighbourhood relations. Contribution introduces moreover the way of ranking and selecting most relevant features. Authors used Neural Network with Gevrey`s concept and recursive feature elimination, to estimate feature importance.

Fast and Exact Fiber Surfaces for Tetrahedral Meshes.

PubMed

Klacansky, Pavol; Tierny, Julien; Carr, Hamish; Zhao Geng

2017-07-01

Isosurfaces are fundamental geometrical objects for the analysis and visualization of volumetric scalar fields. Recent work has generalized them to bivariate volumetric fields with fiber surfaces, the pre-image of polygons in range space. However, the existing algorithm for their computation is approximate, and is limited to closed polygons. Moreover, its runtime performance does not allow instantaneous updates of the fiber surfaces upon user edits of the polygons. Overall, these limitations prevent a reliable and interactive exploration of the space of fiber surfaces. This paper introduces the first algorithm for the exact computation of fiber surfaces in tetrahedral meshes. It assumes no restriction on the topology of the input polygon, handles degenerate cases and better captures sharp features induced by polygon bends. The algorithm also allows visualization of individual fibers on the output surface, better illustrating their relationship with data features in range space. To enable truly interactive exploration sessions, we further improve the runtime performance of this algorithm. In particular, we show that it is trivially parallelizable and that it scales nearly linearly with the number of cores. Further, we study acceleration data-structures both in geometrical domain and range space and we show how to generalize interval trees used in isosurface extraction to fiber surface extraction. Experiments demonstrate the superiority of our algorithm over previous work, both in terms of accuracy and running time, with up to two orders of magnitude speedups. This improvement enables interactive edits of range polygons with instantaneous updates of the fiber surface for exploration purpose. A VTK-based reference implementation is provided as additional material to reproduce our results.

Parametric Accuracy: Building Information Modeling Process Applied to the Cultural Heritage Preservation

NASA Astrophysics Data System (ADS)

Garagnani, S.; Manferdini, A. M.

2013-02-01

Since their introduction, modeling tools aimed to architectural design evolved in today's "digital multi-purpose drawing boards" based on enhanced parametric elements able to originate whole buildings within virtual environments. Semantic splitting and elements topology are features that allow objects to be "intelligent" (i.e. self-aware of what kind of element they are and with whom they can interact), representing this way basics of Building Information Modeling (BIM), a coordinated, consistent and always up to date workflow improved in order to reach higher quality, reliability and cost reductions all over the design process. Even if BIM was originally intended for new architectures, its attitude to store semantic inter-related information can be successfully applied to existing buildings as well, especially if they deserve particular care such as Cultural Heritage sites. BIM engines can easily manage simple parametric geometries, collapsing them to standard primitives connected through hierarchical relationships: however, when components are generated by existing morphologies, for example acquiring point clouds by digital photogrammetry or laser scanning equipment, complex abstractions have to be introduced while remodeling elements by hand, since automatic feature extraction in available software is still not effective. In order to introduce a methodology destined to process point cloud data in a BIM environment with high accuracy, this paper describes some experiences on monumental sites documentation, generated through a plug-in written for Autodesk Revit and codenamed GreenSpider after its capability to layout points in space as if they were nodes of an ideal cobweb.

Design of Polymer-Grafted Particles for Biocompatability

NASA Astrophysics Data System (ADS)

Trombly, David; Ganesan, Venkat

2009-03-01

Drug designers often coat drug particles with grafted polymers in order to introduce a net repulsion between the particles and blood proteins. This net repulsion results from the energy cost of compressing grafted chains on approach of proteins. It thus overcomes the Van Der Waals attraction between drug and protein which would otherwise cause particle-protein agglomeration and ultimately thrombosis. This study proposes to develop a fundamental understanding of the role of different features in controlling the efficacy of the grafted layers. We address this issue by developing a framework to predict the interactions between a polymer-coated spherical particle and a bare spherical particle. In order to fully capture the two-sphere system, a numerical solution of polymer mean field theory is used in a bispherical coordinate system. Results for protein-particle interaction energies for different design parameters will be presented. For biological applications, polyethylene glycol is often used as the grafted polymer. The unique properties of this molecule will be accounted for using the n-cluster model.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q

2017-07-03

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program-Web3DMol-a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamical evolution of motion perception.

PubMed

Kanai, Ryota; Sheth, Bhavin R; Shimojo, Shinsuke

2007-03-01

Motion is defined as a sequence of positional changes over time. However, in perception, spatial position and motion dynamically interact with each other. This reciprocal interaction suggests that the perception of a moving object itself may dynamically evolve following the onset of motion. Here, we show evidence that the percept of a moving object systematically changes over time. In experiments, we introduced a transient gap in the motion sequence or a brief change in some feature (e.g., color or shape) of an otherwise smoothly moving target stimulus. Observers were highly sensitive to the gap or transient change if it occurred soon after motion onset (< or =200 ms), but significantly less so if it occurred later (> or = 300 ms). Our findings suggest that the moving stimulus is initially perceived as a time series of discrete potentially isolatable frames; later failures to perceive change suggests that over time, the stimulus begins to be perceived as a single, indivisible gestalt integrated over space as well as time, which could well be the signature of an emergent stable motion percept.

Modelling of DNA-Mediated of Two- and -Three dimensional Protein-Protein and Protein-Nanoparticle Self-Assembly

NASA Astrophysics Data System (ADS)

Millan, Jaime; McMillan, Janet; Brodin, Jeff; Lee, Byeongdu; Mirkin, Chad; Olvera de La Cruz, Monica

Programmable DNA interactions represent a robust scheme to self-assemble a rich variety of tunable superlattices, where intrinsic and in some cases non-desirable nano-scale building blocks interactions are substituted for DNA hybridization events. Recent advances in synthesis has allowed the extension of this successful scheme to proteins, where DNA distribution can be tuned independently of protein shape by selectively addressing surface residues, giving rise to assembly properties in three dimensional protein-nanoparticle superlattices dependent on DNA distribution. In parallel to this advances, we introduced a scalable coarse-grained model that faithfully reproduces the previously observed co-assemblies from nanoparticles and proteins conjugates. Herein, we implement this numerical model to explain the stability of complex protein-nanoparticle binary superlattices and to elucidate experimentally inaccessible features such as protein orientation. Also, we will discuss systematic studies that highlight the role of DNA distribution and sequence on two-dimensional protein-protein and protein-nanoparticle superlattices.

An extended micromechanics method for probing interphase properties in polymer nanocomposites [An extended micromechanics method for overlapping geometries with application to polymer nanocomposites

DOE PAGES

Liu, Zeliang; Moore, John A.; Liu, Wing Kam

2016-05-03

Inclusions comprised on filler particles and interphase regions commonly form complex morphologies in polymer nanocomposites. Addressing these morphologies as systems of overlapping simple shapes allows for the study of dilute particles, clustered particles, and interacting interphases all in one general modeling framework. To account for the material properties in these overlapping geometries, weighted-mean and additive overlapping conditions are introduced and the corresponding inclusion-wise integral equations are formulated. An extended micromechanics method based on these overlapping conditions for linear elastic and viscoelastic heterogeneous material is then developed. An important feature of the proposed approach is that the effect of both themore » geometric overlapping (clustered particles) and physical overlapping (interacting interphases) on the effective properties can be distinguished. Lastly, we apply the extended micromechanics method to a viscoelastic polymer nanocomposite with interphase regions, and estimate the properties and thickness of the interphase region based on experimental data for carbon-black filled styrene butadiene rubbers.« less

An extended micromechanics method for probing interphase properties in polymer nanocomposites [An extended micromechanics method for overlapping geometries with application to polymer nanocomposites

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

Liu, Zeliang; Moore, John A.; Liu, Wing Kam

Inclusions comprised on filler particles and interphase regions commonly form complex morphologies in polymer nanocomposites. Addressing these morphologies as systems of overlapping simple shapes allows for the study of dilute particles, clustered particles, and interacting interphases all in one general modeling framework. To account for the material properties in these overlapping geometries, weighted-mean and additive overlapping conditions are introduced and the corresponding inclusion-wise integral equations are formulated. An extended micromechanics method based on these overlapping conditions for linear elastic and viscoelastic heterogeneous material is then developed. An important feature of the proposed approach is that the effect of both themore » geometric overlapping (clustered particles) and physical overlapping (interacting interphases) on the effective properties can be distinguished. Lastly, we apply the extended micromechanics method to a viscoelastic polymer nanocomposite with interphase regions, and estimate the properties and thickness of the interphase region based on experimental data for carbon-black filled styrene butadiene rubbers.« less

Brewing and volatiles analysis of three tea beers indicate a potential interaction between tea components and lager yeast.

PubMed

Rong, Lei; Peng, Li-Juan; Ho, Chi-Tang; Yan, Shou-He; Meurens, Marc; Zhang, Zheng-Zhu; Li, Da-Xiang; Wan, Xiao-Chun; Bao, Guan-Hu; Gao, Xue-Ling; Ling, Tie-Jun

2016-04-15

Green tea, oolong tea and black tea were separately introduced to brew three kinds of tea beers. A model was designed to investigate the tea beer flavour character. Comparison of the volatiles between the sample of tea beer plus water mixture (TBW) and the sample of combination of tea infusion and normal beer (CTB) was accomplished by triangular sensory test and HS-SPME GC-MS analysis. The PCA of GC-MS data not only showed a significant difference between volatile features of each TBW and CTB group, but also suggested some key compounds to distinguish TBW from CTB. The results of GC-MS showed that the relative concentrations of many typical tea volatiles were significantly changed after the brewing process. More interestingly, the behaviour of yeast fermentation was influenced by tea components. A potential interaction between tea components and lager yeast could be suggested. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nonlinear stochastic exclusion financial dynamics modeling and time-dependent intrinsic detrended cross-correlation

NASA Astrophysics Data System (ADS)

Zhang, Wei; Wang, Jun

2017-09-01

In attempt to reproduce price dynamics of financial markets, a stochastic agent-based financial price model is proposed and investigated by stochastic exclusion process. The exclusion process, one of interacting particle systems, is usually thought of as modeling particle motion (with the conserved number of particles) in a continuous time Markov process. In this work, the process is utilized to imitate the trading interactions among the investing agents, in order to explain some stylized facts found in financial time series dynamics. To better understand the correlation behaviors of the proposed model, a new time-dependent intrinsic detrended cross-correlation (TDI-DCC) is introduced and performed, also, the autocorrelation analyses are applied in the empirical research. Furthermore, to verify the rationality of the financial price model, the actual return series are also considered to be comparatively studied with the simulation ones. The comparison results of return behaviors reveal that this financial price dynamics model can reproduce some correlation features of actual stock markets.

Modeling birds on wires.

PubMed

Aydoğdu, A; Frasca, P; D'Apice, C; Manzo, R; Thornton, J M; Gachomo, B; Wilson, T; Cheung, B; Tariq, U; Saidel, W; Piccoli, B

2017-02-21

In this paper we introduce a mathematical model to study the group dynamics of birds resting on wires. The model is agent-based and postulates attraction-repulsion forces between the interacting birds: the interactions are "topological", in the sense that they involve a given number of neighbors irrespective of their distance. The model is first mathematically analyzed and then simulated to study its main properties: we observe that the model predicts birds to be more widely spaced near the borders of each group. We compare the results from the model with experimental data, derived from the analysis of pictures of pigeons and starlings taken in New Jersey: two different image elaboration protocols allow us to establish a good agreement with the model and to quantify its main parameters. We also discuss the potential handedness of the birds, by analyzing the group organization features and the group dynamics at the arrival of new birds. Finally, we propose a more refined mathematical model that describes landing and departing birds by suitable stochastic processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Economic networks: Heterogeneity-induced vulnerability and loss of synchronization

NASA Astrophysics Data System (ADS)

Colon, Célian; Ghil, Michael

2017-12-01

Interconnected systems are prone to propagation of disturbances, which can undermine their resilience to external perturbations. Propagation dynamics can clearly be affected by potential time delays in the underlying processes. We investigate how such delays influence the resilience of production networks facing disruption of supply. Interdependencies between economic agents are modeled using systems of Boolean delay equations (BDEs); doing so allows us to introduce heterogeneity in production delays and in inventories. Complex network topologies are considered that reproduce realistic economic features, including a network of networks. Perturbations that would otherwise vanish can, because of delay heterogeneity, amplify and lead to permanent disruptions. This phenomenon is enabled by the interactions between short cyclic structures. Difference in delays between two interacting, and otherwise resilient, structures can in turn lead to loss of synchronization in damage propagation and thus prevent recovery. Finally, this study also shows that BDEs on complex networks can lead to metastable relaxation oscillations, which are damped out in one part of a network while moving on to another part.

Going virtual with quicktime VR: new methods and standardized tools for interactive dynamic visualization of anatomical structures.

PubMed

Trelease, R B; Nieder, G L; Dørup, J; Hansen, M S

2000-04-15

Continuing evolution of computer-based multimedia technologies has produced QuickTime, a multiplatform digital media standard that is supported by stand-alone commercial programs and World Wide Web browsers. While its core functions might be most commonly employed for production and delivery of conventional video programs (e.g., lecture videos), additional QuickTime VR "virtual reality" features can be used to produce photorealistic, interactive "non-linear movies" of anatomical structures ranging in size from microscopic through gross anatomic. But what is really included in QuickTime VR and how can it be easily used to produce novel and innovative visualizations for education and research? This tutorial introduces the QuickTime multimedia environment, its QuickTime VR extensions, basic linear and non-linear digital video technologies, image acquisition, and other specialized QuickTime VR production methods. Four separate practical applications are presented for light and electron microscopy, dissectable preserved specimens, and explorable functional anatomy in magnetic resonance cinegrams.

On the use of information theory for the analysis of synchronous nociceptive withdrawal reflexes and somatosensory evoked potentials elicited by graded electrical stimulation.

PubMed

Arguissain, Federico G; Biurrun Manresa, José A; Mørch, Carsten D; Andersen, Ole K

2015-01-30

To date, few studies have combined the simultaneous acquisition of nociceptive withdrawal reflexes (NWR) and somatosensory evoked potentials (SEPs). In fact, it is unknown whether the combination of these two signals acquired simultaneously could provide additional information on somatosensory processing at spinal and supraspinal level compared to individual NWR and SEP signals. By using the concept of mutual information (MI), it is possible to quantify the relation between electrical stimuli and simultaneous elicited electrophysiological responses in humans based on the estimated stimulus-response signal probability distributions. All selected features from NWR and SEPs were informative in regard to the stimulus when considered individually. Specifically, the information carried by NWR features was significantly higher than the information contained in the SEP features (p<0.05). Moreover, the joint information carried by the combination of features showed an overall redundancy compared to the sum of the individual contributions. Comparison with existing methods MI can be used to quantify the information that single-trial NWR and SEP features convey, as well as the information carried jointly by NWR and SEPs. This is a model-free approach that considers linear and non-linear correlations at any order and is not constrained by parametric assumptions. The current study introduces a novel approach that allows the quantification of the individual and joint information content of single-trial NWR and SEP features. This methodology could be used to decode and interpret spinal and supraspinal interaction in studies modulating the responsiveness of the nociceptive system. Copyright © 2014 Elsevier B.V. All rights reserved.

Rhythm Patterns Interaction - Synchronization Behavior for Human-Robot Joint Action

PubMed Central

Mörtl, Alexander; Lorenz, Tamara; Hirche, Sandra

2014-01-01

Interactive behavior among humans is governed by the dynamics of movement synchronization in a variety of repetitive tasks. This requires the interaction partners to perform for example rhythmic limb swinging or even goal-directed arm movements. Inspired by that essential feature of human interaction, we present a novel concept and design methodology to synthesize goal-directed synchronization behavior for robotic agents in repetitive joint action tasks. The agents’ tasks are described by closed movement trajectories and interpreted as limit cycles, for which instantaneous phase variables are derived based on oscillator theory. Events segmenting the trajectories into multiple primitives are introduced as anchoring points for enhanced synchronization modes. Utilizing both continuous phases and discrete events in a unifying view, we design a continuous dynamical process synchronizing the derived modes. Inverse to the derivation of phases, we also address the generation of goal-directed movements from the behavioral dynamics. The developed concept is implemented to an anthropomorphic robot. For evaluation of the concept an experiment is designed and conducted in which the robot performs a prototypical pick-and-place task jointly with human partners. The effectiveness of the designed behavior is successfully evidenced by objective measures of phase and event synchronization. Feedback gathered from the participants of our exploratory study suggests a subjectively pleasant sense of interaction created by the interactive behavior. The results highlight potential applications of the synchronization concept both in motor coordination among robotic agents and in enhanced social interaction between humanoid agents and humans. PMID:24752212

A feature-based approach to modeling protein–protein interaction hot spots

PubMed Central

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-01-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions. PMID:19273533

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Older Adults Perceptions of Technology and Barriers to Interacting with Tablet Computers: A Focus Group Study.

PubMed

Vaportzis, Eleftheria; Clausen, Maria Giatsi; Gow, Alan J

2017-10-04

New technologies provide opportunities for the delivery of broad, flexible interventions with older adults. Focus groups were conducted to: (1) understand older adults' familiarity with, and barriers to, interacting with new technologies and tablets; and (2) utilize user-engagement in refining an intervention protocol. Eighteen older adults (65-76 years old; 83.3% female) who were novice tablet users participated in discussions about their perceptions of and barriers to interacting with tablets. We conducted three separate focus groups and used a generic qualitative design applying thematic analysis to analyse the data. The focus groups explored attitudes toward tablets and technology in general. We also explored the perceived advantages and disadvantages of using tablets, familiarity with, and barriers to interacting with tablets. In two of the focus groups, participants had previous computing experience (e.g., desktop), while in the other, participants had no previous computing experience. None of the participants had any previous experience with tablet computers. The themes that emerged were related to barriers (i.e., lack of instructions and guidance, lack of knowledge and confidence, health-related barriers, cost); disadvantages and concerns (i.e., too much and too complex technology, feelings of inadequacy, and comparison with younger generations, lack of social interaction and communication, negative features of tablets); advantages (i.e., positive features of tablets, accessing information, willingness to adopt technology); and skepticism about using tablets and technology in general. After brief exposure to tablets, participants emphasized the likelihood of using a tablet in the future. Our findings suggest that most of our participants were eager to adopt new technology and willing to learn using a tablet. However, they voiced apprehension about lack of, or lack of clarity in, instructions and support. Understanding older adults' perceptions of technology is important to assist with introducing it to this population and maximize the potential of technology to facilitate independent living.

Older Adults Perceptions of Technology and Barriers to Interacting with Tablet Computers: A Focus Group Study

PubMed Central

Vaportzis, Eleftheria; Giatsi Clausen, Maria; Gow, Alan J.

2017-01-01

Background: New technologies provide opportunities for the delivery of broad, flexible interventions with older adults. Focus groups were conducted to: (1) understand older adults' familiarity with, and barriers to, interacting with new technologies and tablets; and (2) utilize user-engagement in refining an intervention protocol. Methods: Eighteen older adults (65–76 years old; 83.3% female) who were novice tablet users participated in discussions about their perceptions of and barriers to interacting with tablets. We conducted three separate focus groups and used a generic qualitative design applying thematic analysis to analyse the data. The focus groups explored attitudes toward tablets and technology in general. We also explored the perceived advantages and disadvantages of using tablets, familiarity with, and barriers to interacting with tablets. In two of the focus groups, participants had previous computing experience (e.g., desktop), while in the other, participants had no previous computing experience. None of the participants had any previous experience with tablet computers. Results: The themes that emerged were related to barriers (i.e., lack of instructions and guidance, lack of knowledge and confidence, health-related barriers, cost); disadvantages and concerns (i.e., too much and too complex technology, feelings of inadequacy, and comparison with younger generations, lack of social interaction and communication, negative features of tablets); advantages (i.e., positive features of tablets, accessing information, willingness to adopt technology); and skepticism about using tablets and technology in general. After brief exposure to tablets, participants emphasized the likelihood of using a tablet in the future. Conclusions: Our findings suggest that most of our participants were eager to adopt new technology and willing to learn using a tablet. However, they voiced apprehension about lack of, or lack of clarity in, instructions and support. Understanding older adults' perceptions of technology is important to assist with introducing it to this population and maximize the potential of technology to facilitate independent living. PMID:29071004

Improving deep convolutional neural networks with mixed maxout units

PubMed Central

Liu, Fu-xian; Li, Long-yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that “non-maximal features are unable to deliver” and “feature mapping subspace pooling is insufficient,” we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance. PMID:28727737

Software-aided discussion about classical picture of Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Cavalcanti, C. J. H.; Ostermann, F.; Lima, N. W.; Netto, J. S.

2017-11-01

The Mach-Zehnder interferometer has played an important role both in quantum and classical physics research over the years. In physics education, it has been used as a didactic tool for quantum physics teaching, allowing fundamental concepts, such as particle-wave duality, to be addressed from the very beginning. For a student to understand the novelties of the quantum scenario, it is first worth introducing the classical picture. In this paper, we introduce a new version of the software developed by our research group to deepen the discussion on the classical picture of the Mach-Zehnder interferometer. We present its equivalence with the double slit experiment and we derive the mathematical expressions relating to the interference pattern. We also explore the concept of visibility (which is very important for understanding wave-particle complementarity in quantum physics) to help students become familiar with this experiment and to enhance their knowledge of its counterintuitive aspects. We use the software articulated by the mathematical formalism and phenomenological features. We also present excerpts of the discursive interactions of students using the software in didactic situations.

Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes

PubMed Central

Oliveros, Juan C.; Franch, Mònica; Tabas-Madrid, Daniel; San-León, David; Montoliu, Lluis; Cubas, Pilar; Pazos, Florencio

2016-01-01

The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5′ or 3′ and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request. PMID:27166368

Concierge: Personal Database Software for Managing Digital Research Resources

PubMed Central

Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

2007-01-01

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp). PMID:18974800

Multiresolution saliency map based object segmentation

NASA Astrophysics Data System (ADS)

Yang, Jian; Wang, Xin; Dai, ZhenYou

2015-11-01

Salient objects' detection and segmentation are gaining increasing research interest in recent years. A saliency map can be obtained from different models presented in previous studies. Based on this saliency map, the most salient region (MSR) in an image can be extracted. This MSR, generally a rectangle, can be used as the initial parameters for object segmentation algorithms. However, to our knowledge, all of those saliency maps are represented in a unitary resolution although some models have even introduced multiscale principles in the calculation process. Furthermore, some segmentation methods, such as the well-known GrabCut algorithm, need more iteration time or additional interactions to get more precise results without predefined pixel types. A concept of a multiresolution saliency map is introduced. This saliency map is provided in a multiresolution format, which naturally follows the principle of the human visual mechanism. Moreover, the points in this map can be utilized to initialize parameters for GrabCut segmentation by labeling the feature pixels automatically. Both the computing speed and segmentation precision are evaluated. The results imply that this multiresolution saliency map-based object segmentation method is simple and efficient.

Electronic structure and STM images simulation of defects on hBN/ black-phosphorene heterostructures: A theoretical study

NASA Astrophysics Data System (ADS)

Ospina, D. A.; Cisternas, E.; Duque, C. A.; Correa, J. D.

2018-03-01

By first principles calculations which include van der Waals interactions, we studied the electronic structure of hexagonal boron-nitride/black-phosphorene heterostructures (hBN/BP). In particular the role of several kind of defects on the electronic properties of black-phosphorene monolayer and hBN/BP heterostructure was analyzed. The defects under consideration were single and double vacancies, as well Stone-Wale type defects, all of them present in the phosphorene layer. In this way, we found that the electronic structure of the hBN/BP is modified according the type of defect that is introduced. As a remarkable feature, our results show occupied states at the Fermi Level introduced by a single vacancy in the energy gap of the hBN/BP heterostructure. Additionally, we performed simulations of scanning tunneling microscopy images. These simulations show that is possible to discriminate the kind of defect even when the black-phosphorene monolayer is part of the heterostructure hBN/BP. Our results may help to discriminate among several kind of defects during experimental characterization of these novel materials.

Stacked sparse autoencoder in hyperspectral data classification using spectral-spatial, higher order statistics and multifractal spectrum features

NASA Astrophysics Data System (ADS)

Wan, Xiaoqing; Zhao, Chunhui; Wang, Yanchun; Liu, Wu

2017-11-01

This paper proposes a novel classification paradigm for hyperspectral image (HSI) using feature-level fusion and deep learning-based methodologies. Operation is carried out in three main steps. First, during a pre-processing stage, wave atoms are introduced into bilateral filter to smooth HSI, and this strategy can effectively attenuate noise and restore texture information. Meanwhile, high quality spectral-spatial features can be extracted from HSI by taking geometric closeness and photometric similarity among pixels into consideration simultaneously. Second, higher order statistics techniques are firstly introduced into hyperspectral data classification to characterize the phase correlations of spectral curves. Third, multifractal spectrum features are extracted to characterize the singularities and self-similarities of spectra shapes. To this end, a feature-level fusion is applied to the extracted spectral-spatial features along with higher order statistics and multifractal spectrum features. Finally, stacked sparse autoencoder is utilized to learn more abstract and invariant high-level features from the multiple feature sets, and then random forest classifier is employed to perform supervised fine-tuning and classification. Experimental results on two real hyperspectral data sets demonstrate that the proposed method outperforms some traditional alternatives.

A scale-entropy diffusion equation to describe the multi-scale features of turbulent flames near a wall

NASA Astrophysics Data System (ADS)

Queiros-Conde, D.; Foucher, F.; Mounaïm-Rousselle, C.; Kassem, H.; Feidt, M.

2008-12-01

Multi-scale features of turbulent flames near a wall display two kinds of scale-dependent fractal features. In scale-space, an unique fractal dimension cannot be defined and the fractal dimension of the front is scale-dependent. Moreover, when the front approaches the wall, this dependency changes: fractal dimension also depends on the wall-distance. Our aim here is to propose a general geometrical framework that provides the possibility to integrate these two cases, in order to describe the multi-scale structure of turbulent flames interacting with a wall. Based on the scale-entropy quantity, which is simply linked to the roughness of the front, we thus introduce a general scale-entropy diffusion equation. We define the notion of “scale-evolutivity” which characterises the deviation of a multi-scale system from the pure fractal behaviour. The specific case of a constant “scale-evolutivity” over the scale-range is studied. In this case, called “parabolic scaling”, the fractal dimension is a linear function of the logarithm of scale. The case of a constant scale-evolutivity in the wall-distance space implies that the fractal dimension depends linearly on the logarithm of the wall-distance. We then verified experimentally, that parabolic scaling represents a good approximation of the real multi-scale features of turbulent flames near a wall.

Entanglement and quantum superposition induced by a single photon

NASA Astrophysics Data System (ADS)

Lü, Xin-You; Zhu, Gui-Lei; Zheng, Li-Li; Wu, Ying

2018-03-01

We predict the occurrence of single-photon-induced entanglement and quantum superposition in a hybrid quantum model, introducing an optomechanical coupling into the Rabi model. Originally, it comes from the photon-dependent quantum property of the ground state featured by the proposed hybrid model. It is associated with a single-photon-induced quantum phase transition, and is immune to the A2 term of the spin-field interaction. Moreover, the obtained quantum superposition state is actually a squeezed cat state, which can significantly enhance precision in quantum metrology. This work offers an approach to manipulate entanglement and quantum superposition with a single photon, which might have potential applications in the engineering of new single-photon quantum devices, and also fundamentally broaden the regime of cavity QED.

Application of Virtual, Augmented, and Mixed Reality to Urology.

PubMed

Hamacher, Alaric; Kim, Su Jin; Cho, Sung Tae; Pardeshi, Sunil; Lee, Seung Hyun; Eun, Sung-Jong; Whangbo, Taeg Keun

2016-09-01

Recent developments in virtual, augmented, and mixed reality have introduced a considerable number of new devices into the consumer market. This momentum is also affecting the medical and health care sector. Although many of the theoretical and practical foundations of virtual reality (VR) were already researched and experienced in the 1980s, the vastly improved features of displays, sensors, interactivity, and computing power currently available in devices offer a new field of applications to the medical sector and also to urology in particular. The purpose of this review article is to review the extent to which VR technology has already influenced certain aspects of medicine, the applications that are currently in use in urology, and the future development trends that could be expected.

Application of Virtual, Augmented, and Mixed Reality to Urology

PubMed Central

2016-01-01

Recent developments in virtual, augmented, and mixed reality have introduced a considerable number of new devices into the consumer market. This momentum is also affecting the medical and health care sector. Although many of the theoretical and practical foundations of virtual reality (VR) were already researched and experienced in the 1980s, the vastly improved features of displays, sensors, interactivity, and computing power currently available in devices offer a new field of applications to the medical sector and also to urology in particular. The purpose of this review article is to review the extent to which VR technology has already influenced certain aspects of medicine, the applications that are currently in use in urology, and the future development trends that could be expected. PMID:27706017

Single-Photon-Triggered Quantum Phase Transition

NASA Astrophysics Data System (ADS)

Lü, Xin-You; Zheng, Li-Li; Zhu, Gui-Lei; Wu, Ying

2018-06-01

We propose a hybrid quantum model combining cavity QED and optomechanics, which allows the occurrence of an equilibrium superradiant quantum phase transition (QPT) triggered by a single photon. This single-photon-triggered QPT exists in the cases of both ignoring and including the so-called A2 term; i.e., it is immune to the no-go theorem. It originally comes from the photon-dependent quantum criticality featured by the proposed hybrid quantum model. Moreover, a reversed superradiant QPT is induced by the competition between the introduced A2 term and the optomechanical interaction. This work offers an approach to manipulate QPT with a single photon, which should inspire the exploration of single-photon quantum-criticality physics and the engineering of new single-photon quantum devices.

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

A new Lagrangian method for three-dimensional steady supersonic flows

NASA Technical Reports Server (NTRS)

Loh, Ching-Yuen; Liou, Meng-Sing

1993-01-01

In this report, the new Lagrangian method introduced by Loh and Hui is extended for three-dimensional, steady supersonic flow computation. The derivation of the conservation form and the solution of the local Riemann solver using the Godunov and the high-resolution TVD (total variation diminished) scheme is presented. This new approach is accurate and robust, capable of handling complicated geometry and interactions between discontinuous waves. Test problems show that the extended Lagrangian method retains all the advantages of the two-dimensional method (e.g., crisp resolution of a slip-surface (contact discontinuity) and automatic grid generation). In this report, we also suggest a novel three dimensional Riemann problem in which interesting and intricate flow features are present.

Scientific Networks on Data Landscapes: Question Difficulty, Epistemic Success, and Convergence

PubMed Central

Grim, Patrick; Singer, Daniel J.; Fisher, Steven; Bramson, Aaron; Berger, William J.; Reade, Christopher; Flocken, Carissa; Sales, Adam

2014-01-01

A scientific community can be modeled as a collection of epistemic agents attempting to answer questions, in part by communicating about their hypotheses and results. We can treat the pathways of scientific communication as a network. When we do, it becomes clear that the interaction between the structure of the network and the nature of the question under investigation affects epistemic desiderata, including accuracy and speed to community consensus. Here we build on previous work, both our own and others’, in order to get a firmer grasp on precisely which features of scientific communities interact with which features of scientific questions in order to influence epistemic outcomes. Here we introduce a measure on the landscape meant to capture some aspects of the difficulty of answering an empirical question. We then investigate both how different communication networks affect whether the community finds the best answer and the time it takes for the community to reach consensus on an answer. We measure these two epistemic desiderata on a continuum of networks sampled from the Watts-Strogatz spectrum. It turns out that finding the best answer and reaching consensus exhibit radically different patterns. The time it takes for a community to reach a consensus in these models roughly tracks mean path length in the network. Whether a scientific community finds the best answer, on the other hand, tracks neither mean path length nor clustering coefficient. PMID:24683416

Scientific Networks on Data Landscapes: Question Difficulty, Epistemic Success, and Convergence.

PubMed

Grim, Patrick; Singer, Daniel J; Fisher, Steven; Bramson, Aaron; Berger, William J; Reade, Christopher; Flocken, Carissa; Sales, Adam

2013-12-01

A scientific community can be modeled as a collection of epistemic agents attempting to answer questions, in part by communicating about their hypotheses and results. We can treat the pathways of scientific communication as a network. When we do, it becomes clear that the interaction between the structure of the network and the nature of the question under investigation affects epistemic desiderata, including accuracy and speed to community consensus. Here we build on previous work, both our own and others', in order to get a firmer grasp on precisely which features of scientific communities interact with which features of scientific questions in order to influence epistemic outcomes. Here we introduce a measure on the landscape meant to capture some aspects of the difficulty of answering an empirical question. We then investigate both how different communication networks affect whether the community finds the best answer and the time it takes for the community to reach consensus on an answer. We measure these two epistemic desiderata on a continuum of networks sampled from the Watts-Strogatz spectrum. It turns out that finding the best answer and reaching consensus exhibit radically different patterns. The time it takes for a community to reach a consensus in these models roughly tracks mean path length in the network. Whether a scientific community finds the best answer, on the other hand, tracks neither mean path length nor clustering coefficient.

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

PubMed

Martinez, Hugo M; Maizel, Jacob V; Shapiro, Bruce A

2008-06-01

Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.

Electronically Enhanced Classroom Interaction.

ERIC Educational Resources Information Center

Draper, Stephen; Cargill, Julie; Cutts, Quintin

A design rationale for introducing electronic equipment (a group response system) for student interaction in lecture theaters is presented, linking the instructional design to theory. The effectiveness of the equipment for learning depends mostly on what pedagogic method is employed. Various alternative types are introduced, including: assessment;…

Aladin Lite: Embed your Sky in the Browser

NASA Astrophysics Data System (ADS)

Boch, T.; Fernique, P.

2014-05-01

I will introduce and describe Aladin Lite1, a lightweight interactive sky viewer running natively in the browser. The past five years have seen the emergence of powerful and complex web applications, thanks to major improvements in JavaScript engines and the advent of HTML5. At the same time, browser plugins Java applets, Flash, Silverlight) that were commonly used to run rich Internet applications are declining and are not well suited for mobile devices. The Aladin team took this opportunity to develop Aladin Lite, a lightweight version of Aladin geared towards simple visualization of a sky region. Relying on the widely supported HTML5 canvas element, it provides an intuitive user interface running on desktops and tablets. This first version allows one to interactively visualize multi-resolution HEALPix image and superimpose tabular data and footprints. Aladin Lite is easily embeddable on any web page and may be of interest for data providers which will be able to use it as an interactive previewer for their own image surveys, previously pre-processed as explained in details in the poster "Create & publish your Hierarchical Progressive Survey". I will present the main features of Aladin Lite as well as the JavaScript API which gives the building blocks to create rich interactions between a web page and Aladin Lite.

The Perfect Glass Paradigm: Disordered Hyperuniform Glasses Down to Absolute Zero

NASA Astrophysics Data System (ADS)

Zhang, G.; Stillinger, F. H.; Torquato, S.

2016-11-01

Rapid cooling of liquids below a certain temperature range can result in a transition to glassy states. The traditional understanding of glasses includes their thermodynamic metastability with respect to crystals. However, here we present specific examples of interactions that eliminate the possibilities of crystalline and quasicrystalline phases, while creating mechanically stable amorphous glasses down to absolute zero temperature. We show that this can be accomplished by introducing a new ideal state of matter called a “perfect glass”. A perfect glass represents a soft-interaction analog of the maximally random jammed (MRJ) packings of hard particles. These latter states can be regarded as the epitome of a glass since they are out of equilibrium, maximally disordered, hyperuniform, mechanically rigid with infinite bulk and shear moduli, and can never crystallize due to configuration-space trapping. Our model perfect glass utilizes two-, three-, and four-body soft interactions while simultaneously retaining the salient attributes of the MRJ state. These models constitute a theoretical proof of concept for perfect glasses and broaden our fundamental understanding of glass physics. A novel feature of equilibrium systems of identical particles interacting with the perfect-glass potential at positive temperature is that they have a non-relativistic speed of sound that is infinite.

Tangled nature model of evolutionary dynamics reconsidered: Structural and dynamical effects of trait inheritance

NASA Astrophysics Data System (ADS)

Andersen, Christian Walther; Sibani, Paolo

2016-05-01

Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K . We first show that the interactions generated by our rule are nearly independent of K . Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time tw also survives at t >tw . Finally, survival probabilities of species are shown to decay as powers of the ratio t /tw , a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.

Inquiry style interactive virtual experiments: a case on circular motion

NASA Astrophysics Data System (ADS)

Zhou, Shaona; Han, Jing; Pelz, Nathaniel; Wang, Xiaojun; Peng, Liangyu; Xiao, Hua; Bao, Lei

2011-11-01

Interest in computer-based learning, especially in the use of virtual reality simulations is increasing rapidly. While there are good reasons to believe that technologies have the potential to improve teaching and learning, how to utilize the technology effectively in teaching specific content difficulties is challenging. To help students develop robust understandings of correct physics concepts, we have developed interactive virtual experiment simulations that have the unique feature of enabling students to experience force and motion via an analogue joystick, allowing them to feel the applied force and simultaneously see its effects. The simulations provide students learning experiences that integrate both scientific representations and low-level sensory cues such as haptic cues under a single setting. In this paper, we introduce a virtual experiment module on circular motion. A controlled study has been conducted to evaluate the impact of using this virtual experiment on students' learning of force and motion in the context of circular motion. The results show that the interactive virtual experiment method is preferred by students and is more effective in helping students grasp the physics concepts than the traditional education method such as problem-solving practices. Our research suggests that well-developed interactive virtual experiments can be useful tools in teaching difficult concepts in science.

The Perfect Glass Paradigm: Disordered Hyperuniform Glasses Down to Absolute Zero.

PubMed

Zhang, G; Stillinger, F H; Torquato, S

2016-11-28

Rapid cooling of liquids below a certain temperature range can result in a transition to glassy states. The traditional understanding of glasses includes their thermodynamic metastability with respect to crystals. However, here we present specific examples of interactions that eliminate the possibilities of crystalline and quasicrystalline phases, while creating mechanically stable amorphous glasses down to absolute zero temperature. We show that this can be accomplished by introducing a new ideal state of matter called a "perfect glass". A perfect glass represents a soft-interaction analog of the maximally random jammed (MRJ) packings of hard particles. These latter states can be regarded as the epitome of a glass since they are out of equilibrium, maximally disordered, hyperuniform, mechanically rigid with infinite bulk and shear moduli, and can never crystallize due to configuration-space trapping. Our model perfect glass utilizes two-, three-, and four-body soft interactions while simultaneously retaining the salient attributes of the MRJ state. These models constitute a theoretical proof of concept for perfect glasses and broaden our fundamental understanding of glass physics. A novel feature of equilibrium systems of identical particles interacting with the perfect-glass potential at positive temperature is that they have a non-relativistic speed of sound that is infinite.

The Perfect Glass Paradigm: Disordered Hyperuniform Glasses Down to Absolute Zero

PubMed Central

Zhang, G.; Stillinger, F. H.; Torquato, S.

2016-01-01

Rapid cooling of liquids below a certain temperature range can result in a transition to glassy states. The traditional understanding of glasses includes their thermodynamic metastability with respect to crystals. However, here we present specific examples of interactions that eliminate the possibilities of crystalline and quasicrystalline phases, while creating mechanically stable amorphous glasses down to absolute zero temperature. We show that this can be accomplished by introducing a new ideal state of matter called a “perfect glass”. A perfect glass represents a soft-interaction analog of the maximally random jammed (MRJ) packings of hard particles. These latter states can be regarded as the epitome of a glass since they are out of equilibrium, maximally disordered, hyperuniform, mechanically rigid with infinite bulk and shear moduli, and can never crystallize due to configuration-space trapping. Our model perfect glass utilizes two-, three-, and four-body soft interactions while simultaneously retaining the salient attributes of the MRJ state. These models constitute a theoretical proof of concept for perfect glasses and broaden our fundamental understanding of glass physics. A novel feature of equilibrium systems of identical particles interacting with the perfect-glass potential at positive temperature is that they have a non-relativistic speed of sound that is infinite. PMID:27892452

Eye center localization and gaze gesture recognition for human-computer interaction.

PubMed

Zhang, Wenhao; Smith, Melvyn L; Smith, Lyndon N; Farooq, Abdul

2016-03-01

This paper introduces an unsupervised modular approach for accurate and real-time eye center localization in images and videos, thus allowing a coarse-to-fine, global-to-regional scheme. The trajectories of eye centers in consecutive frames, i.e., gaze gestures, are further analyzed, recognized, and employed to boost the human-computer interaction (HCI) experience. This modular approach makes use of isophote and gradient features to estimate the eye center locations. A selective oriented gradient filter has been specifically designed to remove strong gradients from eyebrows, eye corners, and shadows, which sabotage most eye center localization methods. A real-world implementation utilizing these algorithms has been designed in the form of an interactive advertising billboard to demonstrate the effectiveness of our method for HCI. The eye center localization algorithm has been compared with 10 other algorithms on the BioID database and six other algorithms on the GI4E database. It outperforms all the other algorithms in comparison in terms of localization accuracy. Further tests on the extended Yale Face Database b and self-collected data have proved this algorithm to be robust against moderate head poses and poor illumination conditions. The interactive advertising billboard has manifested outstanding usability and effectiveness in our tests and shows great potential for benefiting a wide range of real-world HCI applications.

Tangled nature model of evolutionary dynamics reconsidered: Structural and dynamical effects of trait inheritance.

PubMed

Andersen, Christian Walther; Sibani, Paolo

2016-05-01

Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K. We first show that the interactions generated by our rule are nearly independent of K. Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time t_{w} also survives at t>t_{w}. Finally, survival probabilities of species are shown to decay as powers of the ratio t/t_{w}, a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.

The "Social Gaze Space": A Taxonomy for Gaze-Based Communication in Triadic Interactions.

PubMed

Jording, Mathis; Hartz, Arne; Bente, Gary; Schulte-Rüther, Martin; Vogeley, Kai

2018-01-01

Humans substantially rely on non-verbal cues in their communication and interaction with others. The eyes represent a "simultaneous input-output device": While we observe others and obtain information about their mental states (including feelings, thoughts, and intentions-to-act), our gaze simultaneously provides information about our own attention and inner experiences. This substantiates its pivotal role for the coordination of communication. The communicative and coordinative capacities - and their phylogenetic and ontogenetic impacts - become fully apparent in triadic interactions constituted in its simplest form by two persons and an object. Technological advances have sparked renewed interest in social gaze and provide new methodological approaches. Here we introduce the 'Social Gaze Space' as a new conceptual framework for the systematic study of gaze behavior during social information processing. It covers all possible categorical states, namely 'partner-oriented,' 'object-oriented,' 'introspective,' 'initiating joint attention,' and 'responding joint attention.' Different combinations of these states explain several interpersonal phenomena. We argue that this taxonomy distinguishes the most relevant interactional states along their distinctive features, and will showcase the implications for prominent social gaze phenomena. The taxonomy allows to identify research desiderates that have been neglected so far. We argue for a systematic investigation of these phenomena and discuss some related methodological issues.

Full three-dimensional investigation of structural contact interactions in turbomachines

NASA Astrophysics Data System (ADS)

Legrand, Mathias; Batailly, Alain; Magnain, Benoît; Cartraud, Patrice; Pierre, Christophe

2012-05-01

Minimizing the operating clearance between rotating bladed-disks and stationary surrounding casings is a primary concern in the design of modern turbomachines since it may advantageously affect their energy efficiency. This technical choice possibly leads to interactions between elastic structural components through direct unilateral contact and dry friction, events which are now accepted as normal operating conditions. Subsequent nonlinear dynamical behaviors of such systems are commonly investigated with simplified academic models mainly due to theoretical difficulties and numerical challenges involved in non-smooth large-scale realistic models. In this context, the present paper introduces an adaptation of a full three-dimensional contact strategy for the prediction of potentially damaging motions that would imply highly demanding computational efforts for the targeted aerospace application in an industrial context. It combines a smoothing procedure including bicubic B-spline patches together with a Lagrange multiplier based contact strategy within an explicit time-marching integration procedure preferred for its versatility. The proposed algorithm is first compared on a benchmark configuration against the more elaborated bi-potential formulation and the commercial software Ansys. The consistency of the provided results and the low energy fluctuations of the introduced approach underlines its reliable numerical properties. A case study featuring blade-tip/casing contact on industrial finite element models is then proposed: it incorporates component mode synthesis and the developed three-dimensional contact algorithm for investigating structural interactions occurring within a turbomachine compressor stage. Both time results and frequency-domain analysis emphasize the practical use of such a numerical tool: detection of severe operating conditions and critical rotational velocities, time-dependent maps of stresses acting within the structures, parameter studies and blade design tests.

The Automation-by-Expertise-by-Training Interaction.

PubMed

Strauch, Barry

2017-03-01

I introduce the automation-by-expertise-by-training interaction in automated systems and discuss its influence on operator performance. Transportation accidents that, across a 30-year interval demonstrated identical automation-related operator errors, suggest a need to reexamine traditional views of automation. I review accident investigation reports, regulator studies, and literature on human computer interaction, expertise, and training and discuss how failing to attend to the interaction of automation, expertise level, and training has enabled operators to commit identical automation-related errors. Automated systems continue to provide capabilities exceeding operators' need for effective system operation and provide interfaces that can hinder, rather than enhance, operator automation-related situation awareness. Because of limitations in time and resources, training programs do not provide operators the expertise needed to effectively operate these automated systems, requiring them to obtain the expertise ad hoc during system operations. As a result, many do not acquire necessary automation-related system expertise. Integrating automation with expected operator expertise levels, and within training programs that provide operators the necessary automation expertise, can reduce opportunities for automation-related operator errors. Research to address the automation-by-expertise-by-training interaction is needed. However, such research must meet challenges inherent to examining realistic sociotechnical system automation features with representative samples of operators, perhaps by using observational and ethnographic research. Research in this domain should improve the integration of design and training and, it is hoped, enhance operator performance.

Multifunctional clickable and protein-repellent magnetic silica nanoparticles

NASA Astrophysics Data System (ADS)

Estupiñán, Diego; Bannwarth, Markus B.; Mylon, Steven E.; Landfester, Katharina; Muñoz-Espí, Rafael; Crespy, Daniel

2016-01-01

Silica nanoparticles are versatile materials whose physicochemical surface properties can be precisely adjusted. Because it is possible to combine several functionalities in a single carrier, silica-based materials are excellent candidates for biomedical applications. However, the functionality of the nanoparticles can get lost upon exposure to biological media due to uncontrolled biomolecule adsorption. Therefore, it is important to develop strategies that reduce non-specific protein-particle interactions without losing the introduced surface functionality. Herein, organosilane chemistry is employed to produce magnetic silica nanoparticles bearing differing amounts of amino and alkene functional groups on their surface as orthogonally addressable chemical functionalities. Simultaneously, a short-chain zwitterion is added to decrease the non-specific adsorption of biomolecules on the nanoparticles surface. The multifunctional particles display reduced protein adsorption after incubation in undiluted fetal bovine serum as well as in single protein solutions (serum albumin and lysozyme). Besides, the particles retain their capacity to selectively react with biomolecules. Thus, they can be covalently bio-functionalized with an antibody by means of orthogonal click reactions. These features make the described multifunctional silica nanoparticles a promising system for the study of surface interactions with biomolecules, targeting, and bio-sensing.Silica nanoparticles are versatile materials whose physicochemical surface properties can be precisely adjusted. Because it is possible to combine several functionalities in a single carrier, silica-based materials are excellent candidates for biomedical applications. However, the functionality of the nanoparticles can get lost upon exposure to biological media due to uncontrolled biomolecule adsorption. Therefore, it is important to develop strategies that reduce non-specific protein-particle interactions without losing the introduced surface functionality. Herein, organosilane chemistry is employed to produce magnetic silica nanoparticles bearing differing amounts of amino and alkene functional groups on their surface as orthogonally addressable chemical functionalities. Simultaneously, a short-chain zwitterion is added to decrease the non-specific adsorption of biomolecules on the nanoparticles surface. The multifunctional particles display reduced protein adsorption after incubation in undiluted fetal bovine serum as well as in single protein solutions (serum albumin and lysozyme). Besides, the particles retain their capacity to selectively react with biomolecules. Thus, they can be covalently bio-functionalized with an antibody by means of orthogonal click reactions. These features make the described multifunctional silica nanoparticles a promising system for the study of surface interactions with biomolecules, targeting, and bio-sensing. Electronic supplementary information (ESI) available: Detailed synthetic procedures and additional experimental light scattering and zeta-potential data. See DOI: 10.1039/c5nr08258g

Waves and mesoscale features in the marginal ice zone

NASA Technical Reports Server (NTRS)

Liu, Antony K.; Peng, Chih Y.

1993-01-01

Ocean-ice interaction processes in the Marginal Ice Zone (MIZ) by waves and mesoscale features, such as upwelling and eddies, are studied using ERS-1 Synthetic Aperture Radar (SAR) imagery and wave-ice interaction models. Satellite observations of mesoscale features can play a crucial role in ocean-ice interaction study.

Web Image Retrieval Using Self-Organizing Feature Map.

ERIC Educational Resources Information Center

Wu, Qishi; Iyengar, S. Sitharama; Zhu, Mengxia

2001-01-01

Provides an overview of current image retrieval systems. Describes the architecture of the SOFM (Self Organizing Feature Maps) based image retrieval system, discussing the system architecture and features. Introduces the Kohonen model, and describes the implementation details of SOFM computation and its learning algorithm. Presents a test example…

Activeness as a key to counter democratic balance

NASA Astrophysics Data System (ADS)

Qian, Shen; Liu, Yijun; Galam, Serge

2015-08-01

According to the classic Galam model of opinion dynamics, each agent participates at each update of an opinion interaction. While the scheme gives everyone the same chance to influence others, in reality, social activity and influence vary considerably from one agent to another. To account for such a feature, we introduce a new individual attribute-"activeness"-which makes some agents more inclined than others at engaging in local discussions. To enhance the corresponding effect, opinion updates are shifted from all-out agent interaction cycles to few agent interaction cycles. Using dynamic analysis and simulations the resulting model is found to exhibit a "Minority Counteroffensive" phenomenon, which under some initial conditions makes the minority to win the opinion competition despite a threshold tipping point at fifty percent. The associated probabilistic phenomenon persists in the case "activeness" is held equal for all agents. The effect of "opinion leaders" is also investigated. Indeed, a leader is an inflexible agent, i.e., an agent who does not change opinion. The results reveal that two opinion leaders with moderate social influence may have a stronger effect than one opinion leader with a strong social influence. The model may shed a new light to the understanding of opinion formation and public voting.

Virtual Reality for Research in Social Neuroscience

PubMed Central

Parsons, Thomas D.; Gaggioli, Andrea; Riva, Giuseppe

2017-01-01

The emergence of social neuroscience has significantly advanced our understanding of the relationship that exists between social processes and their neurobiological underpinnings. Social neuroscience research often involves the use of simple and static stimuli lacking many of the potentially important aspects of real world activities and social interactions. Whilst this research has merit, there is a growing interest in the presentation of dynamic stimuli in a manner that allows researchers to assess the integrative processes carried out by perceivers over time. Herein, we discuss the potential of virtual reality for enhancing ecological validity while maintaining experimental control in social neuroscience research. Virtual reality is a technology that allows for the creation of fully interactive, three-dimensional computerized models of social situations that can be fully controlled by the experimenter. Furthermore, the introduction of interactive virtual characters—either driven by a human or by a computer—allows the researcher to test, in a systematic and independent manner, the effects of various social cues. We first introduce key technical features and concepts related to virtual reality. Next, we discuss the potential of this technology for enhancing social neuroscience protocols, drawing on illustrative experiments from the literature. PMID:28420150

Kinematic design to improve ergonomics in human machine interaction.

PubMed

Schiele, André; van der Helm, Frans C T

2006-12-01

This paper introduces a novel kinematic design paradigm for ergonomic human machine interaction. Goals for optimal design are formulated generically and applied to the mechanical design of an upper-arm exoskeleton. A nine degree-of-freedom (DOF) model of the human arm kinematics is presented and used to develop, test, and optimize the kinematic structure of an human arm interfacing exoskeleton. The resulting device can interact with an unprecedented portion of the natural limb workspace, including motions in the shoulder-girdle, shoulder, elbow, and the wrist. The exoskeleton does not require alignment to the human joint axes, yet is able to actuate each DOF of our redundant limb unambiguously and without reaching into singularities. The device is comfortable to wear and does not create residual forces if misalignments exist. Implemented in a rehabilitation robot, the design features of the exoskeleton could enable longer lasting training sessions, training of fully natural tasks such as activities of daily living and shorter dress-on and dress-off times. Results from inter-subject experiments with a prototype are presented, that verify usability over the entire workspace of the human arm, including shoulder and shoulder girdle.

Entanglement entropy with a time-dependent Hamiltonian

NASA Astrophysics Data System (ADS)

Sivaramakrishnan, Allic

2018-03-01

The time evolution of entanglement tracks how information propagates in interacting quantum systems. We study entanglement entropy in CFT2 with a time-dependent Hamiltonian. We perturb by operators with time-dependent source functions and use the replica trick to calculate higher-order corrections to entanglement entropy. At first order, we compute the correction due to a metric perturbation in AdS3/CFT2 and find agreement on both sides of the duality. Past first order, we find evidence of a universal structure of entanglement propagation to all orders. The central feature is that interactions entangle unentangled excitations. Entanglement propagates according to "entanglement diagrams," proposed structures that are motivated by accessory spacetime diagrams for real-time perturbation theory. To illustrate the mechanisms involved, we compute higher-order corrections to free fermion entanglement entropy. We identify an unentangled operator, one which does not change the entanglement entropy to any order. Then, we introduce an interaction and find it changes entanglement entropy by entangling the unentangled excitations. The entanglement propagates in line with our conjecture. We compute several entanglement diagrams. We provide tools to simplify the computation of loop entanglement diagrams, which probe UV effects in entanglement propagation in CFT and holography.

Virtual Reality for Research in Social Neuroscience.

PubMed

Parsons, Thomas D; Gaggioli, Andrea; Riva, Giuseppe

2017-04-16

The emergence of social neuroscience has significantly advanced our understanding of the relationship that exists between social processes and their neurobiological underpinnings. Social neuroscience research often involves the use of simple and static stimuli lacking many of the potentially important aspects of real world activities and social interactions. Whilst this research has merit, there is a growing interest in the presentation of dynamic stimuli in a manner that allows researchers to assess the integrative processes carried out by perceivers over time. Herein, we discuss the potential of virtual reality for enhancing ecological validity while maintaining experimental control in social neuroscience research. Virtual reality is a technology that allows for the creation of fully interactive, three-dimensional computerized models of social situations that can be fully controlled by the experimenter. Furthermore, the introduction of interactive virtual characters-either driven by a human or by a computer-allows the researcher to test, in a systematic and independent manner, the effects of various social cues. We first introduce key technical features and concepts related to virtual reality. Next, we discuss the potential of this technology for enhancing social neuroscience protocols, drawing on illustrative experiments from the literature.

Interactive outlining: an improved approach using active contours

NASA Astrophysics Data System (ADS)

Daneels, Dirk; van Campenhout, David; Niblack, Carlton W.; Equitz, Will; Barber, Ron; Fierens, Freddy

1993-04-01

The purpose of our work is to outline objects on images in an interactive environment. We use an improved method based on energy minimizing active contours or `snakes.' Kass et al., proposed a variational technique; Amini used dynamic programming; and Williams and Shah introduced a fast, greedy algorithm. We combine the advantages of the latter two methods in a two-stage algorithm. The first stage is a greedy procedure that provides fast initial convergence. It is enhanced with a cost term that extends over a large number of points to avoid oscillations. The second stage, when accuracy becomes important, uses dynamic programming. This step is accelerated by the use of alternating search neighborhoods and by dropping stable points from the iterations. We have also added several features for user interaction. First, the user can define points of high confidence. Mathematically, this results in an extra cost term and, in that way, the robustness in difficult areas (e.g., noisy edges, sharp corners) is improved. We also give the user the possibility of incremental contour tracking, thus providing feedback on the refinement process. The algorithm has been tested on numerous photographic clip art images and extensive tests on medical images are in progress.

Resonant slepton production and right sneutrino dark matter in left-right supersymmetry

NASA Astrophysics Data System (ADS)

Frank, Mariana; Fuks, Benjamin; Huitu, Katri; Rai, Santosh Kumar; Waltari, Harri

2017-05-01

Right-handed sneutrinos are natural components of left-right symmetric supersymmetric models where the gauge sector is extended to include right-handed weak interactions. Unlike in other models where right-handed sneutrinos are gauge singlets, here the right sneutrino is part of a doublet and could be a dark matter candidate whose annihilation proceeds via gauge interactions. We investigate this possibility, and find that relic density, low-energy observable and direct supersymmetry search constraints can be satisfied when the lightest supersymmetric particle is a right-handed sneutrino. We introduce benchmarks for left-right supersymmetric realizations where either a sneutrino or a neutralino is the lightest superpartner. We then study the LHC signals arising through resonant right-handed slepton production via a W R gauge-boson exchange that lead to final states enriched in leptons, additionally containing a large amount of missing transverse momentum, and featuring a low jet multiplicity. We find that such a resonant production would boost the chances of discovering these weakly interacting supersymmetric particles for a mass range extending beyond 1 TeV already with a luminosity of 100 fb-1. Finally, we compare sneutrino versus neutralino scenarios, and comment on differences with other sneutrino dark matter models.

Analysis of high-speed digital phonoscopy pediatric images

NASA Astrophysics Data System (ADS)

Unnikrishnan, Harikrishnan; Donohue, Kevin D.; Patel, Rita R.

2012-02-01

The quantitative characterization of vocal fold (VF) motion can greatly enhance the diagnosis and treatment of speech pathologies. The recent availability of high-speed systems has created new opportunities to understand VF dynamics. This paper presents quantitative methods for analyzing VF dynamics with high-speed digital phonoscopy, with a focus on expected VF changes during childhood. A robust method for automatic VF edge tracking during phonation is introduced and evaluated against 4 expert human observers. Results from 100 test frames show a subpixel difference between the VF edges selected by algorithm and expert observers. Waveforms created from the VF edge displacement are used to created motion features with limited sensitivity to variations of camera resolution on the imaging plane. New features are introduced based on acceleration ratios of critical points over each phonation cycle, which have the potential for studying issues related to impact stress. A novel denoising and hybrid interpolation/extrapolation scheme is also introduced to reduce the impact of quantization errors and large sampling intervals relative to the phonation cycle. Features extracted from groups of 4 adults and 5 children show large differences for features related to asymmetry between the right and left fold and consistent differences for impact acceleration ratio.

16 CFR § 1750.3 - Scope and application.

Code of Federal Regulations, 2013 CFR

2013-01-01

... manufactured and introduced or delivered for introduction into interstate commerce after the effective date... feature(s) of the device shall be accessible from all spaces which (a) are bounded by interior walls or...

Plasmon-Exciton Coupling Interaction for Surface Catalytic Reactions.

PubMed

Wang, Jingang; Lin, Weihua; Xu, Xuefeng; Ma, Fengcai; Sun, Mengtao

2018-05-01

In this review, we firstly reveal the physical principle of plasmon-exciton coupling interaction with steady absorption spectroscopy, and ultrafast transition absorption spectroscopy, based on the pump-prop technology. Secondly, we introduce the fabrication of electro-optical device of two-dimensional semiconductor-nanostructure noble metals hybrid, based on the plasmon-exciton coupling interactions. Thirdly, we introduce the applications of plasmon-exciton coupling interaction in the field of surface catalytic reactions. Lastly, the perspective of plasmon-exciton coupling interaction and applications closed this review. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Neural Mechanisms of Cortical Motion Computation Based on a Neuromorphic Sensory System

PubMed Central

Abdul-Kreem, Luma Issa; Neumann, Heiko

2015-01-01

The visual cortex analyzes motion information along hierarchically arranged visual areas that interact through bidirectional interconnections. This work suggests a bio-inspired visual model focusing on the interactions of the cortical areas in which a new mechanism of feedforward and feedback processing are introduced. The model uses a neuromorphic vision sensor (silicon retina) that simulates the spike-generation functionality of the biological retina. Our model takes into account two main model visual areas, namely V1 and MT, with different feature selectivities. The initial motion is estimated in model area V1 using spatiotemporal filters to locally detect the direction of motion. Here, we adapt the filtering scheme originally suggested by Adelson and Bergen to make it consistent with the spike representation of the DVS. The responses of area V1 are weighted and pooled by area MT cells which are selective to different velocities, i.e. direction and speed. Such feature selectivity is here derived from compositions of activities in the spatio-temporal domain and integrating over larger space-time regions (receptive fields). In order to account for the bidirectional coupling of cortical areas we match properties of the feature selectivity in both areas for feedback processing. For such linkage we integrate the responses over different speeds along a particular preferred direction. Normalization of activities is carried out over the spatial as well as the feature domains to balance the activities of individual neurons in model areas V1 and MT. Our model was tested using different stimuli that moved in different directions. The results reveal that the error margin between the estimated motion and synthetic ground truth is decreased in area MT comparing with the initial estimation of area V1. In addition, the modulated V1 cell activations shows an enhancement of the initial motion estimation that is steered by feedback signals from MT cells. PMID:26554589

Biological and genetic features of introduced aphid populations in agroecosystems.

PubMed

Figueroa, Christian C; Fuentes-Contreras, Eduardo; Molina-Montenegro, Marco A; Ramírez, Claudio C

2018-04-01

In agroecosystems, introduced aphids that reproduce by obligate parthenogenesis (OP) show strong biased representation of a few genotypes (superclones), whereas species with cyclical parthenogenesis (CP) exhibit the opposite trend with many unique genotypes. We analyzed the biological and genetic features of 23 different aphid species introduced in different geographic areas and climates, finding putative superclones in about 60% of them. We have examined the proximal causes for aphid establishment and spread after their introduction, and found that OP, host availability, and phenotypic plasticity are among the main variables underpinning the ability of aphids to succeed in new geographic areas, which may explain the high potential for invasion in this group of pest insects. Copyright © 2018 Elsevier Inc. All rights reserved.

Superstretchable Nacre-Mimetic Graphene/Poly(vinyl alcohol) Composite Film Based on Interfacial Architectural Engineering.

PubMed

Zhao, Nifang; Yang, Miao; Zhao, Qian; Gao, Weiwei; Xie, Tao; Bai, Hao

2017-05-23

Through designing hierarchical structures, particularly optimizing the chemical and architectural interactions at its inorganic/organic interface, nacre has achieved an excellent combination of contradictory mechanical properties such as strength and toughness, which is highly demanded yet difficult to achieve by most synthetic materials. Most techniques applied to develop nacre-mimetic composites have been focused on mimicking the "brick-and-mortar" structure, but the interfacial architectural features, especially the asperities and mineral bridges of "bricks", have been rarely concerned, which are of equal importance for enhancing mechanical properties of nacre. Here, we used a modified bidirectional freezing method followed by uniaxial pressing and chemical reduction to assemble a nacre-mimetic graphene/poly(vinyl alcohol) composite film, with both asperities and bridges introduced in addition to the lamellar layers to mimic the interfacial architectural interactions found in nacre. As such, we have developed a composite film that is not only strong (up to ∼150.9 MPa), but also tough (up to ∼8.50 MJ/m 3 ), and highly stretchable (up to ∼10.44%), difficult to obtain by other methods. This was all achieved by only interfacial architectural engineering within the traditional "brick-and-mortar" structure, without introducing a third component or employing chemical cross-linker as in some other nacre-mimetic systems. More importantly, we believe that the design principles and processing strategies reported here can also be applied to other material systems to develop strong and stretchable materials.

[Ecological agriculture: future of Good Agriculture Practice of Chinese materia medica].

PubMed

Guo, Lan-ping; Zhou, Liang-yun; Mo, Ge; Wang, Sheng; Huang, Lu-qi

2015-09-01

Based on the ecological and economic problems in Good Agriculture Practice (GAP) of Chinese material medica, we introduced the origin, concept, features and operative technology of eco-agriculture worldwide, emphasizing its modes on different biological levels of landscape, ecosystem, community, population, individual and gene in China. And on this basis, we analyzed the background and current situation of eco-agriculture of Chinese materia medica, and proposed its development ideas and key tasks, including: (1) Analysis and planning of the production pattern of Chinese material medica national wide. (2) Typical features extraction of regional agriculture of Chinese materia medica. (3) Investigation of the interaction and its mechanism between typical Chinese materia medica in each region and the micro-ecology of rhizosphere soil. (4) Study on technology of eco-agriculture of Chinese materia medica. (5) Extraction and solidification of eco-agriculture modes of Chinese materia medica. (6) Study on the theory of eco-agriculture of Chinese materia medica. Also we pointed out that GAP and eco-agriculture of Chinese material medica are both different and relative, but they are not contradictory with their own features. It is an irresistible trend to promote eco-agriculture in the GAP of Chinese material medica and coordinate ecological and economic development.

Regional co-location pattern scoping on a street network considering distance decay effects of spatial interaction

PubMed Central

Yu, Wenhao

2017-01-01

Regional co-location scoping intends to identify local regions where spatial features of interest are frequently located together. Most of the previous researches in this domain are conducted on a global scale and they assume that spatial objects are embedded in a 2-D space, but the movement in urban space is actually constrained by the street network. In this paper we refine the scope of co-location patterns to 1-D paths consisting of nodes and segments. Furthermore, since the relations between spatial events are usually inversely proportional to their separation distance, the proposed method introduces the “Distance Decay Effects” to improve the result. Specifically, our approach first subdivides the street edges into continuous small linear segments. Then a value representing the local distribution intensity of events is estimated for each linear segment using the distance-decay function. Each kind of geographic feature can lead to a tessellated network with density attribute, and the generated multiple networks for the pattern of interest will be finally combined into a composite network by calculating the co-location prevalence measure values, which are based on the density variation between different features. Our experiments verify that the proposed approach is effective in urban analysis. PMID:28763496

Exploiting Amino Acid Composition for Predicting Protein-Protein Interactions

PubMed Central

Roy, Sushmita; Martinez, Diego; Platero, Harriett; Lane, Terran; Werner-Washburne, Margaret

2009-01-01

Background Computational prediction of protein interactions typically use protein domains as classifier features because they capture conserved information of interaction surfaces. However, approaches relying on domains as features cannot be applied to proteins without any domain information. In this paper, we explore the contribution of pure amino acid composition (AAC) for protein interaction prediction. This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information. Results AAC performed at par with protein interaction prediction based on domains on three yeast protein interaction datasets. Similar behavior was obtained using different classifiers, indicating that our results are a function of features and not of classifiers. In addition to yeast datasets, AAC performed comparably on worm and fly datasets. Prediction of interactions for the entire yeast proteome identified a large number of novel interactions, the majority of which co-localized or participated in the same processes. Our high confidence interaction network included both well-studied and uncharacterized proteins. Proteins with known function were involved in actin assembly and cell budding. Uncharacterized proteins interacted with proteins involved in reproduction and cell budding, thus providing putative biological roles for the uncharacterized proteins. Conclusion AAC is a simple, yet powerful feature for predicting protein interactions, and can be used alone or in conjunction with protein domains to predict new and validate existing interactions. More importantly, AAC alone performs at par with existing, but more complex, features indicating the presence of sequence-level information that is predictive of interaction, but which is not necessarily restricted to domains. PMID:19936254

Numerical simulations and observations of surface wave fields under an extreme tropical cyclone

USGS Publications Warehouse

Fan, Y.; Ginis, I.; Hara, T.; Wright, C.W.; Walsh, E.J.

2009-01-01

The performance of the wave model WAVEWATCH III under a very strong, category 5, tropical cyclone wind forcing is investigated with different drag coefficient parameterizations and ocean current inputs. The model results are compared with field observations of the surface wave spectra from an airborne scanning radar altimeter, National Data Buoy Center (NDBC) time series, and satellite altimeter measurements in Hurricane Ivan (2004). The results suggest that the model with the original drag coefficient parameterization tends to overestimate the significant wave height and the dominant wavelength and produces a wave spectrum with narrower directional spreading. When an improved drag parameterization is introduced and the wave-current interaction is included, the model yields an improved forecast of significant wave height, but underestimates the dominant wavelength. When the hurricane moves over a preexisting mesoscale ocean feature, such as the Loop Current in the Gulf of Mexico or a warm-and cold-core ring, the current associated with the feature can accelerate or decelerate the wave propagation and significantly modulate the wave spectrum. ?? 2009 American Meteorological Society.

Volumetric data analysis using Morse-Smale complexes

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

Natarajan, V; Pascucci, V

2005-10-13

The 3D Morse-Smale complex is a fundamental topological construct that partitions the domain of a real-valued function into regions having uniform gradient flow behavior. In this paper, we consider the construction and selective presentation of cells of the Morse-Smale complex and their use in the analysis and visualization of scientific datasets. We take advantage of the fact that cells of different dimension often characterize different types of features present in the data. For example, critical points pinpoint changes in topology by showing where components of the level sets are created, destroyed or modified in genus. Edges of the Morse-Smale complexmore » extract filament-like features that are not explicitly modeled in the original data. Interactive selection and rendering of portions of the Morse-Smale complex introduces fundamental data management challenges due to the unstructured nature of the complex even for structured inputs. We describe a data structure that stores the Morse-Smale complex and allows efficient selective traversal of regions of interest. Finally, we illustrate the practical use of this approach by applying it to cryo-electron microscopy data of protein molecules.« less

Evaluating and understanding fish health risks and their consequences in propagated and free-ranging fish populations

USGS Publications Warehouse

Moffitt, C.M.; Haukenes, A.H.; Williams, C.J.

2005-01-01

Fishery managers and resource conservationists are increasingly interested in understanding the fish health and disease risks of free-ranging fishes and whether propagated fishes or features and practices used at fish culture facilities pose a health risk to free-ranging populations. Disease agents are present in most both captive and all free-ranging fish populations, but the consequences and extent of infections in free-ranging populations are often difficult to measure, control, and understand. Sampling methods, protocols, and assay techniques developed to assess the health of captive populations are not as applicable for assessments of free-ranging fishes. The use of chemicals and therapeutics to control diseases and parasites in propagated fishes likely reduces the risk of introducing specific pathogens into the environment, but control measures may have localized effects on the environment surrounding fish culture facilities. To understand health risks of propagated and free ranging fishes, we must consider fish populations, culture facilities, fish releases, and their interactions within the greater geospatial features of the aquatic environment. ?? 2004 by the American Fisheries Society.

Structural features of Fab fragments of rheumatoid factor IgM-RF in solution

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

Volkov, V. V., E-mail: vvo@ns.crys.ras.ru; Lapuk, V. A.; Shtykova, E. V.

The structural features of the Fab fragments of monoclonal (Waldenstroem's disease) immunoglobulin M (IgM) and rheumatoid immunoglobulin M (IgM-RF) were studied by a complex of methods, including small-angle X-ray scattering (SAXS), electron spin resonance (ESR), and mass spectrometry (MS). The Fab-RF fragment was demonstrated to be much more flexible in the region of interdomain contacts, the molecular weights and the shapes of the Fab and Fab-RF macromolecules in solution being only slightly different. According to the ESR data, the rotational correlation time for a spin label introduced into the peptide sequence for Fab is twice as large as that formore » Fab-RF (21{+-}2 and 11{+-}1 ns, respectively), whereas the molecular weights of these fragments differ by only 0.5% (mass-spectrometric data), which correlates with the results of molecular-shape modeling by small-angle X-ray scattering. The conclusion about the higher flexibility of the Fab-RF fragment contributes to an understanding of the specificity of interactions between the rheumatoid factor and the antigens of the own organism.« less

Would you hire me? Selfie portrait images perception in a recruitment context

NASA Astrophysics Data System (ADS)

Mazza, F.; Da Silva, M. P.; Le Callet, P.

2014-02-01

Human content perception has been underlined to be important in multimedia quality evaluation. Recently aesthetic considerations have been subject of research in this field. First attempts in aesthetics took into account perceived low-level features, especially taken from photography theory. However they demonstrated to be insuf- ficient to characterize human content perception. More recently image psychology started to be considered as higher cognitive feature impacting user perception. In this paper we follow this idea introducing social cognitive elements. Our experiments focus on the influence of different versions of portrait pictures in context where they are showed aside some completely unrelated informations; this can happen for example in social networks interactions between users, where profile pictures are present aside almost every user action. In particular, we tested this impact on resumes between professional portrait and self shot pictures. Moreover, as we run tests in crowdsourcing, we will discuss the use of this methodology for these tests. Our final aim is to analyse social biases' impact on multimedia aesthetics evaluation and how this bias influences messages that go along with pictures, as in public online platforms and social networks.

Insights into structural features determining odorant affinities to honey bee odorant binding protein 14.

PubMed

Schwaighofer, Andreas; Pechlaner, Maria; Oostenbrink, Chris; Kotlowski, Caroline; Araman, Can; Mastrogiacomo, Rosa; Pelosi, Paolo; Knoll, Wolfgang; Nowak, Christoph; Larisika, Melanie

2014-04-18

Molecular interactions between odorants and odorant binding proteins (OBPs) are of major importance for understanding the principles of selectivity of OBPs towards the wide range of semiochemicals. It is largely unknown on a structural basis, how an OBP binds and discriminates between odorant molecules. Here we examine this aspect in greater detail by comparing the C-minus OBP14 of the honey bee (Apis mellifera L.) to a mutant form of the protein that comprises the third disulfide bond lacking in C-minus OBPs. Affinities of structurally analogous odorants featuring an aromatic phenol group with different side chains were assessed based on changes of the thermal stability of the protein upon odorant binding monitored by circular dichroism spectroscopy. Our results indicate a tendency that odorants show higher affinity to the wild-type OBP suggesting that the introduced rigidity in the mutant protein has a negative effect on odorant binding. Furthermore, we show that OBP14 stability is very sensitive to the position and type of functional groups in the odorant. Copyright © 2014 Elsevier Inc. All rights reserved.

Building Development Monitoring in Multitemporal Remotely Sensed Image Pairs with Stochastic Birth-Death Dynamics.

PubMed

Benedek, C; Descombes, X; Zerubia, J

2012-01-01

In this paper, we introduce a new probabilistic method which integrates building extraction with change detection in remotely sensed image pairs. A global optimization process attempts to find the optimal configuration of buildings, considering the observed data, prior knowledge, and interactions between the neighboring building parts. We present methodological contributions in three key issues: 1) We implement a novel object-change modeling approach based on Multitemporal Marked Point Processes, which simultaneously exploits low-level change information between the time layers and object-level building description to recognize and separate changed and unaltered buildings. 2) To answer the challenges of data heterogeneity in aerial and satellite image repositories, we construct a flexible hierarchical framework which can create various building appearance models from different elementary feature-based modules. 3) To simultaneously ensure the convergence, optimality, and computation complexity constraints raised by the increased data quantity, we adopt the quick Multiple Birth and Death optimization technique for change detection purposes, and propose a novel nonuniform stochastic object birth process which generates relevant objects with higher probability based on low-level image features.

Automatic detection of solar features in HSOS full-disk solar images using guided filter

NASA Astrophysics Data System (ADS)

Yuan, Fei; Lin, Jiaben; Guo, Jingjing; Wang, Gang; Tong, Liyue; Zhang, Xinwei; Wang, Bingxiang

2018-02-01

A procedure is introduced for the automatic detection of solar features using full-disk solar images from Huairou Solar Observing Station (HSOS), National Astronomical Observatories of China. In image preprocessing, median filter is applied to remove the noises. Guided filter is adopted to enhance the edges of solar features and restrain the solar limb darkening, which is first introduced into the astronomical target detection. Then specific features are detected by Otsu algorithm and further threshold processing technique. Compared with other automatic detection procedures, our procedure has some advantages such as real time and reliability as well as no need of local threshold. Also, it reduces the amount of computation largely, which is benefited from the efficient guided filter algorithm. The procedure has been tested on one month sequences (December 2013) of HSOS full-disk solar images and the result shows that the number of features detected by our procedure is well consistent with the manual one.

Ensemble Classifier Strategy Based on Transient Feature Fusion in Electronic Nose

NASA Astrophysics Data System (ADS)

Bagheri, Mohammad Ali; Montazer, Gholam Ali

2011-09-01

In this paper, we test the performance of several ensembles of classifiers and each base learner has been trained on different types of extracted features. Experimental results show the potential benefits introduced by the usage of simple ensemble classification systems for the integration of different types of transient features.

OLMS: Online Learning Management System for E-Learning

ERIC Educational Resources Information Center

Ippakayala, Vinay Kumar; El-Ocla, Hosam

2017-01-01

In this paper we introduce a learning management system that provides a management system for centralized control of course content. A secure system to record lectures is implemented as a key feature of this application. This feature would be accessed through web camera and mobile recording. These features are mainly designed for e-learning…

A Check List for Evaluating Persuasive Features of Mathematics Courseware

ERIC Educational Resources Information Center

Aris, Baharuddin; Gharbaghi, Alireza; Ahmad, Maizah Hura; Rosli, Mohd Shafie

2013-01-01

The main purpose of this study is to introduce a check list for evaluating persuasive features of mathematics courseware. Since mathematics is a source of anxiety among students (Zeidner & Matthews, 2010), this research is an attempt to employ persuasive features that can be used in mathematics courseware. Specifically, we sought to determine…

Self-Injurious Behavior in Rett Syndrome: Interactions between Features of Rett Syndrome and Operant Conditioning.

ERIC Educational Resources Information Center

Oliver, Chris; And Others

1993-01-01

In this case study, interactions were examined between features of Rett syndrome and operant conditioning as determinants of self-injurious behavior (SIB). Analysis suggested different functions for two forms of SIB: automatic reinforcement by sensory stimulation and escape from social interactions. Features of Rett syndrome tended to maximize the…

Human red blood cell recognition enhancement with three-dimensional morphological features obtained by digital holographic imaging

NASA Astrophysics Data System (ADS)

Jaferzadeh, Keyvan; Moon, Inkyu

2016-12-01

The classification of erythrocytes plays an important role in the field of hematological diagnosis, specifically blood disorders. Since the biconcave shape of red blood cell (RBC) is altered during the different stages of hematological disorders, we believe that the three-dimensional (3-D) morphological features of erythrocyte provide better classification results than conventional two-dimensional (2-D) features. Therefore, we introduce a set of 3-D features related to the morphological and chemical properties of RBC profile and try to evaluate the discrimination power of these features against 2-D features with a neural network classifier. The 3-D features include erythrocyte surface area, volume, average cell thickness, sphericity index, sphericity coefficient and functionality factor, MCH and MCHSD, and two newly introduced features extracted from the ring section of RBC at the single-cell level. In contrast, the 2-D features are RBC projected surface area, perimeter, radius, elongation, and projected surface area to perimeter ratio. All features are obtained from images visualized by off-axis digital holographic microscopy with a numerical reconstruction algorithm, and four categories of biconcave (doughnut shape), flat-disc, stomatocyte, and echinospherocyte RBCs are interested. Our experimental results demonstrate that the 3-D features can be more useful in RBC classification than the 2-D features. Finally, we choose the best feature set of the 2-D and 3-D features by sequential forward feature selection technique, which yields better discrimination results. We believe that the final feature set evaluated with a neural network classification strategy can improve the RBC classification accuracy.

Inferring protein domains associated with drug side effects based on drug-target interaction network.

PubMed

Iwata, Hiroaki; Mizutani, Sayaka; Tabei, Yasuo; Kotera, Masaaki; Goto, Susumu; Yamanishi, Yoshihiro

2013-01-01

Most phenotypic effects of drugs are involved in the interactions between drugs and their target proteins, however, our knowledge about the molecular mechanism of the drug-target interactions is very limited. One of challenging issues in recent pharmaceutical science is to identify the underlying molecular features which govern drug-target interactions. In this paper, we make a systematic analysis of the correlation between drug side effects and protein domains, which we call "pharmacogenomic features," based on the drug-target interaction network. We detect drug side effects and protein domains that appear jointly in known drug-target interactions, which is made possible by using classifiers with sparse models. It is shown that the inferred pharmacogenomic features can be used for predicting potential drug-target interactions. We also discuss advantages and limitations of the pharmacogenomic features, compared with the chemogenomic features that are the associations between drug chemical substructures and protein domains. The inferred side effect-domain association network is expected to be useful for estimating common drug side effects for different protein families and characteristic drug side effects for specific protein domains.

Detecting Service Chains and Feature Interactions in Sensor-Driven Home Network Services

PubMed Central

Inada, Takuya; Igaki, Hiroshi; Ikegami, Kosuke; Matsumoto, Shinsuke; Nakamura, Masahide; Kusumoto, Shinji

2012-01-01

Sensor-driven services often cause chain reactions, since one service may generate an environmental impact that automatically triggers another service. We first propose a framework that can formalize and detect such service chains based on ECA (event, condition, action) rules. Although the service chain can be a major source of feature interactions, not all service chains lead to harmful interactions. Therefore, we then propose a method that identifies feature interactions within the service chains. Specifically, we characterize the degree of deviation of every service chain by evaluating the gap between expected and actual service states. An experimental evaluation demonstrates that the proposed method successfully detects 11 service chains and 6 feature interactions within 7 practical sensor-driven services. PMID:23012499

Unipept web services for metaproteomics analysis.

PubMed

Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-06-01

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Unipept@ugent.be 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.

Ecological prediction with nonlinear multivariate time-frequency functional data models

USGS Publications Warehouse

Yang, Wen-Hsi; Wikle, Christopher K.; Holan, Scott H.; Wildhaber, Mark L.

2013-01-01

Time-frequency analysis has become a fundamental component of many scientific inquiries. Due to improvements in technology, the amount of high-frequency signals that are collected for ecological and other scientific processes is increasing at a dramatic rate. In order to facilitate the use of these data in ecological prediction, we introduce a class of nonlinear multivariate time-frequency functional models that can identify important features of each signal as well as the interaction of signals corresponding to the response variable of interest. Our methodology is of independent interest and utilizes stochastic search variable selection to improve model selection and performs model averaging to enhance prediction. We illustrate the effectiveness of our approach through simulation and by application to predicting spawning success of shovelnose sturgeon in the Lower Missouri River.

Quantum jumps on Anderson attractors

NASA Astrophysics Data System (ADS)

Yusipov, I. I.; Laptyeva, T. V.; Ivanchenko, M. V.

2018-01-01

In a closed single-particle quantum system, spatial disorder induces Anderson localization of eigenstates and halts wave propagation. The phenomenon is vulnerable to interaction with environment and decoherence that is believed to restore normal diffusion. We demonstrate that for a class of experimentally feasible non-Hermitian dissipators, which admit signatures of localization in asymptotic states, quantum particle opts between diffusive and ballistic regimes, depending on the phase parameter of dissipators, with sticking about localization centers. In a diffusive regime, statistics of quantum jumps is non-Poissonian and has a power-law interval, a footprint of intermittent locking in Anderson modes. Ballistic propagation reflects dispersion of an ordered lattice and introduces the second timescale for jumps, resulting in non-nonmonotonous probability distribution. Hermitian dephasing dissipation makes localization features vanish, and Poissonian jump statistics along with normal diffusion are recovered.

[Development of opened instrument for generating and measuring physiological signal].

PubMed

Chen, Longcong; Hu, Guohu; Gao, Bin

2004-12-01

An opened instrument with liquid crystal display (LCD) for generating and measuring physiological signal is introduced in this paper. Based on a single-chip microcomputer. the instrument uses the technique of LCD screen to display signal wave and information, and it realizes man-machine interaction by keyboard. This instrument can produce not only defined signal in common use by utilizing important saved data and relevant arithmetic, but also user-defined signal. Therefore, it is open to produce signal. In addition, this instrument has strong extension because of its modularized design as computer, which has much function such as displaying, measuring and saving physiological signal, and many features such as low power consumption, small volume, low cost and portability. Hence this instrument is convenient for experiment teaching, clinic examining, maintaining of medical instrument.

Nonequilibrium spin transport in integrable spin chains: Persistent currents and emergence of magnetic domains

NASA Astrophysics Data System (ADS)

De Luca, Andrea; Collura, Mario; De Nardis, Jacopo

2017-07-01

We construct exact steady states of unitary nonequilibrium time evolution in the gapless XXZ spin-1/2 chain where integrability preserves ballistic spin transport at long times. We characterize the quasilocal conserved quantities responsible for this feature and introduce a computationally effective way to evaluate their expectation values on generic matrix product initial states. We employ this approach to reproduce the long-time limit of local observables in all quantum quenches which explicitly break particle-hole or time-reversal symmetry. We focus on a class of initial states supporting persistent spin currents and our predictions remarkably agree with numerical simulations at long times. Furthermore, we propose a protocol for this model where interactions, even when antiferromagnetic, are responsible for the unbounded growth of a macroscopic magnetic domain.

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments

PubMed Central

Russo, Francesco; Righelli, Dario

2016-01-01

We present the advancements and novelties recently introduced in RNASeqGUI, a graphical user interface that helps biologists to handle and analyse large data collected in RNA-Seq experiments. This work focuses on the concept of reproducible research and shows how it has been incorporated in RNASeqGUI to provide reproducible (computational) results. The novel version of RNASeqGUI combines graphical interfaces with tools for reproducible research, such as literate statistical programming, human readable report, parallel executions, caching, and interactive and web-explorable tables of results. These features allow the user to analyse big datasets in a fast, efficient, and reproducible way. Moreover, this paper represents a proof of concept, showing a simple way to develop computational tools for Life Science in the spirit of reproducible research. PMID:26977414

Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

PubMed

Lehn, Jean-Marie

2012-01-01

Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

Using GoNoodle to Introduce Health Concepts in the K-5 Classroom

ERIC Educational Resources Information Center

Whitney, Elizabeth A.

2016-01-01

This article introduces readers to the GoNoodle platform for incorporating physical activity throughout the school day, and describes how one of the features, Ultimate Champ Training, can be used to teach health concepts in the elementary school classroom.

Build a Robust Learning Feature Descriptor by Using a New Image Visualization Method for Indoor Scenario Recognition

PubMed Central

Wang, Xin; Deng, Zhongliang

2017-01-01

In order to recognize indoor scenarios, we extract image features for detecting objects, however, computers can make some unexpected mistakes. After visualizing the histogram of oriented gradient (HOG) features, we find that the world through the eyes of a computer is indeed different from human eyes, which assists researchers to see the reasons that cause a computer to make errors. Additionally, according to the visualization, we notice that the HOG features can obtain rich texture information. However, a large amount of background interference is also introduced. In order to enhance the robustness of the HOG feature, we propose an improved method for suppressing the background interference. On the basis of the original HOG feature, we introduce a principal component analysis (PCA) to extract the principal components of the image colour information. Then, a new hybrid feature descriptor, which is named HOG–PCA (HOGP), is made by deeply fusing these two features. Finally, the HOGP is compared to the state-of-the-art HOG feature descriptor in four scenes under different illumination. In the simulation and experimental tests, the qualitative and quantitative assessments indicate that the visualizing images of the HOGP feature are close to the observation results obtained by human eyes, which is better than the original HOG feature for object detection. Furthermore, the runtime of our proposed algorithm is hardly increased in comparison to the classic HOG feature. PMID:28677635

Mathematical approach to nonlocal interactions using a reaction-diffusion system.

PubMed

Tanaka, Yoshitaro; Yamamoto, Hiroko; Ninomiya, Hirokazu

2017-06-01

In recent years, spatial long range interactions during developmental processes have been introduced as a result of the integration of microscopic information, such as molecular events and signaling networks. They are often called nonlocal interactions. If the profile of a nonlocal interaction is determined by experiments, we can easily investigate how patterns generate by numerical simulations without detailed microscopic events. Thus, nonlocal interactions are useful tools to understand complex biosystems. However, nonlocal interactions are often inconvenient for observing specific mechanisms because of the integration of information. Accordingly, we proposed a new method that could convert nonlocal interactions into a reaction-diffusion system with auxiliary unknown variables. In this review, by introducing biological and mathematical studies related to nonlocal interactions, we will present the heuristic understanding of nonlocal interactions using a reaction-diffusion system. © 2017 Japanese Society of Developmental Biologists.

Prediction of interface residue based on the features of residue interaction network.

PubMed

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Constraint programming based biomarker optimization.

PubMed

Zhou, Manli; Luo, Youxi; Sun, Guoquan; Mai, Guoqin; Zhou, Fengfeng

2015-01-01

Efficient and intuitive characterization of biological big data is becoming a major challenge for modern bio-OMIC based scientists. Interactive visualization and exploration of big data is proven to be one of the successful solutions. Most of the existing feature selection algorithms do not allow the interactive inputs from users in the optimizing process of feature selection. This study investigates this question as fixing a few user-input features in the finally selected feature subset and formulates these user-input features as constraints for a programming model. The proposed algorithm, fsCoP (feature selection based on constrained programming), performs well similar to or much better than the existing feature selection algorithms, even with the constraints from both literature and the existing algorithms. An fsCoP biomarker may be intriguing for further wet lab validation, since it satisfies both the classification optimization function and the biomedical knowledge. fsCoP may also be used for the interactive exploration of bio-OMIC big data by interactively adding user-defined constraints for modeling.

Incremental learning of tasks from user demonstrations, past experiences, and vocal comments.

PubMed

Pardowitz, Michael; Knoop, Steffen; Dillmann, Ruediger; Zöllner, Raoul D

2007-04-01

Since many years the robotics community is envisioning robot assistants sharing the same environment with humans. It became obvious that they have to interact with humans and should adapt to individual user needs. Especially the high variety of tasks robot assistants will be facing requires a highly adaptive and user-friendly programming interface. One possible solution to this programming problem is the learning-by-demonstration paradigm, where the robot is supposed to observe the execution of a task, acquire task knowledge, and reproduce it. In this paper, a system to record, interpret, and reason over demonstrations of household tasks is presented. The focus is on the model-based representation of manipulation tasks, which serves as a basis for incremental reasoning over the acquired task knowledge. The aim of the reasoning is to condense and interconnect the data, resulting in more general task knowledge. A measure for the assessment of information content of task features is introduced. This measure for the relevance of certain features relies both on general background knowledge as well as task-specific knowledge gathered from the user demonstrations. Beside the autonomous information estimation of features, speech comments during the execution, pointing out the relevance of features are considered as well. The results of the incremental growth of the task knowledge when more task demonstrations become available and their fusion with relevance information gained from speech comments is demonstrated within the task of laying a table.

A Machine Learning Approach to Measurement of Text Readability for EFL Learners Using Various Linguistic Features

ERIC Educational Resources Information Center

Kotani, Katsunori; Yoshimi, Takehiko; Isahara, Hitoshi

2011-01-01

The present paper introduces and evaluates a readability measurement method designed for learners of EFL (English as a foreign language). The proposed readability measurement method (a regression model) estimates the text readability based on linguistic features, such as lexical, syntactic and discourse features. Text readability refers to the…

Investigation of the interaction between benzaldehyde thiosemicarbazone compounds and xanthine oxidase

NASA Astrophysics Data System (ADS)

Li, Mengrong; Yu, Yanying; Liu, Jing; Chen, Zelu; Cao, Shuwen

2018-05-01

A series of substituted benzaldehyde thiosemicarbazide compounds (1-7) were synthesized as xanthine oxidase (XO) inhibitors, and the interactions between substituted benzaldehyde thiosemicarbazide compounds (1-7) and XO were studied by ultraviolet spectroscopy, fluorescence spectroscopy, and molecular docking. It was found that the hydrogen bond and hydrophobicity were the main interactions between substituted benzaldehyde thiosemicarbazide compounds and XO, and introducing sbnd OH at the para position of the benzene ring and a Ph- or Me-group at the amino terminal of compound 4 increased the modifier's inhibitory activity. The results suggest that the newly introduced benzene ring interacted with the hydrophobic cavity of XO by means of the π-π stacking force between the newly introduced benzene ring and the aromatic amino acid residues, such as the Phe residue, which greatly increased the modifier's inhibitory activity. We conclude that introducing the Ph-group at the amino terminal of compound 4 and the sbnd OH group at the para position of the benzene ring was a good route to obtain novel XO inhibitors. Fluorescence spectroscopy assisted by 8-anilino-1-naphthalenesulfonic acid fluorescence probing and molecular docking were helpful for achieving a preliminary and relatively clear understanding of the interactions between target compounds and XO, which deserve further study.

Generating finite cyclic and dihedral groups using sequential insertion systems with interactions

NASA Astrophysics Data System (ADS)

Fong, Wan Heng; Sarmin, Nor Haniza; Turaev, Sherzod; Yosman, Ahmad Firdaus

2017-04-01

The operation of insertion has been studied extensively throughout the years for its impact in many areas of theoretical computer science such as DNA computing. First introduced as a generalization of the concatenation operation, many variants of insertion have been introduced, each with their own computational properties. In this paper, we introduce a new variant that enables the generation of some special types of groups called sequential insertion systems with interactions. We show that these new systems are able to generate all finite cyclic and dihedral groups.

Analyzing and Visualizing Cosmological Simulations with ParaView

NASA Astrophysics Data System (ADS)

Woodring, Jonathan; Heitmann, Katrin; Ahrens, James; Fasel, Patricia; Hsu, Chung-Hsing; Habib, Salman; Pope, Adrian

2011-07-01

The advent of large cosmological sky surveys—ushering in the era of precision cosmology—has been accompanied by ever larger cosmological simulations. The analysis of these simulations, which currently encompass tens of billions of particles and up to a trillion particles in the near future, is often as daunting as carrying out the simulations in the first place. Therefore, the development of very efficient analysis tools combining qualitative and quantitative capabilities is a matter of some urgency. In this paper, we introduce new analysis features implemented within ParaView, a fully parallel, open-source visualization toolkit, to analyze large N-body simulations. A major aspect of ParaView is that it can live and operate on the same machines and utilize the same parallel power as the simulation codes themselves. In addition, data movement is in a serious bottleneck now and will become even more of an issue in the future; an interactive visualization and analysis tool that can handle data in situ is fast becoming essential. The new features in ParaView include particle readers and a very efficient halo finder that identifies friends-of-friends halos and determines common halo properties, including spherical overdensity properties. In combination with many other functionalities already existing within ParaView, such as histogram routines or interfaces to programming languages like Python, this enhanced version enables fast, interactive, and convenient analyses of large cosmological simulations. In addition, development paths are available for future extensions.

Extensive epistasis for olfactory behaviour, sleep and waking activity in Drosophila melanogaster.

PubMed

Swarup, Shilpa; Harbison, Susan T; Hahn, Lauren E; Morozova, Tatiana V; Yamamoto, Akihiko; Mackay, Trudy F C; Anholt, Robert R H

2012-02-01

Epistasis is an important feature of the genetic architecture of quantitative traits, but the dynamics of epistatic interactions in natural populations and the relationship between epistasis and pleiotropy remain poorly understood. Here, we studied the effects of epistatic modifiers that segregate in a wild-derived Drosophila melanogaster population on the mutational effects of P-element insertions in Semaphorin-5C (Sema-5c) and Calreticulin (Crc), pleiotropic genes that affect olfactory behaviour and startle behaviour and, in the case of Crc, sleep phenotypes. We introduced Canton-S B (CSB) third chromosomes with or without a P-element insertion at the Crc or Sema-5c locus in multiple wild-derived inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and assessed the effects of epistasis on the olfactory response to benzaldehyde and, for Crc, also on sleep. In each case, we found substantial epistasis and significant variation in the magnitude of epistasis. The predominant direction of epistatic effects was to suppress the mutant phenotype. These observations support a previous study on startle behaviour using the same D. melanogaster chromosome substitution lines, which concluded that suppressing epistasis may buffer the effects of new mutations. However, epistatic effects are not correlated among the different phenotypes. Thus, suppressing epistasis appears to be a pervasive general feature of natural populations to protect against the effects of new mutations, but different epistatic interactions modulate different phenotypes affected by mutations at the same pleiotropic gene.

A Qualitative Inquiry into the Complex Features of Strained Interactions: Analysis and Implications for Health Care Personnel.

PubMed

Thunborg, Charlotta; Salzmann-Erikson, Martin

2017-01-01

Communication skills are vital for successful relationships between patients and health care professionals. Failure to communicate may lead to a lack of understanding and may result in strained interactions. Our theoretical point of departure was to make use of chaos and complexity theories. To examine the features of strained interactions and to discuss their relevance for health care settings. A netnography study design was applied. Data were purposefully sampled, and video clips (122 minutes from 30 video clips) from public online venues were used. The results are presented in four categories: 1) unpredictability, 2) sensitivity dependence, 3) resistibility, and 4) iteration. They are all features of strained interactions. Strained interactions are a complex phenomenon that exists in health care settings. The findings provide health care professionals guidance to understand the complexity and the features of strained interactions.

Simulation Engine for Fluid Solid Interaction Problems and its Application to the Modelling of Air Blast Hazards in Block Cave Mining.

NASA Astrophysics Data System (ADS)

Galindo Torres, S. A.; Scheuermann, A.; Ruest, M.

2016-12-01

Air blasts that may occur in a block caving mining operation represent a significant hazard for personnel as well as to mining infrastructure. Uncontrolled caving of a large volume of broken rock into a mine void causes compression of the air within, forcing it to flow at high velocities into connecting tunnels such as extraction points beneath the cave or observation points intersecting the cave. This high velocity flow of air can cause injury to personnel and significant damage to equipment. In this presentation, we introduce a simulation engine for the air blast problem. The solid material is modelled using the Discrete Element Method (DEM) and the fluid (air) is modelled using the Lattice Boltzmann Method (LBM). The combined DEM-LBM approach has been introduced by our group at the University of Queensland[1]. LBM allows us to introduce an appropriate equation of state for the air that simulates compressibility as a function of the speed of sound. Validation examples are presented to justify the use of this tool for an air blasting situation. A section view of one simulation is provided in Fig 1. An investigation into the risk of developing air pockets as a function of fragment size distribution is also conducted and described. The fragment size distribution can be assessed during mining and the risk of air pockets forming (and consequently of air blast occurring) can be deduced and mitigation measures put in place. The effect of other key variables that can be determined from geotechnical investigations, such as fracture frequency, are also systematically explored. It is expected that the results of this study can elucidate key features of the air blasting phenomenon in order to formulate safer mining protocols. references 1. Galindo-Torres, S.A., A coupled Discrete Element Lattice Boltzmann Method for the simulation of fluid-solid interaction with particles of general shapes. Computer Methods in Applied Mechanics and Engineering, 2013. 265(0): p. 107-119.

An analysis of multi-type relational interactions in FMA using graph motifs with disjointness constraints.

PubMed

Zhang, Guo-Qiang; Luo, Lingyun; Ogbuji, Chime; Joslyn, Cliff; Mejino, Jose; Sahoo, Satya S

2012-01-01

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.

An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints

PubMed Central

Zhang, Guo-Qiang; Luo, Lingyun; Ogbuji, Chime; Joslyn, Cliff; Mejino, Jose; Sahoo, Satya S

2012-01-01

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation. PMID:23304382

Landscape Visualisation on the Internet

NASA Astrophysics Data System (ADS)

Imhof, M. P.; Cox, M. T.; Harvey, D. W.; Heemskerk, G. E.; Pettit, C. J.

2012-07-01

The Victorian Resources Online (VRO) website (http://www.dpi.vic.gov.au/vro) is the principal means for accessing landscapebased information in Victoria. In this paper we introduce a range of online landscape visualisations that have been developed to enhance existing static web content around the nature and distribution of Victoria's landforms and soils as well as associated processes. Flash is used to develop online visualisations that include interactive landscape panoramas, animations of soil and landscape processes and videos of experts explaining features in the field as well as landscape "flyovers". The use of interactive visualisations adds rich information multimedia content to otherwise static pages and offers the potential to improve user's appreciation and understanding of soil and landscapes. Visualisation is becoming a key component of knowledge management activities associated with VRO - proving useful for both "knowledge capture" (from subject matter specialists) and "knowledge transfer" to a diverse user base. A range of useful visualisation products have been made available online, with varying degrees of interactivity and suited to a variety of users. The use of video files, animation and interactive visualisations is adding rich information content to otherwise static web pages. These information products offer new possibilities to enhance learning of landscapes and the effectiveness of these will be tested as the next phase of development.

3D Printing Polymers with Supramolecular Functionality for Biological Applications.

PubMed

Pekkanen, Allison M; Mondschein, Ryan J; Williams, Christopher B; Long, Timothy E

2017-09-11

Supramolecular chemistry continues to experience widespread growth, as fine-tuned chemical structures lead to well-defined bulk materials. Previous literature described the roles of hydrogen bonding, ionic aggregation, guest/host interactions, and π-π stacking to tune mechanical, viscoelastic, and processing performance. The versatility of reversible interactions enables the more facile manufacturing of molded parts with tailored hierarchical structures such as tissue engineered scaffolds for biological applications. Recently, supramolecular polymers and additive manufacturing processes merged to provide parts with control of the molecular, macromolecular, and feature length scales. Additive manufacturing, or 3D printing, generates customizable constructs desirable for many applications, and the introduction of supramolecular interactions will potentially increase production speed, offer a tunable surface structure for controlling cell/scaffold interactions, and impart desired mechanical properties through reinforcing interlayer adhesion and introducing gradients or self-assembled structures. This review details the synthesis and characterization of supramolecular polymers suitable for additive manufacture and biomedical applications as well as the use of supramolecular polymers in additive manufacturing for drug delivery and complex tissue scaffold formation. The effect of supramolecular assembly and its dynamic behavior offers potential for controlling the anisotropy of the printed objects with exquisite geometrical control. The potential for supramolecular polymers to generate well-defined parts, hierarchical structures, and scaffolds with gradient properties/tuned surfaces provides an avenue for developing next-generation biomedical devices and tissue scaffolds.

Peptide design using alpha,beta-dehydro amino acids: from beta-turns to helical hairpins.

PubMed

Mathur, Puniti; Ramakumar, S; Chauhan, V S

2004-01-01

Incorporation of alpha,beta-dehydrophenylalanine (DeltaPhe) residue in peptides induces folded conformations: beta-turns in short peptides and 3(10)-helices in larger ones. A few exceptions-namely, alpha-helix or flat beta-bend ribbon structures-have also been reported in a few cases. The most favorable conformation of DeltaPhe residues are (phi,psi) approximately (-60 degrees, -30 degrees ), (-60 degrees, 150 degrees ), (80 degrees, 0 degrees ) or their enantiomers. DeltaPhe is an achiral and planar residue. These features have been exploited in designing DeltaPhe zippers and helix-turn-helix motifs. DeltaPhe can be incorporated in both right and left-handed helices. In fact, consecutive occurrence of three or more DeltaPhe amino acids induce left-handed screw sense in peptides containing L-amino acids. Weak interactions involving the DeltaPhe residue play an important role in molecular association. The C--H.O==C hydrogen bond between the DeltaPhe side-chain and backbone carboxyl moiety, pi-pi stacking interactions between DeltaPhe side chains belonging to enantiomeric helices have shown to stabilize folding. The unusual capability of a DeltaPhe ring to form the hub of multicentered interactions namely, a donor in aromatic C--H.pi and C--H.O==C and an acceptor in a CH(3).pi interaction suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures. Copyright 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004

Inferring protein domains associated with drug side effects based on drug-target interaction network

PubMed Central

2013-01-01

Background Most phenotypic effects of drugs are involved in the interactions between drugs and their target proteins, however, our knowledge about the molecular mechanism of the drug-target interactions is very limited. One of challenging issues in recent pharmaceutical science is to identify the underlying molecular features which govern drug-target interactions. Results In this paper, we make a systematic analysis of the correlation between drug side effects and protein domains, which we call "pharmacogenomic features," based on the drug-target interaction network. We detect drug side effects and protein domains that appear jointly in known drug-target interactions, which is made possible by using classifiers with sparse models. It is shown that the inferred pharmacogenomic features can be used for predicting potential drug-target interactions. We also discuss advantages and limitations of the pharmacogenomic features, compared with the chemogenomic features that are the associations between drug chemical substructures and protein domains. Conclusion The inferred side effect-domain association network is expected to be useful for estimating common drug side effects for different protein families and characteristic drug side effects for specific protein domains. PMID:24565527

Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.

PubMed

Oliveros, Juan C; Franch, Mònica; Tabas-Madrid, Daniel; San-León, David; Montoliu, Lluis; Cubas, Pilar; Pazos, Florencio

2016-07-08

The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Bioinspired Photonic Pigments from Colloidal Self-Assembly.

PubMed

Goerlitzer, Eric S A; Klupp Taylor, Robin N; Vogel, Nicolas

2018-05-07

The natural world is a colorful environment. Stunning displays of coloration have evolved throughout nature to optimize camouflage, warning, and communication. The resulting flamboyant visual effects and remarkable dynamic properties, often caused by an intricate structural design at the nano- and microscale, continue to inspire scientists to unravel the underlying physics and to recreate the observed effects. Here, the methodologies to create bioinspired photonic pigments using colloidal self-assembly approaches are considered. The physics governing the interaction of light with structural features and natural examples of structural coloration are briefly introduced. It is then outlined how the self-assembly of colloidal particles, acting as wavelength-scale building blocks, can be particularly useful to replicate coloration from nature. Different coloration effects that result from the defined structure of the self-assembled colloids are introduced and it is highlighted how these optical properties can be translated into photonic pigments by modifications of the assembly processes. The importance of absorbing elements, as well as the role of surface chemistry and wettability to control structural coloration is discussed. Finally, approaches to integrate dynamic control of coloration into such self-assembled photonic pigments are outlined. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactions between similar and dissimilar charged interfaces in the presence of multivalent anions.

PubMed

Moazzami-Gudarzi, Mohsen; Adam, Pavel; Smith, Alexander M; Trefalt, Gregor; Szilágyi, István; Maroni, Plinio; Borkovec, Michal

2018-04-04

Direct force measurements involving amidine latex (AL) and sulfate latex (SL) particles in aqueous solutions containing multivalent ferrocyanide anions are presented. These measurements feature three different pairs of particles, namely SL-SL, AL-SL, and AL-AL. The force profiles are quantitatively interpreted in terms of the theory by Derjaguin, Landau, Verwey, and Overbeek (DLVO) that is combined with a short-ranged exponential attraction. In monovalent salt solutions, the AL particles are positively charged, while the SL particles are negatively charged. In solutions containing ferrocyanide, the charge of the AL particles is reversed as the concentration is increased. The longer-ranged component of all force profiles is fully compatible with DLVO theory, provided effects of charge regulation are included. At shorter distances, an additional exponential attraction must be introduced, whereby the respective decay length is about 2 nm for the AL-AL pair, and below 1 nm for the SL-SL pair. This non-DLVO force is intermediate for the asymmetric AL-SL pair. These additional forces are probably related to charge fluctuations, patch-charged interactions, or hydrophobic forces.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

Multifunctional Polymer Nanofibers: UV Emission, Optical Gain, Anisotropic Wetting, and High Hydrophobicity for Next Flexible Excitation Sources

PubMed Central

2015-01-01

The use of UV light sources is highly relevant in many fields of science, being directly related to all those detection and diagnosis procedures that are based on fluorescence spectroscopy. Depending on the specific application, UV light-emitting materials are desired to feature a number of opto-mechanical properties, including brightness, optical gain for being used in laser devices, flexibility to conform with different lab-on-chip architectures, and tailorable wettability to control and minimize their interaction with ambient humidity and fluids. In this work, we introduce multifunctional, UV-emitting electrospun fibers with both optical gain and greatly enhanced anisotropic hydrophobicity compared to films. Fibers are described by the onset of a composite wetting state, and their arrangement in uniaxial arrays further favors liquid directional control. The low gain threshold, optical losses, plastic nature, flexibility, and stability of these UV-emitting fibers make them interesting for building light-emitting devices and microlasers. Furthermore, the anisotropic hydrophobicity found is strongly synergic with optical properties, reducing interfacial interactions with liquids and enabling smart functional surfaces for droplet microfluidic and wearable applications. PMID:26401889

Classical emergence of intrinsic spin-orbit interaction of light at the nanoscale

NASA Astrophysics Data System (ADS)

Vázquez-Lozano, J. Enrique; Martínez, Alejandro

2018-03-01

Traditionally, in macroscopic geometrical optics intrinsic polarization and spatial degrees of freedom of light can be treated independently. However, at the subwavelength scale these properties appear to be coupled together, giving rise to the spin-orbit interaction (SOI) of light. In this work we address theoretically the classical emergence of the optical SOI at the nanoscale. By means of a full-vector analysis involving spherical vector waves we show that the spin-orbit factorizability condition, accounting for the mutual influence between the amplitude (spin) and phase (orbit), is fulfilled only in the far-field limit. On the other side, in the near-field region, an additional relative phase introduces an extra term that hinders the factorization and reveals an intricate dynamical behavior according to the SOI regime. As a result, we find a suitable theoretical framework able to capture analytically the main features of intrinsic SOI of light. Besides allowing for a better understanding into the mechanism leading to its classical emergence at the nanoscale, our approach may be useful to design experimental setups that enhance the response of SOI-based effects.

The effect of ICT on CO2 emissions in emerging economies: does the level of income matters?

PubMed

Danish; Khan, Noheed; Baloch, Muhammad Awais; Saud, Shah; Fatima, Tehreem

2018-05-31

In the modern era of globalization, the rapid increase in information and telecommunication technologies (ICTs) contributes in various sectors of an economy; however, the environmental consequences of ICTs cannot be ignored. Therefore, the study investigates the nexus between ICTs, economic growth, financial development, and environmental quality in emerging economies. The novel feature of the study is that the interaction term of ICT is introduced with economic growth and financial development. The empirical findings of the study are based on panel mean group (MG) and augmented mean group (AMG) estimation methods from 1990 to 2015. The following empirical results are established: first the ICTs significantly affect CO 2 emissions. Second, the moderating effect of ICT and financial development stimulate the level of CO 2 emissions. Third, economic growth contributes CO 2 emission; however, the interaction between ICT and GDP mitigates the level of pollution. Policy thresholds with the R&D in ICT sector are required to mitigate the level of CO 2 emission. Introduction of green ICTs projects in the financial sector is a better choice to improve the energy efficiency.

Social interaction shapes babbling: Testing parallels between birdsong and speech

NASA Astrophysics Data System (ADS)

Goldstein, Michael H.; King, Andrew P.; West, Meredith J.

2003-06-01

Birdsong is considered a model of human speech development at behavioral and neural levels. Few direct tests of the proposed analogs exist, however. Here we test a mechanism of phonological development in human infants that is based on social shaping, a selective learning process first documented in songbirds. By manipulating mothers' reactions to their 8-month-old infants' vocalizations, we demonstrate that phonological features of babbling are sensitive to nonimitative social stimulation. Contingent, but not noncontingent, maternal behavior facilitates more complex and mature vocal behavior. Changes in vocalizations persist after the manipulation. The data show that human infants use social feedback, facilitating immediate transitions in vocal behavior. Social interaction creates rapid shifts to developmentally more advanced sounds. These transitions mirror the normal development of speech, supporting the predictions of the avian social shaping model. These data provide strong support for a parallel in function between vocal precursors of songbirds and infants. Because imitation is usually considered the mechanism for vocal learning in both taxa, the findings introduce social shaping as a general process underlying the development of speech and song.

Light Controlling at Subwavelength Scales in Nanophotonic Systems: Physics and Applications

NASA Astrophysics Data System (ADS)

Shen, Yuecheng

The capability of controlling light at scales that are much smaller than the operating wave-length enables new optical functionalities, and opens up a wide range of applications. Such a capability is out of the realm of conventional optical approaches. This dissertation aims to explore the light-matter interactions at nanometer scale, and to investigate the novel scien-tific and industrial applications. In particular, we will explain how to detect nanoparticles using an ultra-sensitive nano-sensor; we will also describe a photonic diode which gener-ates a unidirectional flow of single photons; Moreover, in an one-dimensional waveguide QED system where the fermionic degree of freedom is present, we will show that strong photon-photon interactions can be generated through scattering means, leading to photonic bunching and anti-bunching with various applications. Finally, we will introduce a mecha-nism to achieve super-resolution to discern fine features that are orders of magnitude smaller than the illuminating wavelength. These research projects incorporate recent advances in quantum nanophotonics, nanotechnologies, imaging reconstruction techniques, and rigorous numerical simulations.

Adapting Web content for low-literacy readers by using lexical elaboration and named entities labeling

NASA Astrophysics Data System (ADS)

Watanabe, W. M.; Candido, A.; Amâncio, M. A.; De Oliveira, M.; Pardo, T. A. S.; Fortes, R. P. M.; Aluísio, S. M.

2010-12-01

This paper presents an approach for assisting low-literacy readers in accessing Web online information. The "Educational FACILITA" tool is a Web content adaptation tool that provides innovative features and follows more intuitive interaction models regarding accessibility concerns. Especially, we propose an interaction model and a Web application that explore the natural language processing tasks of lexical elaboration and named entity labeling for improving Web accessibility. We report on the results obtained from a pilot study on usability analysis carried out with low-literacy users. The preliminary results show that "Educational FACILITA" improves the comprehension of text elements, although the assistance mechanisms might also confuse users when word sense ambiguity is introduced, by gathering, for a complex word, a list of synonyms with multiple meanings. This fact evokes a future solution in which the correct sense for a complex word in a sentence is identified, solving this pervasive characteristic of natural languages. The pilot study also identified that experienced computer users find the tool to be more useful than novice computer users do.

Ergonomic guidelines for using notebook personal computers. Technical Committee on Human-Computer Interaction, International Ergonomics Association.

PubMed

Saito, S; Piccoli, B; Smith, M J; Sotoyama, M; Sweitzer, G; Villanueva, M B; Yoshitake, R

2000-10-01

In the 1980's, the visual display terminal (VDT) was introduced in workplaces of many countries. Soon thereafter, an upsurge in reported cases of related health problems, such as musculoskeletal disorders and eyestrain, was seen. Recently, the flat panel display or notebook personal computer (PC) became the most remarkable feature in modern workplaces with VDTs and even in homes. A proactive approach must be taken to avert foreseeable ergonomic and occupational health problems from the use of this new technology. Because of its distinct physical and optical characteristics, the ergonomic requirements for notebook PCs in terms of machine layout, workstation design, lighting conditions, among others, should be different from the CRT-based computers. The Japan Ergonomics Society (JES) technical committee came up with a set of guidelines for notebook PC use following exploratory discussions that dwelt on its ergonomic aspects. To keep in stride with this development, the Technical Committee on Human-Computer Interaction under the auspices of the International Ergonomics Association worked towards the international issuance of the guidelines. This paper unveils the result of this collaborative effort.

Dynamics of entropy and nonclassical properties of the state of a Λ-type three-level atom interacting with a single-mode cavity field with intensity-dependent coupling in a Kerr medium

NASA Astrophysics Data System (ADS)

Faghihi, M. J.; Tavassoly, M. K.

2012-02-01

In this paper, we study the interaction between a three-level atom and a quantized single-mode field with ‘intensity-dependent coupling’ in a ‘Kerr medium’. The three-level atom is considered to be in a Λ-type configuration. Under particular initial conditions, which may be prepared for the atom and the field, the dynamical state vector of the entire system will be explicitly obtained, for the arbitrary nonlinearity function f(n) associated with any physical system. Then, after evaluating the variation of the field entropy against time, we will investigate the quantum statistics as well as some of the nonclassical properties of the introduced state. During our calculations we investigate the effects of intensity-dependent coupling, Kerr medium and detuning parameters on the depth and domain of the nonclassicality features of the atom-field state vector. Finally, we compare our obtained results with those of V-type three-level atoms.

Understanding the value of mixed methods research: the Children’s Safety Initiative-Emergency Medical Services

PubMed Central

Hansen, Matthew; O’Brien, Kerth; Meckler, Garth; Chang, Anna Marie; Guise, Jeanne-Marie

2016-01-01

Mixed methods research has significant potential to broaden the scope of emergency care and specifically emergency medical services investigation. Mixed methods studies involve the coordinated use of qualitative and quantitative research approaches to gain a fuller understanding of practice. By combining what is learnt from multiple methods, these approaches can help to characterise complex healthcare systems, identify the mechanisms of complex problems such as medical errors and understand aspects of human interaction such as communication, behaviour and team performance. Mixed methods approaches may be particularly useful for out-of-hospital care researchers because care is provided in complex systems where equipment, interpersonal interactions, societal norms, environment and other factors influence patient outcomes. The overall objectives of this paper are to (1) introduce the fundamental concepts and approaches of mixed methods research and (2) describe the interrelation and complementary features of the quantitative and qualitative components of mixed methods studies using specific examples from the Children’s Safety Initiative-Emergency Medical Services (CSI-EMS), a large National Institutes of Health-funded research project conducted in the USA. PMID:26949970

Internet for Library Media Specialists.

ERIC Educational Resources Information Center

Simpson, Carol Mann

This guide introduces the library media specialist to the Internet, its history and features, and provides information on specific uses of the Internet in school libraries and specific areas. Section 1, "What is the Internet?" introduces the reader to the Internet; electronic mail; telnet; file transfer protocol (FTP); wide area…

CASTING A BROAD NETWORK: FISHING FOR MECHANISMS OF RETINOID TERATOGENICITY

EPA Science Inventory

This is a short essay that serves to introduce a featured paper for an issue of Toxicological Sciences. The paper being introduced describes a study of mechanisms of retinoid induced abnormal limb development in mice. The paper was notable because the authors used gene expressi...

Predicting protein-protein interactions by combing various sequence- derived features into the general form of Chou's Pseudo amino acid composition.

PubMed

Zhao, Xiao-Wei; Ma, Zhi-Qiang; Yin, Ming-Hao

2012-05-01

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

The interactive contents authoring system for terrestrial digital multimedia broadcasting

NASA Astrophysics Data System (ADS)

Cheong, Won-Sik; Ahn, Sangwoo; Cha, Jihun; Moon, Kyung Ae

2007-02-01

This paper introduces an interactive contents authoring system which can easily and conveniently produce interactive contents for the Terrestrial Digital Multimedia Broadcasting (T-DMB). For interactive broadcasting service, T-DMB adopted MPEG-4 Systems technology. In order to the interactive service becomes flourishing on the market, various types of interactive contents should be well provided prior to the service. In MPEG-4 Systems specification, broadcasting contents are described by the combination of a large number of nodes, routes and descriptors. In order to provide interactive data services through the T-DMB network, it is essential to have an interactive contents authoring system which allows contents authors to compose interactive contents easily and conveniently even if they lack any background on MPEG-4 Systems technology. The introduced authoring system provides powerful graphical user interface and produces interactive broadcasting contents in the forms of binary and textual format. Therefore, the interactive contents authoring system presented in this paper would vastly contribute to the flourishing interactive service.

A Variation on the Use of Interactive Anonymous Quizzes in the Chemistry Classroom

ERIC Educational Resources Information Center

Wagner, Brian D.

2009-01-01

This article describes an interesting variation on the use of interactive anonymous quizzes (IAQs) in the chemistry classroom. In this variation, IAQs are used to introduce new material or topics in a course, as opposed to their traditional use for reviewing previously covered material. Two examples of IAQs used to introduce new topics in a…

Remarks on forensically interesting Sony Playstation 3 console features

NASA Astrophysics Data System (ADS)

Daugs, Gunnar; Kröger, Knut; Creutzburg, Reiner

2012-02-01

This paper deals with forensically interesting features of the Sony Playstation 3 game console. The construction and the internal structure are analyzed more precisely. Interesting forensic features of the operating system and the file system are presented. Differences between a PS3 with and without jailbreak are introduced and possible forensic attempts when using an installed Linux are discussed.

Feature Selection for Evolutionary Commercial-off-the-Shelf Software: Studies Focusing on Time-to-Market, Innovation and Hedonic-Utilitarian Trade-Offs

ERIC Educational Resources Information Center

Kakar, Adarsh Kumar

2013-01-01

Feature selection is one of the most important decisions made by product managers. This three article study investigates the concepts, tools and techniques for making trade-off decisions of introducing new features in evolving Commercial-Off-The-Shelf (COTS) software products. The first article investigates the efficacy of various feature…

Object-Oriented Scientific Programming with Fortran 90

NASA Technical Reports Server (NTRS)

Norton, C.

1998-01-01

Fortran 90 is a modern language that introduces many important new features beneficial for scientific programming. We discuss our experiences in plasma particle simulation and unstructured adaptive mesh refinement on supercomputers, illustrating the features of Fortran 90 that support the object-oriented methodology.

Latent feature decompositions for integrative analysis of multi-platform genomic data

PubMed Central

Gregory, Karl B.; Momin, Amin A.; Coombes, Kevin R.; Baladandayuthapani, Veerabhadran

2015-01-01

Increased availability of multi-platform genomics data on matched samples has sparked research efforts to discover how diverse molecular features interact both within and between platforms. In addition, simultaneous measurements of genetic and epigenetic characteristics illuminate the roles their complex relationships play in disease progression and outcomes. However, integrative methods for diverse genomics data are faced with the challenges of ultra-high dimensionality and the existence of complex interactions both within and between platforms. We propose a novel modeling framework for integrative analysis based on decompositions of the large number of platform-specific features into a smaller number of latent features. Subsequently we build a predictive model for clinical outcomes accounting for both within- and between-platform interactions based on Bayesian model averaging procedures. Principal components, partial least squares and non-negative matrix factorization as well as sparse counterparts of each are used to define the latent features, and the performance of these decompositions is compared both on real and simulated data. The latent feature interactions are shown to preserve interactions between the original features and not only aid prediction but also allow explicit selection of outcome-related features. The methods are motivated by and applied to, a glioblastoma multiforme dataset from The Cancer Genome Atlas to predict patient survival times integrating gene expression, microRNA, copy number and methylation data. For the glioblastoma data, we find a high concordance between our selected prognostic genes and genes with known associations with glioblastoma. In addition, our model discovers several relevant cross-platform interactions such as copy number variation associated gene dosing and epigenetic regulation through promoter methylation. On simulated data, we show that our proposed method successfully incorporates interactions within and between genomic platforms to aid accurate prediction and variable selection. Our methods perform best when principal components are used to define the latent features. PMID:26146492

Learning in data-limited multimodal scenarios: Scandent decision forests and tree-based features.

PubMed

Hor, Soheil; Moradi, Mehdi

2016-12-01

Incomplete and inconsistent datasets often pose difficulties in multimodal studies. We introduce the concept of scandent decision trees to tackle these difficulties. Scandent trees are decision trees that optimally mimic the partitioning of the data determined by another decision tree, and crucially, use only a subset of the feature set. We show how scandent trees can be used to enhance the performance of decision forests trained on a small number of multimodal samples when we have access to larger datasets with vastly incomplete feature sets. Additionally, we introduce the concept of tree-based feature transforms in the decision forest paradigm. When combined with scandent trees, the tree-based feature transforms enable us to train a classifier on a rich multimodal dataset, and use it to classify samples with only a subset of features of the training data. Using this methodology, we build a model trained on MRI and PET images of the ADNI dataset, and then test it on cases with only MRI data. We show that this is significantly more effective in staging of cognitive impairments compared to a similar decision forest model trained and tested on MRI only, or one that uses other kinds of feature transform applied to the MRI data. Copyright © 2016. Published by Elsevier B.V.

Development of a templated approach to fabricate diamond patterns on various substrates.

PubMed

Shimoni, Olga; Cervenka, Jiri; Karle, Timothy J; Fox, Kate; Gibson, Brant C; Tomljenovic-Hanic, Snjezana; Greentree, Andrew D; Prawer, Steven

2014-06-11

We demonstrate a robust templated approach to pattern thin films of chemical vapor deposited nanocrystalline diamond grown from monodispersed nanodiamond (mdND) seeds. The method works on a range of substrates, and we herein demonstrate the method using silicon, aluminum nitride (AlN), and sapphire substrates. Patterns are defined using photo- and e-beam lithography, which are seeded with mdND colloids and subsequently introduced into microwave assisted chemical vapor deposition reactor to grow patterned nanocrystalline diamond films. In this study, we investigate various factors that affect the selective seeding of different substrates to create high quality diamond thin films, including mdND surface termination, zeta potential, surface treatment, and plasma cleaning. Although the electrostatic interaction between mdND colloids and substrates is the main process driving adherence, we found that chemical reaction (esterification) or hydrogen bonding can potentially dominate the seeding process. Leveraging the knowledge on these different interactions, we optimize fabrication protocols to eliminate unwanted diamond nucleation outside the patterned areas. Furthermore, we have achieved the deposition of patterned diamond films and arrays over a range of feature sizes. This study contributes to a comprehensive understanding of the mdND-substrate interaction that will enable the fabrication of integrated nanocrystalline diamond thin films for microelectronics, sensors, and tissue culturing applications.

Acoustic signatures of sound source-tract coupling.

PubMed

Arneodo, Ezequiel M; Perl, Yonatan Sanz; Mindlin, Gabriel B

2011-04-01

Birdsong is a complex behavior, which results from the interaction between a nervous system and a biomechanical peripheral device. While much has been learned about how complex sounds are generated in the vocal organ, little has been learned about the signature on the vocalizations of the nonlinear effects introduced by the acoustic interactions between a sound source and the vocal tract. The variety of morphologies among bird species makes birdsong a most suitable model to study phenomena associated to the production of complex vocalizations. Inspired by the sound production mechanisms of songbirds, in this work we study a mathematical model of a vocal organ, in which a simple sound source interacts with a tract, leading to a delay differential equation. We explore the system numerically, and by taking it to the weakly nonlinear limit, we are able to examine its periodic solutions analytically. By these means we are able to explore the dynamics of oscillatory solutions of a sound source-tract coupled system, which are qualitatively different from those of a sound source-filter model of a vocal organ. Nonlinear features of the solutions are proposed as the underlying mechanisms of observed phenomena in birdsong, such as unilaterally produced "frequency jumps," enhancement of resonances, and the shift of the fundamental frequency observed in heliox experiments. ©2011 American Physical Society

Acoustic signatures of sound source-tract coupling

PubMed Central

Arneodo, Ezequiel M.; Perl, Yonatan Sanz; Mindlin, Gabriel B.

2014-01-01

Birdsong is a complex behavior, which results from the interaction between a nervous system and a biomechanical peripheral device. While much has been learned about how complex sounds are generated in the vocal organ, little has been learned about the signature on the vocalizations of the nonlinear effects introduced by the acoustic interactions between a sound source and the vocal tract. The variety of morphologies among bird species makes birdsong a most suitable model to study phenomena associated to the production of complex vocalizations. Inspired by the sound production mechanisms of songbirds, in this work we study a mathematical model of a vocal organ, in which a simple sound source interacts with a tract, leading to a delay differential equation. We explore the system numerically, and by taking it to the weakly nonlinear limit, we are able to examine its periodic solutions analytically. By these means we are able to explore the dynamics of oscillatory solutions of a sound source-tract coupled system, which are qualitatively different from those of a sound source-filter model of a vocal organ. Nonlinear features of the solutions are proposed as the underlying mechanisms of observed phenomena in birdsong, such as unilaterally produced “frequency jumps,” enhancement of resonances, and the shift of the fundamental frequency observed in heliox experiments. PMID:21599213

Modeling the interactions between compliant microcapsules and pillars in microchannels

NASA Astrophysics Data System (ADS)

Zhu, Guangdong; Alexeev, Alexander; Kumacheva, Eugenia; Balazs, Anna C.

2007-07-01

Using a computational model, we investigate the motion of microcapsules inside a microchannel that encompasses a narrow constriction. The microcapsules are composed of a compliant, elastic shell and an encapsulated fluid; these fluid-filled shells model synthetic polymeric microcapsules or biological cells (e.g., leukocytes). Driven by an imposed flow, the capsules are propelled along the microchannel and through the constricted region, which is formed by two pillars that lie in registry, extending from the top and bottom walls of the channels. The tops of these pillars (facing into the microchannel) are modified to exhibit either a neutral or an attractive interaction with the microcapsules. The pillars (and constriction) model topological features that can be introduced into microfluidic devices or the physical and chemical heterogeneities that are inherently present in biological vessels. To simulate the behavior of this complex system, we employ a hybrid method that integrates the lattice Boltzmann model (LBM) for fluid dynamics and the lattice spring model (LSM) for the micromechanics of elastic solids. Through this LBM/LSM technique, we probe how the capsule's stiffness and interaction with the pillars affect its passage through the chambers. The results yield guidelines for regulating the movement of microcarriers in microfluidic systems and provide insight into the flow properties of biological cells in capillaries.

Tripartite entanglement dynamics and entropic squeezing of a three-level atom interacting with a bimodal cavity field

NASA Astrophysics Data System (ADS)

Faghihi, M. J.; Tavassoly, M. K.; Bagheri Harouni, M.

2014-04-01

In this paper, we study the interaction between a Λ-type three-level atom and two quantized electromagnetic fields which are simultaneously injected in a bichromatic cavity surrounded by a Kerr medium in the presence of field-field interaction (parametric down conversion) and detuning parameters. By applying a canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions which may be prepared for the atom and the field, the time evolution of the state vector of the entire system is analytically evaluated. Then, the dynamics of the atom is studied through the evolution of the atomic population inversion. In addition, two different measures of entanglement between the tripartite system (three entities make the system: two field modes and one atom), i.e., von Neumann and linear entropy are investigated. Also, two kinds of entropic uncertainty relations, from which entropy squeezing can be obtained, are discussed. In each case, the influences of the detuning parameters and Kerr medium on the above nonclassicality features are analyzed in detail via numerical results. It is illustrated that the amount of the above-mentioned physical phenomena can be tuned by choosing the evolved parameters, appropriately.

Exploring Localization in Nuclear Spin Chains

NASA Astrophysics Data System (ADS)

Wei, Ken Xuan; Ramanathan, Chandrasekhar; Cappellaro, Paola

2018-02-01

Characterizing out-of-equilibrium many-body dynamics is a complex but crucial task for quantum applications and understanding fundamental phenomena. A central question is the role of localization in quenching thermalization in many-body systems and whether such localization survives in the presence of interactions. Probing this question in real systems necessitates the development of an experimentally measurable metric that can distinguish between different types of localization. While it is known that the localized phase of interacting systems [many-body localization (MBL)] exhibits a long-time logarithmic growth in entanglement entropy that distinguishes it from the noninteracting case of Anderson localization (AL), entanglement entropy is difficult to measure experimentally. Here, we present a novel correlation metric, capable of distinguishing MBL from AL in high-temperature spin systems. We demonstrate the use of this metric to detect localization in a natural solid-state spin system using nuclear magnetic resonance (NMR). We engineer the natural Hamiltonian to controllably introduce disorder and interactions, and observe the emergence of localization. In particular, while our correlation metric saturates for AL, it slowly keeps increasing for MBL, demonstrating analogous features to entanglement entropy, as we show in simulations. Our results show that our NMR techniques, akin to measuring out-of-time correlations, are well suited for studying localization in spin systems.

Rigorous ILT optimization for advanced patterning and design-process co-optimization

NASA Astrophysics Data System (ADS)

Selinidis, Kosta; Kuechler, Bernd; Cai, Howard; Braam, Kyle; Hoppe, Wolfgang; Domnenko, Vitaly; Poonawala, Amyn; Xiao, Guangming

2018-03-01

Despite the large difficulties involved in extending 193i multiple patterning and the slow ramp of EUV lithography to full manufacturing readiness, the pace of development for new technology node variations has been accelerating. Multiple new variations of new and existing technology nodes have been introduced for a range of device applications; each variation with at least a few new process integration methods, layout constructs and/or design rules. This had led to a strong increase in the demand for predictive technology tools which can be used to quickly guide important patterning and design co-optimization decisions. In this paper, we introduce a novel hybrid predictive patterning method combining two patterning technologies which have each individually been widely used for process tuning, mask correction and process-design cooptimization. These technologies are rigorous lithography simulation and inverse lithography technology (ILT). Rigorous lithography simulation has been extensively used for process development/tuning, lithography tool user setup, photoresist hot-spot detection, photoresist-etch interaction analysis, lithography-TCAD interactions/sensitivities, source optimization and basic lithography design rule exploration. ILT has been extensively used in a range of lithographic areas including logic hot-spot fixing, memory layout correction, dense memory cell optimization, assist feature (AF) optimization, source optimization, complex patterning design rules and design-technology co-optimization (DTCO). The combined optimization capability of these two technologies will therefore have a wide range of useful applications. We investigate the benefits of the new functionality for a few of these advanced applications including correction for photoresist top loss and resist scumming hotspots.

Meet the Alpha-Pets.

ERIC Educational Resources Information Center

Zitlaw, Jo Ann Bruce; Frank, Cheryl Standish

1985-01-01

"Alpha-Pets" are the focal point of an integrated, multidisciplinary curriculum. Each pet is featured for a week in a vocabulary-rich story and introduces related activities beginning with the featured letter, such as the four food groups during Freddie Fish's week or universe during Ulysses Unicorn's week. (MT)

Predicting Good Features for Image Geo-Localization Using Per-Bundle VLAD (Open Access)

DTIC Science & Technology

2016-02-18

transient scene elements (pedestrians, cars, billboards) and ubiquitous objects (trees, fences, signage ) can introduce obfuscating cues into the geo...windows, charac- teristic wall patterns, and letters on signage are detected as positive elements, while features from trees, people, car wheels

Wavelet Packet Entropy for Heart Murmurs Classification

PubMed Central

Safara, Fatemeh; Doraisamy, Shyamala; Azman, Azreen; Jantan, Azrul; Ranga, Sri

2012-01-01

Heart murmurs are the first signs of cardiac valve disorders. Several studies have been conducted in recent years to automatically differentiate normal heart sounds, from heart sounds with murmurs using various types of audio features. Entropy was successfully used as a feature to distinguish different heart sounds. In this paper, new entropy was introduced to analyze heart sounds and the feasibility of using this entropy in classification of five types of heart sounds and murmurs was shown. The entropy was previously introduced to analyze mammograms. Four common murmurs were considered including aortic regurgitation, mitral regurgitation, aortic stenosis, and mitral stenosis. Wavelet packet transform was employed for heart sound analysis, and the entropy was calculated for deriving feature vectors. Five types of classification were performed to evaluate the discriminatory power of the generated features. The best results were achieved by BayesNet with 96.94% accuracy. The promising results substantiate the effectiveness of the proposed wavelet packet entropy for heart sounds classification. PMID:23227043

Statistical process control using optimized neural networks: a case study.

PubMed

Addeh, Jalil; Ebrahimzadeh, Ata; Azarbad, Milad; Ranaee, Vahid

2014-09-01

The most common statistical process control (SPC) tools employed for monitoring process changes are control charts. A control chart demonstrates that the process has altered by generating an out-of-control signal. This study investigates the design of an accurate system for the control chart patterns (CCPs) recognition in two aspects. First, an efficient system is introduced that includes two main modules: feature extraction module and classifier module. In the feature extraction module, a proper set of shape features and statistical feature are proposed as the efficient characteristics of the patterns. In the classifier module, several neural networks, such as multilayer perceptron, probabilistic neural network and radial basis function are investigated. Based on an experimental study, the best classifier is chosen in order to recognize the CCPs. Second, a hybrid heuristic recognition system is introduced based on cuckoo optimization algorithm (COA) algorithm to improve the generalization performance of the classifier. The simulation results show that the proposed algorithm has high recognition accuracy. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Functional Brain Connectivity as a New Feature for P300 Speller.

PubMed

Kabbara, Aya; Khalil, Mohamad; El-Falou, Wassim; Eid, Hassan; Hassan, Mahmoud

2016-01-01

The brain is a large-scale complex network often referred to as the "connectome". Cognitive functions and information processing are mainly based on the interactions between distant brain regions. However, most of the 'feature extraction' methods used in the context of Brain Computer Interface (BCI) ignored the possible functional relationships between different signals recorded from distinct brain areas. In this paper, the functional connectivity quantified by the phase locking value (PLV) was introduced to characterize the evoked responses (ERPs) obtained in the case of target and non-targets visual stimuli. We also tested the possibility of using the functional connectivity in the context of 'P300 speller'. The proposed approach was compared to the well-known methods proposed in the state of the art of "P300 Speller", mainly the peak picking, the area, time/frequency based features, the xDAWN spatial filtering and the stepwise linear discriminant analysis (SWLDA). The electroencephalographic (EEG) signals recorded from ten subjects were analyzed offline. The results indicated that phase synchrony offers relevant information for the classification in a P300 speller. High synchronization between the brain regions was clearly observed during target trials, although no significant synchronization was detected for a non-target trial. The results showed also that phase synchrony provides higher performance than some existing methods for letter classification in a P300 speller principally when large number of trials is available. Finally, we tested the possible combination of both approaches (classical features and phase synchrony). Our findings showed an overall improvement of the performance of the P300-speller when using Peak picking, the area and frequency based features. Similar performances were obtained compared to xDAWN and SWLDA when using large number of trials.

Random Forest Application for NEXRAD Radar Data Quality Control

NASA Astrophysics Data System (ADS)

Keem, M.; Seo, B. C.; Krajewski, W. F.

2017-12-01

Identification and elimination of non-meteorological radar echoes (e.g., returns from ground, wind turbines, and biological targets) are the basic data quality control steps before radar data use in quantitative applications (e.g., precipitation estimation). Although WSR-88Ds' recent upgrade to dual-polarization has enhanced this quality control and echo classification, there are still challenges to detect some non-meteorological echoes that show precipitation-like characteristics (e.g., wind turbine or anomalous propagation clutter embedded in rain). With this in mind, a new quality control method using Random Forest is proposed in this study. This classification algorithm is known to produce reliable results with less uncertainty. The method introduces randomness into sampling and feature selections and integrates consequent multiple decision trees. The multidimensional structure of the trees can characterize the statistical interactions of involved multiple features in complex situations. The authors explore the performance of Random Forest method for NEXRAD radar data quality control. Training datasets are selected using several clear cases of precipitation and non-precipitation (but with some non-meteorological echoes). The model is structured using available candidate features (from the NEXRAD data) such as horizontal reflectivity, differential reflectivity, differential phase shift, copolar correlation coefficient, and their horizontal textures (e.g., local standard deviation). The influence of each feature on classification results are quantified by variable importance measures that are automatically estimated by the Random Forest algorithm. Therefore, the number and types of features in the final forest can be examined based on the classification accuracy. The authors demonstrate the capability of the proposed approach using several cases ranging from distinct to complex rain/no-rain events and compare the performance with the existing algorithms (e.g., MRMS). They also discuss operational feasibility based on the observed strength and weakness of the method.

a Data Field Method for Urban Remotely Sensed Imagery Classification Considering Spatial Correlation

NASA Astrophysics Data System (ADS)

Zhang, Y.; Qin, K.; Zeng, C.; Zhang, E. B.; Yue, M. X.; Tong, X.

2016-06-01

Spatial correlation between pixels is important information for remotely sensed imagery classification. Data field method and spatial autocorrelation statistics have been utilized to describe and model spatial information of local pixels. The original data field method can represent the spatial interactions of neighbourhood pixels effectively. However, its focus on measuring the grey level change between the central pixel and the neighbourhood pixels results in exaggerating the contribution of the central pixel to the whole local window. Besides, Geary's C has also been proven to well characterise and qualify the spatial correlation between each pixel and its neighbourhood pixels. But the extracted object is badly delineated with the distracting salt-and-pepper effect of isolated misclassified pixels. To correct this defect, we introduce the data field method for filtering and noise limitation. Moreover, the original data field method is enhanced by considering each pixel in the window as the central pixel to compute statistical characteristics between it and its neighbourhood pixels. The last step employs a support vector machine (SVM) for the classification of multi-features (e.g. the spectral feature and spatial correlation feature). In order to validate the effectiveness of the developed method, experiments are conducted on different remotely sensed images containing multiple complex object classes inside. The results show that the developed method outperforms the traditional method in terms of classification accuracies.

Pre-produsage and the remediation of virtual products

NASA Astrophysics Data System (ADS)

Skågeby, Jörgen

2011-04-01

This paper introduces and explores cycles of pre-produsage and produsage. It reports on the results from an online ethnographical study of the Apple iPad conducted before the public release of the material product. Consequently, most users had not physically interacted with the device in question. Nevertheless, the release of the technical specifications and marketing material generated a massive amount of produsage-related online discussion. As such this paper explores the concept of pre-produsage. Pre-produsage is a form of predicted or expected use, relating to products or services that are only accessible to users as a form of representation (e.g. technical specification, virtual prototype, and design sketch), but with an added element of user-generated design suggestions, conflict coordination, and software development. Remediation-the process by which new digital media technologies reuses qualities of previous technologies and enters an existing media ecology-is a prevalent theme in pre-produsage and involves a tension between features that support protracted use and features that provide total innovation. The paper argues that an analysis of pre-produsage can provide insights that relate to both anticipated and actual user experience (UX). More specifically, pre-produsage analysis can trace the underlying reasons for a certain problem, intention, or concern and connect it to a specific set of features and potential solutions. Finally, the paper shows how proprietary products become subject to produsage, resulting in artifacts negotiated by cycles of produsage.

"Don't call me 'mom'": how parents want to be greeted by their pediatrician.

PubMed

Amer, Ahdi; Fischer, Howard

2009-09-01

Physician-patient interaction during the medical interview is essential in establishing the rapport necessary for a successful relationship. Physicians are generally encouraged to shake hands with patients, address patients by name, and identify themselves. To define parents expectations for greetings by pediatricians and to determine the frequency with which these expectations are met. Design and methods. A total of 100 parents visiting the General Pediatric Clinic at Children's Hospital of Michigan were recruited. Parents were interviewed at the end of their medical encounter to determine expectations for greeting by their doctor. They were questioned about preferences for shaking hands, the doctors' use of their names, and the way doctors should introduce themselves. They were then asked if the experience at this visit conformed to these expectations. Overall, 81% of the parents were the children's mother and 86% were African-American. Over 80% of parents expected physicians to shake hands; 70% of residents and 66% of attendings did. 88% of parents wanted to be addressed by their names; only 14% of residents and 24% of attending physicians did so. All of the parents wanted the physicians to introduce themselves; 84% of residents and 93% of attendings did so. Physicians neither shook hands with many parents who expected it, nor did they address parents by their last names. About 90% of physicians introduced themselves. These disappointingly low results may predispose to parent dissatisfaction. Attending physicians need to teach these small, but important features, and to model them as well.

Opinion formation models in static and dynamic social networks

NASA Astrophysics Data System (ADS)

Singh, Pramesh

We study models of opinion formation on static as well as dynamic networks where interaction among individuals is governed by widely accepted social theories. In particular, three models of competing opinions based on distinct interaction mechanisms are studied. A common feature in all of these models is the existence of a tipping point in terms of a model parameter beyond which a rapid consensus is reached. In the first model that we study on a static network, a node adopts a particular state (opinion) if a threshold fraction of its neighbors are already in that state. We introduce a few initiator nodes which are in state '1' in a population where every node is in state '0'. Thus, opinion '1' spreads through the population until no further influence is possible. Size of the spread is greatly affected by how these initiator nodes are selected. We find that there exists a critical fraction of initiators pc that is needed to trigger global cascades for a given threshold phi. We also study heuristic strategies for selecting a set of initiator nodes in order to maximize the cascade size. The structural properties of networks also play an important role in the spreading process. We study how the dynamics is affected by changing the clustering in a network. It turns out that local clustering is helpful in spreading. Next, we studied a model where the network is dynamic and interactions are homophilic. We find that homophily-driven rewiring impedes the reaching of consensus and in the absence of committed nodes (nodes that are not influenceable on their opinion), consensus time Tc diverges exponentially with network size N . As we introduce a fraction of committed nodes, beyond a critical value, the scaling of Tc becomes logarithmic in N. We also find that slight change in the interaction rule can produce strikingly different scaling behaviors of T c . However, introducing committed agents in the system drastically improves the scaling of the consensus time regardless of the interaction rules considered. Finally, a three-state (leftist, rightist, centrist) model that couples the dynamics of social balance with an external deradicalizing field is studied. The mean-field analysis shows that for a weak external field, the system exhibits a metastable fixed point and a saddle point in addition to a stable fixed point. However, if the strength of the external field is sufficiently large (larger than a critical value), there is only one (stable) fixed point which corresponds to an all-centrist consensus state (absorbing state). In the weak-field regime, the convergence time to the absorbing state is evaluated using the quasi-stationary(QS) distribution and is found to be in good agreement with the results obtained by numerical simulations.

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.

PubMed

A Santos, Jose C; Nassif, Houssam; Page, David; Muggleton, Stephen H; E Sternberg, Michael J

2012-07-11

There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. In addition to confirming literature results, ProGolem's model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm

PubMed Central

Wang, ShaoPeng; Zhang, Yu-Hang; Lu, Jing; Cui, Weiren; Hu, Jerry; Cai, Yu-Dong

2016-01-01

The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request. PMID:26955638

Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm.

PubMed

Wang, ShaoPeng; Zhang, Yu-Hang; Lu, Jing; Cui, Weiren; Hu, Jerry; Cai, Yu-Dong

2016-01-01

The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request.

New Density Functional Approach for Solid-Liquid-Vapor Transitions in Pure Materials

NASA Astrophysics Data System (ADS)

Kocher, Gabriel; Provatas, Nikolas

2015-04-01

A new phase field crystal (PFC) type theory is presented, which accounts for the full spectrum of solid-liquid-vapor phase transitions within the framework of a single density order parameter. Its equilibrium properties show the most quantitative features to date in PFC modeling of pure substances, and full consistency with thermodynamics in pressure-volume-temperature space is demonstrated. A method to control either the volume or the pressure of the system is also introduced. Nonequilibrium simulations show that 2- and 3-phase growth of solid, vapor, and liquid can be achieved, while our formalism also allows for a full range of pressure-induced transformations. This model opens up a new window for the study of pressure driven interactions of condensed phases with vapor, an experimentally relevant paradigm previously missing from phase field crystal theories.

Automated Monitoring and Analysis of Social Behavior in Drosophila

PubMed Central

Dankert, Heiko; Wang, Liming; Hoopfer, Eric D.; Anderson, David J.; Perona, Pietro

2009-01-01

We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies, and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship “song”) and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression. PMID:19270697

An Argumentation Framework based on Paraconsistent Logic

NASA Astrophysics Data System (ADS)

Umeda, Yuichi; Takahashi, Takehisa; Sawamura, Hajime

Argumentation is the most representative of intelligent activities of humans. Therefore, it is natural to think that it could have many implications for artificial intelligence and computer science as well. Specifically, argumentation may be considered a most primitive capability for interaction among computational agents. In this paper we present an argumentation framework based on the four-valued paraconsistent logic. Tolerance and acceptance of inconsistency that this logic has as its logical feature allow for arguments on inconsistent knowledge bases with which we are often confronted. We introduce various concepts for argumentation, such as arguments, attack relations, argument justification, preferential criteria of arguments based on social norms, and so on, in a way proper to the four-valued paraconsistent logic. Then, we provide the fixpoint semantics and dialectical proof theory for our argumentation framework. We also give the proofs of the soundness and completeness.

Fiber-reinforced superalloy composites provide an added performance edge

NASA Technical Reports Server (NTRS)

Petrasek, D. W.; Mcdaniels, D. L.; Westfall, L. J.; Stephens, J. R.

1986-01-01

Fiber reinforcements are being explored as a means to increasing the performance of superalloys past 980 C. Fiber-reinforced superalloys (FRS), particularly tungsten FRS (TFRS) are candidate materials for rocket-engine turbopump blades for advanced Shuttle engines and in airbreathing and other rocket engines. Refractory metal wires are the reinforcement of choice due to tolerance to fiber/matrix interactions. W alloy fibers have a maximum tensile strength of 2165 MPa at 1095 C and a 100 hr creep rupture strength at stresses up to 1400 MPa. A TFRS has the potential of a service temperature 110 C over the strongest superalloy. Manufacturing processes being evaluated to realize the FRS components are summarized, together with design features which will be introduced in turbine blades to take advantage of the FRS materials and to extend their surface life.

Fractional Factorial Experiment Designs to Minimize Configuration Changes in Wind Tunnel Testing

NASA Technical Reports Server (NTRS)

DeLoach, Richard; Cler, Daniel L.; Graham, Albert B.

2002-01-01

This paper serves as a tutorial to introduce the wind tunnel research community to configuration experiment designs that can satisfy resource constraints in a configuration study involving several variables, without arbitrarily eliminating any of them from the experiment initially. The special case of a configuration study featuring variables at two levels is examined in detail. This is the type of study in which each configuration variable has two natural states - 'on or off', 'deployed or not deployed', 'low or high', and so forth. The basic principles are illustrated by results obtained in configuration studies conducted in the Langley National Transonic Facility and in the ViGYAN Low Speed Tunnel in Hampton, Virginia. The crucial role of interactions among configuration variables is highlighted with an illustration of difficulties that can be encountered when they are not properly taken into account.

Innovation: an emerging focus from cells to societies.

PubMed

Hochberg, Michael E; Marquet, Pablo A; Boyd, Robert; Wagner, Andreas

2017-12-05

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

Innovation: an emerging focus from cells to societies

PubMed Central

Boyd, Robert

2017-01-01

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability. This article is part of the theme issue ‘Process and pattern in innovations from cells to societies’. PMID:29061887

Nonlinearity of the forward-backward correlation function in the model with string fusion

NASA Astrophysics Data System (ADS)

Vechernin, Vladimir

2017-12-01

The behavior of the forward-backward correlation functions and the corresponding correlation coefficients between multiplicities and transverse momenta of particles produced in high energy hadronic interactions is analyzed by analytical and MC calculations in the models with and without string fusion. The string fusion is taking into account in simplified form by introducing the lattice in the transverse plane. The results obtained with two alternative definitions of the forward-backward correlation coefficient are compared. It is shown that the nonlinearity of correlation functions increases with the width of observation windows, leading at small string density to a strong dependence of correlation coefficient value on the definition. The results of the modeling enable qualitatively to explain the experimentally observed features in the behavior of the correlation functions between multiplicities and mean transverse momenta at small and large multiplicities.

Differences in maternal responsive and directive behavior during free play with and without aided AAC.

PubMed

Medeiros, Kara F; Cress, Cynthia J

2016-06-01

Maternal directive and responsive behaviors were compared for 25 mothers and children with complex communication needs using two types of toys (familiar and unfamiliar toys). Each type of toy play was conducted with and without a single message speech-generating communication device (SGD) programmed to say "more." Rate percentages of coded intervals for maternal directive and responsive behaviors were analyzed using repeated measures ANOVAs. Results indicated that mothers used significantly more responsive behaviors when playing with their own familiar toys than with unfamiliar toys, but no differences in directiveness between types of play. Mothers showed no differences in responsivity or directiveness when the SGD was added to play interactions, indicating that the SGD did not introduce task features that detracted from the mothers' existing levels of responsivity with their children. Clinical implications are discussed.

Application of Fuzzy c-Means and Joint-Feature-Clustering to Detect Redundancies of Image-Features in Drug Combinations Studies of Breast Cancer

NASA Astrophysics Data System (ADS)

Brandl, Miriam B.; Beck, Dominik; Pham, Tuan D.

2011-06-01

The high dimensionality of image-based dataset can be a drawback for classification accuracy. In this study, we propose the application of fuzzy c-means clustering, cluster validity indices and the notation of a joint-feature-clustering matrix to find redundancies of image-features. The introduced matrix indicates how frequently features are grouped in a mutual cluster. The resulting information can be used to find data-derived feature prototypes with a common biological meaning, reduce data storage as well as computation times and improve the classification accuracy.

A Framework to Describe, Analyze and Generate Interactive Motor Behaviors

PubMed Central

Jarrassé, Nathanaël; Charalambous, Themistoklis; Burdet, Etienne

2012-01-01

While motor interaction between a robot and a human, or between humans, has important implications for society as well as promising applications, little research has been devoted to its investigation. In particular, it is important to understand the different ways two agents can interact and generate suitable interactive behaviors. Towards this end, this paper introduces a framework for the description and implementation of interactive behaviors of two agents performing a joint motor task. A taxonomy of interactive behaviors is introduced, which can classify tasks and cost functions that represent the way each agent interacts. The role of an agent interacting during a motor task can be directly explained from the cost function this agent is minimizing and the task constraints. The novel framework is used to interpret and classify previous works on human-robot motor interaction. Its implementation power is demonstrated by simulating representative interactions of two humans. It also enables us to interpret and explain the role distribution and switching between roles when performing joint motor tasks. PMID:23226231

A framework to describe, analyze and generate interactive motor behaviors.

PubMed

Jarrassé, Nathanaël; Charalambous, Themistoklis; Burdet, Etienne

2012-01-01

While motor interaction between a robot and a human, or between humans, has important implications for society as well as promising applications, little research has been devoted to its investigation. In particular, it is important to understand the different ways two agents can interact and generate suitable interactive behaviors. Towards this end, this paper introduces a framework for the description and implementation of interactive behaviors of two agents performing a joint motor task. A taxonomy of interactive behaviors is introduced, which can classify tasks and cost functions that represent the way each agent interacts. The role of an agent interacting during a motor task can be directly explained from the cost function this agent is minimizing and the task constraints. The novel framework is used to interpret and classify previous works on human-robot motor interaction. Its implementation power is demonstrated by simulating representative interactions of two humans. It also enables us to interpret and explain the role distribution and switching between roles when performing joint motor tasks.

Evaluation of drug interaction microcomputer software: comparative study.

PubMed

Poirier, T I; Giudici, R

1991-01-01

Twelve drug interaction microcomputer software programs were evaluated and compared using general and specific criteria. This article summarizes and compares the features, ratings, advantages, and disadvantages of each program. Features of an ideal drug interaction program are noted. Recommended programs based on three price ranges are suggested.

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

Rebolini, Elisa, E-mail: rebolini@lct.jussieu.fr; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr; Savin, Andreas, E-mail: savin@lct.jussieu.fr

We present a study of the variation of total energies and excitation energies along a range-separated adiabatic connection. This connection links the non-interacting Kohn–Sham electronic system to the physical interacting system by progressively switching on the electron–electron interactions whilst simultaneously adjusting a one-electron effective potential so as to keep the ground-state density constant. The interactions are introduced in a range-dependent manner, first introducing predominantly long-range, and then all-range, interactions as the physical system is approached, as opposed to the conventional adiabatic connection where the interactions are introduced by globally scaling the standard Coulomb interaction. Reference data are reported for themore » He and Be atoms and the H{sub 2} molecule, obtained by calculating the short-range effective potential at the full configuration-interaction level using Lieb's Legendre-transform approach. As the strength of the electron–electron interactions increases, the excitation energies, calculated for the partially interacting systems along the adiabatic connection, offer increasingly accurate approximations to the exact excitation energies. Importantly, the excitation energies calculated at an intermediate point of the adiabatic connection are much better approximations to the exact excitation energies than are the corresponding Kohn–Sham excitation energies. This is particularly evident in situations involving strong static correlation effects and states with multiple excitation character, such as the dissociating H{sub 2} molecule. These results highlight the utility of long-range interacting reference systems as a starting point for the calculation of excitation energies and are of interest for developing and analyzing practical approximate range-separated density-functional methodologies.« less

Development of a Dehalogenase-Based Protein Fusion Tag Capable of Rapid, Selective and Covalent Attachment to Customizable Ligands

PubMed Central

Encell, Lance P; Friedman Ohana, Rachel; Zimmerman, Kris; Otto, Paul; Vidugiris, Gediminas; Wood, Monika G; Los, Georgyi V; McDougall, Mark G; Zimprich, Chad; Karassina, Natasha; Learish, Randall D; Hurst, Robin; Hartnett, James; Wheeler, Sarah; Stecha, Pete; English, Jami; Zhao, Kate; Mendez, Jacqui; Benink, Hélène A; Murphy, Nancy; Daniels, Danette L; Slater, Michael R; Urh, Marjeta; Darzins, Aldis; Klaubert, Dieter H; Bulleit, Robert F; Wood, Keith V

2012-01-01

Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins. PMID:23248739

Surgeon Training in Telerobotic Surgery via a Hardware-in-the-Loop Simulator

PubMed Central

Alemzadeh, Homa; Chen, Daniel; Kalbarczyk, Zbigniew; Iyer, Ravishankar K.; Kesavadas, Thenkurussi

2017-01-01

This work presents a software and hardware framework for a telerobotic surgery safety and motor skill training simulator. The aims are at providing trainees a comprehensive simulator for acquiring essential skills to perform telerobotic surgery. Existing commercial robotic surgery simulators lack features for safety training and optimal motion planning, which are critical factors in ensuring patient safety and efficiency in operation. In this work, we propose a hardware-in-the-loop simulator directly introducing these two features. The proposed simulator is built upon the Raven-II™ open source surgical robot, integrated with a physics engine and a safety hazard injection engine. Also, a Fast Marching Tree-based motion planning algorithm is used to help trainee learn the optimal instrument motion patterns. The main contributions of this work are (1) reproducing safety hazards events, related to da Vinci™ system, reported to the FDA MAUDE database, with a novel haptic feedback strategy to provide feedback to the operator when the underlying dynamics differ from the real robot's states so that the operator will be aware and can mitigate the negative impact of the safety-critical events, and (2) using motion planner to generate semioptimal path in an interactive robotic surgery training environment. PMID:29065635

Automated computer-based detection of encounter behaviours in groups of honeybees.

PubMed

Blut, Christina; Crespi, Alessandro; Mersch, Danielle; Keller, Laurent; Zhao, Linlin; Kollmann, Markus; Schellscheidt, Benjamin; Fülber, Carsten; Beye, Martin

2017-12-15

Honeybees form societies in which thousands of members integrate their behaviours to act as a single functional unit. We have little knowledge on how the collaborative features are regulated by workers' activities because we lack methods that enable collection of simultaneous and continuous behavioural information for each worker bee. In this study, we introduce the Bee Behavioral Annotation System (BBAS), which enables the automated detection of bees' behaviours in small observation hives. Continuous information on position and orientation were obtained by marking worker bees with 2D barcodes in a small observation hive. We computed behavioural and social features from the tracking information to train a behaviour classifier for encounter behaviours (interaction of workers via antennation) using a machine learning-based system. The classifier correctly detected 93% of the encounter behaviours in a group of bees, whereas 13% of the falsely classified behaviours were unrelated to encounter behaviours. The possibility of building accurate classifiers for automatically annotating behaviours may allow for the examination of individual behaviours of worker bees in the social environments of small observation hives. We envisage that BBAS will be a powerful tool for detecting the effects of experimental manipulation of social attributes and sub-lethal effects of pesticides on behaviour.

A minimal model of an autonomous thermal motor

NASA Astrophysics Data System (ADS)

Fogedby, Hans C.; Imparato, Alberto

2017-09-01

We consider a model of a Brownian motor composed of two coupled overdamped degrees of freedom moving in periodic potentials and driven by two heat reservoirs. This model exhibits a spontaneous breaking of symmetry and gives rise to directed transport in the case of a non-vanishing interparticle interaction strength. For strong coupling between the particles we derive an expression for the propagation velocity valid for arbitrary periodic potentials. In the limit of strong coupling the model is equivalent to the Büttiker-Landauer model for a single particle diffusing in an environment with position-dependent temperature. By using numerical calculations of the Fokker-Planck equation and simulations of the Langevin equations we study the model for arbitrary coupling, retrieving many features of the strong-coupling limit. In particular, directed transport emerges even for symmetric potentials. For distinct heat reservoirs the heat currents are well-defined quantities allowing a study of the motor efficiency. We show that the optimal working regime occurs for moderate coupling. Finally, we introduce a model with discrete phase space which captures the essential features of the continuous model, can be solved in the limit of weak coupling, and exhibits a larger efficiency than the continuous counterpart.

Topological resilience in non-normal networked systems

NASA Astrophysics Data System (ADS)

Asllani, Malbor; Carletti, Timoteo

2018-04-01

The network of interactions in complex systems strongly influences their resilience and the system capability to resist external perturbations or structural damages and to promptly recover thereafter. The phenomenon manifests itself in different domains, e.g., parasitic species invasion in ecosystems or cascade failures in human-made networks. Understanding the topological features of the networks that affect the resilience phenomenon remains a challenging goal for the design of robust complex systems. We hereby introduce the concept of non-normal networks, namely networks whose adjacency matrices are non-normal, propose a generating model, and show that such a feature can drastically change the global dynamics through an amplification of the system response to exogenous disturbances and eventually impact the system resilience. This early stage transient period can induce the formation of inhomogeneous patterns, even in systems involving a single diffusing agent, providing thus a new kind of dynamical instability complementary to the Turing one. We provide, first, an illustrative application of this result to ecology by proposing a mechanism to mute the Allee effect and, second, we propose a model of virus spreading in a population of commuters moving using a non-normal transport network, the London Tube.

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

PubMed

Reimand, Jüri; Arak, Tambet; Adler, Priit; Kolberg, Liis; Reisberg, Sulev; Peterson, Hedi; Vilo, Jaak

2016-07-08

Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene function related terms. Translation of hundreds of gene identifiers is another core feature of g:Profiler. Since its first publication in 2007, our web server has become a popular tool of choice among basic and translational researchers. Timeliness is a major advantage of g:Profiler as genome and pathway information is synchronized with the Ensembl database in quarterly updates. g:Profiler supports 213 species including mammals and other vertebrates, plants, insects and fungi. The 2016 update of g:Profiler introduces several novel features. We have added further functional datasets to interpret gene lists, including transcription factor binding site predictions, Mendelian disease annotations, information about protein expression and complexes and gene mappings of human genetic polymorphisms. Besides the interactive web interface, g:Profiler can be accessed in computational pipelines using our R package, Python interface and BioJS component. g:Profiler is freely available at http://biit.cs.ut.ee/gprofiler/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Network motif frequency vectors reveal evolving metabolic network organisation.

PubMed

Pearcy, Nicole; Crofts, Jonathan J; Chuzhanova, Nadia

2015-01-01

At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over the past decade or so. Such investigations have revealed a number of shared topological features, such as a short characteristic path-length, large clustering coefficient and hierarchical modular structure. However, the extent to which evolutionary and functional properties of metabolism manifest via this underlying network architecture remains unclear. In this paper, we employ a novel graph embedding technique, based upon low-order network motifs, to compare metabolic network structure for 383 bacterial species categorised according to a number of biological features. In particular, we introduce a new global significance score which enables us to quantify important evolutionary relationships that exist between organisms and their physical environments. Using this new approach, we demonstrate a number of significant correlations between environmental factors, such as growth conditions and habitat variability, and network motif structure, providing evidence that organism adaptability leads to increased complexities in the resultant metabolic networks.

Stroboscopic phenomena in superconductors with dynamic pinning landscape

PubMed Central

Jelić, Ž. L.; Milošević, M. V.; Van de Vondel, J.; Silhanek, A. V.

2015-01-01

Introducing artificial pinning centers is a well established strategy to trap quantum vortices and increase the maximal magnetic field and applied electric current that a superconductor can sustain without dissipation. In case of spatially periodic pinning, a clear enhancement of the superconducting critical current arises when commensurability between the vortex configurations and the pinning landscape occurs. With recent achievements in (ultrafast) optics and nanoengineered plasmonics it has become possible to exploit the interaction of light with superconductivity, and create not only spatially periodic imprints on the superconducting condensate, but also temporally periodic ones. Here we show that in the latter case, temporal matching phenomena develop, caused by stroboscopic commensurability between the characteristic frequency of the vortex motion under applied current and the frequency of the dynamic pinning. The matching resonances persist in a broad parameter space, including magnetic field, driving current, or material purity, giving rise to unusual features such as externally variable resistance/impedance and Shapiro steps in current-voltage characteristics. All features are tunable by the frequency of the dynamic pinning landscape. These findings open further exploration avenues for using flashing, spatially engineered, and/or mobile excitations on superconductors, permitting us to achieve advanced functionalities. PMID:26423610

Deeply learnt hashing forests for content based image retrieval in prostate MR images

NASA Astrophysics Data System (ADS)

Shah, Amit; Conjeti, Sailesh; Navab, Nassir; Katouzian, Amin

2016-03-01

Deluge in the size and heterogeneity of medical image databases necessitates the need for content based retrieval systems for their efficient organization. In this paper, we propose such a system to retrieve prostate MR images which share similarities in appearance and content with a query image. We introduce deeply learnt hashing forests (DL-HF) for this image retrieval task. DL-HF effectively leverages the semantic descriptiveness of deep learnt Convolutional Neural Networks. This is used in conjunction with hashing forests which are unsupervised random forests. DL-HF hierarchically parses the deep-learnt feature space to encode subspaces with compact binary code words. We propose a similarity preserving feature descriptor called Parts Histogram which is derived from DL-HF. Correlation defined on this descriptor is used as a similarity metric for retrieval from the database. Validations on publicly available multi-center prostate MR image database established the validity of the proposed approach. The proposed method is fully-automated without any user-interaction and is not dependent on any external image standardization like image normalization and registration. This image retrieval method is generalizable and is well-suited for retrieval in heterogeneous databases other imaging modalities and anatomies.

Introducing time-dependent molecular fields: a new derivation of the wave equations

NASA Astrophysics Data System (ADS)

Baer, Michael

2018-02-01

This article is part of a series of articles trying to establish the concept molecular field. The theory that induced us to introduce this novel concept is based on the Born-Huang expansion as applied to the Schroedinger equation that describes the interaction of a molecular system with an external electric field. Assuming the molecular system is made up of two coupled adiabatic states the theory leads from a single spatial curl equation, two space-time curl equations and one single space-time divergent equation to a pair of decoupled wave equations usually encountered within the theory of fields. In the present study, just like in the previous study [see Baer et al., Mol. Phys. 114, 227 (2016)] the wave equations are derived for an electric field having two features: (a) its intensity is high enough; (b) its duration is short enough. Although not all the findings are new the derivation, in the present case, is new, straightforward, fluent and much friendlier as compared to the previous one and therefore should be presented again. For this situation the study reveals that the just described interaction creates two fields that coexist within a molecule: one is a novel vectorial field formed via the interaction of the electric field with the Born-Huang non-adiabatic coupling terms (NACTs) and the other is an ordinary, scalar, electric field essentially identical to the original electric field. Section 4 devoted to the visualization of the outcomes via two intersecting Jahn-Teller cones which contain NACTs that become singular at the intersection point of these cones. Finally, the fact that eventually we are facing a kind of a cosmic situation may bring us to speculate that singular NACTs are a result of cosmic phenomena. Thus, if indeed this singularity is somehow connected to reality then, like other singularities in physics, it is formed at (or immediately after) the Big Bang and consequently, guarantees the formation of molecules.

Predicting Protein-Protein Interactions by Combing Various Sequence-Derived.

PubMed

Zhao, Xiao-Wei; Ma, Zhi-Qiang; Yin, Ming-Hao

2011-09-20

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

Early relations between language development and the quality of mother-child interaction in very-low-birth-weight children.

PubMed

Stolt, S; Korja, R; Matomäki, J; Lapinleimu, H; Haataja, L; Lehtonen, L

2014-05-01

It is not clearly understood how the quality of early mother-child interaction influences language development in very-low-birth-weight children (VLBW). We aim to analyze associations between early language and the quality of mother-child interaction, and, the predictive value of the features of early mother-child interaction on language development at 24 months of corrected age in VLBW children. A longitudinal prospective follow-up study design was used. The participants were 28 VLBW children and 34 full-term controls. Language development was measured using different methods at 6, 12 and at 24 months of age. The quality of mother-child interaction was assessed using PC-ERA method at 6 and at 12 months of age. Associations between the features of early interaction and language development were different in the groups of VLBW and full-term children. There were no significant correlations between the features of mother-child interaction and language skills when measured at the same age in the VLBW group. Significant longitudinal correlations were detected in the VLBW group especially if the quality of early interactions was measured at six months and language skills at 2 years of age. However, when the predictive value of the features of early interactions for later poor language performance was analyzed separately, the features of early interaction predicted language skills in the VLBW group only weakly. The biological factors may influence on the language development more in the VLBW children than in the full-term children. The results also underline the role of maternal and dyadic factors in early interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Interactive Sections Of An Internet-Based Intervention Increase Patient Empowerment: A Study With Chronic Back Pain Patients

ClinicalTrials.gov

2014-04-12

Group 1 (Control): Access to a Static Version of the Website Containing Only Static Features (i.e. Library, First Aid, and FAQ); Group2 (Intervention) Access to an Interactive Version of the Website Containing Both Static and Interactive Features

Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

Mondrian is state-of-the-art statistical data visualization software featuring modern interactive visualization techniques for a wide range of data types. This article reviews the capabilities, functionality, and interactive properties of this software package. Key features of Mondrian are illustrated with data from the Programme for International…

Drug-target interaction prediction using ensemble learning and dimensionality reduction.

PubMed

Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

2017-10-01

Experimental prediction of drug-target interactions is expensive, time-consuming and tedious. Fortunately, computational methods help narrow down the search space for interaction candidates to be further examined via wet-lab techniques. Nowadays, the number of attributes/features for drugs and targets, as well as the amount of their interactions, are increasing, making these computational methods inefficient or occasionally prohibitive. This motivates us to derive a reduced feature set for prediction. In addition, since ensemble learning techniques are widely used to improve the classification performance, it is also worthwhile to design an ensemble learning framework to enhance the performance for drug-target interaction prediction. In this paper, we propose a framework for drug-target interaction prediction leveraging both feature dimensionality reduction and ensemble learning. First, we conducted feature subspacing to inject diversity into the classifier ensemble. Second, we applied three different dimensionality reduction methods to the subspaced features. Third, we trained homogeneous base learners with the reduced features and then aggregated their scores to derive the final predictions. For base learners, we selected two classifiers, namely Decision Tree and Kernel Ridge Regression, resulting in two variants of ensemble models, EnsemDT and EnsemKRR, respectively. In our experiments, we utilized AUC (Area under ROC Curve) as an evaluation metric. We compared our proposed methods with various state-of-the-art methods under 5-fold cross validation. Experimental results showed EnsemKRR achieving the highest AUC (94.3%) for predicting drug-target interactions. In addition, dimensionality reduction helped improve the performance of EnsemDT. In conclusion, our proposed methods produced significant improvements for drug-target interaction prediction. Copyright © 2017 Elsevier Inc. All rights reserved.

A Review of Integrating Mobile Phones for Language Learning

ERIC Educational Resources Information Center

Darmi, Ramiza; Albion, Peter

2014-01-01

Mobile learning (m-learning) is gradually being introduced in language classrooms. All forms of mobile technology represent portability with smarter features. Studies have proven the concomitant role of technology beneficial for language learning. Various features in the technology have been exploited and researched for acquiring and learning…

Teaching the Conventions of Academic Discourse

ERIC Educational Resources Information Center

Thonney, Teresa

2011-01-01

Given the current emphasis on disciplinary discourses, it's not surprising that so little recent attention has been devoted to identifying conventions that are universal in academic discourse. In this essay, the author argues that there are shared features that unite academic writing, and that by introducing these features to first-year students…

Introduction: Optical trapping and applications feature issue

PubMed Central

López-Mariscal, Carlos; McGloin, David

2013-01-01

The editors introduce the Biomedical Optics Express feature issue on “Optical Trapping and Applications.” The works presented in the papers within this issue include were the focus of the third OTA Topical Meeting that was held on April 14–18, 2013, in Waikoloa, Hawaii. PMID:24298428

Reviewing Student Papers Electronically

ERIC Educational Resources Information Center

Dunford, Spencer

2011-01-01

In order to consistently give quality feedback to students, the author introduces the revision and automation tools in Microsoft Word 2007. These features, Comments, Tracking, and Changes, are part of the Review group in MS Word 2007. Additionally, the AutoCorrect feature can be used to enhance and support editing endeavors. This article offers a…

"I" Is for Iowa Inventors!

ERIC Educational Resources Information Center

Frese, Millie K., Ed.

1998-01-01

"The Goldfinch" is a magazine oriented toward young children and intended to introduce said audience to many different aspects of Iowa history. Each issue focuses on a different topic, and features a number of articles that discuss the topic in more depth. The topic for this issue is Iowa Inventors. Featured articles highlight women…

Features of Computerized Educational Games in Sciences of the Elementary Phase in Jordan from the Point of View of Specialists in Teaching Science and Computer Subjects

ERIC Educational Resources Information Center

Al Sarhan, Khaled Ali; AlZboon, Saleem Odeh; Olimat, Khalaf Mufleh; Al-Zboon, Mohammad Saleem

2013-01-01

The study aims at introducing the features of the computerized educational games in sciences at the elementary school in Jordan according to the specialists in teaching science and computer subjects, through answering some questions such as: What are the features of the computerized educational games in sciences at the elementary schools in Jordan…

Prediction of enhancer-promoter interactions via natural language processing.

PubMed

Zeng, Wanwen; Wu, Mengmeng; Jiang, Rui

2018-05-09

Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting ones since the power of traditional experimental methods is limited due to low resolution or low throughput. We propose a novel computational framework EP2vec to assay three-dimensional genomic interactions. We first extract sequence embedding features, defined as fixed-length vector representations learned from variable-length sequences using an unsupervised deep learning method in natural language processing. Then, we train a classifier to predict EPIs using the learned representations in supervised way. Experimental results demonstrate that EP2vec obtains F1 scores ranging from 0.841~ 0.933 on different datasets, which outperforms existing methods. We prove the robustness of sequence embedding features by carrying out sensitivity analysis. Besides, we identify motifs that represent cell line-specific information through analysis of the learned sequence embedding features by adopting attention mechanism. Last, we show that even superior performance with F1 scores 0.889~ 0.940 can be achieved by combining sequence embedding features and experimental features. EP2vec sheds light on feature extraction for DNA sequences of arbitrary lengths and provides a powerful approach for EPIs identification.

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

PubMed

Pancaldi, Vera; Carrillo-de-Santa-Pau, Enrique; Javierre, Biola Maria; Juan, David; Fraser, Peter; Spivakov, Mikhail; Valencia, Alfonso; Rico, Daniel

2016-07-08

Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts. We use high-resolution promoter capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse embryonic stem cells to investigate promoter-centered chromatin interaction networks and calculate the presence of specific epigenomic features in the chromatin fragments constituting the nodes of the network. We estimate the association of these features with the topology of four chromatin interaction networks and identify features localized in connected areas of the network. Polycomb group proteins and associated histone marks are the features with the highest chromatin assortativity in promoter-centered networks. We then ask which features distinguish contacts amongst promoters from contacts between promoters and other genomic elements. We observe higher chromatin assortativity of the actively elongating form of RNA polymerase 2 (RNAPII) compared with inactive forms only in interactions between promoters and other elements. Contacts among promoters and between promoters and other elements have different characteristic epigenomic features. We identify a possible role for the elongating form of RNAPII in mediating interactions among promoters, enhancers, and transcribed gene bodies. Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing the comparison of chromatin interaction networks.

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

PubMed Central

2012-01-01

Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners. PMID:22783946

Interaction of Solar Wind and Magnetic Anomalies - Modelling from Moon to Mars

NASA Astrophysics Data System (ADS)

Alho, Markku; Kallio, Esa; Wedlund, Cyril Simon; Wurz, Peter

2015-04-01

The crustal magnetic anomalies on both the Moon and Mars strongly affect the local plasma environment. On the Moon, the impinging solar wind is decelerated or deflected when interacting with the magnetic field anomaly, visible in the lunar surface as energetic neutral atom (ENA) emissions or as reflected protons, and may play a part in the space weathering of the lunar soil. At Mars, the crustal magnetic fields have been shown to be associated with, e.g., enhanced electron scale heights and modified convection of ionospheric plasma, resulting in the plasma environment being dominated by crustal magnetic fields up to altitudes of 400km. Our previous modelling work suggested that Hall currents are a dominant feature in a Moon-like magnetic anomaly interaction at scales at or below the proton inertial length. In this work we study the solar wind interaction with magnetic anomalies and compare the plasma environments of a Moon-like anomaly with a Mars-like anomaly by introducing an ionosphere and an exosphere to probe the transition from an atmosphere-less anomaly interaction to an ionospheric one. We utilize a 3D hybrid plasma model, in which ions are modelled as particles while electrons form a charge-neutralizing massless fluid. The hybrid model gives a full description of ion kinetics and associated plasma phenomena at the simulation region ranging from instabilities to possible reconnection. The model can thus be used to interpret both in-situ particle and field observations and remotely-sensed ENA emissions. A self-consistent ionosphere package for the model is additionally in development.

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids.

PubMed

Wu, Yang; Li, Yao; Hu, Na; Hong, Mei

2014-02-14

Recently, experimental and theoretical studies on amino acid ionic liquid (AAIL) systems have attracted much attention. A transferable intermolecular potential approach that includes fluctuating charges and a flexible body based on a combination of the electronegativity equalization method and molecular mechanics (EEM/MM), and its application to an AAIL system containing 1-ethyl-3-methylimidazolium ([Emim](+)) and glycine ([Gly](-)) are explored and tested in this study. A consistent integration of EEM with MM requires the input of the EEM charges of all atoms into the MM intermolecular electrostatic interaction term. Compared with ionic liquid (IL) force fields, the EEM/MM model has an outstanding feature: the EEM/MM model not only presents the electrostatic interaction of atoms and their changes in response to different ambient environments but also introduces "the H-bond interaction region" in which a new parameter kHB(RHB) is used to describe the electrostatic interaction of hydrogen atoms in [Emim](+) and oxygen atoms in [Gly](-), which can form hydrogen bonds. The EEM/MM model gives quite accurate predictions for gas-phase state properties of [Emim](+), [Gly](-), and ion pairs, such as optimized geometries, dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and hydrogen bonds, the EEM/MM model also performs well for the liquid-phase properties of [Emim][Gly] under ambient conditions. The calculated properties, such as density, heat of vaporization, the self-diffusion coefficient, and ionic conductivity, are fairly consistent with available experimental results.

Agile Multi-Scale Decompositions for Automatic Image Registration

NASA Technical Reports Server (NTRS)

Murphy, James M.; Leija, Omar Navarro; Le Moigne, Jacqueline

2016-01-01

In recent works, the first and third authors developed an automatic image registration algorithm based on a multiscale hybrid image decomposition with anisotropic shearlets and isotropic wavelets. This prototype showed strong performance, improving robustness over registration with wavelets alone. However, this method imposed a strict hierarchy on the order in which shearlet and wavelet features were used in the registration process, and also involved an unintegrated mixture of MATLAB and C code. In this paper, we introduce a more agile model for generating features, in which a flexible and user-guided mix of shearlet and wavelet features are computed. Compared to the previous prototype, this method introduces a flexibility to the order in which shearlet and wavelet features are used in the registration process. Moreover, the present algorithm is now fully coded in C, making it more efficient and portable than the MATLAB and C prototype. We demonstrate the versatility and computational efficiency of this approach by performing registration experiments with the fully-integrated C algorithm. In particular, meaningful timing studies can now be performed, to give a concrete analysis of the computational costs of the flexible feature extraction. Examples of synthetically warped and real multi-modal images are analyzed.

FAST TRACK COMMUNICATION: A Temperley-Lieb quantum chain with two- and three-site interactions

NASA Astrophysics Data System (ADS)

Ikhlef, Y.; Jacobsen, J. L.; Saleur, H.

2009-07-01

We study the phase diagram of a quantum chain of spin-1/2 particles whose world lines form a dense loop gas with loop weight n. In addition to the usual two-site interaction corresponding to the XXZ spin chain, we introduce a three-site interaction. The resulting model contains a Majumdar-Ghosh-like gapped phase and a new integrable point, which we solve exactly. We also locate a critical line realizing dilute O(n) criticality, without introducing explicit dilution in the loops. Our results have implications for anisotropic spin chains, as well as anyonic quantum chains.

Life events and borderline personality features: the influence of gene-environment interaction and gene-environment correlation.

PubMed

Distel, M A; Middeldorp, C M; Trull, T J; Derom, C A; Willemsen, G; Boomsma, D I

2011-04-01

Traumatic life events are generally more common in patients with borderline personality disorder (BPD) than in non-patients or patients with other personality disorders. This study investigates whether exposure to life events moderates the genetic architecture of BPD features. As the presence of genotype-environment correlation (rGE) can lead to spurious findings of genotype-environment interaction (G × E), we also test whether BPD features increase the likelihood of exposure to life events. The extent to which an individual is at risk to develop BPD was assessed with the Personality Assessment Inventory - Borderline features scale (PAI-BOR). Life events under study were a divorce/break-up, traffic accident, violent assault, sexual assault, robbery and job loss. Data were available for 5083 twins and 1285 non-twin siblings. Gene-environment interaction and correlation were assessed by using structural equation modelling (SEM) and the co-twin control design. There was evidence for both gene-environment interaction and correlation. Additive genetic influences on BPD features interacted with the exposure to sexual assault, with genetic variance being lower in exposed individuals. In individuals who had experienced a divorce/break-up, violent assault, sexual assault or job loss, environmental variance for BPD features was higher, leading to a lower heritability of BPD features in exposed individuals. Gene-environment correlation was present for some life events. The genes that influence BPD features thus also increased the likelihood of being exposed to certain life events. To our knowledge, this study is the first to test the joint effect of genetic and environmental influences and the exposure to life events on BPD features in the general population. Our results indicate the importance of both genetic vulnerability and life events.

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches.

PubMed

Yugandhar, K; Gromiha, M Michael

2014-09-01

Protein-protein interactions are intrinsic to virtually every cellular process. Predicting the binding affinity of protein-protein complexes is one of the challenging problems in computational and molecular biology. In this work, we related sequence features of protein-protein complexes with their binding affinities using machine learning approaches. We set up a database of 185 protein-protein complexes for which the interacting pairs are heterodimers and their experimental binding affinities are available. On the other hand, we have developed a set of 610 features from the sequences of protein complexes and utilized Ranker search method, which is the combination of Attribute evaluator and Ranker method for selecting specific features. We have analyzed several machine learning algorithms to discriminate protein-protein complexes into high and low affinity groups based on their Kd values. Our results showed a 10-fold cross-validation accuracy of 76.1% with the combination of nine features using support vector machines. Further, we observed accuracy of 83.3% on an independent test set of 30 complexes. We suggest that our method would serve as an effective tool for identifying the interacting partners in protein-protein interaction networks and human-pathogen interactions based on the strength of interactions. © 2014 Wiley Periodicals, Inc.

Computational Models of Laryngeal Aerodynamics: Potentials and Numerical Costs.

PubMed

Sadeghi, Hossein; Kniesburges, Stefan; Kaltenbacher, Manfred; Schützenberger, Anne; Döllinger, Michael

2018-02-07

Human phonation is based on the interaction between tracheal airflow and laryngeal dynamics. This fluid-structure interaction is based on the energy exchange between airflow and vocal folds. Major challenges in analyzing the phonatory process in-vivo are the small dimensions and the poor accessibility of the region of interest. For improved analysis of the phonatory process, numerical simulations of the airflow and the vocal fold dynamics have been suggested. Even though most of the models reproduced the phonatory process fairly well, development of comprehensive larynx models is still a subject of research. In the context of clinical application, physiological accuracy and computational model efficiency are of great interest. In this study, a simple numerical larynx model is introduced that incorporates the laryngeal fluid flow. It is based on a synthetic experimental model with silicone vocal folds. The degree of realism was successively increased in separate computational models and each model was simulated for 10 oscillation cycles. Results show that relevant features of the laryngeal flow field, such as glottal jet deflection, develop even when applying rather simple static models with oscillating flow rates. Including further phonatory components such as vocal fold motion, mucosal wave propagation, and ventricular folds, the simulations show phonatory key features like intraglottal flow separation and increased flow rate in presence of ventricular folds. The simulation time on 100 CPU cores ranged between 25 and 290 hours, currently restricting clinical application of these models. Nevertheless, results show high potential of numerical simulations for better understanding of phonatory process. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

The Third Tibetan Plateau Atmospheric Scientific Experiment for Understanding the Earth-Atmosphere Coupled System

NASA Astrophysics Data System (ADS)

Zhao, P.; Xu, X.; Chen, F.; Guo, X.; Zheng, X.; Liu, L. P.; Hong, Y.; Li, Y.; La, Z.; Peng, H.; Zhong, L. Z.; Ma, Y.; Tang, S. H.; Liu, Y.; Liu, H.; Li, Y. H.; Zhang, Q.; Hu, Z.; Sun, J. H.; Zhang, S.; Dong, L.; Zhang, H.; Zhao, Y.; Yan, X.; Xiao, A.; Wan, W.; Zhou, X.

2016-12-01

The Third Tibetan Plateau atmospheric scientific experiment (TIPEX-III) was initiated jointly by the China Meteorological Administration, the National Natural Scientific Foundation, and the Chinese Academy of Sciences. This paper presents the background, scientific objectives, and overall experimental design of TIPEX-III. It was designed to conduct an integrated observation of the earth-atmosphere coupled system over the Tibetan Plateau (TP) from land surface, planetary boundary layer (PBL), troposphere, and stratosphere for eight to ten years by coordinating ground- and air-based measurement facilities for understanding spatial heterogeneities of complex land-air interactions, cloud-precipitation physical processes, and interactions between troposphere and stratosphere. TIPEX-III originally began in 2014, and is ongoing. It established multiscale land-surface and PBL observation networks over the TP and a tropospheric meteorological radiosonde network over the western TP, and executed an integrated observation mission for cloud-precipitation physical features using ground-based radar systems and aircraft campaigns and an observation task for atmospheric ozone, aerosol, and water vapor. The archive, management, and share policy of the observation data are also introduced herein. Some TIPEX-III data have been preliminarily applied to analyze the features of surface sensible and latent heat fluxes, cloud-precipitation physical processes, and atmospheric water vapor and ozone over the TP, and to improve the local precipitation forecast. Furthermore, TIPEX-III intends to promote greater scientific and technological cooperation with international research communities and broader organizations. Scientists working internationally are invited to participate in the field campaigns and to use the TIPEX-III data for their own research.

Moving force identification based on redundant concatenated dictionary and weighted l1-norm regularization

NASA Astrophysics Data System (ADS)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin; Chen, Ze-Peng; Luo, Wen-Feng

2018-01-01

Moving force identification (MFI) is an important inverse problem in the field of bridge structural health monitoring (SHM). Reasonable signal structures of moving forces are rarely considered in the existing MFI methods. Interaction forces are complex because they contain both slowly-varying harmonic and impact signals due to bridge vibration and bumps on a bridge deck, respectively. Therefore, the interaction forces are usually hard to be expressed completely and sparsely by using a single basis function set. Based on the redundant concatenated dictionary and weighted l1-norm regularization method, a hybrid method is proposed for MFI in this study. The redundant dictionary consists of both trigonometric functions and rectangular functions used for matching the harmonic and impact signal features of unknown moving forces. The weighted l1-norm regularization method is introduced for formulation of MFI equation, so that the signal features of moving forces can be accurately extracted. The fast iterative shrinkage-thresholding algorithm (FISTA) is used for solving the MFI problem. The optimal regularization parameter is appropriately chosen by the Bayesian information criterion (BIC) method. In order to assess the accuracy and the feasibility of the proposed method, a simply-supported beam bridge subjected to a moving force is taken as an example for numerical simulations. Finally, a series of experimental studies on MFI of a steel beam are performed in laboratory. Both numerical and experimental results show that the proposed method can accurately identify the moving forces with a strong robustness, and it has a better performance than the Tikhonov regularization method. Some related issues are discussed as well.

Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome.

PubMed

Cheng, Lixin; Leung, Kwong-Sak

2018-05-16

Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA-protein interactions, and functional annotation of proteins. We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a variable localization pattern with a high chance of residing in the cytoplasmic compartment in comparison to the other lncRNAs. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases. The code implementing MoonFinder is supplied as an R package in the supplementary material. lxcheng@cse.cuhk.edu.hk or ksleung@cse.cuhk.edu.hk. Supplementary data are available at Bioinformatics online.

Vertical Feature Mask Feature Classification Flag Extraction

Atmospheric Science Data Center

2013-03-28

  Vertical Feature Mask Feature Classification Flag Extraction This routine demonstrates extraction of the ... in a CALIPSO Lidar Level 2 Vertical Feature Mask feature classification flag value. It is written in Interactive Data Language (IDL) ...

CRIE: An automated analyzer for Chinese texts.

PubMed

Sung, Yao-Ting; Chang, Tao-Hsing; Lin, Wei-Chun; Hsieh, Kuan-Sheng; Chang, Kuo-En

2016-12-01

Textual analysis has been applied to various fields, such as discourse analysis, corpus studies, text leveling, and automated essay evaluation. Several tools have been developed for analyzing texts written in alphabetic languages such as English and Spanish. However, currently there is no tool available for analyzing Chinese-language texts. This article introduces a tool for the automated analysis of simplified and traditional Chinese texts, called the Chinese Readability Index Explorer (CRIE). Composed of four subsystems and incorporating 82 multilevel linguistic features, CRIE is able to conduct the major tasks of segmentation, syntactic parsing, and feature extraction. Furthermore, the integration of linguistic features with machine learning models enables CRIE to provide leveling and diagnostic information for texts in language arts, texts for learning Chinese as a foreign language, and texts with domain knowledge. The usage and validation of the functions provided by CRIE are also introduced.

The effects of missing data on global ozone estimates

NASA Technical Reports Server (NTRS)

Drewry, J. W.; Robbins, J. L.

1981-01-01

The effects of missing data and model truncation on estimates of the global mean, zonal distribution, and global distribution of ozone are considered. It is shown that missing data can introduce biased estimates with errors that are not accounted for in the accuracy calculations of empirical modeling techniques. Data-fill techniques are introduced and used for evaluating error bounds and constraining the estimate in areas of sparse and missing data. It is found that the accuracy of the global mean estimate is more dependent on data distribution than model size. Zonal features can be accurately described by 7th order models over regions of adequate data distribution. Data variance accounted for by higher order models appears to represent climatological features of columnar ozone rather than pure error. Data-fill techniques can prevent artificial feature generation in regions of sparse or missing data without degrading high order estimates over dense data regions.

Effects of Interactive Vocabulary Instruction on the Vocabulary Learning and Reading Comprehension of Junior-High Learning Disabled Students.

ERIC Educational Resources Information Center

Bos, Candace S.; Anders, Patricia L.

1990-01-01

The study, involving 61 learning-disabled junior high students, compared the short-term and long-term effectiveness of definition instruction with interactive vocabulary strategies (semantic mapping, semantic feature analysis, and semantic/syntactic feature analysis). Students participating in the interactive strategies demonstrated greater…

Introducing Adaptivity Features to a Regular Learning Management System to Support Creation of Advanced eLessons

ERIC Educational Resources Information Center

Komlenov, Zivana; Budimac, Zoran; Ivanovic, Mirjana

2010-01-01

In order to improve the learning process for students with different pre-knowledge, personal characteristics and preferred learning styles, a certain degree of adaptability must be introduced to online courses. In learning environments that support such kind of functionalities students can explicitly choose different paths through course contents…

Computing and visualizing time-varying merge trees for high-dimensional data

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

Oesterling, Patrick; Heine, Christian; Weber, Gunther H.

2017-06-03

We introduce a new method that identifies and tracks features in arbitrary dimensions using the merge tree -- a structure for identifying topological features based on thresholding in scalar fields. This method analyzes the evolution of features of the function by tracking changes in the merge tree and relates features by matching subtrees between consecutive time steps. Using the time-varying merge tree, we present a structural visualization of the changing function that illustrates both features and their temporal evolution. We demonstrate the utility of our approach by applying it to temporal cluster analysis of high-dimensional point clouds.

Human infrastructure and invasive plant occurrence across rangelands of southwestern Wyoming, U.S.A.

USGS Publications Warehouse

Manier, Daniel J.; Aldridge, Cameron L.; O'Donnell, Michael S.; Schell, Spencer

2014-01-01

Although human influence across rural landscapes is often discussed, interactions between the native, natural systems and human activities are challenging to measure explicitly. We assessed the distribution of introduced, invasive species as related to anthropogenic infrastructure and environmental conditions across southwestern Wyoming. to discern direct correlations as well as covariate influences between land use, land cover, and abundance of invasive plants, and assess the supposition that these features affect surrounding rangeland conditions. Our sample units were 1 000 m long and extended outward from target features, which included roads, oil and gas well pads, pipelines, power lines, and featureless background sites. Sample sites were distributed across the region using a stratified, random design with a frame that represented features and land-use intensity. In addition to land-use gradients, we captured a representative, but limited, range of variability in climate, soils, geology, topography, and dominant vegetation. Several of these variables proved significant, in conjunction with distance from anthropogenic features, in regression models of invasive plant abundance. We used general linear models to demonstrate and compare associations between invasive plant frequency and Euclidian distance from features, natural logarithm transformed distances (log-linear), and environmental variables which were presented as potential covariates. We expected a steep curvilinear (log or exponential) decline trending towards an asymptote along the axis representing high abundance near features with rapid decrease beyond approximately 50–100 m. Some of the associations we document exhibit this pattern, but we also found some invasive plant distributions that extended beyond our expectations, suggesting a broader distribution than anticipated. Our results provide details that can inform local efforts for management and control of invasive species, and they provide evidence of the different associations between natural patterns and human land use exhibited by nonnative species in this rural setting, such as the indirect effects of humans beyond impact areas.

Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers

PubMed Central

Tabei, Yasuo; Pauwels, Edouard; Stoven, Véronique; Takemoto, Kazuhiro; Yamanishi, Yoshihiro

2012-01-01

Motivation: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug–target interactions is crucial in the drug design process. Results: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug–target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L1 regularized classifiers over the tensor product space of possible drug–target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug–target interactions and the extracted features are biologically meaningful. The extracted substructure–domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families. Availability: Softwares are available at the supplemental website. Contact: yamanishi@bioreg.kyushu-u.ac.jp Supplementary Information: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/ . PMID:22962471

The Canadian Jobs Strategy. A Review of the First Years.

ERIC Educational Resources Information Center

Canada Employment and Immigration Commission, Ottawa (Ontario).

In September 1985, the Canadian government introduced the Canadian Jobs Strategy. Two features distinguish the jobs strategy program from Canada's old job development programs and programs for purchasing job training from colleges. These features are: (1) focusing of federal support for labor market adjustment on those individuals who are most in…

Playing with Plug-ins

ERIC Educational Resources Information Center

Thompson, Douglas E.

2013-01-01

In today's complex music software packages, many features can remain unexplored and unused. Software plug-ins--available in most every music software package, yet easily overlooked in the software's basic operations--are one such feature. In this article, I introduce readers to plug-ins and offer tips for purchasing plug-ins I have…

The Linguistic Special Features of the Sami Education

ERIC Educational Resources Information Center

Keskitalo, Pigga; Maatta, Kaarina

2011-01-01

This article focuses on the features of Sami language instruction at the first school grades in Norway. The most important part is to describe what kind of challenges Sami language instruction at the first grades as an indigenous people's language and with the status of a minority language has. This situation introduces some differences and…

Brief Report: Major Depressive Disorder with Psychotic Features in Williams Syndrome--A Case Series

ERIC Educational Resources Information Center

Valdes, Francisca; Keary, Christopher J.; Mullett, Jennifer E.; Palumbo, Michelle L.; Waxler, Jessica L.; Pober, Barbara R.; McDougle, Christopher J.

2018-01-01

Descriptions of individuals with Williams syndrome (WS) and co-morbid major depressive disorder (MDD) with psychotic features have not appeared in the literature. In addition to reviewing previous reports of psychotic symptoms in persons with WS, this paper introduces clinical histories and therapeutic management strategies for three previously…

An experimental and theoretical analysis of a foil-air bearing rotor system

NASA Astrophysics Data System (ADS)

Bonello, P.; Hassan, M. F. Bin

2018-01-01

Although there is considerable research on the experimental testing of foil-air bearing (FAB) rotor systems, only a small fraction has been correlated with simulations from a full nonlinear model that links the rotor, air film and foil domains, due to modelling complexity and computational burden. An approach for the simultaneous solution of the three domains as a coupled dynamical system, introduced by the first author and adopted by independent researchers, has recently demonstrated its capability to address this problem. This paper uses this approach, with further developments, in an experimental and theoretical study of a FAB-rotor test rig. The test rig is described in detail, including issues with its commissioning. The theoretical analysis uses a recently introduced modal-based bump foil model that accounts for interaction between the bumps and their inertia. The imposition of pressure constraints on the air film is found to delay the predicted onset of instability speed. The results lend experimental validation to a recent theoretically-based claim that the Gümbel condition may not be appropriate for a practical single-pad FAB. The satisfactory prediction of the salient features of the measured nonlinear behavior shows that the air film is indeed highly influential on the response, in contrast to an earlier finding.

A novel feature ranking method for prediction of cancer stages using proteomics data

PubMed Central

Saghapour, Ehsan; Sehhati, Mohammadreza

2017-01-01

Proteomic analysis of cancers' stages has provided new opportunities for the development of novel, highly sensitive diagnostic tools which helps early detection of cancer. This paper introduces a new feature ranking approach called FRMT. FRMT is based on the Technique for Order of Preference by Similarity to Ideal Solution method (TOPSIS) which select the most discriminative proteins from proteomics data for cancer staging. In this approach, outcomes of 10 feature selection techniques were combined by TOPSIS method, to select the final discriminative proteins from seven different proteomic databases of protein expression profiles. In the proposed workflow, feature selection methods and protein expressions have been considered as criteria and alternatives in TOPSIS, respectively. The proposed method is tested on seven various classifier models in a 10-fold cross validation procedure that repeated 30 times on the seven cancer datasets. The obtained results proved the higher stability and superior classification performance of method in comparison with other methods, and it is less sensitive to the applied classifier. Moreover, the final introduced proteins are informative and have the potential for application in the real medical practice. PMID:28934234

Why are dunkels sticky? Preschoolers infer functionality and intentional creation for artifact properties learned from generic language.

PubMed

Cimpian, Andrei; Cadena, Cristina

2010-10-01

Artifacts pose a potential learning problem for children because the mapping between their features and their functions is often not transparent. In solving this problem, children are likely to rely on a number of information sources (e.g., others' actions, affordances). We argue that children's sensitivity to nuances in the language used to describe artifacts is an important, but so far unacknowledged, piece of this puzzle. Specifically, we hypothesize that children are sensitive to whether an unfamiliar artifact's features are highlighted using generic (e.g., "Dunkels are sticky") or non-generic (e.g., "This dunkel is sticky") language. Across two studies, older-but not younger-preschoolers who heard such features introduced via generic statements inferred that they are a functional part of the artifact's design more often than children who heard the same features introduced via non-generic statements. The ability to pick up on this linguistic cue may expand considerably the amount of conceptual information about artifacts that children derive from conversations with adults. Copyright 2010 Elsevier B.V. All rights reserved.

Web 1.0 to Web 3.0 Evolution: Reviewing the Impacts on Tourism Development and Opportunities

NASA Astrophysics Data System (ADS)

Eftekhari, M. Hossein; Barzegar, Zeynab; Isaai, M. T.

The most important event following the establishmenet of the Internet network was the Web introduced by Tim Berners-Lee. Websites give their owners features that allow sharing with which they can publish their content with users and visitors. In the last 5 years, we have seen some changes in the use of web. Users want to participate in content sharing and they like to interact with each other. This is known as Web 2.0. In the last year, Web 2.0 has reached maturity and now we need a smart web which will be accordingly be called Web 3.0. Web 3.0 is based on semantic web definition. Changing the way of using the web has had a clear impact on E-Tourism and its development and also on business models. In this paper, we review the definitions and describe the impacts of web evolution on E-Tourism.

Observsational Planet Formation

NASA Astrophysics Data System (ADS)

Dong, Ruobing; Zhu, Zhaohuan; Fung, Jeffrey

2017-06-01

Planets form in gaseous protoplanetary disks surrounding newborn stars. As such, the most direct way to learn how they form from observations, is to directly watch them forming in disks. In the past, this was very difficult due to a lack of observational capabilities; as such, planet formation was largely a subject of pure theoretical astrophysics. Now, thanks to a fleet of new instruments with unprecedented resolving power that have come online recently, we have just started to unveil features in resolve images of protoplanetary disks, such as gaps and spiral arms, that are most likely associated with embedded (unseen) planets. By comparing observations with theoretical models of planet-disk interactions, the masses and orbits of these still forming planets may be constrained. Such planets may help us to directly test various planet formation models. This marks the onset of a new field — observational planet formation. I will introduce the current status of this field.

A computer program (MACPUMP) for interactive aquifer-test analysis

USGS Publications Warehouse

Day-Lewis, F. D.; Person, M.A.; Konikow, Leonard F.

1995-01-01

This report introduces MACPUMP (Version 1.0), an aquifer-test-analysis package for use with Macintosh4 computers. The report outlines the input- data format, describes the solutions encoded in the program, explains the menu-items, and offers a tutorial illustrating the use of the program. The package reads list-directed aquifer-test data from a file, plots the data to the screen, generates and plots type curves for several different test conditions, and allows mouse-controlled curve matching. MACPUMP features pull-down menus, a simple text viewer for displaying data-files, and optional on-line help windows. This version includes the analytical solutions for nonleaky and leaky confined aquifers, using both type curves and straight-line methods, and for the analysis of single-well slug tests using type curves. An executable version of the code and sample input data sets are included on an accompanying floppy disk.

Self-Assembled Ag-MXA Superclusters with Structure-Dependent Mechanical Properties.

PubMed

Qin, Xiaoyun; Luo, Dan; Xue, Zhenjie; Song, Qian; Wang, Tie

2018-03-01

The low elastic modulus and time-consuming formation process represent the major challenges that impede the penetration of nanoparticle superstructures into daily life applications. As observed in the molecular or atomic crystals, more effective interactions between adjacent nanoparticles would introduce beneficial features to assemblies enabling optimized mechanical properties. Here, a straightforward synthetic strategy is showed that allows fast and scalable fabrication of 2D Ag-mercaptoalkyl acid superclusters of either hexagonal or lamellar topology. Remarkably, these ordered superstructures exhibit a structure-dependent elastic modulus which is subject to the tether length of straight-chain mercaptoalkyl acids or the ratio between silver and tether molecules. These superclusters are plastic and moldable against arbitrarily shaped masters of macroscopic dimensions, thereby opening a wealth of possibilities to develop more nanocrystals with practically useful nanoscopic properties. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pedagogy and Academic Success in Prelicensure Nursing Education.

PubMed

Murray, Teri A

2016-01-01

The purpose of this article is to provide a brief description of the New Careers in Nursing (NCIN) program; highlight the features of the NCIN Preentry Immersion program designed to help students achieve academic success; introduce two NCIN innovation teaching projects that used active learning strategies to foster student engagement; and conduct an integrative review on the pedagogies used to foster academic success in nursing education. The integrative review revealed that interactive pedagogies fostered student engagement and increased the students' knowledge acquisition, competence, confidence, and satisfaction. Significant variations in the methodological rigor for the studies included in this review were noted in addition to nebulousness between nursing education research and evaluation. The review validated the need for more rigorous research in nursing education to improve the students' academic experience and subsequent success of all nursing students, including those from underrepresented or disadvantaged backgrounds, enrolled in prelicensure nursing education programs. Copyright © 2016 Elsevier Inc. All rights reserved.

Boltzmann-type control of opinion consensus through leaders

PubMed Central

Albi, G.; Pareschi, L.; Zanella, M.

2014-01-01

The study of formations and dynamics of opinions leading to the so-called opinion consensus is one of the most important areas in mathematical modelling of social sciences. Following the Boltzmann-type control approach recently introduced by the first two authors, we consider a group of opinion leaders who modify their strategy accordingly to an objective functional with the aim of achieving opinion consensus. The main feature of the Boltzmann-type control is that, owing to an instantaneous binary control formulation, it permits the minimization of the cost functional to be embedded into the microscopic leaders’ interactions of the corresponding Boltzmann equation. The related Fokker–Planck asymptotic limits are also derived, which allow one to give explicit expressions of stationary solutions. The results demonstrate the validity of the Boltzmann-type control approach and the capability of the leaders’ control to strategically lead the followers’ opinion. PMID:25288820

Systems Science Methods in Public Health

PubMed Central

Luke, Douglas A.; Stamatakis, Katherine A.

2012-01-01

Complex systems abound in public health. Complex systems are made up of heterogeneous elements that interact with one another, have emergent properties that are not explained by understanding the individual elements of the system, persist over time and adapt to changing circumstances. Public health is starting to use results from systems science studies to shape practice and policy, for example in preparing for global pandemics. However, systems science study designs and analytic methods remain underutilized and are not widely featured in public health curricula or training. In this review we present an argument for the utility of systems science methods in public health, introduce three important systems science methods (system dynamics, network analysis, and agent-based modeling), and provide three case studies where these methods have been used to answer important public health science questions in the areas of infectious disease, tobacco control, and obesity. PMID:22224885

Mexican-origin Early Adolescents' Ethnic Socialization, Ethnic Identity, and Psychosocial Functioning.

PubMed

Umaña-Taylor, Adriana J; O'Donnell, Megan; Knight, George P; Roosa, Mark W; Berkel, Cady; Nair, Rajni

2014-02-01

The current study examined how parental ethnic socialization informed adolescents' ethnic identity development and, in turn, youths' psychosocial functioning (i.e., mental health, social competence, academic efficacy, externalizing behaviors) among 749 Mexican-origin families. In addition, school ethnic composition was examined as a moderator of these associations. Findings indicated that mothers' and fathers' ethnic socialization were significant longitudinal predictors of adolescents' ethnic identity, although fathers' ethnic socialization interacted significantly with youths' school ethnic composition in 5 th grade to influence ethnic identity in 7 th grade. Furthermore, adolescents' ethnic identity was significantly associated with increased academic self-efficacy and social competence, and decreased depressive symptoms and externalizing behaviors. Findings support theoretical predictions regarding the central role parents play in Mexican-origin adolescents' normative developmental processes and adjustment and, importantly, underscore the need to consider variability that is introduced into these processes by features of the social context such as school ethnic composition.

Structural analyses of the JPL Mars Pathfinder impact

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

Gwinn, K.W.

1994-12-31

The purpose of this paper is to demonstrate that finite element analysis can be used in the design process for high performance fabric structures. These structures exhibit extreme geometric nonlinearity; specifically, the contact and interaction of fabric surfaces with the large deformation which necessarily results from membrane structures introduces great complexity to analyses of this type. All of these features are demonstrated here in the analysis of the Jet Propulsion Laboratory (JPL) Mars Pathfinder impact onto Mars. This lander system uses airbags to envelope the lander experiment package, protecting it with large deformation upon contact. Results from the analysis showmore » the stress in the fabric airbags, forces in the internal tendon support system, forces in the latches and hinges which allow the lander to deploy after impact, and deceleration of the lander components. All of these results provide the JPL engineers with design guidance for the success of this novel lander system.« less

Structural analyses of the JPL Mars Pathfinder impact

NASA Astrophysics Data System (ADS)

Gwinn, Kenneth W.

The purpose of this paper is to demonstrate that finite element analysis can be used in the design process for high performance fabric structures. These structures exhibit extreme geometric nonlinearity; specifically, the contact and interaction of fabric surfaces with the large deformation which necessarily results from membrane structures introduces great complexity to analyses of this type. All of these features are demonstrated here in the analysis of the Jet Propulsion Laboratory (JPL) Mars Pathfinder impact onto Mars. This lander system uses airbags to envelope the lander experiment package, protecting it with large deformation upon contact. Results from the analysis show the stress in the fabric airbags, forces in the internal tendon support system, forces in the latches and hinges which allow the lander to deploy after impact, and deceleration of the lander components. All of these results provide the JPL engineers with design guidance for the success of this novel lander system.

Ka-Band Phased Array System Characterization

NASA Technical Reports Server (NTRS)

Acosta, R.; Johnson, S.; Sands, O.; Lambert, K.

2001-01-01

Phased Array Antennas (PAAs) using patch-radiating elements are projected to transmit data at rates several orders of magnitude higher than currently offered with reflector-based systems. However, there are a number of potential sources of degradation in the Bit Error Rate (BER) performance of the communications link that are unique to PAA-based links. Short spacing of radiating elements can induce mutual coupling between radiating elements, long spacing can induce grating lobes, modulo 2 pi phase errors can add to Inter Symbol Interference (ISI), phase shifters and power divider network introduce losses into the system. This paper describes efforts underway to test and evaluate the effects of the performance degrading features of phased-array antennas when used in a high data rate modulation link. The tests and evaluations described here uncover the interaction between the electrical characteristics of a PAA and the BER performance of a communication link.

Nonminimal couplings, gravitational waves, and torsion in Horndeski's theory

NASA Astrophysics Data System (ADS)

Barrientos, José; Cordonier-Tello, Fabrizio; Izaurieta, Fernando; Medina, Perla; Narbona, Daniela; Rodríguez, Eduardo; Valdivia, Omar

2017-10-01

The Horndeski Lagrangian brings together all possible interactions between gravity and a scalar field that yield second-order field equations in four-dimensional spacetime. As originally proposed, it only addresses phenomenology without torsion, which is a non-Riemannian feature of geometry. Since torsion can potentially affect interesting phenomena such as gravitational waves and early universe inflation, in this paper we allow torsion to exist and propagate within the Horndeski framework. To achieve this goal, we cast the Horndeski Lagrangian in Cartan's first-order formalism and introduce wave operators designed to act covariantly on p -form fields that carry Lorentz indices. We find that nonminimal couplings and second-order derivatives of the scalar field in the Lagrangian are indeed generic sources of torsion. Metric perturbations couple to the background torsion, and new torsional modes appear. These may be detected via gravitational waves but not through Yang-Mills gauge bosons.

Real-Time Considerations for Rugged Embedded Systems

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

Tumeo, Antonino; Ceriani, Marco; Palermo, Gianluca

This chapter introduces the characterizing aspects of embedded systems, and discusses the specific features that a designer should address to an embedded system “rugged”, i.e., able to operate reliably in harsh environments. The chapter addresses both the hardware and the less obvious software aspect. After presenting a current list of certifications for ruggedization, the chapters present a case study that focuses on the interaction of the hardware and software layers in reactive real-time system. In particular, it shows how the use of fast FPGA prototyping could provide insights on unexpected factors that influence the performance and thus responsiveness to eventsmore » of a scheduling algorithm for multiprocessor systems that manages both periodic, hard real-time task, and aperiodic tasks. The main lesson is that to make the system “rugged”, a designer should consider these issues by, for example, overprovisioning resources and/or computation capabilities.« less

Smart glove: hand master using magnetorheological fluid actuators

NASA Astrophysics Data System (ADS)

Nam, Y. J.; Park, M. K.; Yamane, R.

2007-12-01

In this study, a hand master using five miniature magneto-rheological (MR) actuators, which is called 'the smart glove', is introduced. This hand master is intended to display haptic feedback to the fingertip of the human user interacting with any virtual objects in virtual environment. For the smart glove, two effective approaches are proposed: (i) by using the MR actuator which can be considered as a passive actuator, the smart glove is made simple in structure, high in power, low in inertia, safe in interface and stable in haptic feedback, and (ii) with a novel flexible link mechanism designed for the position-force transmission between the fingertips and the actuators, the number of the actuator and the weight of the smart glove can be reduced. These features lead to the improvement in the manipulability and portability of the smart glove. The feasibility of the constructed smart glove is verified through basic performance evaluation.

Simulation of wind turbine wakes using the actuator line technique

PubMed Central

Sørensen, Jens N.; Mikkelsen, Robert F.; Henningson, Dan S.; Ivanell, Stefan; Sarmast, Sasan; Andersen, Søren J.

2015-01-01

The actuator line technique was introduced as a numerical tool to be employed in combination with large eddy simulations to enable the study of wakes and wake interaction in wind farms. The technique is today largely used for studying basic features of wakes as well as for making performance predictions of wind farms. In this paper, we give a short introduction to the wake problem and the actuator line methodology and present a study in which the technique is employed to determine the near-wake properties of wind turbines. The presented results include a comparison of experimental results of the wake characteristics of the flow around a three-bladed model wind turbine, the development of a simple analytical formula for determining the near-wake length behind a wind turbine and a detailed investigation of wake structures based on proper orthogonal decomposition analysis of numerically generated snapshots of the wake. PMID:25583862

Programming languages for synthetic biology.

PubMed

Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

2010-12-01

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

Could the 2012 Drought in Central U.S. Have Been Anticipated? A Review of NASA Working Group Research

NASA Technical Reports Server (NTRS)

Wang, S.-Y. Simon; Barandiaran, Danny; Hilburn, Kyle; Houser, Paul; Oglesby, Bob; Pan, Ming; Pinker, Rachel; Santanello, Joe; Schubert, Siegfried; Wang, Hailan;

>From individual choice to group decision-making

NASA Astrophysics Data System (ADS)

Galam, Serge; Zucker, Jean-Daniel

2000-12-01

Some universal features are independent of both the social nature of the individuals making the decision and the nature of the decision itself. On this basis a simple magnet like model is built. Pair interactions are introduced to measure the degree of exchange among individuals while discussing. An external uniform field is included to account for a possible pressure from outside. Individual biases with respect to the issue at stake are also included using local random fields. A unique postulate of minimum conflict is assumed. The model is then solved with emphasis on its psycho-sociological implications. Counter-intuitive results are obtained. At this stage no new physical technicality is involved. Instead the full psycho-sociological implications of the model are drawn. Few cases are then detailed to enlight them. In addition, several numerical experiments based on our model are shown to give both an insight on the dynamics of the model and suggest further research directions.

Improving activity recognition using temporal coherence.

PubMed

Ataya, Abbas; Jallon, Pierre; Bianchi, Pascal; Doron, Maeva

2013-01-01

Assessment of daily physical activity using data from wearable sensors has recently become a prominent research area in the biomedical engineering field and a substantial application for pattern recognition. In this paper, we present an accelerometer-based activity recognition scheme on the basis of a hierarchical structured classifier. A first step consists of distinguishing static activities from dynamic ones in order to extract relevant features for each activity type. Next, a separate classifier is applied to detect more specific activities of the same type. On top of our activity recognition system, we introduce a novel approach to take into account the temporal coherence of activities. Inter-activity transition information is modeled by a directed graph Markov chain. Confidence measures in activity classes are then evaluated from conventional classifier's outputs and coupled with the graph to reinforce activity estimation. Accurate results and significant improvement of activity detection are obtained when applying our system for the recognition of 9 activities for 48 subjects.

Magnetic gates and guides for superconducting vortices

DOE PAGES

Vlasko-Vlasov, V. K.; Colauto, F.; Buzdin, A. I.; ...

2017-04-04

Here, we image the motion of superconducting vortices in niobium film covered with a regular array of thin permalloy stripes. By altering the magnetization orientation in the stripes using a small in-plane magnetic field, we can tune the strength of interactions between vortices and the stripe edges, enabling acceleration or retardation of the superconducting vortices in the sample and consequently introducing strong tunable anisotropy into the vortex dynamics. We discuss our observations in terms of the attraction/repulsion between point magnetic charges carried by vortices and lines of magnetic charges at the stripe edges, and derive analytical formulas for the vortex-magneticmore » stripes coupling. Our approach demonstrates the analogy between the vortex motion regulated by the magnetic stripe array and electric carrier flow in gated semiconducting devices. Scaling down the geometrical features of the proposed design may enable controlled manipulation of single vortices, paving the way for Abrikosov vortex microcircuits and memories.« less

New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content

PubMed Central

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT. PMID:23304293

A Coarse-Grained Protein Model in a Water-like Solvent

NASA Astrophysics Data System (ADS)

Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene

2013-05-01

Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.

New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

PubMed

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT.

Self-assembling graphene-anthraquinone-2-sulphonate supramolecular nanostructures with enhanced energy density for supercapacitors

NASA Astrophysics Data System (ADS)

Gao, Lifang; Gan, Shiyu; Li, Hongyan; Han, Dongxue; Li, Fenghua; Bao, Yu; Niu, Li

2017-07-01

Boosting the energy density of capacitive energy storage devices remains a crucial issue for facilitating applications. Herein, we report a graphene-anthraquinone supramolecular nanostructure by self-assembly for supercapacitors. The sulfonated anthraquinone exhibits high water solubility, a π-conjugated structure and redox active features, which not only serve as a spacer to interact with and stabilize graphene but also introduce extra pseudocapacitance contributions. The formed nest-like three-dimensional (3D) nanostructure with further hydrothermal treatment enhances the accessibility of ion transfer and exposes the redox-active quinone groups in the electrolytes. A fabricated all-solid-state flexible symmetric device delivers a high specific capacitance of 398.5 F g-1 at 1 A g-1 (1.5 times higher than graphene), superior energy density (52.24 Wh kg-1 at about 1 kW kg-1) and good stability (82% capacitance retention after 10 000 cycles).

Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

NASA Astrophysics Data System (ADS)

McKinney, B. A.; Crowe, J. E., Jr.; Voss, H. U.; Crooke, P. S.; Barney, N.; Moore, J. H.

2006-02-01

We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual’s response to the smallpox vaccine.

VisGets: coordinated visualizations for web-based information exploration and discovery.

PubMed

Dörk, Marian; Carpendale, Sheelagh; Collins, Christopher; Williamson, Carey

2008-01-01

In common Web-based search interfaces, it can be difficult to formulate queries that simultaneously combine temporal, spatial, and topical data filters. We investigate how coordinated visualizations can enhance search and exploration of information on the World Wide Web by easing the formulation of these types of queries. Drawing from visual information seeking and exploratory search, we introduce VisGets--interactive query visualizations of Web-based information that operate with online information within a Web browser. VisGets provide the information seeker with visual overviews of Web resources and offer a way to visually filter the data. Our goal is to facilitate the construction of dynamic search queries that combine filters from more than one data dimension. We present a prototype information exploration system featuring three linked VisGets (temporal, spatial, and topical), and used it to visually explore news items from online RSS feeds.

Black phosphorus: a two-dimension saturable absorption material for mid-infrared Q-switched and mode-locked fiber lasers

PubMed Central

Li, Jianfeng; Luo, Hongyu; Zhai, Bo; Lu, Rongguo; Guo, Zhinan; Zhang, Han; Liu, Yong

2016-01-01

Black phosphorus (BP) as a novel class of two-dimension (2D) materials has recently attracted enormous attention as a result of its unique physical and chemical features. The remarkably strong light-matter interaction and tunable direct band-gap at a wide range make it an ideal candidate especially in the mid-infrared wavelength region as the saturable absorber (SA). In this paper, the simple and effective liquid phase exfoliation (LPE) method was used to fabricate BP. By introducing the same BP SA into two specifically designed rare earth ions doped fluoride fiber lasers at mid-infrared wavebands, Q-switching with the pulse energy of 4.93 μJ and mode-locking with the pulse duration of 8.6 ps were obtained, respectively. The operation wavelength of ~2970 nm for generated pulse is the reported longest wavelength for BP SA based fiber lasers. PMID:27457338

Magnetic gates and guides for superconducting vortices

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

Vlasko-Vlasov, V. K.; Colauto, F.; Buzdin, A. I.

Here, we image the motion of superconducting vortices in niobium film covered with a regular array of thin permalloy stripes. By altering the magnetization orientation in the stripes using a small in-plane magnetic field, we can tune the strength of interactions between vortices and the stripe edges, enabling acceleration or retardation of the superconducting vortices in the sample and consequently introducing strong tunable anisotropy into the vortex dynamics. We discuss our observations in terms of the attraction/repulsion between point magnetic charges carried by vortices and lines of magnetic charges at the stripe edges, and derive analytical formulas for the vortex-magneticmore » stripes coupling. Our approach demonstrates the analogy between the vortex motion regulated by the magnetic stripe array and electric carrier flow in gated semiconducting devices. Scaling down the geometrical features of the proposed design may enable controlled manipulation of single vortices, paving the way for Abrikosov vortex microcircuits and memories.« less

Scattering engineering in continuously shaped metasurface: An approach for electromagnetic illusion

PubMed Central

Guo, Yinghui; Yan, Lianshan; Pan, Wei; Shao, Liyang

2016-01-01

The control of electromagnetic waves scattering is critical in wireless communications and stealth technology. Discrete metasurfaces not only increase the design and fabrication complex but also cause difficulties in obtaining simultaneous electric and optical functionality. On the other hand, discontinuous phase profiles fostered by discrete systems inevitably introduce phase noises to the scattering fields. Here we propose the principle of a scattering-harness mechanism by utilizing continuous gradient phase stemming from the spin-orbit interaction via sinusoidal metallic strips. Furthermore, by adjusting the amplitude and period of the sinusoidal metallic strip, the scattering characteristics of the underneath object can be greatly changed and thus result in electromagnetic illusion. The proposal is validated by full-wave simulations and experiment characterization in microwave band. Our approach featured by continuous phase profile, polarization independent performance and facile implementation may find widespread applications in electromagnetic wave manipulation. PMID:27439474

Weyl solitons in three-dimensional optical lattices

NASA Astrophysics Data System (ADS)

Shang, Ce; Zheng, Yuanlin; Malomed, Boris A.

2018-04-01

Weyl fermions are massless chiral quasiparticles existing in materials known as Weyl semimetals. Topological surface states, associated with the unusual electronic structure in the Weyl semimetals, have been recently demonstrated in linear systems. Ultracold atomic gases, featuring laser-assisted tunneling in three-dimensional optical lattices, can be used for the emulation of Weyl semimetals, including nonlinear effects induced by the collisional nonlinearity of atomic Bose-Einstein condensates. We demonstrate that this setting gives rise to topological states in the form of Weyl solitons at the surface of the underlying optical lattice. These nonlinear modes, being exceptionally robust, bifurcate from linear states for a given quasimomentum. The Weyl solitons may be used to design an efficient control scheme for topologically protected unidirectional propagation of excitations in light-matter-interaction physics. After the recently introduced Majorana and Dirac solitons, the Weyl solitons proposed in this work constitute the third (and the last) member in this family of topological solitons.

Importance-sampling computation of statistical properties of coupled oscillators

NASA Astrophysics Data System (ADS)

Gupta, Shamik; Leitão, Jorge C.; Altmann, Eduardo G.

2017-07-01

We introduce and implement an importance-sampling Monte Carlo algorithm to study systems of globally coupled oscillators. Our computational method efficiently obtains estimates of the tails of the distribution of various measures of dynamical trajectories corresponding to states occurring with (exponentially) small probabilities. We demonstrate the general validity of our results by applying the method to two contrasting cases: the driven-dissipative Kuramoto model, a paradigm in the study of spontaneous synchronization; and the conservative Hamiltonian mean-field model, a prototypical system of long-range interactions. We present results for the distribution of the finite-time Lyapunov exponent and a time-averaged order parameter. Among other features, our results show most notably that the distributions exhibit a vanishing standard deviation but a skewness that is increasing in magnitude with the number of oscillators, implying that nontrivial asymmetries and states yielding rare or atypical values of the observables persist even for a large number of oscillators.

Overview of the Helios Version 2.0 Computational Platform for Rotorcraft Simulations

NASA Technical Reports Server (NTRS)

Sankaran, Venkateswaran; Wissink, Andrew; Datta, Anubhav; Sitaraman, Jayanarayanan; Jayaraman, Buvna; Potsdam, Mark; Katz, Aaron; Kamkar, Sean; Roget, Beatrice; Mavriplis, Dimitri;

Scattering engineering in continuously shaped metasurface: An approach for electromagnetic illusion

NASA Astrophysics Data System (ADS)

Guo, Yinghui; Yan, Lianshan; Pan, Wei; Shao, Liyang

2016-07-01

The control of electromagnetic waves scattering is critical in wireless communications and stealth technology. Discrete metasurfaces not only increase the design and fabrication complex but also cause difficulties in obtaining simultaneous electric and optical functionality. On the other hand, discontinuous phase profiles fostered by discrete systems inevitably introduce phase noises to the scattering fields. Here we propose the principle of a scattering-harness mechanism by utilizing continuous gradient phase stemming from the spin-orbit interaction via sinusoidal metallic strips. Furthermore, by adjusting the amplitude and period of the sinusoidal metallic strip, the scattering characteristics of the underneath object can be greatly changed and thus result in electromagnetic illusion. The proposal is validated by full-wave simulations and experiment characterization in microwave band. Our approach featured by continuous phase profile, polarization independent performance and facile implementation may find widespread applications in electromagnetic wave manipulation.

Specific features of direct formation of graphite-like microstructures in polycarbonate samples by single femtosecond laser pulses

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

Ganin, D V; Lapshin, K E; Obidin, A Z

2015-11-30

We present the result of the experiments on producing graphite-like cylindrical microstructures by focusing single femtosecond laser pulses into the bulk of a transparent polymer (polycarbonate). The microstructures are embedded in a cladding with a modified refractive index, possessing waveguide properties. In the experiments with nontransparent screens and diaphragms, placed in the laser beam in front of the entrance pupil of the objective with a large numerical aperture, we have found that the paraxial rays are blocked by the peripheral ones, which reduces the length of the destruction region in the pre-focal zone. In the experiments with transparent screens andmore » diaphragms, introducing optical delays τ{sub d} between the paraxial and peripheral rays, the quantitative dependence of the destruction region length in the pre-focal zone on the value of τ{sub d} is determined. (interaction of laser radiation with matter. laser plasma)« less

Mexican-origin Early Adolescents’ Ethnic Socialization, Ethnic Identity, and Psychosocial Functioning

PubMed Central

Umaña-Taylor, Adriana J.; O’Donnell, Megan; Knight, George P.; Roosa, Mark W.; Berkel, Cady; Nair, Rajni

2013-01-01

The current study examined how parental ethnic socialization informed adolescents’ ethnic identity development and, in turn, youths’ psychosocial functioning (i.e., mental health, social competence, academic efficacy, externalizing behaviors) among 749 Mexican-origin families. In addition, school ethnic composition was examined as a moderator of these associations. Findings indicated that mothers’ and fathers’ ethnic socialization were significant longitudinal predictors of adolescents’ ethnic identity, although fathers’ ethnic socialization interacted significantly with youths’ school ethnic composition in 5th grade to influence ethnic identity in 7th grade. Furthermore, adolescents’ ethnic identity was significantly associated with increased academic self-efficacy and social competence, and decreased depressive symptoms and externalizing behaviors. Findings support theoretical predictions regarding the central role parents play in Mexican-origin adolescents’ normative developmental processes and adjustment and, importantly, underscore the need to consider variability that is introduced into these processes by features of the social context such as school ethnic composition. PMID:24465033

Deep Direct Reinforcement Learning for Financial Signal Representation and Trading.

PubMed

Deng, Yue; Bao, Feng; Kong, Youyong; Ren, Zhiquan; Dai, Qionghai

2017-03-01

Can we train the computer to beat experienced traders for financial assert trading? In this paper, we try to address this challenge by introducing a recurrent deep neural network (NN) for real-time financial signal representation and trading. Our model is inspired by two biological-related learning concepts of deep learning (DL) and reinforcement learning (RL). In the framework, the DL part automatically senses the dynamic market condition for informative feature learning. Then, the RL module interacts with deep representations and makes trading decisions to accumulate the ultimate rewards in an unknown environment. The learning system is implemented in a complex NN that exhibits both the deep and recurrent structures. Hence, we propose a task-aware backpropagation through time method to cope with the gradient vanishing issue in deep training. The robustness of the neural system is verified on both the stock and the commodity future markets under broad testing conditions.

Adverse outcome pathway networks II: Network analytics.

PubMed

Villeneuve, Daniel L; Angrish, Michelle M; Fortin, Marie C; Katsiadaki, Ioanna; Leonard, Marc; Margiotta-Casaluci, Luigi; Munn, Sharon; O'Brien, Jason M; Pollesch, Nathan L; Smith, L Cody; Zhang, Xiaowei; Knapen, Dries

2018-06-01

Toxicological responses to stressors are more complex than the simple one-biological-perturbation to one-adverse-outcome model portrayed by individual adverse outcome pathways (AOPs). Consequently, the AOP framework was designed to facilitate de facto development of AOP networks that can aid in the understanding and prediction of pleiotropic and interactive effects more common to environmentally realistic, complex exposure scenarios. The present study introduces nascent concepts related to the qualitative analysis of AOP networks. First, graph theory-based approaches for identifying important topological features are illustrated using 2 example AOP networks derived from existing AOP descriptions. Second, considerations for identifying the most significant path(s) through an AOP network from either a biological or risk assessment perspective are described. Finally, approaches for identifying interactions among AOPs that may result in additive, synergistic, or antagonistic responses (or previously undefined emergent patterns of response) are introduced. Along with a companion article (part I), these concepts set the stage for the development of tools and case studies that will facilitate more rigorous analysis of AOP networks, and the utility of AOP network-based predictions, for use in research and regulatory decision-making. The present study addresses one of the major themes identified through a Society of Environmental Toxicology and Chemistry Horizon Scanning effort focused on advancing the AOP framework. Environ Toxicol Chem 2018;37:1734-1748. © 2018 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. © 2018 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

Broadening the cofactor specificity of a thermostable alcohol dehydrogenase using rational protein design introduces novel kinetic transient behavior.

PubMed

Campbell, Elliot; Wheeldon, Ian R; Banta, Scott

2010-12-01

Cofactor specificity in the aldo-keto reductase (AKR) superfamily has been well studied, and several groups have reported the rational alteration of cofactor specificity in these enzymes. Although most efforts have focused on mesostable AKRs, several putative AKRs have recently been identified from hyperthermophiles. The few that have been characterized exhibit a strong preference for NAD(H) as a cofactor, in contrast to the NADP(H) preference of the mesophilic AKRs. Using the design rules elucidated from mesostable AKRs, we introduced two site-directed mutations in the cofactor binding pocket to investigate cofactor specificity in a thermostable AKR, AdhD, which is an alcohol dehydrogenase from Pyrococcus furiosus. The resulting double mutant exhibited significantly improved activity and broadened cofactor specificity as compared to the wild-type. Results of previous pre-steady-state kinetic experiments suggest that the high affinity of the mesostable AKRs for NADP(H) stems from a conformational change upon cofactor binding which is mediated by interactions between a canonical arginine and the 2'-phosphate of the cofactor. Pre-steady-state kinetics with AdhD and the new mutants show a rich conformational behavior that is independent of the canonical arginine or the 2'-phosphate. Additionally, experiments with the highly active double mutant using NADPH as a cofactor demonstrate an unprecedented transient behavior where the binding mechanism appears to be dependent on cofactor concentration. These results suggest that the structural features involved in cofactor specificity in the AKRs are conserved within the superfamily, but the dynamic interactions of the enzyme with cofactors are unexpectedly complex. © 2010 Wiley Periodicals, Inc.

Development and utilization of a web-based application as a robust radiology teaching tool (radstax) for medical student anatomy teaching.

PubMed

Colucci, Philip G; Kostandy, Petro; Shrauner, William R; Arleo, Elizabeth; Fuortes, Michele; Griffin, Andrew S; Huang, Yun-Han; Juluru, Krishna; Tsiouris, Apostolos John

2015-02-01

Rationale and Objectives: The primary role of radiology in the preclinical setting is the use of imaging to improve students' understanding of anatomy. Many currently available Web-based anatomy programs include either suboptimal or overwhelming levels of detail for medical students.Our objective was to develop a user-friendly software program that anatomy instructors can completely tailor to match the desired level of detail for their curriculum, meets the unique needs of the first- and the second-year medical students, and is compatible with most Internet browsers and tablets.Materials and Methods: RadStax is a Web-based application developed using free, open-source, ubiquitous software. RadStax was first introduced as an interactive resource for independent study and later incorporated into lectures. First- and second-year medical students were surveyed for quantitative feedback regarding their experience.Results: RadStax was successfully introduced into our medical school curriculum. It allows the creation of learning modules with labeled multiplanar (MPR) image sets, basic anatomic information, and a self-assessment feature. The program received overwhelmingly positive feedback from students. Of 115 students surveyed, 87.0% found it highly effective as a study tool and 85.2% reported high user satisfaction with the program.Conclusions: RadStax is a novel application for instructors wishing to create an atlas of labeled MPR radiologic studies tailored to meet the specific needs their curriculum. Simple and focused, it provides an interactive experience for students similar to the practice of radiologists.This program is a robust anatomy teaching tool that effectively aids in educating the preclinical medical student.

Development and Utilization of a Web-Based Application as a Robust Radiology Teaching Tool (RadStax) for Medical Student Anatomy Teaching

PubMed Central

Colucci, Philip G.; Kostandy, Petro; Shrauner, William R.; Arleo, Elizabeth; Fuortes, Michele; Griffin, Andrew S.; Huang, Yun-Han; Juluru, Krishna; Tsiouris, Apostolos John

2016-01-01

Rationale and Objectives The primary role of radiology in the preclinical setting is the use of imaging to improve students’ understanding of anatomy. Many currently available Web-based anatomy programs include either suboptimal or overwhelming levels of detail for medical students. Our objective was to develop a user-friendly software program that anatomy instructors can completely tailor to match the desired level of detail for their curriculum, meets the unique needs of the first- and the second-year medical students, and is compatible with most Internet browsers and tablets. Materials and Methods RadStax is a Web-based application developed using free, open-source, ubiquitous software. RadStax was first introduced as an interactive resource for independent study and later incorporated into lectures. First- and second-year medical students were surveyed for quantitative feedback regarding their experience. Results RadStax was successfully introduced into our medical school curriculum. It allows the creation of learning modules with labeled multiplanar (MPR) image sets, basic anatomic information, and a self-assessment feature. The program received overwhelmingly positive feedback from students. Of 115 students surveyed, 87.0% found it highly effective as a study tool and 85.2% reported high user satisfaction with the program. Conclusions RadStax is a novel application for instructors wishing to create an atlas of labeled MPR radiologic studies tailored to meet the specific needs their curriculum. Simple and focused, it provides an interactive experience for students similar to the practice of radiologists. This program is a robust anatomy teaching tool that effectively aids in educating the preclinical medical student. PMID:25964956

Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

PubMed

Sun, Yunxiang; Ming, Dengming

2014-01-01

Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

Recognition of blurred images by the method of moments.

PubMed

Flusser, J; Suk, T; Saic, S

1996-01-01

The article is devoted to the feature-based recognition of blurred images acquired by a linear shift-invariant imaging system against an image database. The proposed approach consists of describing images by features that are invariant with respect to blur and recognizing images in the feature space. The PSF identification and image restoration are not required. A set of symmetric blur invariants based on image moments is introduced. A numerical experiment is presented to illustrate the utilization of the invariants for blurred image recognition. Robustness of the features is also briefly discussed.

Acorns Alive.

ERIC Educational Resources Information Center

Matthews, Catherine; Vickers, Valerie; Patrick, Patricia

2002-01-01

Introduces a lesson plan on the role of the acorn and its complex community of biotic relationships between animal and fungal organisms. Introduces students to ecological concepts through acorn investigations including dissection of acorns and exploring the organisms' interaction web. (YDS)

Feature Interactions Enable Decoding of Sensorimotor Transformations for Goal-Directed Movement

PubMed Central

Barany, Deborah A.; Della-Maggiore, Valeria; Viswanathan, Shivakumar; Cieslak, Matthew

2014-01-01

Neurophysiology and neuroimaging evidence shows that the brain represents multiple environmental and body-related features to compute transformations from sensory input to motor output. However, it is unclear how these features interact during goal-directed movement. To investigate this issue, we examined the representations of sensory and motor features of human hand movements within the left-hemisphere motor network. In a rapid event-related fMRI design, we measured cortical activity as participants performed right-handed movements at the wrist, with either of two postures and two amplitudes, to move a cursor to targets at different locations. Using a multivoxel analysis technique with rigorous generalization tests, we reliably distinguished representations of task-related features (primarily target location, movement direction, and posture) in multiple regions. In particular, we identified an interaction between target location and movement direction in the superior parietal lobule, which may underlie a transformation from the location of the target in space to a movement vector. In addition, we found an influence of posture on primary motor, premotor, and parietal regions. Together, these results reveal the complex interactions between different sensory and motor features that drive the computation of sensorimotor transformations. PMID:24828640

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

Circuit variability interacts with excitatory-inhibitory diversity of interneurons to regulate network encoding capacity.

PubMed

Tsai, Kuo-Ting; Hu, Chin-Kun; Li, Kuan-Wei; Hwang, Wen-Liang; Chou, Ya-Hui

2018-05-23

Local interneurons (LNs) in the Drosophila olfactory system exhibit neuronal diversity and variability, yet it is still unknown how these features impact information encoding capacity and reliability in a complex LN network. We employed two strategies to construct a diverse excitatory-inhibitory neural network beginning with a ring network structure and then introduced distinct types of inhibitory interneurons and circuit variability to the simulated network. The continuity of activity within the node ensemble (oscillation pattern) was used as a readout to describe the temporal dynamics of network activity. We found that inhibitory interneurons enhance the encoding capacity by protecting the network from extremely short activation periods when the network wiring complexity is very high. In addition, distinct types of interneurons have differential effects on encoding capacity and reliability. Circuit variability may enhance the encoding reliability, with or without compromising encoding capacity. Therefore, we have described how circuit variability of interneurons may interact with excitatory-inhibitory diversity to enhance the encoding capacity and distinguishability of neural networks. In this work, we evaluate the effects of different types and degrees of connection diversity on a ring model, which may simulate interneuron networks in the Drosophila olfactory system or other biological systems.

Trail networks formed by populations of immune cells

NASA Astrophysics Data System (ADS)

Yang, Taeseok Daniel; Kwon, Tae Goo; Park, Jin-sung; Lee, Kyoung J.

2014-02-01

Populations of biological cells that communicate with each other can organize themselves to generate large-scale patterns. Examples can be found in diverse systems, ranging from developing embryos, cardiac tissues, chemotaxing ameba and swirling bacteria. The similarity, often shared by the patterns, suggests the existence of some general governing principle. On the other hand, rich diversity and system-specific properties are exhibited, depending on the type of involved cells and the nature of their interactions. The study on the similarity and the diversity constitutes a rapidly growing field of research. Here, we introduce a new class of self-organized patterns of cell populations that we term as ‘cellular trail networks’. They were observed with populations of rat microglia, the immune cells of the brain and the experimental evidence suggested that haptotaxis is the key element responsible for them. The essential features of the observed patterns are well captured by the mathematical model cells that actively crawl and interact with each other through a decomposing but non-diffusing chemical attractant laid down by the cells. Our finding suggests an unusual mechanism of socially cooperative long-range signaling for the crawling immune cells.

Dynamics of elastic systems

NASA Astrophysics Data System (ADS)

Sankovich, Vladimir

1998-12-01

The goal of this paper is to build a consistent physical theory of the dynamics of the bat-ball interaction. This requires creating realistic models for both the softball bat and the softball. Some of the features of these models are known phenomenologically, from experiments conducted in our laboratory, others will be introduced and computed from first principles here for the first time. Both interacting objects are treated from the viewpoint of the theory of elasticity, and it is shown how a computer can be used to accurately calculate all the relevant characteristics of batball collisions. It is shown also how the major elastic parameters of the material constituting the interior of a softball can be determined using the existing experimental data. These parameters, such as the Young's modulus, the Poisson ratio and the damping coefficient are vital for the accurate description of the ball's dynamics. We are demonstrating how the existing theories of the elastic behavior of solid bars and hollow shells can be augmented to simplify the resulting equations and make the subsequent computer analysis feasible. The standard system of fourth-order PDE's is reduced to a system of the second order, because of the inclusion of the usually ignored effects of the shear forces in the bat.