Hierarchical Neural Representation of Dreamed Objects Revealed by Brain Decoding with Deep Neural Network Features.

Science.gov (United States)

Horikawa, Tomoyasu; Kamitani, Yukiyasu

2017-01-01

Dreaming is generally thought to be generated by spontaneous brain activity during sleep with patterns common to waking experience. This view is supported by a recent study demonstrating that dreamed objects can be predicted from brain activity during sleep using statistical decoders trained with stimulus-induced brain activity. However, it remains unclear whether and how visual image features associated with dreamed objects are represented in the brain. In this study, we used a deep neural network (DNN) model for object recognition as a proxy for hierarchical visual feature representation, and DNN features for dreamed objects were analyzed with brain decoding of fMRI data collected during dreaming. The decoders were first trained with stimulus-induced brain activity labeled with the feature values of the stimulus image from multiple DNN layers. The decoders were then used to decode DNN features from the dream fMRI data, and the decoded features were compared with the averaged features of each object category calculated from a large-scale image database. We found that the feature values decoded from the dream fMRI data positively correlated with those associated with dreamed object categories at mid- to high-level DNN layers. Using the decoded features, the dreamed object category could be identified at above-chance levels by matching them to the averaged features for candidate categories. The results suggest that dreaming recruits hierarchical visual feature representations associated with objects, which may support phenomenal aspects of dream experience.

Inferring the conservative causal core of gene regulatory networks

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Emmert-Streib Frank

2010-09-01

Full Text Available Abstract Background Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically. Results In this paper, we introduce a novel gene regulatory network inference (GRNI algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently. Conclusions For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.

Inferring the conservative causal core of gene regulatory networks.

Science.gov (United States)

Altay, Gökmen; Emmert-Streib, Frank

2010-09-28

Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically. In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently. For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.

A new asynchronous parallel algorithm for inferring large-scale gene regulatory networks.

Directory of Open Access Journals (Sweden)

Xiangyun Xiao

Full Text Available The reconstruction of gene regulatory networks (GRNs from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM, experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.

A new asynchronous parallel algorithm for inferring large-scale gene regulatory networks.

Science.gov (United States)

Xiao, Xiangyun; Zhang, Wei; Zou, Xiufen

2015-01-01

The reconstruction of gene regulatory networks (GRNs) from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE)-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM), experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.

Fused Regression for Multi-source Gene Regulatory Network Inference.

Directory of Open Access Journals (Sweden)

Kari Y Lam

2016-12-01

Full Text Available Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression. This approach improves network inference performance even when orthology mapping and conservation are incomplete. We refine this method by presenting an algorithm that extracts the true conserved subnetwork from a larger set of potentially conserved interactions and demonstrate the utility of our method in cross species network inference. Last, we demonstrate our method's utility in learning from data collected on different experimental platforms.

Compiling Relational Bayesian Networks for Exact Inference

DEFF Research Database (Denmark)

Jaeger, Manfred; Chavira, Mark; Darwiche, Adnan

2004-01-01

We describe a system for exact inference with relational Bayesian networks as defined in the publicly available \\primula\\ tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference by evaluating...

When dreaming is believing: the (motivated) interpretation of dreams.

Science.gov (United States)

Morewedge, Carey K; Norton, Michael I

2009-02-01

This research investigated laypeople's interpretation of their dreams. Participants from both Eastern and Western cultures believed that dreams contain hidden truths (Study 1) and considered dreams to provide more meaningful information about the world than similar waking thoughts (Studies 2 and 3). The meaningfulness attributed to specific dreams, however, was moderated by the extent to which the content of those dreams accorded with participants' preexisting beliefs--from the theories they endorsed to attitudes toward acquaintances, relationships with friends, and faith in God (Studies 3-6). Finally, dream content influenced judgment: Participants reported greater affection for a friend after considering a dream in which a friend protected rather than betrayed them (Study 5) and were equally reluctant to fly after dreaming or learning of a plane crash (Studies 2 and 3). Together, these results suggest that people engage in motivated interpretation of their dreams and that these interpretations impact their everyday lives.

Compiling Relational Bayesian Networks for Exact Inference

DEFF Research Database (Denmark)

Jaeger, Manfred; Darwiche, Adnan; Chavira, Mark

2006-01-01

We describe in this paper a system for exact inference with relational Bayesian networks as defined in the publicly available PRIMULA tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference...

An algebra-based method for inferring gene regulatory networks.

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Vera-Licona, Paola; Jarrah, Abdul; Garcia-Puente, Luis David; McGee, John; Laubenbacher, Reinhard

2014-03-26

The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that infer network dynamics. Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models. Finally, it is also important to have an understanding of how a given inference method is affected by experimental and other noise in the data used. This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and recall for the network reconstruction task, while also predicting several of the

An analysis pipeline for the inference of protein-protein interaction networks

Energy Technology Data Exchange (ETDEWEB)

Taylor, Ronald C.; Singhal, Mudita; Daly, Don S.; Gilmore, Jason M.; Cannon, William R.; Domico, Kelly O.; White, Amanda M.; Auberry, Deanna L.; Auberry, Kenneth J.; Hooker, Brian S.; Hurst, G. B.; McDermott, Jason E.; McDonald, W. H.; Pelletier, Dale A.; Schmoyer, Denise A.; Wiley, H. S.

2009-12-01

An analysis pipeline has been created for deployment of a novel algorithm, the Bayesian Estimator of Protein-Protein Association Probabilities (BEPro), for use in the reconstruction of protein-protein interaction networks. We have combined the Software Environment for BIological Network Inference (SEBINI), an interactive environment for the deployment and testing of network inference algorithms that use high-throughput data, and the Collective Analysis of Biological Interaction Networks (CABIN), software that allows integration and analysis of protein-protein interaction and gene-to-gene regulatory evidence obtained from multiple sources, to allow interactions computed by BEPro to be stored, visualized, and further analyzed. Incorporating BEPro into SEBINI and automatically feeding the resulting inferred network into CABIN, we have created a structured workflow for protein-protein network inference and supplemental analysis from sets of mass spectrometry bait-prey experiment data. SEBINI demo site: https://www.emsl.pnl.gov /SEBINI/ Contact: ronald.taylor@pnl.gov. BEPro is available at http://www.pnl.gov/statistics/BEPro3/index.htm. Contact: ds.daly@pnl.gov. CABIN is available at http://www.sysbio.org/dataresources/cabin.stm. Contact: mudita.singhal@pnl.gov.

Dream Skepticism and the Conditionality Problem

DEFF Research Database (Denmark)

Ahlström, Kristoffer

2011-01-01

Recently, Ernest Sosa (2007) has proposed two novel solutions to the problem of dream skepticism. In the present paper, I argue that Sosa's first solution falls prey to what I will refer to as the conditionality problem, i.e., the problem of only establishing a conditional---in this case, "if x......, then I am awake," x being a placeholder for a condition incompatible with dreaming---in a context where it also needs to be established that we can know that the antecedent holds, and as such can infer the consequent, i.e., "I am awake." Sosa's second solution in terms of so-called reflective knowledge......, I conclude that Sosa has not solved the problem of dream skepticism....

Dearfield Dream Project: Developing an Interdisciplinary Historical/Cultural Research Network

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Robert Brunswig

2013-08-01

Full Text Available The Dearfield Dream Project is a collaborative research initiative to conduct historical, cultural, archaeological, and environmental studies on the early 20th Century African-American colony site of Dearfield, Colorado, USA. Because the breadth and significance of the Dearfield Project requires an interdisciplinary research team, a network of research collaborators has been assembled. This research network seeks to discover, preserve, and disseminate knowledge of the site and its surrounding farmsteads’ economic, social, political, and environmental history for better understanding and interpretation of its contributions to Colorado and U.S. history. Herein, we detail progress that has been made on this important historical/cultural research project. Further, we outline the future of the Dearfield research network along with our current and anticipated subjects of inquiry.

Dopaminergic system and dream recall: An MRI study in Parkinson's disease patients.

Science.gov (United States)

De Gennaro, Luigi; Lanteri, Olimpia; Piras, Fabrizio; Scarpelli, Serena; Assogna, Francesca; Ferrara, Michele; Caltagirone, Carlo; Spalletta, Gianfranco

2016-03-01

We investigated the role of the dopamine system [i.e., subcortical-medial prefrontal cortex (mPFC) network] in dreaming, by studying patients with Parkinson's Disease (PD) as a model of altered dopaminergic transmission. Subcortical volumes and cortical thickness were extracted by 3T-MR images of 27 PD patients and 27 age-matched controls, who were asked to fill out a dream diary upon morning awakening for one week. PD patients do not substantially differ from healthy controls with respect to the sleep, dream, and neuroanatomical measures. Multivariate correlational analyses in PD patients show that dopamine agonist dosage is associated to qualitatively impoverished dreams, as expressed by lower bizarreness and lower emotional load values. Visual vividness (VV) of their dream reports positively correlates with volumes of both the amygdalae and with thickness of the left mPFC. Emotional load also positively correlates with hippocampal volume. Beside the replication of our previous finding on the role of subcortical nuclei in dreaming experience of healthy subjects, this represents the first evidence of a specific role of the amygdala-mPFC dopaminergic network system in dream recall. The association in PD patients between higher dopamine agonist dosages and impoverished dream reports, however, and the significant correlations between VV and mesolimbic regions, however, provide an empirical support to the hypothesis that a dopamine network plays a key role in dream generation. The causal relation is however precluded by the intrinsic limitation of assuming the dopamine agonist dosage as a measure of the hypodopaminergic state in PD. Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Inferring epidemic network topology from surveillance data.

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Xiang Wan

Full Text Available The transmission of infectious diseases can be affected by many or even hidden factors, making it difficult to accurately predict when and where outbreaks may emerge. One approach at the moment is to develop and deploy surveillance systems in an effort to detect outbreaks as timely as possible. This enables policy makers to modify and implement strategies for the control of the transmission. The accumulated surveillance data including temporal, spatial, clinical, and demographic information, can provide valuable information with which to infer the underlying epidemic networks. Such networks can be quite informative and insightful as they characterize how infectious diseases transmit from one location to another. The aim of this work is to develop a computational model that allows inferences to be made regarding epidemic network topology in heterogeneous populations. We apply our model on the surveillance data from the 2009 H1N1 pandemic in Hong Kong. The inferred epidemic network displays significant effect on the propagation of infectious diseases.

Testing the implicit processing hypothesis of precognitive dream experience.

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Valášek, Milan; Watt, Caroline; Hutton, Jenny; Neill, Rebecca; Nuttall, Rachel; Renwick, Grace

2014-08-01

Seemingly precognitive (prophetic) dreams may be a result of one's unconscious processing of environmental cues and having an implicit inference based on these cues manifest itself in one's dreams. We present two studies exploring this implicit processing hypothesis of precognitive dream experience. Study 1 investigated the relationship between implicit learning, transliminality, and precognitive dream belief and experience. Participants completed the Serial Reaction Time task and several questionnaires. We predicted a positive relationship between the variables. With the exception of relationships between transliminality and precognitive dream belief and experience, this prediction was not supported. Study 2 tested the hypothesis that differences in the ability to notice subtle cues explicitly might account for precognitive dream beliefs and experiences. Participants completed a modified version of the flicker paradigm. We predicted a negative relationship between the ability to explicitly detect changes and precognitive dream variables. This relationship was not found. There was also no relationship between precognitive dream belief and experience and implicit change detection. Copyright © 2014 Elsevier Inc. All rights reserved.

Bayesian Inference and Online Learning in Poisson Neuronal Networks.

Science.gov (United States)

Huang, Yanping; Rao, Rajesh P N

2016-08-01

Motivated by the growing evidence for Bayesian computation in the brain, we show how a two-layer recurrent network of Poisson neurons can perform both approximate Bayesian inference and learning for any hidden Markov model. The lower-layer sensory neurons receive noisy measurements of hidden world states. The higher-layer neurons infer a posterior distribution over world states via Bayesian inference from inputs generated by sensory neurons. We demonstrate how such a neuronal network with synaptic plasticity can implement a form of Bayesian inference similar to Monte Carlo methods such as particle filtering. Each spike in a higher-layer neuron represents a sample of a particular hidden world state. The spiking activity across the neural population approximates the posterior distribution over hidden states. In this model, variability in spiking is regarded not as a nuisance but as an integral feature that provides the variability necessary for sampling during inference. We demonstrate how the network can learn the likelihood model, as well as the transition probabilities underlying the dynamics, using a Hebbian learning rule. We present results illustrating the ability of the network to perform inference and learning for arbitrary hidden Markov models.

Inference in hybrid Bayesian networks

DEFF Research Database (Denmark)

Lanseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

2009-01-01

Since the 1980s, Bayesian Networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability-techniques (like fault trees...... decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability....

The China Dream and the American Dream

Institute of Scientific and Technical Information of China (English)

WILLIAM; A.CALLAHAN

2014-01-01

Since Xi Jinping invoked"The China Dream"as a key concept in November 2012,this phrase has come to dominate discussions of China’s future.This paper will examine the China dream phenomenon first by placing it in the context of debates that have been raging in Chinese civil society over the past few years.It will analyze the works of20 prominent"China dreamers"in terms of debates over the proper relationship between(1)politics and economics,(2)equality and hierarchy,(3)civilization and civility,and(4)nationalism and statism.The other main context for the China dream concept is the American dream.While it is common to dismiss the American dream as crass materialism,this essay will examine how it stresses the complementary ideals of freedom and equality.More importantly,it will examine how the American dream has been used as a critical tool to comment on problems in the United States,and relate this to examples in the PRC where the China dream is being used as a critical tool as well.

The China Dream and the American Dream

Institute of Scientific and Technical Information of China (English)

WILLIAM A.CALLAHAN

2014-01-01

Since Xi Jinping invoked "The China Dream" as a key concept in November 2012,this phrase has come to dominate discussions of China's future.This paper will examine the China dream phenomenon first by placing it in the context of debates that have been raging in Chinese civil society over the past few years.It will analyze the works of 20 prominent "China dreamers" in terms of debates over the proper relationship between (1) politics and economics,(2) equality and hierarchy,(3) civilization and civility,and (4) nationalism and statism.The other main context for the China dream concept is the American dream.While it is common to dismiss the American dream as crass materialism,this essay will examine how it stresses the complementary (i)deals of freedom and equality.More importantly,it will examine how the American dream has been used as a critical tool to comment on problems in the United States,and relate this to examples in the PRC where the China dream is being used as a critical tool as well.

Inferring time-varying network topologies from gene expression data.

Science.gov (United States)

Rao, Arvind; Hero, Alfred O; States, David J; Engel, James Douglas

2007-01-01

Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has been a need to infer and represent networks in a dynamic, that is, time-varying fashion, in order to account for different cellular states affecting the interactions amongst genes. In this work, we present an approach, regime-SSM, to understand gene regulatory networks within such a dynamic setting. The approach uses a clustering method based on these underlying dynamics, followed by system identification using a state-space model for each learnt cluster--to infer a network adjacency matrix. We finally indicate our results on the mouse embryonic kidney dataset as well as the T-cell activation-based expression dataset and demonstrate conformity with reported experimental evidence.

A Bayesian Network Schema for Lessening Database Inference

National Research Council Canada - National Science Library

Chang, LiWu; Moskowitz, Ira S

2001-01-01

.... The authors introduce a formal schema for database inference analysis, based upon a Bayesian network structure, which identifies critical parameters involved in the inference problem and represents...

An Intuitive Dashboard for Bayesian Network Inference

International Nuclear Information System (INIS)

Reddy, Vikas; Farr, Anna Charisse; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K D V

2014-01-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++

An Intuitive Dashboard for Bayesian Network Inference

Science.gov (United States)

Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

2014-03-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors

Directory of Open Access Journals (Sweden)

Frank Emmert-Streib

2013-02-01

Full Text Available The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I observational gene expression data: normal environmental condition, (II interventional gene expression data: growth in rich media, (III interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.

Information-Theoretic Inference of Large Transcriptional Regulatory Networks

Directory of Open Access Journals (Sweden)

Meyer Patrick

2007-01-01

Full Text Available The paper presents MRNET, an original method for inferring genetic networks from microarray data. The method is based on maximum relevance/minimum redundancy (MRMR, an effective information-theoretic technique for feature selection in supervised learning. The MRMR principle consists in selecting among the least redundant variables the ones that have the highest mutual information with the target. MRNET extends this feature selection principle to networks in order to infer gene-dependence relationships from microarray data. The paper assesses MRNET by benchmarking it against RELNET, CLR, and ARACNE, three state-of-the-art information-theoretic methods for large (up to several thousands of genes network inference. Experimental results on thirty synthetically generated microarray datasets show that MRNET is competitive with these methods.

Information-Theoretic Inference of Large Transcriptional Regulatory Networks

Directory of Open Access Journals (Sweden)

Patrick E. Meyer

2007-06-01

Full Text Available The paper presents MRNET, an original method for inferring genetic networks from microarray data. The method is based on maximum relevance/minimum redundancy (MRMR, an effective information-theoretic technique for feature selection in supervised learning. The MRMR principle consists in selecting among the least redundant variables the ones that have the highest mutual information with the target. MRNET extends this feature selection principle to networks in order to infer gene-dependence relationships from microarray data. The paper assesses MRNET by benchmarking it against RELNET, CLR, and ARACNE, three state-of-the-art information-theoretic methods for large (up to several thousands of genes network inference. Experimental results on thirty synthetically generated microarray datasets show that MRNET is competitive with these methods.

Resting brain activity varies with dream recall frequency between subjects.

Science.gov (United States)

Eichenlaub, Jean-Baptiste; Nicolas, Alain; Daltrozzo, Jérôme; Redouté, Jérôme; Costes, Nicolas; Ruby, Perrine

2014-06-01

Dreaming is still poorly understood. Notably, its cerebral underpinning remains unclear. Neuropsychological studies have shown that lesions in the temporoparietal junction (TPJ) and/or the white matter of the medial prefrontal cortex (MPFC) lead to the global cessation of dream reports, suggesting that these regions of the default mode network have key roles in the dreaming process (forebrain 'dream-on' hypothesis). To test this hypothesis, we measured regional cerebral blood flow (rCBF) using [(15)O]H2O positron emission tomography in healthy subjects with high and low dream recall frequencies (DRFs) during wakefulness (rest) and sleep (rapid eye movement (REM) sleep, N2, and N3). Compared with Low recallers (0.5 ± 0.3 dream recall per week in average), High recallers (5.2 ± 1.4) showed higher rCBF in the TPJ during REM sleep, N3, and wakefulness, and in the MPFC during REM sleep and wakefulness. We demonstrate that the resting states of High recallers and Low recallers differ during sleep and wakefulness. It coheres with previous ERP results and confirms that a high/low DRF is associated with a specific functional organization of the brain. These results support the forebrain 'dream-on' hypothesis and suggest that TPJ and MPFC are not only involved in dream recall during wakefulness but also have a role in dreaming during sleep (production and/or encoding). Increased activity in the TPJ and MPFC might promote the mental imagery and/or memory encoding of dreams. Notably, increased activity in TPJ might facilitate attention orienting toward external stimuli and promote intrasleep wakefulness, facilitating the encoding of the dreams in memory.

Gene regulatory network inference by point-based Gaussian approximation filters incorporating the prior information.

Science.gov (United States)

Jia, Bin; Wang, Xiaodong

2013-12-17

: The extended Kalman filter (EKF) has been applied to inferring gene regulatory networks. However, it is well known that the EKF becomes less accurate when the system exhibits high nonlinearity. In addition, certain prior information about the gene regulatory network exists in practice, and no systematic approach has been developed to incorporate such prior information into the Kalman-type filter for inferring the structure of the gene regulatory network. In this paper, an inference framework based on point-based Gaussian approximation filters that can exploit the prior information is developed to solve the gene regulatory network inference problem. Different point-based Gaussian approximation filters, including the unscented Kalman filter (UKF), the third-degree cubature Kalman filter (CKF3), and the fifth-degree cubature Kalman filter (CKF5) are employed. Several types of network prior information, including the existing network structure information, sparsity assumption, and the range constraint of parameters, are considered, and the corresponding filters incorporating the prior information are developed. Experiments on a synthetic network of eight genes and the yeast protein synthesis network of five genes are carried out to demonstrate the performance of the proposed framework. The results show that the proposed methods provide more accurate inference results than existing methods, such as the EKF and the traditional UKF.

A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium

Energy Technology Data Exchange (ETDEWEB)

Taylor, Ronald C.; Singhal, Mudita; Weller, Jennifer B.; Khoshnevis, Saeed; Shi, Liang; McDermott, Jason E.

2009-04-20

Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene expression data now available for that organism, and describe our results obtained by following this workflow. The primary tool is one of the network inference algorithms deployed in the Software Environment for BIological Network Inference (SEBINI). Specifically, we selected the algorithm called Context Likelihood of Relatedness (CLR), which uses the mutual information contained in the gene expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological of Biological Interaction Networks (CABIN) tool for further post-analysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.

Inferring network structure from cascades

Science.gov (United States)

Ghonge, Sushrut; Vural, Dervis Can

2017-07-01

Many physical, biological, and social phenomena can be described by cascades taking place on a network. Often, the activity can be empirically observed, but not the underlying network of interactions. In this paper we offer three topological methods to infer the structure of any directed network given a set of cascade arrival times. Our formulas hold for a very general class of models where the activation probability of a node is a generic function of its degree and the number of its active neighbors. We report high success rates for synthetic and real networks, for several different cascade models.

Inferring network topology from complex dynamics

International Nuclear Information System (INIS)

Shandilya, Srinivas Gorur; Timme, Marc

2011-01-01

Inferring the network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method for inferring the structural connection topology of a network, given an observation of one collective dynamical trajectory. The general theoretical framework is applicable to arbitrary network dynamical systems described by ordinary differential equations. No interference (external driving) is required and the type of dynamics is hardly restricted in any way. In particular, the observed dynamics may be arbitrarily complex; stationary, invariant or transient; synchronous or asynchronous and chaotic or periodic. Presupposing a knowledge of the functional form of the dynamical units and of the coupling functions between them, we present an analytical solution to the inverse problem of finding the network topology from observing a time series of state variables only. Robust reconstruction is achieved in any sufficiently long generic observation of the system. We extend our method to simultaneously reconstructing both the entire network topology and all parameters appearing linear in the system's equations of motion. Reconstruction of network topology and system parameters is viable even in the presence of external noise that distorts the original dynamics substantially. The method provides a conceptually new step towards reconstructing a variety of real-world networks, including gene and protein interaction networks and neuronal circuits.

Congested Link Inference Algorithms in Dynamic Routing IP Network

Directory of Open Access Journals (Sweden)

Yu Chen

2017-01-01

Full Text Available The performance descending of current congested link inference algorithms is obviously in dynamic routing IP network, such as the most classical algorithm CLINK. To overcome this problem, based on the assumptions of Markov property and time homogeneity, we build a kind of Variable Structure Discrete Dynamic Bayesian (VSDDB network simplified model of dynamic routing IP network. Under the simplified VSDDB model, based on the Bayesian Maximum A Posteriori (BMAP and Rest Bayesian Network Model (RBNM, we proposed an Improved CLINK (ICLINK algorithm. Considering the concurrent phenomenon of multiple link congestion usually happens, we also proposed algorithm CLILRS (Congested Link Inference algorithm based on Lagrangian Relaxation Subgradient to infer the set of congested links. We validated our results by the experiments of analogy, simulation, and actual Internet.

Causal Inference and Explaining Away in a Spiking Network

Science.gov (United States)

Moreno-Bote, Rubén; Drugowitsch, Jan

2015-01-01

While the brain uses spiking neurons for communication, theoretical research on brain computations has mostly focused on non-spiking networks. The nature of spike-based algorithms that achieve complex computations, such as object probabilistic inference, is largely unknown. Here we demonstrate that a family of high-dimensional quadratic optimization problems with non-negativity constraints can be solved exactly and efficiently by a network of spiking neurons. The network naturally imposes the non-negativity of causal contributions that is fundamental to causal inference, and uses simple operations, such as linear synapses with realistic time constants, and neural spike generation and reset non-linearities. The network infers the set of most likely causes from an observation using explaining away, which is dynamically implemented by spike-based, tuned inhibition. The algorithm performs remarkably well even when the network intrinsically generates variable spike trains, the timing of spikes is scrambled by external sources of noise, or the network is mistuned. This type of network might underlie tasks such as odor identification and classification. PMID:26621426

Facility Activity Inference Using Radiation Networks

Energy Technology Data Exchange (ETDEWEB)

Rao, Nageswara S. [ORNL; Ramirez Aviles, Camila A. [ORNL

2017-11-01

We consider the problem of inferring the operational status of a reactor facility using measurements from a radiation sensor network deployed around the facility’s ventilation off-gas stack. The intensity of stack emissions decays with distance, and the sensor counts or measurements are inherently random with parameters determined by the intensity at the sensor’s location. We utilize the measurements to estimate the intensity at the stack, and use it in a one-sided Sequential Probability Ratio Test (SPRT) to infer on/off status of the reactor. We demonstrate the superior performance of this method over conventional majority fusers and individual sensors using (i) test measurements from a network of 21 NaI detectors, and (ii) effluence measurements collected at the stack of a reactor facility. We also analytically establish the superior detection performance of the network over individual sensors with fixed and adaptive thresholds by utilizing the Poisson distribution of the counts. We quantify the performance improvements of the network detection over individual sensors using the packing number of the intensity space.

[Neuropsychology of dreams].

Science.gov (United States)

Tirapu-Ustarroz, J

2012-07-16

Dreams are a universal human experience and studying them from the point of view of neuroscience, consciousness, emotions and cognition is quite a challenge for researchers. Thus, dreams have been addressed from a number of different perspectives ranging from philosophy to clinical medicine, as well as psychiatry, psychology, artificial intelligence, neural network models, psychophysiology or neurobiology. The main models are grounded on the biological function of dreams, especially those based on processes involving the consolidation of memory and forgetting, and models of simulation. Similarly, current models are developed upon the neurobiology and the neuropsychology of the REM phases of sleep and how they are differentiated from wakefulness. Thus, neurobiologically speaking, dreams are related to the role of acetylcholine and, neuropsychologically, to the activation of the limbic and paralimbic regions, the activation of the basal ganglia, the activation of cortical areas with a specific modality (especially Brodmann's areas 19, 22 and 37) and the deactivation of the ventromedial, parietal and dorsolateral prefrontal cortex and posterior cingulate. Dreams can be considered a state of consciousness that is characterised by a reduced control over their content, visual images and activation of the memory, and which is mediated by motivational incentives and emotional salience.

Inference of neuronal network spike dynamics and topology from calcium imaging data

Directory of Open Access Journals (Sweden)

Henry eLütcke

2013-12-01

Full Text Available Two-photon calcium imaging enables functional analysis of neuronal circuits by inferring action potential (AP occurrence ('spike trains' from cellular fluorescence signals. It remains unclear how experimental parameters such as signal-to-noise ratio (SNR and acquisition rate affect spike inference and whether additional information about network structure can be extracted. Here we present a simulation framework for quantitatively assessing how well spike dynamics and network topology can be inferred from noisy calcium imaging data. For simulated AP-evoked calcium transients in neocortical pyramidal cells, we analyzed the quality of spike inference as a function of SNR and data acquisition rate using a recently introduced peeling algorithm. Given experimentally attainable values of SNR and acquisition rate, neural spike trains could be reconstructed accurately and with up to millisecond precision. We then applied statistical neuronal network models to explore how remaining uncertainties in spike inference affect estimates of network connectivity and topological features of network organization. We define the experimental conditions suitable for inferring whether the network has a scale-free structure and determine how well hub neurons can be identified. Our findings provide a benchmark for future calcium imaging studies that aim to reliably infer neuronal network properties.

Dreams of the rarebit fiend: Food and diet as instigators of bizarre and disturbing dreams

Directory of Open Access Journals (Sweden)

Tore eNielsen

2015-02-01

Full Text Available In the early 1900s, the Dream of the Rarebit Fiend comic strip conveyed how the spicy cheese dish Welsh rarebit leads to bizarre and disturbing dreams. Today, the perception that foods disturb dreaming persists. But apart from case studies, some exploratory surveys, and a few lab studies on how hunger affects dreaming, there is little empirical evidence addressing this topic. The present study examines 3 aspects of the food/dreaming relationship; it attempts to: 1 assess the prevalence of the perception of food-dependent dreaming and the types of foods most commonly blamed; 2 determine if perceived food-dependent dreaming is associated with dietary, sleep or motivational factors; and 3 explore whether these factors, independent of food/dreaming perceptions, are associated with reports of vivid and disturbing dreaming. 396 students completed questionnaires evaluating sleep, dreams, and dietary habits and motivations. Items queried whether they had noticed if foods produced bizarre or disturbing dreams and if eating late at night influenced their dreams. The perception of food-dependent dreaming had a prevalence of 17.8%; dairy products were the most frequently blamed food type (39%-44%. Those who perceived food-dependent dreaming differed from others by reporting more frequent and disturbing dreams, poorer sleep, higher coffee intake, and lower Intuitive Eating Scale scores. Reports of disturbing dreams were associated with a pathological constellation of measures that include poorer sleep, binge-eating, and eating for emotional reasons. Reports of vivid dreams were associated with measures indicative of wellness: better sleep, a healthier diet, and longer times between meals (fasting. Results clarify the relationship between food and dreaming and suggest 4 explanations for the perception of food-dependent dreaming: 1 food specific effects; 2 food-induced distress; 3 folklore influences, and 4 causal misattributions. Clinical implications are

Dream Symbol or Dream Process?

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Himelstein, Philip

1984-01-01

Discusses the relationship of the symbolic content of dreams to the theory of the dream in psychoanalysis and Gestalt therapy. Points out that the utility of the dream depends upon the techniques of the therapist and not on the validity of the underlying theory of the dream. (LLL)

Impact of noise on molecular network inference.

Directory of Open Access Journals (Sweden)

Radhakrishnan Nagarajan

Full Text Available Molecular entities work in concert as a system and mediate phenotypic outcomes and disease states. There has been recent interest in modelling the associations between molecular entities from their observed expression profiles as networks using a battery of algorithms. These networks have proven to be useful abstractions of the underlying pathways and signalling mechanisms. Noise is ubiquitous in molecular data and can have a pronounced effect on the inferred network. Noise can be an outcome of several factors including: inherent stochastic mechanisms at the molecular level, variation in the abundance of molecules, heterogeneity, sensitivity of the biological assay or measurement artefacts prevalent especially in high-throughput settings. The present study investigates the impact of discrepancies in noise variance on pair-wise dependencies, conditional dependencies and constraint-based Bayesian network structure learning algorithms that incorporate conditional independence tests as a part of the learning process. Popular network motifs and fundamental connections, namely: (a common-effect, (b three-chain, and (c coherent type-I feed-forward loop (FFL are investigated. The choice of these elementary networks can be attributed to their prevalence across more complex networks. Analytical expressions elucidating the impact of discrepancies in noise variance on pairwise dependencies and conditional dependencies for special cases of these motifs are presented. Subsequently, the impact of noise on two popular constraint-based Bayesian network structure learning algorithms such as Grow-Shrink (GS and Incremental Association Markov Blanket (IAMB that implicitly incorporate tests for conditional independence is investigated. Finally, the impact of noise on networks inferred from publicly available single cell molecular expression profiles is investigated. While discrepancies in noise variance are overlooked in routine molecular network inference, the

Nonparametric inference of network structure and dynamics

Science.gov (United States)

Peixoto, Tiago P.

The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among

Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient.

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Mohamed Salleh, Faridah Hani; Arif, Shereena Mohd; Zainudin, Suhaila; Firdaus-Raih, Mohd

2015-12-01

A gene regulatory network (GRN) is a large and complex network consisting of interacting elements that, over time, affect each other's state. The dynamics of complex gene regulatory processes are difficult to understand using intuitive approaches alone. To overcome this problem, we propose an algorithm for inferring the regulatory interactions from knock-out data using a Gaussian model combines with Pearson Correlation Coefficient (PCC). There are several problems relating to GRN construction that have been outlined in this paper. We demonstrated the ability of our proposed method to (1) predict the presence of regulatory interactions between genes, (2) their directionality and (3) their states (activation or suppression). The algorithm was applied to network sizes of 10 and 50 genes from DREAM3 datasets and network sizes of 10 from DREAM4 datasets. The predicted networks were evaluated based on AUROC and AUPR. We discovered that high false positive values were generated by our GRN prediction methods because the indirect regulations have been wrongly predicted as true relationships. We achieved satisfactory results as the majority of sub-networks achieved AUROC values above 0.5. Copyright © 2015 Elsevier Ltd. All rights reserved.

Causal inference in biology networks with integrated belief propagation.

Science.gov (United States)

Chang, Rui; Karr, Jonathan R; Schadt, Eric E

2015-01-01

Inferring causal relationships among molecular and higher order phenotypes is a critical step in elucidating the complexity of living systems. Here we propose a novel method for inferring causality that is no longer constrained by the conditional dependency arguments that limit the ability of statistical causal inference methods to resolve causal relationships within sets of graphical models that are Markov equivalent. Our method utilizes Bayesian belief propagation to infer the responses of perturbation events on molecular traits given a hypothesized graph structure. A distance measure between the inferred response distribution and the observed data is defined to assess the 'fitness' of the hypothesized causal relationships. To test our algorithm, we infer causal relationships within equivalence classes of gene networks in which the form of the functional interactions that are possible are assumed to be nonlinear, given synthetic microarray and RNA sequencing data. We also apply our method to infer causality in real metabolic network with v-structure and feedback loop. We show that our method can recapitulate the causal structure and recover the feedback loop only from steady-state data which conventional method cannot.

Inferring topologies of complex networks with hidden variables.

Science.gov (United States)

Wu, Xiaoqun; Wang, Weihan; Zheng, Wei Xing

2012-10-01

Network topology plays a crucial role in determining a network's intrinsic dynamics and function, thus understanding and modeling the topology of a complex network will lead to greater knowledge of its evolutionary mechanisms and to a better understanding of its behaviors. In the past few years, topology identification of complex networks has received increasing interest and wide attention. Many approaches have been developed for this purpose, including synchronization-based identification, information-theoretic methods, and intelligent optimization algorithms. However, inferring interaction patterns from observed dynamical time series is still challenging, especially in the absence of knowledge of nodal dynamics and in the presence of system noise. The purpose of this work is to present a simple and efficient approach to inferring the topologies of such complex networks. The proposed approach is called "piecewise partial Granger causality." It measures the cause-effect connections of nonlinear time series influenced by hidden variables. One commonly used testing network, two regular networks with a few additional links, and small-world networks are used to evaluate the performance and illustrate the influence of network parameters on the proposed approach. Application to experimental data further demonstrates the validity and robustness of our method.

Efficient probabilistic inference in generic neural networks trained with non-probabilistic feedback.

Science.gov (United States)

Orhan, A Emin; Ma, Wei Ji

2017-07-26

Animals perform near-optimal probabilistic inference in a wide range of psychophysical tasks. Probabilistic inference requires trial-to-trial representation of the uncertainties associated with task variables and subsequent use of this representation. Previous work has implemented such computations using neural networks with hand-crafted and task-dependent operations. We show that generic neural networks trained with a simple error-based learning rule perform near-optimal probabilistic inference in nine common psychophysical tasks. In a probabilistic categorization task, error-based learning in a generic network simultaneously explains a monkey's learning curve and the evolution of qualitative aspects of its choice behavior. In all tasks, the number of neurons required for a given level of performance grows sublinearly with the input population size, a substantial improvement on previous implementations of probabilistic inference. The trained networks develop a novel sparsity-based probabilistic population code. Our results suggest that probabilistic inference emerges naturally in generic neural networks trained with error-based learning rules.Behavioural tasks often require probability distributions to be inferred about task specific variables. Here, the authors demonstrate that generic neural networks can be trained using a simple error-based learning rule to perform such probabilistic computations efficiently without any need for task specific operations.

Dreams of the Rarebit Fiend: food and diet as instigators of bizarre and disturbing dreams

Science.gov (United States)

Nielsen, Tore; Powell, Russell A.

2015-01-01

In the early 1900s, the Dream of the Rarebit Fiend comic strip conveyed how the spicy cheese dish Welsh rarebit leads to bizarre and disturbing dreams. Today, the perception that foods disturb dreaming persists. But apart from case studies, some exploratory surveys, and a few lab studies on how hunger affects dreaming, there is little empirical evidence addressing this topic. The present study examines three aspects of the food/dreaming relationship; it attempts to: (1) assess the prevalence of the perception of food-dependent dreaming and the types of foods most commonly blamed; (2) determine if perceived food-dependent dreaming is associated with dietary, sleep or motivational factors; and (3) explore whether these factors, independent of food/dreaming perceptions, are associated with reports of vivid and disturbing dreams. Three hundred and ninety six students completed questionnaires evaluating sleep, dreams, and dietary habits and motivations. Items queried whether they had noticed if foods produced bizarre or disturbing dreams and if eating late at night influenced their dreams. The perception of food-dependent dreaming had a prevalence of 17.8%; with dairy products being the most frequently blamed food category (39–44%). Those who perceived food-dependent dreaming differed from others by reporting more frequent and disturbing dreams, poorer sleep, higher coffee intake, and lower Intuitive Eating Scale scores. Reports of disturbing dreams were associated with a pathological constellation of measures that includes poorer sleep, binge-eating, and eating for emotional reasons. Reports of vivid dreams were associated with measures indicative of wellness: better sleep, a healthier diet, and longer times between meals (fasting). Results clarify the relationship between food and dreaming and suggest four explanations for the perception of food-dependent dreaming: (1) food specific effects; (2) food-induced distress; (3) folklore influences, and (4) causal

Using neutral network to infer the hydrodynamic yield of aspherical sources

International Nuclear Information System (INIS)

Moran, B.; Glenn, L.A.

1993-07-01

We distinguish two kinds of difficulties with yield determination from aspherical sources. The first kind, the spoofing difficulty, occurs when a fraction of the energy of the explosion is channeled in such a way that it is not detected by the CORRTEX cable. In this case, neither neural networks nor any expert system can be expected to accurately estimate the yield without detailed information about device emplacement within the canister. Numerical simulations however, can provide an upper bound on the undetected fraction of the explosive energy. In the second instance, the interpretation difficulty, the data appear abnormal when analyzed using similar-explosion-scaling and the assumption of a spherical front. The inferred yield varies with time and the confidence in the yield estimate decreases. It is this kind of problem we address in this paper and for which neural networks can make a contribution. We used a back propagation neural network to infer the hydrodynamic yield of simulated aspherical sources. We trained the network using a subset of simulations from 3 different aspherical sources, with 3 different yields, and 3 satellite offset separations. The trained network was able to predict the yield within 15% in all cases and to identify the correct type of aspherical source in most cases. The predictive capability of the network increased with a larger training set. The neural network approach can easily incorporate information from new calculations or experiments and is therefore flexible and easy to maintain. We describe the potential capabilities and limitations in using such networks for yield estimations

Using neural networks to infer the hydrodynamic yield of aspherical sources

International Nuclear Information System (INIS)

Moran, B.; Glenn, L.

1993-01-01

We distinguish two kinds of difficulties with yield determination from aspherical sources. The first kind, the spoofing difficulty, occurs when a fraction of the energy of the explosion is channeled in such a way that it is not detected by the CORRTEX cable. In this case, neither neural networks nor any expert system can be expected to accurately estimate the yield without detailed information about device emplacement within the canister. Numerical simulations however, can provide an upper bound on the undetected fraction of the explosive energy. In the second instance, the interpretation difficulty, the data appear abnormal when analyzed using similar-explosion-scaling and the assumption of a spherical front. The inferred yield varies with time and the confidence in the yield estimate decreases. It is this kind of problem we address in this paper and for which neural networks can make a contribution. We used a back propagation neural network to infer the hydrodynamic yield of simulated aspherical sources. We trained the network using a subset of simulations from 3 different aspherical sources, with 3 different yield, and 3 satellite offset separations. The trained network was able to predict the yield within 15% in all cases and to identify the correct type of aspherical source in most cases. The predictive capability of the network increased with a larger training set. The neural network approach can easily incorporate information from new calculations or experiments and is therefore flexible and easy to maintain. We describe the potential capabilities and limitations in using such networks for yield estimations

The Network Completion Problem: Inferring Missing Nodes and Edges in Networks

Energy Technology Data Exchange (ETDEWEB)

Kim, M; Leskovec, J

2011-11-14

Network structures, such as social networks, web graphs and networks from systems biology, play important roles in many areas of science and our everyday lives. In order to study the networks one needs to first collect reliable large scale network data. While the social and information networks have become ubiquitous, the challenge of collecting complete network data still persists. Many times the collected network data is incomplete with nodes and edges missing. Commonly, only a part of the network can be observed and we would like to infer the unobserved part of the network. We address this issue by studying the Network Completion Problem: Given a network with missing nodes and edges, can we complete the missing part? We cast the problem in the Expectation Maximization (EM) framework where we use the observed part of the network to fit a model of network structure, and then we estimate the missing part of the network using the model, re-estimate the parameters and so on. We combine the EM with the Kronecker graphs model and design a scalable Metropolized Gibbs sampling approach that allows for the estimation of the model parameters as well as the inference about missing nodes and edges of the network. Experiments on synthetic and several real-world networks show that our approach can effectively recover the network even when about half of the nodes in the network are missing. Our algorithm outperforms not only classical link-prediction approaches but also the state of the art Stochastic block modeling approach. Furthermore, our algorithm easily scales to networks with tens of thousands of nodes.

Comparing the Chinese Dream with the American Dream

Institute of Scientific and Technical Information of China (English)

David S.Pena

2015-01-01

Comparison of the Chinese Dream with the American Dream reveals that the Chinese Dream has four main themes:national rejuvenation,common prosperity,democracy,and the people's happiness;whereas,the American Dream emphasizes personal liberty,individual success,and upward social and economic mobility.Investigation of the historical origins and development of the two dreams,conjoined with an account of their aims and purposes,shows that full realization of the Chinese Dream is achieved by successfully building socialism with Chinese characteristics;the American Dream,by contrast,serves as an ideological prop for a particularly aggressive,predatory,and imperialistic form of capitalism.Furthermore,a comparison of each dream in actual practice shows that the Chinese Dream of fully developed socialism has been more successful at promoting common prosperity and peaceful,sustainable development,while the American Dream of unbridled capitalism encourages unsustainable development,growing poverty and inequality,and imperialist wars.Finally,an enumeration of the fundamental differences between the Chinese and American Dreams concludes that the Chinese Dream is fundamentally benign,whereas the American Dream is basically malignant.In order for the American Dream to shed its harmful characteristics,it must reject its capitalist underpinnings and adopt socialism as its ultimate goal.

Quantum Enhanced Inference in Markov Logic Networks.

Science.gov (United States)

Wittek, Peter; Gogolin, Christian

2017-04-19

Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network. We analyze the graph structures that are produced by various lifting methods and investigate the extent to which quantum protocols can be used to speed up Gibbs sampling with state preparation and measurement schemes. We review different such approaches, discuss their advantages, theoretical limitations, and their appeal to implementations. We find that a straightforward application of a recent result yields exponential speedup compared to classical heuristics in approximate probabilistic inference, thereby demonstrating another example where advanced quantum resources can potentially prove useful in machine learning.

Quantum Enhanced Inference in Markov Logic Networks

Science.gov (United States)

Wittek, Peter; Gogolin, Christian

2017-04-01

Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network. We analyze the graph structures that are produced by various lifting methods and investigate the extent to which quantum protocols can be used to speed up Gibbs sampling with state preparation and measurement schemes. We review different such approaches, discuss their advantages, theoretical limitations, and their appeal to implementations. We find that a straightforward application of a recent result yields exponential speedup compared to classical heuristics in approximate probabilistic inference, thereby demonstrating another example where advanced quantum resources can potentially prove useful in machine learning.

Automatic physical inference with information maximizing neural networks

Science.gov (United States)

Charnock, Tom; Lavaux, Guilhem; Wandelt, Benjamin D.

2018-04-01

Compressing large data sets to a manageable number of summaries that are informative about the underlying parameters vastly simplifies both frequentist and Bayesian inference. When only simulations are available, these summaries are typically chosen heuristically, so they may inadvertently miss important information. We introduce a simulation-based machine learning technique that trains artificial neural networks to find nonlinear functionals of data that maximize Fisher information: information maximizing neural networks (IMNNs). In test cases where the posterior can be derived exactly, likelihood-free inference based on automatically derived IMNN summaries produces nearly exact posteriors, showing that these summaries are good approximations to sufficient statistics. In a series of numerical examples of increasing complexity and astrophysical relevance we show that IMNNs are robustly capable of automatically finding optimal, nonlinear summaries of the data even in cases where linear compression fails: inferring the variance of Gaussian signal in the presence of noise, inferring cosmological parameters from mock simulations of the Lyman-α forest in quasar spectra, and inferring frequency-domain parameters from LISA-like detections of gravitational waveforms. In this final case, the IMNN summary outperforms linear data compression by avoiding the introduction of spurious likelihood maxima. We anticipate that the automatic physical inference method described in this paper will be essential to obtain both accurate and precise cosmological parameter estimates from complex and large astronomical data sets, including those from LSST and Euclid.

Multi-Agent Inference in Social Networks: A Finite Population Learning Approach.

Science.gov (United States)

Fan, Jianqing; Tong, Xin; Zeng, Yao

When people in a society want to make inference about some parameter, each person may want to use data collected by other people. Information (data) exchange in social networks is usually costly, so to make reliable statistical decisions, people need to trade off the benefits and costs of information acquisition. Conflicts of interests and coordination problems will arise in the process. Classical statistics does not consider people's incentives and interactions in the data collection process. To address this imperfection, this work explores multi-agent Bayesian inference problems with a game theoretic social network model. Motivated by our interest in aggregate inference at the societal level, we propose a new concept, finite population learning , to address whether with high probability, a large fraction of people in a given finite population network can make "good" inference. Serving as a foundation, this concept enables us to study the long run trend of aggregate inference quality as population grows.

Evaluating the impact of DREAMS on HIV incidence among young women who sell sex: protocol for a non-randomised study in Zimbabwe.

Science.gov (United States)

Hensen, Bernadette; Hargreaves, James R; Chiyaka, Tarisai; Chabata, Sungai; Mushati, Phillis; Floyd, Sian; Birdthistle, Isolde; Busza, Joanna; Cowan, Frances

2018-01-31

"Determined, Resilient, AIDS-free, Mentored and Safe" (DREAMS) is a package of biomedical, social and economic interventions offered to adolescent girls and young women aged 10-24 years with the aim of reducing HIV incidence. In four of the six DREAMS districts in Zimbabwe, DREAMS includes an offer of oral pre-exposure prophylaxis (DREAMS+PrEP), alongside interventions to support demand and adherence, to women aged 18-24 who are at highest risk of HIV infection, including young women who sell sex (YWSS). This evaluation study addresses the question: does the delivery of DREAMS+PrEP through various providers reduce HIV incidence among YWSS Zimbabwe? We describe our approach to designing a rigorous study to assess whether DREAMS+PrEP had an impact on HIV incidence. The study design needed to account for the fact that: 1) DREAMS+PrEP was non-randomly allocated; 2) there is no sampling frame for the target population for the evaluation; 3) there are a small number of DREAMS districts (N = 6), and 4) DREAMS+PrEP is being implemented by various providers. The study will use a cohort analysis approach to compare HIV incidence among YWSS in two DREAMS+PrEP districts to HIV incidence among YWSS in non-DREAMS comparison sites. YWSS will be referred to services and recruited into the cohort through a network-based (respondent-driven) recruitment strategy, and followed-up 12- and 24-months after enrolment. Women will be asked to complete a questionnaire and offered HIV testing. Additional complications of this study include identifying comparable populations of YWSS in the DREAMS+PrEP and non-DREAMS comparison sites, and retention of YWSS over the 24-month period. The primary outcome is HIV incidence among YWSS HIV-negative at study enrolment measured by repeat, rapid HIV testing over 24-months. Inference will be based on plausibility that DREAMS+PrEP had an impact on HIV incidence. A process evaluation will be conducted to understand intervention implementation, and

What physicians need to know about dreams and dreaming.

Science.gov (United States)

Pagel, James F

2012-11-01

An overview of the current status of dream science is given, designed to provide a basic background of this field for the sleep-interested physician. No cognitive state has been more extensively studied and is yet more misunderstood than dreaming. Much older work is methodologically limited by lack of definitions, small sample size, and constraints of theoretical perspective, with evidence equivocal as to whether any special relationship exists between rapid eye movement (REM) sleep and dreaming. As the relationship between dreams and REM sleep is so poorly defined, evidence-based studies of dreaming require a dream report. The different aspects of dreaming that can be studied include dream and nightmare recall frequency, dream content, dreaming effect on waking behaviors, dream/nightmare associated medications, and pathophysiology affecting dreaming. Whether studied from behavioral, neuroanatomical, neurochemical, pathophysiological or electrophysiological perspectives, dreaming reveals itself to be a complex cognitive state affected by a wide variety of medical, psychological, sleep and social variables.

Inferring the gene network underlying the branching of tomato inflorescence.

Directory of Open Access Journals (Sweden)

Laura Astola

Full Text Available The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

Science.gov (United States)

Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

A consideration of ketamine dreams.

Science.gov (United States)

Hejja, P; Galloon, S

1975-01-01

This study was designed to see whether covering of the eyes during and after ketamine anaesthesia would reduce the incidence of dreams. One hundred and fifty patients, randomly divided into three groups, underwent therapeutic abortion with ketamine as the sole anaesthesia. One hundred patients had their eyes completely covered, 50 in the operating room only and 50 in the operating room and in the recovery room. The third 50 were controls, with their eyes uncovered. All patients were questioned post-operatively about dreams, nausea and vomiting, headache, dizziness and experiences, and also how frequently they dreamed at home. Although covering the eyes in the recovery room only reduced the incidence of dreams marginally, it became obvious that the patients who dreamed after ketamine (in all 3 groups) were those who normally dreamed at home. There were 82 patients who were recorded as not being home-dreamers, and only two of these dreamed after ketamine. In contrast, of the 68 home-dreamers, 50 dreamed after ketamine, and 17 of these had unpleasant dreams. In the home-dreamers, covering the eyes reduced the incidence of dreams from 86 per cent in Group 1 to 72 per cent in Group 2 and 64 per cent in Group 3. It is suggested that goggles may be advantageous when dealing with home-dreamers, and a question about the patient's tendency to dream should be included in the preoperative questioning. Alterations in premedication and the use of a quiet dark room during recovery may even further reduce unpleasant dreams in this group.

Network inference via adaptive optimal design

Directory of Open Access Journals (Sweden)

Stigter Johannes D

2012-09-01

Full Text Available Abstract Background Current research in network reverse engineering for genetic or metabolic networks very often does not include a proper experimental and/or input design. In this paper we address this issue in more detail and suggest a method that includes an iterative design of experiments based, on the most recent data that become available. The presented approach allows a reliable reconstruction of the network and addresses an important issue, i.e., the analysis and the propagation of uncertainties as they exist in both the data and in our own knowledge. These two types of uncertainties have their immediate ramifications for the uncertainties in the parameter estimates and, hence, are taken into account from the very beginning of our experimental design. Findings The method is demonstrated for two small networks that include a genetic network for mRNA synthesis and degradation and an oscillatory network describing a molecular network underlying adenosine 3’-5’ cyclic monophosphate (cAMP as observed in populations of Dyctyostelium cells. In both cases a substantial reduction in parameter uncertainty was observed. Extension to larger scale networks is possible but needs a more rigorous parameter estimation algorithm that includes sparsity as a constraint in the optimization procedure. Conclusion We conclude that a careful experiment design very often (but not always pays off in terms of reliability in the inferred network topology. For large scale networks a better parameter estimation algorithm is required that includes sparsity as an additional constraint. These algorithms are available in the literature and can also be used in an adaptive optimal design setting as demonstrated in this paper.

Inference in hybrid Bayesian networks

International Nuclear Information System (INIS)

Langseth, Helge; Nielsen, Thomas D.; Rumi, Rafael; Salmeron, Antonio

2009-01-01

Since the 1980s, Bayesian networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability techniques (like fault trees and reliability block diagrams). However, limitations in the BNs' calculation engine have prevented BNs from becoming equally popular for domains containing mixtures of both discrete and continuous variables (the so-called hybrid domains). In this paper we focus on these difficulties, and summarize some of the last decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability.

Evaluation of artificial time series microarray data for dynamic gene regulatory network inference.

Science.gov (United States)

Xenitidis, P; Seimenis, I; Kakolyris, S; Adamopoulos, A

2017-08-07

High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process. We examined the effect of various factors on the inference performance such as the network size, the presence of noise in microarray data, and the network sparseness. We used a system theory approach and examined the relationship between the pole placement of the inferred system and the inference performance. We examined the relationship between the inference performance in the time domain and the true system parameter identification. Simulation results indicated that time separation and the percentage of directly triggered genes are crucial factors. Also, network sparseness, the triggering function type and noise in input data affect the inference performance. When two factors were simultaneously varied, it was found that variation of one parameter significantly affects the dynamic response of the other. Crucial factors were also examined using a real GRN and acquired results confirmed simulation findings with artificial data. Different initial conditions were also used as an alternative triggering approach. Relevant results confirmed that the number of datasets constitutes the most significant parameter with regard to the inference performance. Copyright © 2017 Elsevier

Beat Dreams?

DEFF Research Database (Denmark)

Sørensen, Bent

2009-01-01

Two of the founding members of the Beat Generation of the 1950s wrote dream books with almost identical titles: Jack Kerouac's Book of Dreams (1961) and William Burroughs' My Education: A Book of Dreams (1995). This paper queries the function of such dream books, both from a perspective of seeing...... dream writing as a confessional genre, and from the perspective of didacticism implicit in sharing one's dream life with one's readers. What role does memory, politics, fantasies and reality play in communicating with and via dreams?...

Learning a Markov Logic network for supervised gene regulatory network inference.

Science.gov (United States)

Brouard, Céline; Vrain, Christel; Dubois, Julie; Castel, David; Debily, Marie-Anne; d'Alché-Buc, Florence

2013-09-12

Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already available, supervised network inference is appropriate. Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. Once learnt, the pairwise classifier can be used to predict new regulations. In this work, we explore the framework of Markov Logic Networks (MLN) that combine features of probabilistic graphical models with the expressivity of first-order logic rules. We propose to learn a Markov Logic network, e.g. a set of weighted rules that conclude on the predicate "regulates", starting from a known gene regulatory network involved in the switch proliferation/differentiation of keratinocyte cells, a set of experimental transcriptomic data and various descriptions of genes all encoded into first-order logic. As training data are unbalanced, we use asymmetric bagging to learn a set of MLNs. The prediction of a new regulation can then be obtained by averaging predictions of individual MLNs. As a side contribution, we propose three in silico tests to assess the performance of any pairwise classifier in various network inference tasks on real datasets. A first test consists of measuring the average performance on balanced edge prediction problem; a second one deals with the ability of the classifier, once enhanced by asymmetric bagging, to update a given network. Finally our main result concerns a third test that measures the ability of the method to predict regulations with a new set of genes. As expected, MLN, when provided with only numerical discretized gene expression data, does not perform as well as a pairwise SVM in terms of AUPR. However, when a more complete description of gene properties is provided by heterogeneous sources, MLN achieves the same performance as a black-box model such as a

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks.

Science.gov (United States)

Gillani, Zeeshan; Akash, Muhammad Sajid Hamid; Rahaman, M D Matiur; Chen, Ming

2014-11-30

Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM). There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size. We developed a tool (CompareSVM) based on SVM to compare different kernel methods for inference of GRN. Using CompareSVM, we investigated and evaluated different SVM kernel methods on simulated datasets of microarray of different sizes in detail. The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network. For network with nodes (SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods. For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. CompareSVM is available at http://bis.zju.edu.cn/CompareSVM/ .

Probabilistic Inference of Biological Networks via Data Integration

Directory of Open Access Journals (Sweden)

Mark F. Rogers

2015-01-01

Full Text Available There is significant interest in inferring the structure of subcellular networks of interaction. Here we consider supervised interactive network inference in which a reference set of known network links and nonlinks is used to train a classifier for predicting new links. Many types of data are relevant to inferring functional links between genes, motivating the use of data integration. We use pairwise kernels to predict novel links, along with multiple kernel learning to integrate distinct sources of data into a decision function. We evaluate various pairwise kernels to establish which are most informative and compare individual kernel accuracies with accuracies for weighted combinations. By associating a probability measure with classifier predictions, we enable cautious classification, which can increase accuracy by restricting predictions to high-confidence instances, and data cleaning that can mitigate the influence of mislabeled training instances. Although one pairwise kernel (the tensor product pairwise kernel appears to work best, different kernels may contribute complimentary information about interactions: experiments in S. cerevisiae (yeast reveal that a weighted combination of pairwise kernels applied to different types of data yields the highest predictive accuracy. Combined with cautious classification and data cleaning, we can achieve predictive accuracies of up to 99.6%.

Dreams

Institute of Scientific and Technical Information of China (English)

L.Hughes; 徐觉庆

2006-01-01

@@ Dreams L.Hughes Hold fast to dreams, For if dreams die, Life is a broken-winged bird That cannot fly. Hold fast to dreams, For when dreams go, Lire is a barren field Frozen with snow. 梦想 徐觉庆 译 紧紧地攥住梦想, 因为梦想一旦天亡, 生活就像折翼的鸟儿 再也不能飞翔. 紧紧地攥住梦想, 因为梦想一旦消逝, 生活犹如荒芜的田地覆盖着雪霜.

Effective network inference through multivariate information transfer estimation

Science.gov (United States)

Dahlqvist, Carl-Henrik; Gnabo, Jean-Yves

2018-06-01

Network representation has steadily gained in popularity over the past decades. In many disciplines such as finance, genetics, neuroscience or human travel to cite a few, the network may not directly be observable and needs to be inferred from time-series data, leading to the issue of separating direct interactions between two entities forming the network from indirect interactions coming through its remaining part. Drawing on recent contributions proposing strategies to deal with this problem such as the so-called "global silencing" approach of Barzel and Barabasi or "network deconvolution" of Feizi et al. (2013), we propose a novel methodology to infer an effective network structure from multivariate conditional information transfers. Its core principal is to test the information transfer between two nodes through a step-wise approach by conditioning the transfer for each pair on a specific set of relevant nodes as identified by our algorithm from the rest of the network. The methodology is model free and can be applied to high-dimensional networks with both inter-lag and intra-lag relationships. It outperforms state-of-the-art approaches for eliminating the redundancies and more generally retrieving simulated artificial networks in our Monte-Carlo experiments. We apply the method to stock market data at different frequencies (15 min, 1 h, 1 day) to retrieve the network of US largest financial institutions and then document how bank's centrality measurements relate to bank's systemic vulnerability.

Network Model-Assisted Inference from Respondent-Driven Sampling Data.

Science.gov (United States)

Gile, Krista J; Handcock, Mark S

2015-06-01

Respondent-Driven Sampling is a widely-used method for sampling hard-to-reach human populations by link-tracing over their social networks. Inference from such data requires specialized techniques because the sampling process is both partially beyond the control of the researcher, and partially implicitly defined. Therefore, it is not generally possible to directly compute the sampling weights for traditional design-based inference, and likelihood inference requires modeling the complex sampling process. As an alternative, we introduce a model-assisted approach, resulting in a design-based estimator leveraging a working network model. We derive a new class of estimators for population means and a corresponding bootstrap standard error estimator. We demonstrate improved performance compared to existing estimators, including adjustment for an initial convenience sample. We also apply the method and an extension to the estimation of HIV prevalence in a high-risk population.

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

Science.gov (United States)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

DREAM DIAGNOSTICS: FRITZ MORGENTHALER'S WORK ON DREAMS.

Science.gov (United States)

Binswanger, Ralf

2016-07-01

The unique approach to dreams of Swiss psychoanalyst Fritz Morgenthaler (1919-1984) is presented and discussed. Although rarely discussed in the English-speaking psychoanalytic world, this approach is very alive in German-speaking countries. Focusing on the distinction between the remembered hallucinatory experience of dreamers and the event of telling dreams within psychoanalytic sessions, Morgenthaler made two major innovations: first, he proposed a new understanding and handling of associations to dreams, and second, he offered what he called dream diagnostics as an instrument with which to integrate both resistance and transference into clinical work with dreams. © 2016 The Psychoanalytic Quarterly, Inc.

Dreaming and offline memory consolidation.

Science.gov (United States)

Wamsley, Erin J

2014-03-01

Converging evidence suggests that dreaming is influenced by the consolidation of memory during sleep. Following encoding, recently formed memory traces are gradually stabilized and reorganized into a more permanent form of long-term storage. Sleep provides an optimal neurophysiological state to facilitate this process, allowing memory networks to be repeatedly reactivated in the absence of new sensory input. The process of memory reactivation and consolidation in the sleeping brain appears to influence conscious experience during sleep, contributing to dream content recalled on awakening. This article outlines several lines of evidence in support of this hypothesis, and responds to some common objections.

What Do Young Children Dream about?

Science.gov (United States)

Honig, Alice Sterling; Nealis, Arlene L.

2012-01-01

Young children's dreams can be a way for teachers and caregivers to share with children and an opportunity for children to describe and even draw dreams. In two different preschool settings, in two different geographical locales, 94 children, aged 3-5 years, shared 266 dreams with a trusted, familiar teacher. Dreams were coded anonymously. The…

A Bayesian Framework That Integrates Heterogeneous Data for Inferring Gene Regulatory Networks

Energy Technology Data Exchange (ETDEWEB)

Santra, Tapesh, E-mail: tapesh.santra@ucd.ie [Systems Biology Ireland, University College Dublin, Dublin (Ireland)

2014-05-20

Reconstruction of gene regulatory networks (GRNs) from experimental data is a fundamental challenge in systems biology. A number of computational approaches have been developed to infer GRNs from mRNA expression profiles. However, expression profiles alone are proving to be insufficient for inferring GRN topologies with reasonable accuracy. Recently, it has been shown that integration of external data sources (such as gene and protein sequence information, gene ontology data, protein–protein interactions) with mRNA expression profiles may increase the reliability of the inference process. Here, I propose a new approach that incorporates transcription factor binding sites (TFBS) and physical protein interactions (PPI) among transcription factors (TFs) in a Bayesian variable selection (BVS) algorithm which can infer GRNs from mRNA expression profiles subjected to genetic perturbations. Using real experimental data, I show that the integration of TFBS and PPI data with mRNA expression profiles leads to significantly more accurate networks than those inferred from expression profiles alone. Additionally, the performance of the proposed algorithm is compared with a series of least absolute shrinkage and selection operator (LASSO) regression-based network inference methods that can also incorporate prior knowledge in the inference framework. The results of this comparison suggest that BVS can outperform LASSO regression-based method in some circumstances.

A Bayesian Framework That Integrates Heterogeneous Data for Inferring Gene Regulatory Networks

International Nuclear Information System (INIS)

Santra, Tapesh

2014-01-01

Reconstruction of gene regulatory networks (GRNs) from experimental data is a fundamental challenge in systems biology. A number of computational approaches have been developed to infer GRNs from mRNA expression profiles. However, expression profiles alone are proving to be insufficient for inferring GRN topologies with reasonable accuracy. Recently, it has been shown that integration of external data sources (such as gene and protein sequence information, gene ontology data, protein–protein interactions) with mRNA expression profiles may increase the reliability of the inference process. Here, I propose a new approach that incorporates transcription factor binding sites (TFBS) and physical protein interactions (PPI) among transcription factors (TFs) in a Bayesian variable selection (BVS) algorithm which can infer GRNs from mRNA expression profiles subjected to genetic perturbations. Using real experimental data, I show that the integration of TFBS and PPI data with mRNA expression profiles leads to significantly more accurate networks than those inferred from expression profiles alone. Additionally, the performance of the proposed algorithm is compared with a series of least absolute shrinkage and selection operator (LASSO) regression-based network inference methods that can also incorporate prior knowledge in the inference framework. The results of this comparison suggest that BVS can outperform LASSO regression-based method in some circumstances.

Inference of cancer-specific gene regulatory networks using soft computing rules.

Science.gov (United States)

Wang, Xiaosheng; Gotoh, Osamu

2010-03-24

Perturbations of gene regulatory networks are essentially responsible for oncogenesis. Therefore, inferring the gene regulatory networks is a key step to overcoming cancer. In this work, we propose a method for inferring directed gene regulatory networks based on soft computing rules, which can identify important cause-effect regulatory relations of gene expression. First, we identify important genes associated with a specific cancer (colon cancer) using a supervised learning approach. Next, we reconstruct the gene regulatory networks by inferring the regulatory relations among the identified genes, and their regulated relations by other genes within the genome. We obtain two meaningful findings. One is that upregulated genes are regulated by more genes than downregulated ones, while downregulated genes regulate more genes than upregulated ones. The other one is that tumor suppressors suppress tumor activators and activate other tumor suppressors strongly, while tumor activators activate other tumor activators and suppress tumor suppressors weakly, indicating the robustness of biological systems. These findings provide valuable insights into the pathogenesis of cancer.

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

Science.gov (United States)

Vlaic, Sebastian; Hoffmann, Bianca; Kupfer, Peter; Weber, Michael; Dräger, Andreas

2013-09-01

GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http://www.hki-jena.de/index.php/0/2/490. General information on GRN2SBML, examples and tutorials are available at the tool's web page.

Spotlight on dream recall: the ages of dreams.

Science.gov (United States)

Mangiaruga, Anastasia; Scarpelli, Serena; Bartolacci, Chiara; De Gennaro, Luigi

2018-01-01

Brain and sleep maturation covary across different stages of life. At the same time, dream generation and dream recall are intrinsically dependent on the development of neural systems. The aim of this paper is to review the existing studies about dreaming in infancy, adulthood, and the elderly stage of life, assessing whether dream mentation may reflect changes of the underlying cerebral activity and cognitive processes. It should be mentioned that some evidence from childhood investigations, albeit still weak and contrasting, revealed a certain correlation between cognitive skills and specific features of dream reports. In this respect, infantile amnesia, confabulatory reports, dream-reality discerning, and limitation in language production and emotional comprehension should be considered as important confounding factors. Differently, growing evidence in adults suggests that the neurophysiological mechanisms underlying the encoding and retrieval of episodic memories may remain the same across different states of consciousness. More directly, some studies on adults point to shared neural mechanisms between waking cognition and corresponding dream features. A general decline in the dream recall frequency is commonly reported in the elderly, and it is explained in terms of a diminished interest in dreaming and in its emotional salience. Although empirical evidence is not yet available, an alternative hypothesis associates this reduction to an age-related cognitive decline. The state of the art of the existing knowledge is partially due to the variety of methods used to investigate dream experience. Very few studies in elderly and no investigations in childhood have been performed to understand whether dream recall is related to specific electrophysiological pattern at different ages. Most of all, the lack of longitudinal psychophysiological studies seems to be the main issue. As a main message, we suggest that future longitudinal studies should collect dream reports

Network Model-Assisted Inference from Respondent-Driven Sampling Data

Science.gov (United States)

Gile, Krista J.; Handcock, Mark S.

2015-01-01

Summary Respondent-Driven Sampling is a widely-used method for sampling hard-to-reach human populations by link-tracing over their social networks. Inference from such data requires specialized techniques because the sampling process is both partially beyond the control of the researcher, and partially implicitly defined. Therefore, it is not generally possible to directly compute the sampling weights for traditional design-based inference, and likelihood inference requires modeling the complex sampling process. As an alternative, we introduce a model-assisted approach, resulting in a design-based estimator leveraging a working network model. We derive a new class of estimators for population means and a corresponding bootstrap standard error estimator. We demonstrate improved performance compared to existing estimators, including adjustment for an initial convenience sample. We also apply the method and an extension to the estimation of HIV prevalence in a high-risk population. PMID:26640328

A Hierarchical Poisson Log-Normal Model for Network Inference from RNA Sequencing Data

Science.gov (United States)

Gallopin, Mélina; Rau, Andrea; Jaffrézic, Florence

2013-01-01

Gene network inference from transcriptomic data is an important methodological challenge and a key aspect of systems biology. Although several methods have been proposed to infer networks from microarray data, there is a need for inference methods able to model RNA-seq data, which are count-based and highly variable. In this work we propose a hierarchical Poisson log-normal model with a Lasso penalty to infer gene networks from RNA-seq data; this model has the advantage of directly modelling discrete data and accounting for inter-sample variance larger than the sample mean. Using real microRNA-seq data from breast cancer tumors and simulations, we compare this method to a regularized Gaussian graphical model on log-transformed data, and a Poisson log-linear graphical model with a Lasso penalty on power-transformed data. For data simulated with large inter-sample dispersion, the proposed model performs better than the other methods in terms of sensitivity, specificity and area under the ROC curve. These results show the necessity of methods specifically designed for gene network inference from RNA-seq data. PMID:24147011

Spotlight on dream recall: the ages of dreams

Directory of Open Access Journals (Sweden)

Mangiaruga A

2018-01-01

Full Text Available Anastasia Mangiaruga, Serena Scarpelli, Chiara Bartolacci, Luigi De Gennaro Department of Psychology, University of Rome “Sapienza”, Rome, Italy Abstract: Brain and sleep maturation covary across different stages of life. At the same time, dream generation and dream recall are intrinsically dependent on the development of neural systems. The aim of this paper is to review the existing studies about dreaming in infancy, adulthood, and the elderly stage of life, assessing whether dream mentation may reflect changes of the underlying cerebral activity and cognitive processes. It should be mentioned that some evidence from childhood investigations, albeit still weak and contrasting, revealed a certain correlation between cognitive skills and specific features of dream reports. In this respect, infantile amnesia, confabulatory reports, dream-reality discerning, and limitation in language production and emotional comprehension should be considered as important confounding factors. Differently, growing evidence in adults suggests that the neurophysiological mechanisms underlying the encoding and retrieval of episodic memories may remain the same across different states of consciousness. More directly, some studies on adults point to shared neural mechanisms between waking cognition and corresponding dream features. A general decline in the dream recall frequency is commonly reported in the elderly, and it is explained in terms of a diminished interest in dreaming and in its emotional salience. Although empirical evidence is not yet available, an alternative hypothesis associates this reduction to an age-related cognitive decline. The state of the art of the existing knowledge is partially due to the variety of methods used to investigate dream experience. Very few studies in elderly and no investigations in childhood have been performed to understand whether dream recall is related to specific electrophysiological pattern at different ages. Most

Inference of financial networks using the normalised mutual information rate

Science.gov (United States)

2018-01-01

In this paper, we study data from financial markets, using the normalised Mutual Information Rate. We show how to use it to infer the underlying network structure of interrelations in the foreign currency exchange rates and stock indices of 15 currency areas. We first present the mathematical method and discuss its computational aspects, and apply it to artificial data from chaotic dynamics and to correlated normal-variates data. We then apply the method to infer the structure of the financial system from the time-series of currency exchange rates and stock indices. In particular, we study and reveal the interrelations among the various foreign currency exchange rates and stock indices in two separate networks, of which we also study their structural properties. Our results show that both inferred networks are small-world networks, sharing similar properties and having differences in terms of assortativity. Importantly, our work shows that global economies tend to connect with other economies world-wide, rather than creating small groups of local economies. Finally, the consistent interrelations depicted among the 15 currency areas are further supported by a discussion from the viewpoint of economics. PMID:29420644

Inference of financial networks using the normalised mutual information rate.

Science.gov (United States)

Goh, Yong Kheng; Hasim, Haslifah M; Antonopoulos, Chris G

2018-01-01

In this paper, we study data from financial markets, using the normalised Mutual Information Rate. We show how to use it to infer the underlying network structure of interrelations in the foreign currency exchange rates and stock indices of 15 currency areas. We first present the mathematical method and discuss its computational aspects, and apply it to artificial data from chaotic dynamics and to correlated normal-variates data. We then apply the method to infer the structure of the financial system from the time-series of currency exchange rates and stock indices. In particular, we study and reveal the interrelations among the various foreign currency exchange rates and stock indices in two separate networks, of which we also study their structural properties. Our results show that both inferred networks are small-world networks, sharing similar properties and having differences in terms of assortativity. Importantly, our work shows that global economies tend to connect with other economies world-wide, rather than creating small groups of local economies. Finally, the consistent interrelations depicted among the 15 currency areas are further supported by a discussion from the viewpoint of economics.

Mathematical inference and control of molecular networks from perturbation experiments

Science.gov (United States)

Mohammed-Rasheed, Mohammed

One of the main challenges facing biologists and mathematicians in the post genomic era is to understand the behavior of molecular networks and harness this understanding into an educated intervention of the cell. The cell maintains its function via an elaborate network of interconnecting positive and negative feedback loops of genes, RNA and proteins that send different signals to a large number of pathways and molecules. These structures are referred to as genetic regulatory networks (GRNs) or molecular networks. GRNs can be viewed as dynamical systems with inherent properties and mechanisms, such as steady-state equilibriums and stability, that determine the behavior of the cell. The biological relevance of the mathematical concepts are important as they may predict the differentiation of a stem cell, the maintenance of a normal cell, the development of cancer and its aberrant behavior, and the design of drugs and response to therapy. Uncovering the underlying GRN structure from gene/protein expression data, e.g., microarrays or perturbation experiments, is called inference or reverse engineering of the molecular network. Because of the high cost and time consuming nature of biological experiments, the number of available measurements or experiments is very small compared to the number of molecules (genes, RNA and proteins). In addition, the observations are noisy, where the noise is due to the measurements imperfections as well as the inherent stochasticity of genetic expression levels. Intra-cellular activities and extra-cellular environmental attributes are also another source of variability. Thus, the inference of GRNs is, in general, an under-determined problem with a highly noisy set of observations. The ultimate goal of GRN inference and analysis is to be able to intervene within the network, in order to force it away from undesirable cellular states and into desirable ones. However, it remains a major challenge to design optimal intervention strategies

Reporting dream experience: Why (not) to be skeptical about dream reports

OpenAIRE

Windt, Jennifer M.

2013-01-01

Are dreams subjective experiences during sleep? Is it like something to dream, or is it only like something to remember dreams after awakening? Specifically, can dream reports be trusted to reveal what it is like to dream, and should they count as evidence for saying that dreams are conscious experiences at all? The goal of this article is to investigate the relationship between dreaming, dream reporting and subjective experience during sleep. I discuss different variants of philosophical ske...

Dream

Institute of Scientific and Technical Information of China (English)

白永康

1994-01-01

People have beliefs since ancient times that dreams were veryimportant. More recently psychiatrist Sigmand Freud believed dreamsshowed a person’s true hidden feelings. He said dreams were theresult of sexual and aggressive needs and represented a person’s deepestdesires. Many psychiatrists now dispute the importance of dreams in

Reporting dream experience: Why (not) to be skeptical about dream reports

Science.gov (United States)

Windt, Jennifer M.

2013-01-01

Are dreams subjective experiences during sleep? Is it like something to dream, or is it only like something to remember dreams after awakening? Specifically, can dream reports be trusted to reveal what it is like to dream, and should they count as evidence for saying that dreams are conscious experiences at all? The goal of this article is to investigate the relationship between dreaming, dream reporting and subjective experience during sleep. I discuss different variants of philosophical skepticism about dream reporting and argue that they all fail. Consequently, skeptical doubts about the trustworthiness of dream reports are misguided, and for systematic reasons. I suggest an alternative, anti-skeptical account of the trustworthiness of dream reports. On this view, dream reports, when gathered under ideal reporting conditions and according to the principle of temporal proximity, are trustworthy (or transparent) with respect to conscious experience during sleep. The transparency assumption has the status of a methodologically necessary default assumption and is theoretically justified because it provides the best explanation of dream reporting. At the same time, it inherits important insights from the discussed variants of skepticism about dream reporting, suggesting that the careful consideration of these skeptical arguments ultimately leads to a positive account of why and under which conditions dream reports can and should be trusted. In this way, moderate distrust can be fruitfully combined with anti-skepticism about dream reporting. Several perspectives for future dream research and for the comparative study of dreaming and waking experience are suggested. PMID:24223542

Reporting dream experience: Why (not) to be skeptical about dream reports.

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Windt, Jennifer M

2013-01-01

Are dreams subjective experiences during sleep? Is it like something to dream, or is it only like something to remember dreams after awakening? Specifically, can dream reports be trusted to reveal what it is like to dream, and should they count as evidence for saying that dreams are conscious experiences at all? The goal of this article is to investigate the relationship between dreaming, dream reporting and subjective experience during sleep. I discuss different variants of philosophical skepticism about dream reporting and argue that they all fail. Consequently, skeptical doubts about the trustworthiness of dream reports are misguided, and for systematic reasons. I suggest an alternative, anti-skeptical account of the trustworthiness of dream reports. On this view, dream reports, when gathered under ideal reporting conditions and according to the principle of temporal proximity, are trustworthy (or transparent) with respect to conscious experience during sleep. The transparency assumption has the status of a methodologically necessary default assumption and is theoretically justified because it provides the best explanation of dream reporting. At the same time, it inherits important insights from the discussed variants of skepticism about dream reporting, suggesting that the careful consideration of these skeptical arguments ultimately leads to a positive account of why and under which conditions dream reports can and should be trusted. In this way, moderate distrust can be fruitfully combined with anti-skepticism about dream reporting. Several perspectives for future dream research and for the comparative study of dreaming and waking experience are suggested.

Reporting dream experience:Why (not to be skeptical about dream reports

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Jennifer Michelle Windt

2013-11-01

Full Text Available Are dreams subjective experiences during sleep? Is it like something to dream, or is it only like something to remember dreams after awakening? Specifically, can dream reports be trusted to reveal what it is like to dream, and should they count as evidence for saying that dreams are conscious experiences at all? The goal of this article is to investigate the relationship between dreaming, dream reporting and subjective experience during sleep. I discuss different variants of philosophical skepticism about dream reporting and argue that they all fail. Consequently, skeptical doubts about the trustworthiness of dream reports are misguided, and for systematic reasons. I suggest an alternative, anti-skeptical account of the trustworthiness of dream reports. On this view, dream reports, when gathered under ideal reporting conditions and according to the principle of temporal proximity, are trustworthy (or transparent with respect to conscious experience during sleep. The transparency assumption has the status of a methodologically necessary default assumption and is theoretically justified because it provides the best explanation of dream reporting. At the same time, it inherits important insights from the discussed variants of skepticism about dream reporting, suggesting that the careful consideration of these skeptical arguments ultimately leads to a positive account of why and under which conditions dream reports can and should be trusted. In this way, moderate distrust can be fruitfully combined with anti-skepticism about dream reporting. Several perspectives for future dream research and for the comparative study of dreaming and waking experience are suggested.

Sensorimotor Network Crucial for Inferring Amusement from Smiles.

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Paracampo, Riccardo; Tidoni, Emmanuele; Borgomaneri, Sara; di Pellegrino, Giuseppe; Avenanti, Alessio

2017-11-01

Understanding whether another's smile reflects authentic amusement is a key challenge in social life, yet, the neural bases of this ability have been largely unexplored. Here, we combined transcranial magnetic stimulation (TMS) with a novel empathic accuracy (EA) task to test whether sensorimotor and mentalizing networks are critical for understanding another's amusement. Participants were presented with dynamic displays of smiles and explicitly requested to infer whether the smiling individual was feeling authentic amusement or not. TMS over sensorimotor regions representing the face (i.e., in the inferior frontal gyrus (IFG) and ventral primary somatosensory cortex (SI)), disrupted the ability to infer amusement authenticity from observed smiles. The same stimulation did not affect performance on a nonsocial task requiring participants to track the smiling expression but not to infer amusement. Neither TMS over prefrontal and temporo-parietal areas supporting mentalizing, nor peripheral control stimulations, affected performance on either task. Thus, motor and somatosensory circuits for controlling and sensing facial movements are causally essential for inferring amusement from another's smile. These findings highlight the functional relevance of IFG and SI to amusement understanding and suggest that EA abilities may be grounded in sensorimotor networks for moving and feeling the body. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Inference of Transmission Network Structure from HIV Phylogenetic Trees.

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Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan; Britton, Tom; Leitner, Thomas

2017-01-01

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.

Dream emotionality. Selected formal properties of dreams

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Grzywacz Kinga

2015-09-01

Full Text Available The aim of the study was to verify hypotheses about time changeability of dream characteristics depending on the participants’ age and affective value of the dream. The study was conducted online. Participants of the study were 68 individuals between the age of 17 and 85. The participants were asked to prepare detailed descriptions of their dreams, next they had to identify elements of the dreams, refer them to their real life, and assess their affective value. In the dreams of late adolescents, and young and middle-aged adults the most frequently recalled period in a positive context turned out to be late adolescence and early adulthood, whereas in a negative context the participants would recall their present developmental phase and the period of late childhood. Unpleasant dreams of older individuals were mainly connected with the period of middle adulthood, whereas those pleasant ones referred to various periods of their entire life.

Inferring topologies via driving-based generalized synchronization of two-layer networks

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Wang, Yingfei; Wu, Xiaoqun; Feng, Hui; Lu, Jun-an; Xu, Yuhua

2016-05-01

The interaction topology among the constituents of a complex network plays a crucial role in the network’s evolutionary mechanisms and functional behaviors. However, some network topologies are usually unknown or uncertain. Meanwhile, coupling delays are ubiquitous in various man-made and natural networks. Hence, it is necessary to gain knowledge of the whole or partial topology of a complex dynamical network by taking into consideration communication delay. In this paper, topology identification of complex dynamical networks is investigated via generalized synchronization of a two-layer network. Particularly, based on the LaSalle-type invariance principle of stochastic differential delay equations, an adaptive control technique is proposed by constructing an auxiliary layer and designing proper control input and updating laws so that the unknown topology can be recovered upon successful generalized synchronization. Numerical simulations are provided to illustrate the effectiveness of the proposed method. The technique provides a certain theoretical basis for topology inference of complex networks. In particular, when the considered network is composed of systems with high-dimension or complicated dynamics, a simpler response layer can be constructed, which is conducive to circuit design. Moreover, it is practical to take into consideration perturbations caused by control input. Finally, the method is applicable to infer topology of a subnetwork embedded within a complex system and locate hidden sources. We hope the results can provide basic insight into further research endeavors on understanding practical and economical topology inference of networks.

Such stuff as NREM dreams are made on?

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Cicogna, PierCarla; Occhionero, Miranda

2013-12-01

The question that we deal with in this commentary is the need to clarify the synergistic role of different non-rapid eye movement (NREM) sleep stages (stages 2 and 3-4) with REM and while awake in elaborative encoding of episodic memory. If the assumption is that there is isomorphism between neuronal and cognitive networks, then more detailed analysis of NREM sleep and dreams is absolutely necessary.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

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Marbach, Daniel; Roy, Sushmita; Ay, Ferhat; Meyer, Patrick E.; Candeias, Rogerio; Kahveci, Tamer; Bristow, Christopher A.; Kellis, Manolis

2012-01-01

Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein–protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network to identify putative functions for hundreds of previously uncharacterized genes, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level. PMID:22456606

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

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Marbach, Daniel; Roy, Sushmita; Ay, Ferhat; Meyer, Patrick E; Candeias, Rogerio; Kahveci, Tamer; Bristow, Christopher A; Kellis, Manolis

2012-07-01

Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein-protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network to identify putative functions for hundreds of previously uncharacterized genes, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level.

Lucid Dreaming in Narcolepsy

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Dodet, Pauline; Chavez, Mario; Leu-Semenescu, Smaranda; Golmard, Jean-Louis; Arnulf, Isabelle

2015-01-01

Objective: To evaluate the frequency, determinants and sleep characteristics of lucid dreaming in narcolepsy Settings: University hospital sleep disorder unit Design: Case-control study Participants: Consecutive patients with narcolepsy and healthy controls Methods: Participants were interviewed regarding the frequency and determinants of lucid dreaming. Twelve narcolepsy patients and 5 controls who self-identified as frequent lucid dreamers underwent nighttime and daytime sleep monitoring after being given instructions regarding how to give an eye signal when lucid. Results: Compared to 53 healthy controls, the 53 narcolepsy patients reported more frequent dream recall, nightmares and recurrent dreams. Lucid dreaming was achieved by 77.4% of narcoleptic patients and 49.1% of controls (P dreams/month (P dreaming. Seven of 12 narcoleptic (and 0 non-narcoleptic) lucid dreamers achieved lucid REM sleep across a total of 33 naps, including 14 episodes with eye signal. The delta power in the electrode average, in delta, theta, and alpha powers in C4, and coherences between frontal electrodes were lower in lucid than non-lucid REM sleep in spectral EEG analysis. The duration of REM sleep was longer, the REM sleep onset latency tended to be shorter, and the percentage of atonia tended to be higher in lucid vs. non-lucid REM sleep; the arousal index and REM density and amplitude were unchanged. Conclusion: Narcoleptics have a high propensity for lucid dreaming without differing in REM sleep characteristics from people without narcolepsy. This suggests narcolepsy patients may provide useful information in future studies on the nature of lucid dreaming. Citation: Dodet P, Chavez M, Leu-Semenescu S, Golmard JL, Arnulf I. Lucid dreaming in narcolepsy. SLEEP 2015;38(3):487–497. PMID:25348131

Probabilistic logic networks a comprehensive framework for uncertain inference

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Goertzel, Ben; Goertzel, Izabela Freire; Heljakka, Ari

2008-01-01

This comprehensive book describes Probabilistic Logic Networks (PLN), a novel conceptual, mathematical and computational approach to uncertain inference. A broad scope of reasoning types are considered.

Inference of Cancer-specific Gene Regulatory Networks Using Soft Computing Rules

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Xiaosheng Wang

2010-03-01

Full Text Available Perturbations of gene regulatory networks are essentially responsible for oncogenesis. Therefore, inferring the gene regulatory networks is a key step to overcoming cancer. In this work, we propose a method for inferring directed gene regulatory networks based on soft computing rules, which can identify important cause-effect regulatory relations of gene expression. First, we identify important genes associated with a specific cancer (colon cancer using a supervised learning approach. Next, we reconstruct the gene regulatory networks by inferring the regulatory relations among the identified genes, and their regulated relations by other genes within the genome. We obtain two meaningful findings. One is that upregulated genes are regulated by more genes than downregulated ones, while downregulated genes regulate more genes than upregulated ones. The other one is that tumor suppressors suppress tumor activators and activate other tumor suppressors strongly, while tumor activators activate other tumor activators and suppress tumor suppressors weakly, indicating the robustness of biological systems. These findings provide valuable insights into the pathogenesis of cancer.

DREAM plays an important role in platelet activation and thrombogenesis

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Kim, Kyungho; Tseng, Alan; Barazia, Andrew; Italiano, Joseph E.

2017-01-01

Downstream regulatory element antagonist modulator (DREAM), a transcriptional repressor, is known to modulate pain responses. However, it is unknown whether DREAM is expressed in anucleate platelets and plays a role in thrombogenesis. By using intravital microscopy with DREAM-null mice and their bone marrow chimeras, we demonstrated that both hematopoietic and nonhematopoietic cell DREAMs are required for platelet thrombus formation following laser-induced arteriolar injury. In a FeCl3-induced thrombosis model, we found that compared with wild-type (WT) control and nonhematopoietic DREAM knockout (KO) mice, DREAM KO control and hematopoietic DREAM KO mice showed a significant delay in time to occlusion. Tail bleeding time was prolonged in DREAM KO control mice, but not in WT or DREAM bone marrow chimeric mice. In vivo adoptive transfer experiments further indicated the importance of platelet DREAM in thrombogenesis. We found that DREAM deletion does not alter the ultrastructural features of platelets but significantly impairs platelet aggregation and adenosine triphosphate secretion induced by numerous agonists (collagen-related peptide, adenosine 5′-diphosphate, A23187, thrombin, or U46619). Biochemical studies revealed that platelet DREAM positively regulates phosphoinositide 3-kinase (PI3K) activity during platelet activation. Using DREAM-null platelets and PI3K isoform-specific inhibitors, we observed that platelet DREAM is important for α-granule secretion, Ca2+ mobilization, and aggregation through PI3K class Iβ (PI3K-Iβ). Genetic and pharmacological studies in human megakaryoblastic MEG-01 cells showed that DREAM is important for A23187-induced Ca2+ mobilization and its regulatory function requires Ca2+ binding and PI3K-Iβ activation. These results suggest that platelet DREAM regulates PI3K-Iβ activity and plays an important role during thrombus formation. PMID:27903531

Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium

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McDermott, Jason E.; Taylor, Ronald C.; Yoon, Hyunjin; Heffron, Fred

2009-02-01

Recent advances in experimental methods have provided sufficient data to consider systems as large networks of interconnected components. High-throughput determination of protein-protein interaction networks has led to the observation that topological bottlenecks, that is proteins defined by high centrality in the network, are enriched in proteins with systems-level phenotypes such as essentiality. Global transcriptional profiling by microarray analysis has been used extensively to characterize systems, for example, cellular response to environmental conditions and genetic mutations. These transcriptomic datasets have been used to infer regulatory and functional relationship networks based on co-regulation. We use the context likelihood of relatedness (CLR) method to infer networks from two datasets gathered from the pathogen Salmonella typhimurium; one under a range of environmental culture conditions and the other from deletions of 15 regulators found to be essential in virulence. Bottleneck nodes were identified from these inferred networks and we show that these nodes are significantly more likely to be essential for virulence than their non-bottleneck counterparts. A network generated using Pearson correlation did not display this behavior. Overall this study demonstrates that topology of networks inferred from global transcriptional profiles provides information about the systems-level roles of bottleneck genes. Analysis of the differences between the two CLR-derived networks suggests that the bottleneck nodes are either mediators of transitions between system states or sentinels that reflect the dynamics of these transitions.

This art of psychoanalysis. Dreaming undreamt dreams and interrupted cries.

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Ogden, Thomas H

2004-08-01

It is the art of psychoanalysis in the making, a process inventing itself as it goes, that is the subject of this paper. The author articulates succinctly how he conceives of psychoanalysis, and offers a detailed clinical illustration. He suggests that each analysand unconsciously (and ambivalently) is seeking help in dreaming his 'night terrors' (his undreamt and undreamable dreams) and his 'nightmares' (his dreams that are interrupted when the pain of the emotional experience being dreamt exceeds his capacity for dreaming). Undreamable dreams are understood as manifestations of psychotic and psychically foreclosed aspects of the personality; interrupted dreams are viewed as reflections of neurotic and other non-psychotic parts of the personality. The analyst's task is to generate conditions that may allow the analysand--with the analyst's participation--to dream the patient's previously undreamable and interrupted dreams. A significant part of the analyst's participation in the patient's dreaming takes the form of the analyst's reverie experience. In the course of this conjoint work of dreaming in the analytic setting, the analyst may get to know the analysand sufficiently well for the analyst to be able to say something that is true to what is occurring at an unconscious level in the analytic relationship. The analyst's use of language contributes significantly to the possibility that the patient will be able to make use of what the analyst has said for purposes of dreaming his own experience, thereby dreaming himself more fully into existence.

Connectivity in the yeast cell cycle transcription network: inferences from neural networks.

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Christopher E Hart

2006-12-01

Full Text Available A current challenge is to develop computational approaches to infer gene network regulatory relationships based on multiple types of large-scale functional genomic data. We find that single-layer feed-forward artificial neural network (ANN models can effectively discover gene network structure by integrating global in vivo protein:DNA interaction data (ChIP/Array with genome-wide microarray RNA data. We test this on the yeast cell cycle transcription network, which is composed of several hundred genes with phase-specific RNA outputs. These ANNs were robust to noise in data and to a variety of perturbations. They reliably identified and ranked 10 of 12 known major cell cycle factors at the top of a set of 204, based on a sum-of-squared weights metric. Comparative analysis of motif occurrences among multiple yeast species independently confirmed relationships inferred from ANN weights analysis. ANN models can capitalize on properties of biological gene networks that other kinds of models do not. ANNs naturally take advantage of patterns of absence, as well as presence, of factor binding associated with specific expression output; they are easily subjected to in silico "mutation" to uncover biological redundancies; and they can use the full range of factor binding values. A prominent feature of cell cycle ANNs suggested an analogous property might exist in the biological network. This postulated that "network-local discrimination" occurs when regulatory connections (here between MBF and target genes are explicitly disfavored in one network module (G2, relative to others and to the class of genes outside the mitotic network. If correct, this predicts that MBF motifs will be significantly depleted from the discriminated class and that the discrimination will persist through evolution. Analysis of distantly related Schizosaccharomyces pombe confirmed this, suggesting that network-local discrimination is real and complements well-known enrichment of

fastBMA: scalable network inference and transitive reduction.

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Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

2017-10-01

Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

Walking dreams in congenital and acquired paraplegia.

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Saurat, Marie-Thérèse; Agbakou, Maité; Attigui, Patricia; Golmard, Jean-Louis; Arnulf, Isabelle

2011-12-01

To test if dreams contain remote or never-experienced motor skills, we collected during 6 weeks dream reports from 15 paraplegics and 15 healthy subjects. In 9/10 subjects with spinal cord injury and in 5/5 with congenital paraplegia, voluntary leg movements were reported during dream, including feelings of walking (46%), running (8.6%), dancing (8%), standing up (6.3%), bicycling (6.3%), and practicing sports (skiing, playing basketball, swimming). Paraplegia patients experienced walking dreams (38.2%) just as often as controls (28.7%). There was no correlation between the frequency of walking dreams and the duration of paraplegia. In contrast, patients were rarely paraplegic in dreams. Subjects who had never walked or stopped walking 4-64 years prior to this study still experience walking in their dreams, suggesting that a cerebral walking program, either genetic or more probably developed via mirror neurons (activated when observing others performing an action) is reactivated during sleep. Copyright © 2011 Elsevier Inc. All rights reserved.

Inference on network statistics by restricting to the network space: applications to sexual history data.

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Goyal, Ravi; De Gruttola, Victor

2018-01-30

Analysis of sexual history data intended to describe sexual networks presents many challenges arising from the fact that most surveys collect information on only a very small fraction of the population of interest. In addition, partners are rarely identified and responses are subject to reporting biases. Typically, each network statistic of interest, such as mean number of sexual partners for men or women, is estimated independently of other network statistics. There is, however, a complex relationship among networks statistics; and knowledge of these relationships can aid in addressing concerns mentioned earlier. We develop a novel method that constrains a posterior predictive distribution of a collection of network statistics in order to leverage the relationships among network statistics in making inference about network properties of interest. The method ensures that inference on network properties is compatible with an actual network. Through extensive simulation studies, we also demonstrate that use of this method can improve estimates in settings where there is uncertainty that arises both from sampling and from systematic reporting bias compared with currently available approaches to estimation. To illustrate the method, we apply it to estimate network statistics using data from the Chicago Health and Social Life Survey. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

CHINA DREAM or CHINESE DREAM based on COCA

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LIU Meng-qing

2016-01-01

There has a lot of discussion about the correct expression of CHINESE DREAM or CHINA DREAM. This paper aims to make well use of COCA, a free online corpus, to clear this question. After contrast, we finally find that the exact expression is CHINESE DREAM instead of the original CHINA DREAM. The application of corpus can also be a new pattern for us to pur-sue our study career and will also be an effective way to help us in research field.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

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Lee, Wei-Po; Hsiao, Yu-Ting; Hwang, Wei-Che

2014-01-16

To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high

Inferring the role of transcription factors in regulatory networks

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Le Borgne Michel

2008-05-01

Full Text Available Abstract Background Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneous sources of information, as well as to comply with practical observability issues: measurements can be scarce or noisy. In this work, we show how to combine a network of genetic regulations with a set of expression profiles, in order to infer the functional effect of the regulations, as inducer or repressor. Our approach is based on a consistency rule between a network and the signs of variation given by expression arrays. Results We evaluate our approach in several settings of increasing complexity. First, we generate artificial expression data on a transcriptional network of E. coli extracted from the literature (1529 nodes and 3802 edges, and we estimate that 30% of the regulations can be annotated with about 30 profiles. We additionally prove that at most 40.8% of the network can be inferred using our approach. Second, we use this network in order to validate the predictions obtained with a compendium of real expression profiles. We describe a filtering algorithm that generates particularly reliable predictions. Finally, we apply our inference approach to S. cerevisiae transcriptional network (2419 nodes and 4344 interactions, by combining ChIP-chip data and 15 expression profiles. We are able to detect and isolate inconsistencies between the expression profiles and a significant portion of the model (15% of all the interactions. In addition, we report predictions for 14.5% of all interactions. Conclusion Our approach does not require accurate expression levels nor times series. Nevertheless, we show on both data, real and artificial, that a relatively small number of perturbation experiments are enough to determine

Measuring consciousness in dreams: the lucidity and consciousness in dreams scale.

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Voss, Ursula; Schermelleh-Engel, Karin; Windt, Jennifer; Frenzel, Clemens; Hobson, Allan

2013-03-01

In this article, we present results from an interdisciplinary research project aimed at assessing consciousness in dreams. For this purpose, we compared lucid dreams with normal non-lucid dreams from REM sleep. Both lucid and non-lucid dreams are an important contrast condition for theories of waking consciousness, giving valuable insights into the structure of conscious experience and its neural correlates during sleep. However, the precise differences between lucid and non-lucid dreams remain poorly understood. The construction of the Lucidity and Consciousness in Dreams scale (LuCiD) was based on theoretical considerations and empirical observations. Exploratory factor analysis of the data from the first survey identified eight factors that were validated in a second survey using confirmatory factor analysis: INSIGHT, CONTROL, THOUGHT, REALISM, MEMORY, DISSOCIATION, NEGATIVE EMOTION, and POSITIVE EMOTION. While all factors are involved in dream consciousness, realism and negative emotion do not differentiate between lucid and non-lucid dreams, suggesting that lucid insight is separable from both bizarreness in dreams and a change in the subjectively experienced realism of the dream. Copyright © 2012 Elsevier Inc. All rights reserved.

Dreams and the temporality of consciousness.

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MacDuffie, Katherine; Mashour, George A

2010-01-01

Understanding dreams has long been considered fundamental to the development of a theory of consciousness. Evidence from neurobiology and neuroimaging research has paved the way for new theories of dreaming that are empirically supported. In this article we argue that dreaming is a unique state of consciousness that incorporates 3 temporal dimensions: experience of the present, processing of the past, and preparation for the future. The temporal complexity of dreams is made possible in part by the unique neurobiological environment of sleep, in which stimuli are internally generated and many of the restrictions associated with waking thought are absent. Because dream consciousness is not determined by sensory stimuli, a flexible integration of past experiences and the forging of novel connections are possible. We argue that disparate dream theories may not be mutually exclusive but rather relate to different temporal domains of the dream state.

Functional inference of complex anatomical tendinous networks at a macroscopic scale via sparse experimentation.

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Saxena, Anupam; Lipson, Hod; Valero-Cuevas, Francisco J

2012-01-01

In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16(th) century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines.

Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks.

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Fischer, Martin; Grossmann, Patrick; Padi, Megha; DeCaprio, James A

2016-07-27

Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dreaming of you: client and therapist dreams about each other during psychodynamic psychotherapy.

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Hill, Clara E; Knox, Sarah; Crook-Lyon, Rachel E; Hess, Shirley A; Miles, Joe; Spangler, Patricia T; Pudasaini, Sakar

2014-01-01

Our objectives were to describe the frequency of therapists' dreams about their clients and clients' dreams about their therapists, to determine how therapists and clients who had such dreams differed from those who did not have such dreams, whether therapy process and outcome differed for those who had and did not have such dreams, and to describe the content and consequences of these dreams. Thirteen doctoral student therapists conducted psychodynamic psychotherapy with 63 clients in a community clinic. Therapists who had dreams about clients had higher estimated and actual dream recall than did therapists who did not dream about clients. Qualitative analyses indicated that therapists' dreams yielded insights about the therapist, clients, and therapy; therapists used insights in their work with the clients. Among the clients, only two (who were particularly high in attachment anxiety and who feared abandonment from their therapists) reported dreams that were manifestly about their therapists. Therapists-in-training dreamed more about their clients than their clients dreamed about them. Dreams about clients can be used by therapists to understand themselves, clients, and the dynamics of the therapy relationship.

Trait and neurobiological correlates of individual differences in dream recall and dream content.

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Blagrove, Mark; Pace-Schott, Edward F

2010-01-01

Individuals differ greatly in their dream recall frequency, in their incidence of recalling types of dreams, such as nightmares, and in the content of their dreams. This chapter reviews work on the waking life correlates of these differences between people in their experience of dreaming and reviews some of the neurobiological correlates of these individual differences. The chapter concludes that despite there being trait-like aspects of general dream recall and of dream content, very few psychometrically assessed correlates for dream recall frequency and dream content have been found. More successful has been the investigation of correlates of frequency of particular types of dreams, such as nightmares and lucid dreams, and also of how waking-life experience is associated with dream content. There is also potential in establishing neurobiological correlates of individual differences in dream recall and dream content, and recent work on this is reviewed. Copyright © 2010 Elsevier Inc. All rights reserved.

On China dream

Institute of Scientific and Technical Information of China (English)

卿恒健

2016-01-01

What is china dream? Different people may have different opinions. But there is no doubt everyone to the understanding of the Chinese dream is good. every Chinese yearning for a better life with this kind of good , and hope for a wealthy and prosperous China is saddled with everyone, this dream is a dream that every Chinese people, and is also the China dream.

Dream as a subject of psychological research

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P.A. Egorova,

2014-08-01

Full Text Available We discuss the main theoretical concepts of a dream: dream definitions, ideas about its genesis, functions, dream location in the structure of activity. We analyze the similarities and differences between the approaches. The results of empirical studies of adolescent and adult dreams are generalized, dream functions in adolescence are analyzed. Based on the analysis of different approaches, we chose theoretical basis of our own research – A. Leontiev activity theory, L.S. Vygotsky concept, K. Lewin's model. We formulated and substantiated the definition of dream as emotionally colored image of the desired future, having a subjective significance. We show the significance and hypotheses of our research: 1 the content of dreams is connected not only with a situation of frustration, but also with the teenager abilities, 2 the dream is involved in regulating of values choice; 3 restoration and development of the ability to dream can be used in the practice of counseling and psychotherapy as an effective tool to help adolescents and adults

Dreaming and insight

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Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

2013-01-01

This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

[Unusual dreams in epileptics].

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Boldyrev, A I

1984-01-01

The author discusses bizarre dreams characteristic of epileptics and never occurring in normal subjects which have an important practical implication especially for early detection of epilepsy and the prevention of severe forms of the disease. This group of dreams includes vivid nightmares with vital fear, dreams not infrequently transforming into pro-dream states; persistently repeated stereotyped dreams and dreams with invariably the same unpleasant sensations representing an isolated aura of subsequent epileptic attacks. Diagnostically important may also be dreams with the symptoms of derealization and depersonalization, vague dream images and the deja vu phenomenon.

Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

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Ji Wei

2010-10-01

Full Text Available Abstract Background Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data. Results In this study, we propose a new discretization method "bikmeans", and compare its performance with four other widely-used discretization methods using different datasets, modeling algorithms and number of intervals. Sensitivities, specificities and total accuracies were calculated and statistical analysis was carried out. Bikmeans method always gave high total accuracies. Conclusions Our results indicate that proper discretization methods can consistently improve gene regulatory network inference independent of network modeling algorithms and datasets. Our new method, bikmeans, resulted in significant better total accuracies than other methods.

Assessing the dream-lag effect for REM and NREM stage 2 dreams.

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Blagrove, Mark; Fouquet, Nathalie C; Henley-Einion, Josephine A; Pace-Schott, Edward F; Davies, Anna C; Neuschaffer, Jennifer L; Turnbull, Oliver H

2011-01-01

This study investigates evidence, from dream reports, for memory consolidation during sleep. It is well-known that events and memories from waking life can be incorporated into dreams. These incorporations can be a literal replication of what occurred in waking life, or, more often, they can be partial or indirect. Two types of temporal relationship have been found to characterize the time of occurrence of a daytime event and the reappearance or incorporation of its features in a dream. These temporal relationships are referred to as the day-residue or immediate incorporation effect, where there is the reappearance of features from events occurring on the immediately preceding day, and the dream-lag effect, where there is the reappearance of features from events occurring 5-7 days prior to the dream. Previous work on the dream-lag effect has used spontaneous home recalled dream reports, which can be from Rapid Eye Movement Sleep (REM) and from non-Rapid Eye Movement Sleep (NREM). This study addresses whether the dream-lag effect occurs only for REM sleep dreams, or for both REM and NREM stage 2 (N2) dreams. 20 participants kept a daily diary for over a week before sleeping in the sleep laboratory for 2 nights. REM and N2 dreams collected in the laboratory were transcribed and each participant rated the level of correspondence between every dream report and every diary record. The dream-lag effect was found for REM but not N2 dreams. Further analysis indicated that this result was not due to N2 dream reports being shorter, in terms of number of words, than the REM dream reports. These results provide evidence for a 7-day sleep-dependent non-linear memory consolidation process that is specific to REM sleep, and accord with proposals for the importance of REM sleep to emotional memory consolidation.

Assessing the Dream-Lag Effect for REM and NREM Stage 2 Dreams

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Blagrove, Mark; Fouquet, Nathalie C.; Henley-Einion, Josephine A.; Pace-Schott, Edward F.; Davies, Anna C.; Neuschaffer, Jennifer L.; Turnbull, Oliver H.

2011-01-01

This study investigates evidence, from dream reports, for memory consolidation during sleep. It is well-known that events and memories from waking life can be incorporated into dreams. These incorporations can be a literal replication of what occurred in waking life, or, more often, they can be partial or indirect. Two types of temporal relationship have been found to characterize the time of occurrence of a daytime event and the reappearance or incorporation of its features in a dream. These temporal relationships are referred to as the day-residue or immediate incorporation effect, where there is the reappearance of features from events occurring on the immediately preceding day, and the dream-lag effect, where there is the reappearance of features from events occurring 5–7 days prior to the dream. Previous work on the dream-lag effect has used spontaneous home recalled dream reports, which can be from Rapid Eye Movement Sleep (REM) and from non-Rapid Eye Movement Sleep (NREM). This study addresses whether the dream-lag effect occurs only for REM sleep dreams, or for both REM and NREM stage 2 (N2) dreams. 20 participants kept a daily diary for over a week before sleeping in the sleep laboratory for 2 nights. REM and N2 dreams collected in the laboratory were transcribed and each participant rated the level of correspondence between every dream report and every diary record. The dream-lag effect was found for REM but not N2 dreams. Further analysis indicated that this result was not due to N2 dream reports being shorter, in terms of number of words, than the REM dream reports. These results provide evidence for a 7-day sleep-dependent non-linear memory consolidation process that is specific to REM sleep, and accord with proposals for the importance of REM sleep to emotional memory consolidation. PMID:22046336

Assessing the dream-lag effect for REM and NREM stage 2 dreams.

Directory of Open Access Journals (Sweden)

Mark Blagrove

Full Text Available This study investigates evidence, from dream reports, for memory consolidation during sleep. It is well-known that events and memories from waking life can be incorporated into dreams. These incorporations can be a literal replication of what occurred in waking life, or, more often, they can be partial or indirect. Two types of temporal relationship have been found to characterize the time of occurrence of a daytime event and the reappearance or incorporation of its features in a dream. These temporal relationships are referred to as the day-residue or immediate incorporation effect, where there is the reappearance of features from events occurring on the immediately preceding day, and the dream-lag effect, where there is the reappearance of features from events occurring 5-7 days prior to the dream. Previous work on the dream-lag effect has used spontaneous home recalled dream reports, which can be from Rapid Eye Movement Sleep (REM and from non-Rapid Eye Movement Sleep (NREM. This study addresses whether the dream-lag effect occurs only for REM sleep dreams, or for both REM and NREM stage 2 (N2 dreams. 20 participants kept a daily diary for over a week before sleeping in the sleep laboratory for 2 nights. REM and N2 dreams collected in the laboratory were transcribed and each participant rated the level of correspondence between every dream report and every diary record. The dream-lag effect was found for REM but not N2 dreams. Further analysis indicated that this result was not due to N2 dream reports being shorter, in terms of number of words, than the REM dream reports. These results provide evidence for a 7-day sleep-dependent non-linear memory consolidation process that is specific to REM sleep, and accord with proposals for the importance of REM sleep to emotional memory consolidation.

Protein Inference from the Integration of Tandem MS Data and Interactome Networks.

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Zhong, Jiancheng; Wang, Jianxing; Ding, Xiaojun; Zhang, Zhen; Li, Min; Wu, Fang-Xiang; Pan, Yi

2017-01-01

Since proteins are digested into a mixture of peptides in the preprocessing step of tandem mass spectrometry (MS), it is difficult to determine which specific protein a shared peptide belongs to. In recent studies, besides tandem MS data and peptide identification information, some other information is exploited to infer proteins. Different from the methods which first use only tandem MS data to infer proteins and then use network information to refine them, this study proposes a protein inference method named TMSIN, which uses interactome networks directly. As two interacting proteins should co-exist, it is reasonable to assume that if one of the interacting proteins is confidently inferred in a sample, its interacting partners should have a high probability in the same sample, too. Therefore, we can use the neighborhood information of a protein in an interactome network to adjust the probability that the shared peptide belongs to the protein. In TMSIN, a multi-weighted graph is constructed by incorporating the bipartite graph with interactome network information, where the bipartite graph is built with the peptide identification information. Based on multi-weighted graphs, TMSIN adopts an iterative workflow to infer proteins. At each iterative step, the probability that a shared peptide belongs to a specific protein is calculated by using the Bayes' law based on the neighbor protein support scores of each protein which are mapped by the shared peptides. We carried out experiments on yeast data and human data to evaluate the performance of TMSIN in terms of ROC, q-value, and accuracy. The experimental results show that AUC scores yielded by TMSIN are 0.742 and 0.874 in yeast dataset and human dataset, respectively, and TMSIN yields the maximum number of true positives when q-value less than or equal to 0.05. The overlap analysis shows that TMSIN is an effective complementary approach for protein inference.

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds

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Neelam Redekar

2017-11-01

Full Text Available A dominant loss of function mutation in myo-inositol phosphate synthase (MIPS gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified a set of putative candidate transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling, and seed dormancy. We evaluated the performance of our unsupervised network inference method by comparing the predicted regulatory network with published regulatory interactions in Arabidopsis. Some contrasting regulatory interactions were observed in low phytic acid mutants compared to non-mutant lines. These findings provide important hypotheses on expression regulation of myo-inositol metabolism and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons

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Pecevski, Dejan; Buesing, Lars; Maass, Wolfgang

2011-01-01

An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows (“explaining away”) and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons. PMID:22219717

Probabilistic inference in general graphical models through sampling in stochastic networks of spiking neurons.

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Dejan Pecevski

2011-12-01

Full Text Available An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows ("explaining away" and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons.

Probabilistic inference in general graphical models through sampling in stochastic networks of spiking neurons.

Science.gov (United States)

Pecevski, Dejan; Buesing, Lars; Maass, Wolfgang

2011-12-01

An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows ("explaining away") and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons.

Dream characteristics in a Brazilian sample: an online survey focusing on lucid dreaming

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Mota-Rolim, Sérgio A.; Targino, Zé H.; Souza, Bryan C.; Blanco, Wilfredo; Araujo, John F.; Ribeiro, Sidarta

2013-01-01

During sleep, humans experience the offline images and sensations that we call dreams, which are typically emotional and lacking in rational judgment of their bizarreness. However, during lucid dreaming (LD), subjects know that they are dreaming, and may control oneiric content. Dreaming and LD features have been studied in North Americans, Europeans and Asians, but not among Brazilians, the largest population in Latin America. Here we investigated dreams and LD characteristics in a Brazilian sample (n = 3,427; median age = 25 years) through an online survey. The subjects reported recalling dreams at least once a week (76%), and that dreams typically depicted actions (93%), known people (92%), sounds/voices (78%), and colored images (76%). The oneiric content was associated with plans for the upcoming days (37%), memories of the previous day (13%), or unrelated to the dreamer (30%). Nightmares usually depicted anxiety/fear (65%), being stalked (48%), or other unpleasant sensations (47%). These data corroborate Freudian notion of day residue in dreams, and suggest that dreams and nightmares are simulations of life situations that are related to our psychobiological integrity. Regarding LD, we observed that 77% of the subjects experienced LD at least once in life (44% up to 10 episodes ever), and for 48% LD subjectively lasted less than 1 min. LD frequency correlated weakly with dream recall frequency (r = 0.20, p < 0.01), and LD control was rare (29%). LD occurrence was facilitated when subjects did not need to wake up early (38%), a situation that increases rapid eye movement sleep (REMS) duration, or when subjects were under stress (30%), which increases REMS transitions into waking. These results indicate that LD is relatively ubiquitous but rare, unstable, difficult to control, and facilitated by increases in REMS duration and transitions to wake state. Together with LD incidence in USA, Europe and Asia, our data from Latin America strengthen the notion that LD

Dream characteristics in a Brazilian sample: an online survey focusing on lucid dreaming.

Science.gov (United States)

Mota-Rolim, Sérgio A; Targino, Zé H; Souza, Bryan C; Blanco, Wilfredo; Araujo, John F; Ribeiro, Sidarta

2013-01-01

During sleep, humans experience the offline images and sensations that we call dreams, which are typically emotional and lacking in rational judgment of their bizarreness. However, during lucid dreaming (LD), subjects know that they are dreaming, and may control oneiric content. Dreaming and LD features have been studied in North Americans, Europeans and Asians, but not among Brazilians, the largest population in Latin America. Here we investigated dreams and LD characteristics in a Brazilian sample (n = 3,427; median age = 25 years) through an online survey. The subjects reported recalling dreams at least once a week (76%), and that dreams typically depicted actions (93%), known people (92%), sounds/voices (78%), and colored images (76%). The oneiric content was associated with plans for the upcoming days (37%), memories of the previous day (13%), or unrelated to the dreamer (30%). Nightmares usually depicted anxiety/fear (65%), being stalked (48%), or other unpleasant sensations (47%). These data corroborate Freudian notion of day residue in dreams, and suggest that dreams and nightmares are simulations of life situations that are related to our psychobiological integrity. Regarding LD, we observed that 77% of the subjects experienced LD at least once in life (44% up to 10 episodes ever), and for 48% LD subjectively lasted less than 1 min. LD frequency correlated weakly with dream recall frequency (r = 0.20, p < 0.01), and LD control was rare (29%). LD occurrence was facilitated when subjects did not need to wake up early (38%), a situation that increases rapid eye movement sleep (REMS) duration, or when subjects were under stress (30%), which increases REMS transitions into waking. These results indicate that LD is relatively ubiquitous but rare, unstable, difficult to control, and facilitated by increases in REMS duration and transitions to wake state. Together with LD incidence in USA, Europe and Asia, our data from Latin America strengthen the notion that LD

The underlying emotion and the dream relating dream imagery to the dreamer's underlying emotion can help elucidate the nature of dreaming.

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Hartmann, Ernest

2010-01-01

There is a widespread consensus that emotion is important in dreams, deriving from both biological and psychological studies. However, the emphasis on examining emotions explicitly mentioned in dreams is misplaced. The dream is basically made of imagery. The focus of our group has been on relating the dream imagery to the dreamer's underlying emotion. What is most important is the underlying emotion--the emotion of the dreamer, not the emotion in the dream. This chapter discusses many studies relating the dream-especially the central image of the dream--to the dreamer's underlying emotion. Focusing on the underlying emotion leads to a coherent and testable view of the nature of dreaming. It also helps to clarify some important puzzling features of the literature on dreams, such as why the clinical literature is different in so many ways from the experimental literature, especially the laboratory-based experimental literature. Based on central image intensity and the associated underlying emotion, we can identify a hierarchy of dreams, from the highest-intensity, "big dreams," to the lowest-intensity dreams from laboratory awakenings. Copyright © 2010 Elsevier Inc. All rights reserved.

From the dreams of a generation to the theory of dreams: Freud's Roman dreams.

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Meghnagi, David

2011-06-01

In The Interpretation of Dreams, Freud's interpretation of oedipal desires does not occur at the expense of historical and personal desires, which are always there as a backdrop. In the relentless examination of his own dreams that Freud makes in order to show the mechanisms inherent in all oneiric deformation, we are also led to another, specifically historical, aspect of the issue of Jewish emancipation, which he experiences at first hand. By analysing his own dreams, Freud not only shows us the mechanisms governing dream formation, but also develops a pointed critique of his contemporary society and its prejudices. Copyright © 2011 Institute of Psychoanalysis.

My Dream, My World

Institute of Scientific and Technical Information of China (English)

Joseph DeVeto; 赵惠妙

2005-01-01

@@ I often dream the same dream: I am driving together with my mother on a stretched straight path1.The birds are singing and playing2 around the car, the flowers are opening3 richly4 which decorate5 the land.The breeze is flirting with ourhair, my long, black waterfall and my mother's short gray hair6.

Inferring general relations between network characteristics from specific network ensembles.

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Cardanobile, Stefano; Pernice, Volker; Deger, Moritz; Rotter, Stefan

2012-01-01

Different network models have been suggested for the topology underlying complex interactions in natural systems. These models are aimed at replicating specific statistical features encountered in real-world networks. However, it is rarely considered to which degree the results obtained for one particular network class can be extrapolated to real-world networks. We address this issue by comparing different classical and more recently developed network models with respect to their ability to generate networks with large structural variability. In particular, we consider the statistical constraints which the respective construction scheme imposes on the generated networks. After having identified the most variable networks, we address the issue of which constraints are common to all network classes and are thus suitable candidates for being generic statistical laws of complex networks. In fact, we find that generic, not model-related dependencies between different network characteristics do exist. This makes it possible to infer global features from local ones using regression models trained on networks with high generalization power. Our results confirm and extend previous findings regarding the synchronization properties of neural networks. Our method seems especially relevant for large networks, which are difficult to map completely, like the neural networks in the brain. The structure of such large networks cannot be fully sampled with the present technology. Our approach provides a method to estimate global properties of under-sampled networks in good approximation. Finally, we demonstrate on three different data sets (C. elegans neuronal network, R. prowazekii metabolic network, and a network of synonyms extracted from Roget's Thesaurus) that real-world networks have statistical relations compatible with those obtained using regression models.

Dreaming and Schizophrenia.

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Stickney, Jeffrey L.

Parallels between dream states and schizophrenia suggest that the study of dreams may offer some information about schizophrenia. A major theoretical assumption of the research on dreaming and schizophrenia is that, in schizophrenics, the dream state intrudes on the awake state creating a dreamlike symptomatology. This theory, called the REM…

VIRTUAL REALITY IN WAKING AND DREAMING CONSCIOUSNESS

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Allan eHobson

2014-10-01

Full Text Available This article explores the notion that the brain is genetically endowed with an innate virtual reality generator that – through experience-dependent plasticity –becomes a generative or predictive model of the world. This model, which is most clearly revealed in rapid eye movement (REM sleep dreaming, may provide the theatre for conscious experience. Functional neuroimaging evidence for brain activations that are time-locked to rapid eye movements endorses the view that waking consciousness emerges from REM sleep – and dreaming lays the foundations for waking perception. In this view, the brain is equipped with a virtual model of the world that generates predictions of its sensations. This model is continually updated and entrained by sensory prediction errors in wakefulness to ensure veridical perception, but not in dreaming. In contrast, dreaming plays an essential role in maintaining and enhancing the capacity to model the world by minimizing model complexity and thereby maximizing both statistical and thermodynamic efficiency. This perspective suggests that consciousness corresponds to the embodied process of inference, realized through the generation of virtual realities (in both sleep and wakefulness. In short, our premise or hypothesis is that the waking brain engages with the sensorium to predict the causes of sensations, while in sleep the brain's generative model is actively refined so that it generates more efficient predictions during waking. We review the evidence in support of this hypothesis – evidence that grounds consciousness in biophysical computations whose neuronal and neurochemical infrastructure has been disclosed by sleep research.

Sign Inference for Dynamic Signed Networks via Dictionary Learning

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Yi Cen

2013-01-01

Full Text Available Mobile online social network (mOSN is a burgeoning research area. However, most existing works referring to mOSNs deal with static network structures and simply encode whether relationships among entities exist or not. In contrast, relationships in signed mOSNs can be positive or negative and may be changed with time and locations. Applying certain global characteristics of social balance, in this paper, we aim to infer the unknown relationships in dynamic signed mOSNs and formulate this sign inference problem as a low-rank matrix estimation problem. Specifically, motivated by the Singular Value Thresholding (SVT algorithm, a compact dictionary is selected from the observed dataset. Based on this compact dictionary, the relationships in the dynamic signed mOSNs are estimated via solving the formulated problem. Furthermore, the estimation accuracy is improved by employing a dictionary self-updating mechanism.

Dreaming in the Classroom: Practices, Methods, and Resources in Dream Education. SUNY Series in Dream Studies

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King, Philip; Bulkeley, Kelly; Welt, Bernard

2011-01-01

"Dreaming in the Classroom" provides teachers from virtually all fields with a uniquely informative guidebook for introducing their students to the universal human phenomenon of dreaming. Although dreaming may not be held in high esteem in mainstream Western society, students at all education levels consistently enjoy learning about…

Memory in dreams.

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Giustino, Gabriella

2009-10-01

In this paper the author discusses a specific type of dreams encountered in her clinical experience, which in her view provide an opportunity of reconstructing the traumatic emotional events of the patient's past. In 1900, Freud described a category of dreams--which he called 'biographical dreams'--that reflect historical infantile experience without the typical defensive function. Many authors agree that some traumatic dreams perform a function of recovery and working through. Bion contributed to the amplification of dream theory by linking it to the theory of thought and emphasizing the element of communication in dreams as well as their defensive aspect. The central hypothesis of this paper is that the predominant aspect of such dreams is the communication of an experience which the dreamer has in the dream but does not understand. It is often possible to reconstruct, and to help the patient to comprehend and make sense of, the emotional truth of the patient's internal world, which stems from past emotional experience with primary objects. The author includes some clinical examples and references to various psychoanalytic and neuroscientific conceptions of trauma and memory. She discusses a particular clinical approach to such dreams and how the analyst should listen to them.

Embracing equifinality with efficiency: Limits of Acceptability sampling using the DREAM(LOA) algorithm

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Vrugt, Jasper A.; Beven, Keith J.

2018-04-01

This essay illustrates some recent developments to the DiffeRential Evolution Adaptive Metropolis (DREAM) MATLAB toolbox of Vrugt (2016) to delineate and sample the behavioural solution space of set-theoretic likelihood functions used within the GLUE (Limits of Acceptability) framework (Beven and Binley, 1992, 2014; Beven and Freer, 2001; Beven, 2006). This work builds on the DREAM(ABC) algorithm of Sadegh and Vrugt (2014) and enhances significantly the accuracy and CPU-efficiency of Bayesian inference with GLUE. In particular it is shown how lack of adequate sampling in the model space might lead to unjustified model rejection.

Dreams and acting out.

Science.gov (United States)

Grinberg, L

1987-01-01

Dreams can be used as containers that free patients from increased tension. This may be the principal function of certain types of dreams, called "evacuative dreams." They are dreams used for getting rid of unbearable affects and unconscious fantasies, or as a safety valve for partial discharge of instinctual drives. These dreams are observed primarily in borderline and psychotic patients, but can also be seen in the regressive states of neurotic patients during weekends and other periods of separation. Such dreams have to be differentiated from "elaborative dreams," which have a working-through function and stand in an inverse relationship to acting out: the greater the production of elaborative dreams, the less the tendency to act out, and vice versa.

Dream characteristics in a Brazilian sample: an online survey focusing on lucid dreaming

Directory of Open Access Journals (Sweden)

Sérgio Arthuro Mota-Rolim

2013-12-01

Full Text Available During sleep, humans experience the offline images and sensations that we call dreams, which are typically emotional and lacking in rational judgment of their bizarreness. However, during lucid dreaming (LD, subjects know that they are dreaming, and may control oneiric content. Dreaming and LD features have been studied in North Americans, Europeans and Asians, but not among Brazilians, the largest population in Latin America. Here we investigated dreams and LD characteristics in a Brazilian sample (n=3,427; median age=25 years through an online survey. The subjects reported recalling dreams at least once a week (76%. Dreams typically depicted actions (93%, known people (92%, sounds/voices (78%, and colored images (76%. The oneiric content was associated with plans for the upcoming days (37%, memories of the previous day (13%, or unrelated to the dreamer (30%. Nightmares usually depicted anxiety/fear (65%, being stalked (48%, or other unpleasant sensations (47%. These data corroborate Freudian notion of day residue, and suggest that dreams are simulations of life situations that are related to our psychobiological integrity. Regarding LD, we observed that 77% of the subjects experienced LD at least once in life (44% up to 10 episodes ever, and for 48% LD subjectively lasted less than 1 minute. LD frequency correlated weakly with dream recall frequency (r=0.20, p<0.01, and LD control was rare (29%. LD occurrence was facilitated when subjects did not need to wake up early (38%, a situation that increases REMS duration, or when subjects were under stress (30%, which increases REMS transitions into waking. These results indicate that LD is a relatively ubiquitous but not frequent state, being unstable, difficult to control, and facilitated by increases in REMS duration and transitions to wake state. Together with LD incidence in USA, Europe and Asia, our data from Latin America strengthen the notion that LD is a general phenomenon of the human

Inference of Transcriptional Network for Pluripotency in Mouse Embryonic Stem Cells

International Nuclear Information System (INIS)

Aburatani, S

2015-01-01

In embryonic stem cells, various transcription factors (TFs) maintain pluripotency. To gain insights into the regulatory system controlling pluripotency, I inferred the regulatory relationships between the TFs expressed in ES cells. In this study, I applied a method based on structural equation modeling (SEM), combined with factor analysis, to 649 expression profiles of 19 TF genes measured in mouse Embryonic Stem Cells (ESCs). The factor analysis identified 19 TF genes that were regulated by several unmeasured factors. Since the known cell reprogramming TF genes (Pou5f1, Sox2 and Nanog) are regulated by different factors, each estimated factor is considered to be an input for signal transduction to control pluripotency in mouse ESCs. In the inferred network model, TF proteins were also arranged as unmeasured factors that control other TFs. The interpretation of the inferred network model revealed the regulatory mechanism for controlling pluripotency in ES cells

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

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Dhaeseleer, Patrik; Liang, Shoudan; Somogyi, Roland

2000-01-01

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

[Phenomenology of dreams].

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Pringuey, Dominique

2011-10-01

A phenomenology of dreams searches for meaning, with the aim not only of explaining but also of understanding the experience. What and who is it for? And what about the nearly forgotten dream among the moderns, the banal returning to the nightmare, sleepiness, or dreamlike reverie. Nostalgia for the dream, where we saw a very early state of light, not a ordinaire qu duel. Regret for the dreamlike splendor exceeded by the modeling power of modern aesthetics--film and the explosion of virtual imaging technologies. Disappointment at the discovery of a cognitive permanence throughout sleep and a unique fit with the real upon awaking? An excess of methodological rigor where we validate the logic of the dream, correlating the clinical improvement in psychotherapy and the ability to interpret one's own dreams. The dangerous psychological access when the dream primarily is mine, viewed as a veiled expression of an unspoken desire, or when the dream reveals to me, in an existential conception of man, through time and space, my daily life, my freedom beyond my needs. Might its ultimate sense also mean its abolition? From the story of a famous forgotten dream, based on unexpected scientific data emerges the question: do we dream to forget? The main thing would not be consciousness but confidence, when " the sleeping man, his regard extinguished, dead to himself seizes the light in the night " (Heraclitus).

Network inference from functional experimental data (Conference Presentation)

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Desrosiers, Patrick; Labrecque, Simon; Tremblay, Maxime; Bélanger, Mathieu; De Dorlodot, Bertrand; Côté, Daniel C.

2016-03-01

Functional connectivity maps of neuronal networks are critical tools to understand how neurons form circuits, how information is encoded and processed by neurons, how memory is shaped, and how these basic processes are altered under pathological conditions. Current light microscopy allows to observe calcium or electrical activity of thousands of neurons simultaneously, yet assessing comprehensive connectivity maps directly from such data remains a non-trivial analytical task. There exist simple statistical methods, such as cross-correlation and Granger causality, but they only detect linear interactions between neurons. Other more involved inference methods inspired by information theory, such as mutual information and transfer entropy, identify more accurately connections between neurons but also require more computational resources. We carried out a comparative study of common connectivity inference methods. The relative accuracy and computational cost of each method was determined via simulated fluorescence traces generated with realistic computational models of interacting neurons in networks of different topologies (clustered or non-clustered) and sizes (10-1000 neurons). To bridge the computational and experimental works, we observed the intracellular calcium activity of live hippocampal neuronal cultures infected with the fluorescent calcium marker GCaMP6f. The spontaneous activity of the networks, consisting of 50-100 neurons per field of view, was recorded from 20 to 50 Hz on a microscope controlled by a homemade software. We implemented all connectivity inference methods in the software, which rapidly loads calcium fluorescence movies, segments the images, extracts the fluorescence traces, and assesses the functional connections (with strengths and directions) between each pair of neurons. We used this software to assess, in real time, the functional connectivity from real calcium imaging data in basal conditions, under plasticity protocols, and epileptic

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.

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Bellot, Pau; Olsen, Catharina; Salembier, Philippe; Oliveras-Vergés, Albert; Meyer, Patrick E

2015-09-29

In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.

Inferring gene networks from discrete expression data

KAUST Repository

Zhang, L.

2013-07-18

The modeling of gene networks from transcriptional expression data is an important tool in biomedical research to reveal signaling pathways and to identify treatment targets. Current gene network modeling is primarily based on the use of Gaussian graphical models applied to continuous data, which give a closedformmarginal likelihood. In this paper,we extend network modeling to discrete data, specifically data from serial analysis of gene expression, and RNA-sequencing experiments, both of which generate counts of mRNAtranscripts in cell samples.We propose a generalized linear model to fit the discrete gene expression data and assume that the log ratios of the mean expression levels follow a Gaussian distribution.We restrict the gene network structures to decomposable graphs and derive the graphs by selecting the covariance matrix of the Gaussian distribution with the hyper-inverse Wishart priors. Furthermore, we incorporate prior network models based on gene ontology information, which avails existing biological information on the genes of interest. We conduct simulation studies to examine the performance of our discrete graphical model and apply the method to two real datasets for gene network inference. © The Author 2013. Published by Oxford University Press. All rights reserved.

Are delusional contents replayed during dreams?

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D'Agostino, Armando; Aletti, Giacomo; Carboni, Martina; Cavallotti, Simone; Limosani, Ivan; Manzone, Marialaura; Scarone, Silvio

2013-09-01

The relationship between dream content and waking life experiences remains difficult to decipher. However, some neurobiological findings suggest that dreaming can, at least in part, be considered epiphenomenal to ongoing memory consolidation processes in sleep. Both abnormalities in sleep architecture and impairment in memory consolidation mechanisms are thought to be involved in the development of psychosis. The objective of this study was to assess the continuity between delusional contents and dreams in acutely psychotic patients. Ten patients with a single fixed and recurring delusional content were asked to report their dreams during an acute psychotic break. Sixteen judges with four different levels of acquaintance to the specific content of the patients' delusions were asked to group the dreams, expecting that fragments of the delusional thought would guide the task. A mathematical index (f,t) was developed in order to compare correct groupings between the four groups of judges. Most judges grouped the dreams slightly above chance level and no relevant differences could be found between the four groups [F(3,12)=1.297; p=n.s.]. Scoring of dreams for specific delusional themes suggested a continuity in terms of dream and waking mentation for two contents (Grandiosity and Religion). These findings seem to suggest that at least some delusional contents recur within patients' dreams. Future studies will need to determine whether such continuity reflects ongoing consolidation processes that are relevant to current theories of delusion formation and stabilization. Copyright © 2013 Elsevier Inc. All rights reserved.

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

Science.gov (United States)

Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

2016-09-19

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

Right hemisphere neural activations in the recall of waking fantasies and of dreams.

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Benedetti, Francesco; Poletti, Sara; Radaelli, Daniele; Ranieri, Rebecca; Genduso, Valeria; Cavallotti, Simone; Castelnovo, Anna; Smeraldi, Enrico; Scarone, Silvio; D'Agostino, Armando

2015-10-01

The story-like organization of dreams is characterized by a pervasive bizarreness of events and actions that resembles psychotic thought, and largely exceeds that observed in normal waking fantasies. Little is known about the neural correlates of the confabulatory narrative construction of dreams. In this study, dreams, fantasies elicited by ambiguous pictorial stimuli, and non-imaginative first- and third-person narratives from healthy participants were recorded, and were then studied for brain blood oxygen level-dependent functional magnetic resonance imaging on a 3.0-Tesla scanner while listening to their own narrative reports and attempting a retrieval of the corresponding experience. In respect to non-bizarre reports of daytime activities, the script-driven recall of dreams and fantasies differentially activated a right hemisphere network including areas in the inferior frontal gyrus, and superior and middle temporal gyrus. Neural responses were significantly greater for fantasies than for dreams in all regions, and inversely proportional to the degree of bizarreness observed in narrative reports. The inferior frontal gyrus, superior and middle temporal gyrus have been implicated in the semantic activation, integration and selection needed to build a coherent story representation and to resolve semantic ambiguities; in deductive and inferential reasoning; in self- and other-perspective taking, theory of mind, moral and autobiographical reasoning. Their degree of activation could parallel the level of logical robustness or inconsistency experienced when integrating information and mental representations in the process of building fantasy and dream narratives. © 2015 European Sleep Research Society.

Characteristics and contents of dreams.

Science.gov (United States)

Schredl, Michael

2010-01-01

Dreams have been studied from different perspectives: psychoanalysis, academic psychology, and neurosciences. After presenting the definition of dreaming and the methodological tools of dream research, the major findings regarding the phenomenology of dreaming and the factors influencing dream content are briefly reviewed. The so-called continuity hypothesis stating that dreams reflect waking-life experiences is supported by studies investigating the dreams of psychiatric patients and patients with sleep disorders, i.e., their daytime symptoms and problems are reflected in their dreams. Dreams also have an effect on subsequent waking life, e.g., on daytime mood and creativity. The question about the functions of dreaming is still unanswered and open to future research. Copyright © 2010 Elsevier Inc. All rights reserved.

Feature network models for proximity data : statistical inference, model selection, network representations and links with related models

NARCIS (Netherlands)

Frank, Laurence Emmanuelle

2006-01-01

Feature Network Models (FNM) are graphical structures that represent proximity data in a discrete space with the use of features. A statistical inference theory is introduced, based on the additivity properties of networks and the linear regression framework. Considering features as predictor

Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.

Directory of Open Access Journals (Sweden)

Xiaodong Cai

Full Text Available Integrating genetic perturbations with gene expression data not only improves accuracy of regulatory network topology inference, but also enables learning of causal regulatory relations between genes. Although a number of methods have been developed to integrate both types of data, the desiderata of efficient and powerful algorithms still remains. In this paper, sparse structural equation models (SEMs are employed to integrate both gene expression data and cis-expression quantitative trait loci (cis-eQTL, for modeling gene regulatory networks in accordance with biological evidence about genes regulating or being regulated by a small number of genes. A systematic inference method named sparsity-aware maximum likelihood (SML is developed for SEM estimation. Using simulated directed acyclic or cyclic networks, the SML performance is compared with that of two state-of-the-art algorithms: the adaptive Lasso (AL based scheme, and the QTL-directed dependency graph (QDG method. Computer simulations demonstrate that the novel SML algorithm offers significantly better performance than the AL-based and QDG algorithms across all sample sizes from 100 to 1,000, in terms of detection power and false discovery rate, in all the cases tested that include acyclic or cyclic networks of 10, 30 and 300 genes. The SML method is further applied to infer a network of 39 human genes that are related to the immune function and are chosen to have a reliable eQTL per gene. The resulting network consists of 9 genes and 13 edges. Most of the edges represent interactions reasonably expected from experimental evidence, while the remaining may just indicate the emergence of new interactions. The sparse SEM and efficient SML algorithm provide an effective means of exploiting both gene expression and perturbation data to infer gene regulatory networks. An open-source computer program implementing the SML algorithm is freely available upon request.

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.

Science.gov (United States)

Gong, Wuming; Koyano-Nakagawa, Naoko; Li, Tongbin; Garry, Daniel J

2015-03-07

Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been employed to systematically study the dynamic and coordinated nature of cardiac differentiation at the global level with multiple dimensions. Therefore, there is a pressing need to develop a systems approach to integrate these data from individual studies and infer the dynamic regulatory networks in an unbiased fashion. We developed a two-step strategy to integrate data from (1) temporal RNA-seq, (2) temporal histone modification ChIP-seq, (3) transcription factor (TF) ChIP-seq and (4) gene perturbation experiments to reconstruct the dynamic network during heart development. First, we trained a logistic regression model to predict the probability (LR score) of any base being bound by 543 TFs with known positional weight matrices. Second, four dimensions of data were combined using a time-varying dynamic Bayesian network model to infer the dynamic networks at four developmental stages in the mouse [mouse embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CP) and cardiomyocytes (CM)]. Our method not only infers the time-varying networks between different stages of heart development, but it also identifies the TF binding sites associated with promoter or enhancers of downstream genes. The LR scores of experimentally verified ESCs and heart enhancers were significantly higher than random regions (p network inference model identified a region with an elevated LR score approximately -9400 bp upstream of the transcriptional start site of Nkx2-5, which overlapped with a previously reported enhancer region (-9435 to -8922 bp). TFs such as Tead1, Gata4, Msx2, and Tgif1 were predicted to bind to this region and participate in the regulation of Nkx2-5 gene expression. Our model also predicted the key regulatory networks for the ESC-MES, MES-CP and CP

Dream-Enacting Behaviors in a Normal Population

Science.gov (United States)

Nielsen, Tore; Svob, Connie; Kuiken, Don

2009-01-01

Study Objectives: Determine the prevalence and gender distributions of behaviors enacted during dreaming (“dream-enacting [DE] behaviors”) in a normal population; the independence of such behaviors from other parasomnias; and the influence of different question wordings, socially desirable responding and personality on prevalence. Design: 3-group questionnaire study Setting: University classrooms Participants: Three undergraduate samples (Ns = 443, 201, 496; mean ages = 19.9 ± 3.2 y; 20.1 ± 3.4 y; 19.1 ± 1.6 y) Interventions: N/A Measurements and Results: Subjects completed questionnaires about DE behaviors and Social Desirability. Study 1 employed a nonspecific question about the behaviors, Study 2 employed the same question with examples, and Study 3 employed 7 questions describing specific behavior subtypes (speaking, crying, smiling/laughing, fear, anger, movement, sexual arousal). Somnambulism, somniloquy, nightmares, dream recall, alexithymia, and absorption were also assessed. Factor analyses were conducted to determine relationships among DE behaviors and their independence from other parasomnias. Prevalence increased with increasing question specificity (35.9%, 76.7%, and 98.2% for the 3 samples). No gender difference obtained for the nonspecific question, but robust differences occurred for more specific questions. Females reported more speaking, crying, fear and smiling/laughing than did males; males reported more sexual arousal. When controlling other parasomnias and dream recall frequency, these differences persisted. Factor solutions revealed that DE behaviors were independent of other parasomnias and of dream recall frequency, except for an association between dream-talking and somniloquy. Sexual arousal was related only to age. Behaviors were independent of alexithymia but moderately related to absorption. Conclusions: Dream-enacting behaviors are prevalent in healthy subjects and sensitive to question wording but not social desirability

(Deconstructing “America”: the Case of Emir Kusturica’s Arizona Dream (1993

Directory of Open Access Journals (Sweden)

David Roche

2010-11-01

Full Text Available By means of an analysis of Kusturica’s only film about America, Arizona Dream, this article argues that while the United States offers a vision of a united society founded on diversity, it also represses, altering in the process both society and the landscape. National unity is consequently a dream – a dream the film suggests that has often been dreamed up by un-Americans. Filtered through Kusturica’s own perceptions of America – and his position on the Balkan War (1991-2001 – the film seems to suggest sadness at the loss of a multi-ethnic, multi-cultural perspective. Through its representations of geography and ethnic diversity, and its dense network of filmic citations, what Arizona Dream ultimately offers is consequently a European auteur’s view of the United States rather than a systematic deconstruction of the “imagined community” of “America.”

Approach/avoidance in dreams.

Science.gov (United States)

Malcolm-Smith, Susan; Koopowitz, Sheri; Pantelis, Eleni; Solms, Mark

2012-03-01

The influential threat simulation theory (TST) asserts that dreaming yields adaptive advantage by providing a virtual environment in which threat-avoidance may be safely rehearsed. We have previously found the incidence of biologically threatening dreams to be around 20%, with successful threat avoidance occurring in approximately one-fifth of such dreams. TST asserts that threat avoidance is over-represented relative to other possible dream contents. To begin assessing this issue, we contrasted the incidence of 'avoidance' dreams with that of their opposite: 'approach' dreams. Because TST states that the threat-avoidance function is only fully activated in ecologically valid (biologically threatening) contexts, we also performed this contrast for populations living in both high- and low-threat environments. We find that 'approach' dreams are significantly more prevalent across both contexts. We suggest these results are more consistent with the view that dreaming is generated by reward-seeking systems than by fear-conditioning systems, although reward-seeking is clearly not the only factor determining the content of dreams. Copyright © 2011 Elsevier Inc. All rights reserved.

Dream Recall and Dream Content in Children with Attention Deficit/Hyperactivity Disorder

Science.gov (United States)

Schredl, Michael; Sartorius, Heiko

2010-01-01

Although sleep is widely investigated in children with ADHD, dream studies in this group are completely lacking. The continuity hypothesis of dreaming stating that waking life is reflected in dreams would predict that waking-life symptoms are reflected in the dreams of such children. 103 children with ADHD and 100 controls completed a dream…

Inferring Phylogenetic Networks from Gene Order Data

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Alexey Anatolievich Morozov

2013-01-01

Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

Statistical inference to advance network models in epidemiology.

Science.gov (United States)

Welch, David; Bansal, Shweta; Hunter, David R

2011-03-01

Contact networks are playing an increasingly important role in the study of epidemiology. Most of the existing work in this area has focused on considering the effect of underlying network structure on epidemic dynamics by using tools from probability theory and computer simulation. This work has provided much insight on the role that heterogeneity in host contact patterns plays on infectious disease dynamics. Despite the important understanding afforded by the probability and simulation paradigm, this approach does not directly address important questions about the structure of contact networks such as what is the best network model for a particular mode of disease transmission, how parameter values of a given model should be estimated, or how precisely the data allow us to estimate these parameter values. We argue that these questions are best answered within a statistical framework and discuss the role of statistical inference in estimating contact networks from epidemiological data. Copyright © 2011 Elsevier B.V. All rights reserved.

Inferring personal economic status from social network location

Science.gov (United States)

Luo, Shaojun; Morone, Flaviano; Sarraute, Carlos; Travizano, Matías; Makse, Hernán A.

2017-05-01

It is commonly believed that patterns of social ties affect individuals' economic status. Here we translate this concept into an operational definition at the network level, which allows us to infer the economic well-being of individuals through a measure of their location and influence in the social network. We analyse two large-scale sources: telecommunications and financial data of a whole country's population. Our results show that an individual's location, measured as the optimal collective influence to the structural integrity of the social network, is highly correlated with personal economic status. The observed social network patterns of influence mimic the patterns of economic inequality. For pragmatic use and validation, we carry out a marketing campaign that shows a threefold increase in response rate by targeting individuals identified by our social network metrics as compared to random targeting. Our strategy can also be useful in maximizing the effects of large-scale economic stimulus policies.

A novel mutual information-based Boolean network inference method from time-series gene expression data.

Directory of Open Access Journals (Sweden)

Shohag Barman

Full Text Available Inferring a gene regulatory network from time-series gene expression data in systems biology is a challenging problem. Many methods have been suggested, most of which have a scalability limitation due to the combinatorial cost of searching a regulatory set of genes. In addition, they have focused on the accurate inference of a network structure only. Therefore, there is a pressing need to develop a network inference method to search regulatory genes efficiently and to predict the network dynamics accurately.In this study, we employed a Boolean network model with a restricted update rule scheme to capture coarse-grained dynamics, and propose a novel mutual information-based Boolean network inference (MIBNI method. Given time-series gene expression data as an input, the method first identifies a set of initial regulatory genes using mutual information-based feature selection, and then improves the dynamics prediction accuracy by iteratively swapping a pair of genes between sets of the selected regulatory genes and the other genes. Through extensive simulations with artificial datasets, MIBNI showed consistently better performance than six well-known existing methods, REVEAL, Best-Fit, RelNet, CST, CLR, and BIBN in terms of both structural and dynamics prediction accuracy. We further tested the proposed method with two real gene expression datasets for an Escherichia coli gene regulatory network and a fission yeast cell cycle network, and also observed better results using MIBNI compared to the six other methods.Taken together, MIBNI is a promising tool for predicting both the structure and the dynamics of a gene regulatory network.

Metacognitive mechanisms underlying lucid dreaming

OpenAIRE

Filevich, E.; Dresler, M.; Brick, T.R.; Kuhn, S.

2015-01-01

Lucid dreaming is a state of awareness that one is dreaming, without leaving the sleep state. Dream reports show that self-reflection and volitional control are more pronounced in lucid compared with nonlucid dreams. Mostly on these grounds, lucid dreaming has been associated with metacognition. However, the link to lucid dreaming at the neural level has not yet been explored. We sought for relationships between the neural correlates of lucid dreaming and thought monitoring. Human participant...

Metaphor and hyperassociativity: the imagination mechanisms behind emotion assimilation in sleep and dreaming.

Science.gov (United States)

Malinowski, Josie E; Horton, Caroline L

2015-01-01

In this paper we propose an emotion assimilation function of sleep and dreaming. We offer explanations both for the mechanisms by which waking-life memories are initially selected for processing during sleep, and for the mechanisms by which those memories are subsequently transformed during sleep. We propose that emotions act as a marker for information to be selectively processed during sleep, including consolidation into long term memory structures and integration into pre-existing memory networks; that dreaming reflects these emotion assimilation processes; and that the associations between memory fragments activated during sleep give rise to measureable elements of dream metaphor and hyperassociativity. The latter are a direct reflection, and the phenomenological experience, of emotional memory assimilation processes occurring during sleep. While many theories previously have posited a role for emotion processing and/or emotional memory consolidation during sleep and dreaming, sleep theories often do not take enough account of important dream science data, yet dream research, when conducted systematically and under ideal conditions, can greatly enhance theorizing around the functions of sleep. Similarly, dream theories often fail to consider the implications of sleep-dependent memory research, which can augment our understanding of dream functioning. Here, we offer a synthesized view, taking detailed account of both sleep and dream data and theories. We draw on extensive literature from sleep and dream experiments and theories, including often-overlooked data from dream science which we believe reflects sleep phenomenology, to bring together important ideas and findings from both domains.

A Local Poisson Graphical Model for inferring networks from sequencing data.

Science.gov (United States)

Allen, Genevera I; Liu, Zhandong

2013-09-01

Gaussian graphical models, a class of undirected graphs or Markov Networks, are often used to infer gene networks based on microarray expression data. Many scientists, however, have begun using high-throughput sequencing technologies such as RNA-sequencing or next generation sequencing to measure gene expression. As the resulting data consists of counts of sequencing reads for each gene, Gaussian graphical models are not optimal for this discrete data. In this paper, we propose a novel method for inferring gene networks from sequencing data: the Local Poisson Graphical Model. Our model assumes a Local Markov property where each variable conditional on all other variables is Poisson distributed. We develop a neighborhood selection algorithm to fit our model locally by performing a series of l1 penalized Poisson, or log-linear, regressions. This yields a fast parallel algorithm for estimating networks from next generation sequencing data. In simulations, we illustrate the effectiveness of our methods for recovering network structure from count data. A case study on breast cancer microRNAs (miRNAs), a novel application of graphical models, finds known regulators of breast cancer genes and discovers novel miRNA clusters and hubs that are targets for future research.

Theoretical trajectories: Dreams and dreaming from Freud to Bion.

Science.gov (United States)

Vinocur Fischbein, Susana; Miramón, Beatriz

2015-08-01

This paper aims at comparing Freud's and Bion's conceptual models on dreams and dreaming. Beyond both authors' shared disposition vis-à-vis problems posed by knowledge, a critical gap opens regarding their differing clinical practices. It is hypothesized that their ideas do not belong to irreconcilable paradigms, but that there are continuities besides discontinuities more frequently highlighted between Freudian statements on psychic functioning--described in his theory on dreams--and Bion's findings in his development of both the original theory and the connections between dreaming and thinking. Firstly, Freud's and Bion's epistemological sources are examined as well as their creative use and historical environment. Then certain general theoretical and clinical issues are considered concerning their theories on dreams, the evolution of their ideas and corresponding clinical contexts. In a third section, their confluences and dissimilarities are dealt with, including clinical vignettes belonging to the authors to illustrate their interpretative modes of working. This is meant to show both an implicit theoretical-clinical complementarity and the fact that, though their routes bifurcate about the function of dreams, there remain connecting paths. Lastly, the final remarks review certain issues that have frequently been controversial between these lines of thought. Copyright © 2015 Institute of Psychoanalysis.

Minding the dream self: perspectives from the analysis of self-experience in dreams.

Science.gov (United States)

Windt, Jennifer Michelle

2013-12-01

Can ancient art of memory (AAOM) principles explain the function of dreaming? The analysis of self-experience in dreams suggests that the answer is no: The phenomenal dream self lacks certain dimensions that are crucial for the efficacy of AAOM in wakefulness. However, the comparison between dreams and AAOM may be fruitful by suggesting new perspectives for the study of lucid dreaming as well an altered perspective on the efficacy of AAOM itself.

Dream recall and dream content in obsessive-compulsive patients: is there a change during exposure treatment?

Science.gov (United States)

Kuelz, Anne K; Stotz, Ulrike; Riemann, Dieter; Schredl, Michael; Voderholzer, Ulrich

2010-08-01

Very little is known about dreams in patients with obsessive compulsive disorder, especially regarding changes over the course of treatment with stimulus exposure and response prevention. By use of dream content analysis, 40 dreams of 9 obsessive compulsive (OC) inpatients were compared with 84 dreams of 10 matched OC outpatients and 63 dreams of 11 healthy control participants. Dream protocols of inpatients were collected at the beginning of treatment and after the first exposure exercises. Controls filled in dream protocols in respective intervals. Before treatment, dreams of patients showed significantly less positive contents than dreams of healthy controls. Under treatment with exposure, a significant reduction of OC themes was observed. The findings support the continuity hypothesis of dreaming by showing a link between day-time symptoms and OC symptoms in dreams. Contrary to expectations, however, exposure treatment does not intensify dreams.

Aphotic Dream

OpenAIRE

Nassiroghli, Fakhteh

2012-01-01

One hour and ten minutes theatre production of Aphotic Dream, written and directed by Fay Nassiroghli. The production took place at Studio T at SFU (Goldcorp Campus). Aphotic Dream was a multidisciplinary piece combining dance, text, lighting, surround audio system and music. Aphotic Dream included a cast of eleven people from diverse cultural and professional backgrounds as well as 4 major collaborators in the areas of lighting, sound and audio design, dramaturgy and directing. The audience ...

Dreaming and personality: Wake-dream continuity, thought suppression, and the Big Five Inventory.

Science.gov (United States)

Malinowski, Josie E

2015-12-15

Studies have found relationships between dream content and personality traits, but there are still many traits that have been underexplored or have had questionable conclusions drawn about them. Experimental work has found a 'rebound' effect in dreams when thoughts are suppressed prior to sleep, but the effect of trait thought suppression on dream content has not yet been researched. In the present study participants (N=106) reported their Most Recent Dream, answered questions about the content of the dream, and completed questionnaires measuring trait thought suppression and the 'Big Five' personality traits. Of these, 83 were suitably recent for analyses. A significant positive correlation was found between trait thought suppression and participants' ratings of dreaming of waking-life emotions, and high suppressors reported dreaming more of their waking-life emotions than low suppressors did. The results may lend support to the compensation theory of dreams, and/or the ironic process theory of mental control. Copyright © 2015 Elsevier Inc. All rights reserved.

Metaphor and hyperassociativity: the imagination mechanisms behind emotion assimilation in sleep and dreaming

Directory of Open Access Journals (Sweden)

Josie Elizabeth Malinowski

2015-08-01

Full Text Available In this paper we propose an emotion assimilation function of sleep and dreaming. We offer explanations both for the mechanisms by which waking-life memories are initially selected for processing during sleep, and for the mechanisms by which those memories are subsequently transformed during sleep, as reflected by dreams. We propose that emotions act as marker for information to be selectively processed during sleep, including consolidation into long term memory structures and integration into pre-existing memory networks; that dreaming reflects these emotion assimilation processes; and that the associations between memory fragments activated during sleep give rise to measureable elements of dream metaphor and hyperassociativity. The latter are a direct reflection, and the phenomenological experience, of emotional memory assimilation processes occurring during sleep. While many theories previously have posited a role for emotion processing and/or emotional memory consolidation during sleep and dreaming, sleep theories often do not take enough account of important dream science data, yet dream research, when conducted systematically and under ideal conditions, can greatly enhance theorising around the functions of sleep. Similarly, dream theories often fail to consider the implications of sleep-dependent memory research, which can augment our understanding of dream functioning. Here we offer a synthesised view, taking detailed account of both sleep and dream data and theories. We draw on extensive literature from sleep and dream experiments and theories, including often-overlooked data from dream science which we believe reflects sleep phenomenology, to bring together important ideas and findings from both domains.

Metacognitive mechanisms underlying lucid dreaming

NARCIS (Netherlands)

Filevich, E.; Dresler, M.; Brick, T.R.; Kuhn, S.

2015-01-01

Lucid dreaming is a state of awareness that one is dreaming, without leaving the sleep state. Dream reports show that self-reflection and volitional control are more pronounced in lucid compared with nonlucid dreams. Mostly on these grounds, lucid dreaming has been associated with metacognition.

Bereavement dream? Successful antidepressant treatment for bereavement-related distressing dreams in patients with major depression.

Science.gov (United States)

Ishida, Mayumi; Onishi, Hideki; Wada, Mei; Wada, Tomomi; Wada, Makoto; Uchitomi, Yosuke; Nomura, Shinobu

2010-03-01

The death of a person is a stressful event. Such stress affects the physical and psychological well-being of the bereaved. As an associated mental disorder, major depressive disorder (MDD) is common. Some dream of the deceased, and these dreams are called bereavement dreams. Some MDD patients also experience dreams. These two types of dreams are sometimes difficult to differentiate. The dream of the bereaved might be only a bereavement-related dream, yet it might be a symptom of MDD. Herein, we report one patient who had distressing dreams after the death of her mother. A 63-year-old woman was referred for psychiatric consultation because of generalized fatigue and insomnia. Questioning her about recent events, she said that her mother had died of colonic carcinoma 5 months previously. Two months after the death, she suddenly started dreaming of her mother, getting angry with her almost every night. Generalized fatigue, insomnia, and distressing dreams appeared simultaneously. The dream caused much distress, making her afraid to fall asleep. Her psychiatric features fulfilled the DSM-IV-TR criteria for MDD, single episode. The death of her mother was considered to be one of the causes of MDD. She was administered 25 mg/day of sertraline hydrochloride. After that, her symptoms gradually disappeared, and the frequency of distressing dreams was reduced. Five months later, physical and psychiatric symptoms of MDD were completely resolved. Subsequently, she has not suffered from any distressing dreams of her mother. This case indicates that dreams experienced after the death of a loved one should not be regarded simply as bereavement dreams. Some of the dreams may be symptoms of MDD. If the dreams are the symptoms of MDD, antidepressant treatment as well as psychotherapy may be useful. Therefore, we should avoid regarding symptoms of MDD as reactions to bereavement.

Volitional components of consciousness vary across wakefulness, dreaming and lucid dreaming

Directory of Open Access Journals (Sweden)

Martin eDresler

2014-01-01

Full Text Available Consciousness is a multifaceted concept; its different aspects vary across species, vigilance states or health conditions. While basal aspects of consciousness like perceptions and emotions are present in many states and species, higher-order aspects like reflective or volitional capabilities seem to be most pronounced in awake humans. Here we assess the experience of volition across different states of consciousness: 10 frequent lucid dreamers rated different aspects of volition according to the Volitional Components Questionnaire for phases of normal dreaming, lucid dreaming and wakefulness. Overall, experienced volition was comparable for lucid dreaming and wakefulness, and rated significantly higher for both states compared to non-lucid dreaming. However, three subscales showed specific differences across states of consciousness: planning ability was most pronounced during wakefulness, intention enactment most pronounced during lucid dreaming, and self-determination most pronounced during both wakefulness and lucid dreaming. Our data confirm the multifaceted nature of consciousness: different higher-order aspects of consciousness are differentially expressed across different conscious states.

Volitional components of consciousness vary across wakefulness, dreaming and lucid dreaming.

Science.gov (United States)

Dresler, Martin; Eibl, Leandra; Fischer, Christian F J; Wehrle, Renate; Spoormaker, Victor I; Steiger, Axel; Czisch, Michael; Pawlowski, Marcel

2014-01-01

Consciousness is a multifaceted concept; its different aspects vary across species, vigilance states, or health conditions. While basal aspects of consciousness like perceptions and emotions are present in many states and species, higher-order aspects like reflective or volitional capabilities seem to be most pronounced in awake humans. Here we assess the experience of volition across different states of consciousness: 10 frequent lucid dreamers rated different aspects of volition according to the Volitional Components Questionnaire for phases of normal dreaming, lucid dreaming, and wakefulness. Overall, experienced volition was comparable for lucid dreaming and wakefulness, and rated significantly higher for both states compared to non-lucid dreaming. However, three subscales showed specific differences across states of consciousness: planning ability was most pronounced during wakefulness, intention enactment most pronounced during lucid dreaming, and self-determination most pronounced during both wakefulness and lucid dreaming. Our data confirm the multifaceted nature of consciousness: different higher-order aspects of consciousness are differentially expressed across different conscious states.

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling.

Directory of Open Access Journals (Sweden)

Junha Shin

Full Text Available Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life-Archaea, Bacteria, and Eukaryota-suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co

Retrospective dream components and musical preferences.

Science.gov (United States)

Kroth, Jerry; Lamas, Jasmin; Pisca, Nicholas; Bourret, Kristy; Kollath, Miranda

2008-08-01

Retrospective dream components endorsed on the KJP Dream Inventory were correlated with those on the Short Test of Musical Preference for 68 graduate students in counseling psychology (11 men). Among 40 correlations, 6 were significant between preferences for Heavy Metal and Dissociative avoidance dreams (.32), Dreaming that you are dreaming (.40), Dreaming that you have fallen unconscious or asleep (.41), Recurring pleasantness (.31), and Awakening abruptly from a dream (-.31); between preferences for Rap/Hip-Hop and Sexual dreams (.27); and between preferences for Jazz and Recurring pleasantness in dreams (.33). Subjects preferring Classical music reported a higher incidence of Dreams of flying (.33) and rated higher Discontentedness in dreams (-.26). The meaning of these low values awaits research based on personality inventories and full dream reports.

Ground calibration of DREAMS-H relative humidity device

Science.gov (United States)

Komu, M.; Genzer, M.; Nikkanen, T.; Schmidt, W.; Haukka, H.; Kemppinen, O.; Harri, A.-M.

2014-04-01

DREAMS (Dust Characterization, Risk Assessment and Environmental Analyzer on the Martian Surface) instrument suite is to be launched as part of ESA ExoMars 2016/Entry, Descent and Landing Demonstration Module (EDM). DREAMS consists of an environmental package for monitoring temperature, pressure, relative humidity, winds and dust opacity, as well as atmospheric electricity of Martian atmosphere. DREAMS instruments and scientific goals are described in [1]. Here we describe ground calibration of the relative humidity device, DREAMS-H, provided to DREAMS payload by Finnish Meteorological Institute and based on proprietary technology of Vaisala, Inc. Same kind of device is part of REMS instrument package onboard MSL Curiosity Rover [2][3].

A novel gene network inference algorithm using predictive minimum description length approach.

Science.gov (United States)

Chaitankar, Vijender; Ghosh, Preetam; Perkins, Edward J; Gong, Ping; Deng, Youping; Zhang, Chaoyang

2010-05-28

Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to find the optimal parameter. In this work, we proposed a new inference algorithm which incorporated mutual information (MI), conditional mutual information (CMI) and predictive minimum description length (PMDL) principle to infer gene regulatory networks from DNA microarray data. In this algorithm, the information theoretic quantities MI and CMI determine the regulatory relationships between genes and the PMDL principle method attempts to determine the best MI threshold without the need of a user-specified fine tuning parameter. The performance of the proposed algorithm was evaluated using both synthetic time series data sets and a biological time series data set for the yeast Saccharomyces cerevisiae. The benchmark quantities precision and recall were used as performance measures. The results show that the proposed algorithm produced less false edges and significantly improved the precision, as compared to the existing algorithm. For further analysis the performance of the algorithms was observed over different sizes of data. We have proposed a new algorithm that implements the PMDL principle for inferring gene regulatory networks from time series DNA microarray data that eliminates the need of a fine tuning parameter. The evaluation results obtained from both synthetic and actual biological data sets show that the

The dynamic radiation environment assimilation model (DREAM)

International Nuclear Information System (INIS)

Reeves, Geoffrey D.; Koller, Josef; Tokar, Robert L.; Chen, Yue; Henderson, Michael G.; Friedel, Reiner H.

2010-01-01

The Dynamic Radiation Environment Assimilation Model (DREAM) is a 3-year effort sponsored by the US Department of Energy to provide global, retrospective, or real-time specification of the natural and potential nuclear radiation environments. The DREAM model uses Kalman filtering techniques that combine the strengths of new physical models of the radiation belts with electron observations from long-term satellite systems such as GPS and geosynchronous systems. DREAM includes a physics model for the production and long-term evolution of artificial radiation belts from high altitude nuclear explosions. DREAM has been validated against satellites in arbitrary orbits and consistently produces more accurate results than existing models. Tools for user-specific applications and graphical displays are in beta testing and a real-time version of DREAM has been in continuous operation since November 2009.

Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference.

Science.gov (United States)

Morcos, Faruck; Lamanna, Charles; Sikora, Marcin; Izaguirre, Jesús

2008-10-01

Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website. http://cytoprophet.cse.nd.edu.

MATRIX-VECTOR ALGORITHMS OF LOCAL POSTERIORI INFERENCE IN ALGEBRAIC BAYESIAN NETWORKS ON QUANTA PROPOSITIONS

Directory of Open Access Journals (Sweden)

A. A. Zolotin

2015-07-01

Full Text Available Posteriori inference is one of the three kinds of probabilistic-logic inferences in the probabilistic graphical models theory and the base for processing of knowledge patterns with probabilistic uncertainty using Bayesian networks. The paper deals with a task of local posteriori inference description in algebraic Bayesian networks that represent a class of probabilistic graphical models by means of matrix-vector equations. The latter are essentially based on the use of tensor product of matrices, Kronecker degree and Hadamard product. Matrix equations for calculating posteriori probabilities vectors within posteriori inference in knowledge patterns with quanta propositions are obtained. Similar equations of the same type have already been discussed within the confines of the theory of algebraic Bayesian networks, but they were built only for the case of posteriori inference in the knowledge patterns on the ideals of conjuncts. During synthesis and development of matrix-vector equations on quanta propositions probability vectors, a number of earlier results concerning normalizing factors in posteriori inference and assignment of linear projective operator with a selector vector was adapted. We consider all three types of incoming evidences - deterministic, stochastic and inaccurate - combined with scalar and interval estimation of probability truth of propositional formulas in the knowledge patterns. Linear programming problems are formed. Their solution gives the desired interval values of posterior probabilities in the case of inaccurate evidence or interval estimates in a knowledge pattern. That sort of description of a posteriori inference gives the possibility to extend the set of knowledge pattern types that we can use in the local and global posteriori inference, as well as simplify complex software implementation by use of existing third-party libraries, effectively supporting submission and processing of matrices and vectors when

HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation

KAUST Repository

Deng, Yue

2017-08-05

Motivation: The use of differential equations (ODE) is one of the most promising approaches to network inference. The success of ODE-based approaches has, however, been limited, due to the difficulty in estimating parameters and by their lack of scalability. Here, we introduce a novel method and pipeline to reverse engineer gene regulatory networks from gene expression of time series and perturbation data based upon an improvement on the calculation scheme of the derivatives and a pre-filtration step to reduce the number of possible links. The method introduces a linear differential equation model with adaptive numerical differentiation that is scalable to extremely large regulatory networks. Results: We demonstrate the ability of this method to outperform current state-of-the-art methods applied to experimental and synthetic data using test data from the DREAM4 and DREAM5 challenges. Our method displays greater accuracy and scalability. We benchmark the performance of the pipeline with respect to dataset size and levels of noise. We show that the computation time is linear over various network sizes.

Predictive minimum description length principle approach to inferring gene regulatory networks.

Science.gov (United States)

Chaitankar, Vijender; Zhang, Chaoyang; Ghosh, Preetam; Gong, Ping; Perkins, Edward J; Deng, Youping

2011-01-01

Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold that defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to find the optimal parameter. In this work, we propose a new inference algorithm that incorporates mutual information (MI), conditional mutual information (CMI), and predictive minimum description length (PMDL) principle to infer gene regulatory networks from DNA microarray data. In this algorithm, the information theoretic quantities MI and CMI determine the regulatory relationships between genes and the PMDL principle method attempts to determine the best MI threshold without the need of a user-specified fine tuning parameter. The performance of the proposed algorithm is evaluated using both synthetic time series data sets and a biological time series data set (Saccharomyces cerevisiae). The results show that the proposed algorithm produced fewer false edges and significantly improved the precision when compared to existing MDL algorithm.

An association between geomagnetic activity and dream bizarreness.

Science.gov (United States)

Lipnicki, Darren M

2009-07-01

Daily disturbances of the earth's magnetic field produce variations in geomagnetic activity (GMA) that are reportedly associated with widespread effects on human health and behaviour. Some of these effects could be mediated by an established influence of GMA on the secretion of melatonin. There is evidence from unrelated research that melatonin influences dream bizarreness, and it is hypothesised here that there is an association between GMA and dream bizarreness. Also reported is a preliminary test of this hypothesis, a case study in which the dreams recorded over 6.5 years by a young adult male were analysed. Reports of dreams from the second of two consecutive days of either low or high GMA (K index sum or = 28) were self-rated for bizarreness on a 1-5 scale. Dreams from low GMA periods (n=69, median bizarreness=4) were found to be significantly more bizarre than dreams from high GMA periods (n=85, median bizarreness=3; p=0.006), supporting the hypothesised association between GMA and dream bizarreness. Studies with larger samples are needed to verify this association, and to determine the extent to which melatonin may be involved. Establishing that there is an association between GMA and dream bizarreness would have relevance for neurophysiological theories of dreaming, and for models of psychotic symptoms resembling bizarre dream events.

Dreaming, fenfluramine, and vitamin C.

Science.gov (United States)

Mullen, A; Wilson, C W; Wilson, B P

1977-01-08

The effect of increasing doses of fenfluramine on dream patterns was studied in 20 patients receiving a reducing diet with or without a controlled dietary intake of vitamin C daily. The dream pattern was unchanged in six patients and dreams disappeared in another who normally dreamed often. In 13 patients dreams increased in frequency and intensity, and in five the dreams assumed frightening proportions. There was a significant straight-line relation between response and the size of the dose. When placebo tablets were given to four patients their dreams disappeared or assumed their pretreatment normal pattern. Absence of vitamin C from the diet did not significantly affect the dream pattern. That fenfluramine has dose-related cerebral effects should be remembered in patients with a history of mental illness.

Metacognitive mechanisms underlying lucid dreaming.

Science.gov (United States)

Filevich, Elisa; Dresler, Martin; Brick, Timothy R; Kühn, Simone

2015-01-21

Lucid dreaming is a state of awareness that one is dreaming, without leaving the sleep state. Dream reports show that self-reflection and volitional control are more pronounced in lucid compared with nonlucid dreams. Mostly on these grounds, lucid dreaming has been associated with metacognition. However, the link to lucid dreaming at the neural level has not yet been explored. We sought for relationships between the neural correlates of lucid dreaming and thought monitoring. Human participants completed a questionnaire assessing lucid dreaming ability, and underwent structural and functional MRI. We split participants based on their reported dream lucidity. Participants in the high-lucidity group showed greater gray matter volume in the frontopolar cortex (BA9/10) compared with those in the low-lucidity group. Further, differences in brain structure were mirrored by differences in brain function. The BA9/10 regions identified through structural analyses showed increases in blood oxygen level-dependent signal during thought monitoring in both groups, and more strongly in the high-lucidity group. Our results reveal shared neural systems between lucid dreaming and metacognitive function, in particular in the domain of thought monitoring. This finding contributes to our understanding of the mechanisms enabling higher-order consciousness in dreams. Copyright © 2015 the authors 0270-6474/15/351082-07$15.00/0.

Colorful Dreams

Institute of Scientific and Technical Information of China (English)

李汉峰; 李永浩; 王雷; 刘玉; 李娜

2007-01-01

Every young student has a beautiful dream in his/her heart.In order to make it come true,we work hard.Sometimes we want to give it up when facing difficulties, but we still go on.Dreams make our lives wonderful...

The brain as a dream state generator: an activation-synthesis hypothesis of the dream process.

Science.gov (United States)

Hobson, J A; McCarley, R W

1977-12-01

Recent research in the neurobiology of dreaming sleep provides new evidence for possible structural and functional substrates of formal aspects of the dream process. The data suggest that dreaming sleep is physiologically determined and shaped by a brain stem neuronal mechanism that can be modeled physiologically and mathematically. Formal features of the generator processes with strong implications for dream theory include periodicity and automaticity of forebrain activation, suggesting a preprogrammed neural basis for dream mentation in sleep; intense and sporadic activation of brain stem sensorimotor circuits including reticular, oculomotor, and vestibular neurons, possibly determining spatiotemporal aspects of dream imagery; and shifts in transmitter ratios, possibly accounting for dream amnesia. The authors suggest that the automatically activated forebrain synthesizes the dream by comparing information generated in specific brain stem circuits with information stored in memory.

Fine-granularity inference and estimations to network traffic for SDN.

Directory of Open Access Journals (Sweden)

Dingde Jiang

Full Text Available An end-to-end network traffic matrix is significantly helpful for network management and for Software Defined Networks (SDN. However, the end-to-end network traffic matrix's inferences and estimations are a challenging problem. Moreover, attaining the traffic matrix in high-speed networks for SDN is a prohibitive challenge. This paper investigates how to estimate and recover the end-to-end network traffic matrix in fine time granularity from the sampled traffic traces, which is a hard inverse problem. Different from previous methods, the fractal interpolation is used to reconstruct the finer-granularity network traffic. Then, the cubic spline interpolation method is used to obtain the smooth reconstruction values. To attain an accurate the end-to-end network traffic in fine time granularity, we perform a weighted-geometric-average process for two interpolation results that are obtained. The simulation results show that our approaches are feasible and effective.

Fine-granularity inference and estimations to network traffic for SDN.

Science.gov (United States)

Jiang, Dingde; Huo, Liuwei; Li, Ya

2018-01-01

An end-to-end network traffic matrix is significantly helpful for network management and for Software Defined Networks (SDN). However, the end-to-end network traffic matrix's inferences and estimations are a challenging problem. Moreover, attaining the traffic matrix in high-speed networks for SDN is a prohibitive challenge. This paper investigates how to estimate and recover the end-to-end network traffic matrix in fine time granularity from the sampled traffic traces, which is a hard inverse problem. Different from previous methods, the fractal interpolation is used to reconstruct the finer-granularity network traffic. Then, the cubic spline interpolation method is used to obtain the smooth reconstruction values. To attain an accurate the end-to-end network traffic in fine time granularity, we perform a weighted-geometric-average process for two interpolation results that are obtained. The simulation results show that our approaches are feasible and effective.

The dream in contemporary psychiatry.

Science.gov (United States)

Reiser, M F

2001-03-01

This article offers selective reviews of cogent sectors of research regarding the dream in contemporary psychiatry. First, the author discusses relatively recent research (1953-1999) on the neurobiology and clinical psychophysiology of dreaming sleep; second, he reviews experimental cognitive neuroscientific studies of perception, emotion, and memory and the putative interrelationships among them in generating dream imagery; and third, he interprets psychoanalytic studies (1900-1999) on related aspects of dreams and the dream process. Exploration for interrelationships among information from these three areas entails discussion of the mind/brain problem. These considerations illuminate some of the logical and interpretive dilemmas that enter into debates about Freud's theory of the dream. The author proposes a preliminary psychobiologic concept of the dream process and discusses, in light of the foregoing considerations, the importance of collaborative research for developing a realistic perspective concerning the proper place of the dream in contemporary psychiatry.

Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks.

Science.gov (United States)

Wang, Yi Kan; Hurley, Daniel G; Schnell, Santiago; Print, Cristin G; Crampin, Edmund J

2013-01-01

We develop a new regression algorithm, cMIKANA, for inference of gene regulatory networks from combinations of steady-state and time-series gene expression data. Using simulated gene expression datasets to assess the accuracy of reconstructing gene regulatory networks, we show that steady-state and time-series data sets can successfully be combined to identify gene regulatory interactions using the new algorithm. Inferring gene networks from combined data sets was found to be advantageous when using noisy measurements collected with either lower sampling rates or a limited number of experimental replicates. We illustrate our method by applying it to a microarray gene expression dataset from human umbilical vein endothelial cells (HUVECs) which combines time series data from treatment with growth factor TNF and steady state data from siRNA knockdown treatments. Our results suggest that the combination of steady-state and time-series datasets may provide better prediction of RNA-to-RNA interactions, and may also reveal biological features that cannot be identified from dynamic or steady state information alone. Finally, we consider the experimental design of genomics experiments for gene regulatory network inference and show that network inference can be improved by incorporating steady-state measurements with time-series data.

The effects of suppressing intrusive thoughts on dream content, dream distress and psychological parameters.

Science.gov (United States)

Kröner-Borowik, Tana; Gosch, Stefanie; Hansen, Kathrin; Borowik, Benjamin; Schredl, Michael; Steil, Regina

2013-10-01

Suppressing unwanted thoughts can lead to an increased occurrence of the suppressed thought in dreams. This is explainable by the ironic control theory, which theorizes why the suppression of thoughts might make them more persistent. The present study examined the influence of thought suppression on dream rebound, dream distress, general psychiatric symptomatology, depression, sleep quality and perceived stress. Thirty healthy participants (good sleepers) were investigated over a period of 1 week. Half were instructed to suppress an unwanted thought 5 min prior to sleep, whereas the other half were allowed to think of anything at all. Dream content was assessed through a dream diary. Independent raters assessed whether or not the dreams were related to the suppressed target thought. The results demonstrated increased target-related dreams and a tendency to have more distressing dreams in the suppression condition. Moreover, the data imply that thought suppression may lead to significantly increased general psychiatric symptomatology. No significant effects were found for the other secondary outcomes. © 2013 European Sleep Research Society.

Older people's experiences of dream coaching.

Science.gov (United States)

Wadensten, Barbro

2009-12-01

Recalling and talking about dreams could initiate dream work among older people and provide an opportunity for self-confrontation and personal growth, which could in turn promote gerotranscendental development. The present article describes older people's opinions about participating in a dream-coaching group; it also briefly describes the theoretical foundation of dream coaching. The study aim was to investigate older people's experience of participating in a dream-coaching group based on Jungian psychology. A descriptive design was used. Retrospective interviews were explored using qualitative content analysis. The participants were satisfied with the arrangement of the dream-coaching groups. All participants believed that they had recalled their dreams and thought much more about their dreams during the period in which the dream-coaching group met. Three diverse appraisals of participating in a dream-coaching group, which had different effects on the participants, were identified: "An activity like any other activity," "An activity that led to deeper thoughts about the meaning of dreams," and "An activity that led to deeper thoughts both about the meaning of dreams and about how dreams can improve one's understanding of the life situation." It is possible to arrange dream-coaching groups for older people and could be a way to promote personal development using this type of intervention. The study provides some guidance as to how such a group could be organized, thus facilitating use of dream-coaching groups in gerontological care.

The Use of Dreams in Psychotherapy

Science.gov (United States)

Schredl, Michael; Bohusch, Claudia; Kahl, Johanna; Mader, Andrea; Somesan, Alexandra

2000-01-01

Since the publication of Sigmund Freud's The Interpretation of Dreams, dream interpretation has been a standard technique often used in psychotherapy. However, empirical studies about the frequency of working on dreams in therapy are lacking. The present study elicited, via a self-developed questionnaire, various aspects of work on dreams applied by psychotherapists in private practice. The findings indicate that dreams were often used in therapy, especially in psychoanalysis. In addition, a significant relationship was found between the frequency of the therapists' working on their own dreams and frequency of work on dreams in therapy. Because work on dreams was rated as beneficial for the clients, further studies investigating the effectiveness and the process of working on dreams will be of interest. PMID:10793127

Opinion Dynamics on Networks with Inference of Unobservable States of Others

Science.gov (United States)

Fujie, Ryo

In most opinion formation models which have been proposed, the agents decide their states (i.e. opinions) by referring to the states of others. However, the referred states of others are not necessarily observable and may be inferred. To investigate the effect of an inference of the states of others on opinion dynamics, I propose an extended voter model on networks where observable and referable node sets are different. These sets for a node defined as the nearest to the mo-th neighbors for observable nodes and the nearest to the mr-th neighbors for referable nodes. The state of referable but unobservable node which is the m-th neighbor (mo pagerank'' is conserved. This conserved quantity coincides with the fixation probability. On the other hand, in the case of mo =mr = 1 , the model comes down to the standard voter model on networks and the conserved quantity is a degree-weighted superposition of the states. Thus, the introduction of the inference changes the important opinion spreaders from the high-degree nodes to the high-betweenness pagerank nodes. This work is supported by the Collaboration Research Program of IDEAS, Chubu University IDEAS2016233.

Intraoperative dreams reported after general anaesthesia are not early interpretations of delayed awareness.

Science.gov (United States)

Samuelsson, P; Brudin, L; Sandin, R H

2008-07-01

Dreams are more frequently reported than awareness after surgery. We define awareness as explicit recall of real intraoperative events during anaesthesia. The importance of intraoperative dreaming is poorly understood. This study was performed to evaluate whether intraoperative dreams can be associated with, or precede, awareness. We also studied whether dreams can be related to case-specific parameters. A cohort of 6991 prospectively included patients given inhalational anaesthesia were interviewed for dreams and awareness at three occasions; before they left the post-anaesthesia care unit, days 1-3 and days 7-14 after the operation. Uni- and multivariate statistical relations between dreams, awareness and case-specific parameters were assessed. Two hundred and thirty-two of 6991 patients (3.3%) reported a dream. Four of those also reported awareness and remembered real events that were distinguishable from their dream. Awareness was 19 times more common among patients who after surgery reported a dream [1.7% vs. 0.09%; odds ratio (OR) 18.7; P=0.000007], but memories of dreams did not precede memories of awareness in any of the 232 patients reporting a dream. Unpleasant dreams were significantly more common when thiopentone was used compared with propofol (OR 2.22; P=0.005). Neutral or pleasant dreams were related to lower body mass index, female gender and shorter duration of anaesthesia. We found a statistically significant association between dreams reported after general anaesthesia and awareness, although intraoperative dreams were not an early interpretation of delayed awareness in any case. A typical dreamer in this study is a lean female having a short procedure.

Dreaming and Neuroesthetics

Science.gov (United States)

Barcaro, Umberto; Paoli, Marco

2015-01-01

This paper, which is limited to the art of painting, aims to support the idea that a substantial insertion of concepts and methods drawn on dream psychology and dream neuroscience can contribute to the advancements of Neuroesthetics. The historical and scientific reasons are discussed that have determined the so far poor role played by the dream phenomenon in the developments of Neuroesthetics. In the light of recent advancements in psychophysiological research, a method of analyzing artistic products is proposed that is based on the recognition of precise features proper of the dreaming experience. Four examples are given for application of this method, regarding works by Giorgione, Leonardo da Vinci, Vermeer, and Millais, respectively. PMID:26157373

Mocapy++ - a toolkit for inference and learning in dynamic Bayesian networks

DEFF Research Database (Denmark)

Paluszewski, Martin; Hamelryck, Thomas Wim

2010-01-01

Background Mocapy++ is a toolkit for parameter learning and inference in dynamic Bayesian networks (DBNs). It supports a wide range of DBN architectures and probability distributions, including distributions from directional statistics (the statistics of angles, directions and orientations...

An approach for reduction of false predictions in reverse engineering of gene regulatory networks.

Science.gov (United States)

Khan, Abhinandan; Saha, Goutam; Pal, Rajat Kumar

2018-05-14

A gene regulatory network discloses the regulatory interactions amongst genes, at a particular condition of the human body. The accurate reconstruction of such networks from time-series genetic expression data using computational tools offers a stiff challenge for contemporary computer scientists. This is crucial to facilitate the understanding of the proper functioning of a living organism. Unfortunately, the computational methods produce many false predictions along with the correct predictions, which is unwanted. Investigations in the domain focus on the identification of as many correct regulations as possible in the reverse engineering of gene regulatory networks to make it more reliable and biologically relevant. One way to achieve this is to reduce the number of incorrect predictions in the reconstructed networks. In the present investigation, we have proposed a novel scheme to decrease the number of false predictions by suitably combining several metaheuristic techniques. We have implemented the same using a dataset ensemble approach (i.e. combining multiple datasets) also. We have employed the proposed methodology on real-world experimental datasets of the SOS DNA Repair network of Escherichia coli and the IMRA network of Saccharomyces cerevisiae. Subsequently, we have experimented upon somewhat larger, in silico networks, namely, DREAM3 and DREAM4 Challenge networks, and 15-gene and 20-gene networks extracted from the GeneNetWeaver database. To study the effect of multiple datasets on the quality of the inferred networks, we have used four datasets in each experiment. The obtained results are encouraging enough as the proposed methodology can reduce the number of false predictions significantly, without using any supplementary prior biological information for larger gene regulatory networks. It is also observed that if a small amount of prior biological information is incorporated here, the results improve further w.r.t. the prediction of true positives

Daydreams and nap dreams: Content comparisons.

Science.gov (United States)

Carr, Michelle; Nielsen, Tore

2015-11-01

Differences between nighttime REM and NREM dreams are well-established but only rarely are daytime REM and NREM nap dreams compared with each other or with daydreams. Fifty-one participants took daytime naps (with REM or NREM awakenings) and provided both waking daydream and nap dream reports. They also provided ratings of their bizarreness, sensory experience, and emotion intensity. Recall rates for REM (96%) and NREM (89%) naps were elevated compared to typical recall rates for nighttime dreams (80% and 43% respectively), suggesting an enhanced circadian influence. All attribute ratings were higher for REM than for NREM dreams, replicating findings for nighttime dreams. Compared with daydreams, NREM dreams had lower ratings for emotional intensity and sensory experience while REM dreams had higher ratings for bizarreness and sensory experience. Results support using daytime naps in dream research and suggest that there occurs selective enhancement and inhibition of specific dream attributes by REM, NREM and waking state mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Dreaming Your Fear Away: A Computational Model for Fear Extinction Learning During Dreaming

NARCIS (Netherlands)

Treur, J.; Lu et al., B.L.

2011-01-01

In this paper a computational model is presented that models how dreaming is used to learn fear extinction. The approach addresses dreaming as internal simulation incorporating memory elements in the form of sensory representations and their associated fear. During dream episodes regulation of fear

A relative variation-based method to unraveling gene regulatory networks.

Directory of Open Access Journals (Sweden)

Yali Wang

Full Text Available Gene regulatory network (GRN reconstruction is essential in understanding the functioning and pathology of a biological system. Extensive models and algorithms have been developed to unravel a GRN. The DREAM project aims to clarify both advantages and disadvantages of these methods from an application viewpoint. An interesting yet surprising observation is that compared with complicated methods like those based on nonlinear differential equations, etc., methods based on a simple statistics, such as the so-called Z-score, usually perform better. A fundamental problem with the Z-score, however, is that direct and indirect regulations can not be easily distinguished. To overcome this drawback, a relative expression level variation (RELV based GRN inference algorithm is suggested in this paper, which consists of three major steps. Firstly, on the basis of wild type and single gene knockout/knockdown experimental data, the magnitude of RELV of a gene is estimated. Secondly, probability for the existence of a direct regulation from a perturbed gene to a measured gene is estimated, which is further utilized to estimate whether a gene can be regulated by other genes. Finally, the normalized RELVs are modified to make genes with an estimated zero in-degree have smaller RELVs in magnitude than the other genes, which is used afterwards in queuing possibilities of the existence of direct regulations among genes and therefore leads to an estimate on the GRN topology. This method can in principle avoid the so-called cascade errors under certain situations. Computational results with the Size 100 sub-challenges of DREAM3 and DREAM4 show that, compared with the Z-score based method, prediction performances can be substantially improved, especially the AUPR specification. Moreover, it can even outperform the best team of both DREAM3 and DREAM4. Furthermore, the high precision of the obtained most reliable predictions shows that the suggested algorithm may be

[Reconsidering children's dreams. A critical review of methods and results in developmental dream research from Freud to contemporary works].

Science.gov (United States)

Sándor, Piroska; Bódizs, Róbert

2014-01-01

Examining children's dream development is a significant challenge for researchers. Results from studies on children's dreaming may enlighten us on the nature and role of dreaming as well as broaden our knowledge of consciousness and cognitive development. This review summarizes the main questions and historical progress in developmental dream research, with the aim of shedding light on the advantages, disadvantages and effects of different settings and methods on research outcomes. A typical example would be the dreams of 3 to 5 year-olds: they are simple and static, with a relative absence of emotions and active self participation according to laboratory studies; studies using different methodology however found them to be vivid, rich in emotions, with the self as an active participant. Questions about the validity of different methods arise, and are considered within this review. Given that methodological differences can result in highly divergent outcomes, it is strongly recommended for future research to select methodology and treat results more carefully.

The future of dream science.

Science.gov (United States)

Bulkeley, Kelly

2017-10-01

This article describes the future prospects of scientific dream research. Three frontiers of investigation hold special promise: neuroscientific studies of the brain-mind system's activities during sleep (such as during lucid dreaming); systematic analyses of large collections of dream reports from diverse populations of people; and psychotherapeutic explorations of the multiple dimensions of personal and collective meaning woven into the dream experiences of each individual. Several helpful books on the science of sleep and dreaming are mentioned for further study. © 2017 New York Academy of Sciences.

[Brief history of dreams].

Science.gov (United States)

Rosselli, D

Throughout history dreams have played a crucial role. Dreams have inspired great works of art, solved scientific problems and, because of the premonitory value attached to them, have influenced transcendental decisions. This paper reviews some of the dreams that have been a part of the world's literature and historical tradition.

Do "Undocumented Aliens" Dream of Neoliberal Sheep?: Conditional DREAMing and Decolonial Imaginaries

Science.gov (United States)

Ríos-Rojas, Anne; Stern, Mark

2018-01-01

Dreams have long been thought to be a space of fantasy and utopic hope. From Paulo Freire to Gloria Anzaldúa to Robin Kelley, many scholars have related the ability to dream with the ability to act collectively, to self-actualize, and to call into being worlds yet to be realized--dreaming as a radical political act. What happens, then, when dreams…

Dream-associated Behaviors Affecting Pregnant and Postpartum Women

Science.gov (United States)

Nielsen, Tore; Paquette, Tyna

2007-01-01

Study objectives: Evaluate the prevalence and phenomenology of dream-associated behaviors affecting pregnant and postpartum mothers. Episodes consist of anxious dreams and nightmares about the new infant that are accompanied by complex behaviors (motor activity, speaking, expressing emotion). Design: Three-group design (postpartum, pregnant, null gravida), self-report, and repeated measures. Setting: Pregnancy and postpartum groups: completion of questionnaires in hospital room within 48 hours of giving birth and home telephone interviews; null gravida group: completion of questionnaires and interview in person or by telephone. Participants: Two hundred seventy-three women in 3 groups: postpartum: n = 202 (mean age = 29.7 ± 4.94 years; 95 primiparas, 107 multiparas); pregnant: n = 50 (mean age = 31.1 ± 5.44 years); null gravida: n = 21 (mean age = 28.5 ± 6.34 years). Interventions: Subjects completed questionnaires about pregnancy and birth factors, personality, and sleep and participated in interviews concerning the prevalence of recent infant dreams and nightmares, associated behaviors, anxiety, depression, and other psychopathologic factors. Measurements and Results: Most women in all groups recalled dreams (88%-91%). Postpartum and pregnant women recalled infant dreams and nightmares with equal prevalence, but more postpartum women reported they contained anxiety (75%) and the infant in peril (73%) than did pregnant women (59%, P dream-associated behaviors (P dream anxiety and, among postpartum women, post-awakening anxiety (41%), confusion (51%), and a need to check on the infant (60%). Primiparas and multiparas differed in dream and nightmare recall but not in prevalence of dream-associated behaviors. Conclusion: The prevalent occurrence of pregnancy and postpartum infant dreams and associated behaviors may reflect the pervasive emotional influence of maternal concerns or changes instigated by severe sleep disruption, rapid eye movement sleep deprivation

Collaborative Wireless Sensor Networks in Industrial and Business Processes

NARCIS (Netherlands)

Marin Perianu, Mihai

2008-01-01

Personal computers, mobile telephony and the Internet made the vision of everyone being networked real, at such a level of quality and speed that people could only dream of, one hundred years ago. Nowadays, another dream starts to become reality: the dream of networking everything. The limits of

Dreaming: a gateway to the unconscious?

Science.gov (United States)

Paulson, Steve; Barrett, Deirdre; Bulkeley, Kelly; Naiman, Rubin

2017-10-01

Where do our dreams originate from, and what do they tell us? Is there a universal set of symbols that are common to all dreams, regardless of a person's ethnicity or culture? What does dreaming reveal about the unconscious? Why do some dreams remain etched in our memories, whereas others are almost instantly forgotten? Some scientists have adopted the position that dreams are little more than noise in the brain, without any substantive purpose or function. Yet, such a stance seemingly runs counter to the experience of many people who reflect upon and even analyze their dreams, often in search of clues to their daily lives or insights into their deeper selves. Similarly, in virtually all wisdom traditions, dreams are invoked as an important source of revelation or prophecy. Steve Paulson, executive producer and host of To the Best of Our Knowledge, moderated a discussion that included psychologist Deirdre Barrett, dream researcher Kelly Bulkeley, and psychologist and sleep/dream medicine specialist Rubin Naiman; they examined dreams from a variety of perspectives to answer these questions. © 2017 New York Academy of Sciences.

The use of dreams in spiritual care.

Science.gov (United States)

Stranahan, Susan

2011-01-01

This paper explores the use of dreams in the context of pastoral care. Although many people dream and consider their dreams to hold some significant spiritual meaning, spiritual care providers have been reluctant to incorporate patients' dreams into the therapeutic conversation. Not every dream can be considered insightful, but probing the meaning of some dreams can enhance spiritual care practice. Hill's Cognitive-Experimental Dream Interpretation Model is applied in the current article as a useful framework for exploring dreams, gaining insight about spiritual problems, and developing a therapeutic plan of action. Bulkeley's criteria for dream interpretation were used to furnish safeguards against inappropriate application of dream interpretation to spiritual assessment and interventions.

Recalling and forgetting dreams: theta and alpha oscillations during sleep predict subsequent dream recall.

Science.gov (United States)

Marzano, Cristina; Ferrara, Michele; Mauro, Federica; Moroni, Fabio; Gorgoni, Maurizio; Tempesta, Daniela; Cipolli, Carlo; De Gennaro, Luigi

2011-05-04

Under the assumption that dream recall is a peculiar form of declarative memory, we have hypothesized that (1) the encoding of dream contents during sleep should share some electrophysiological mechanisms with the encoding of episodic memories of the awake brain and (2) recalling a dream(s) after awakening from non-rapid eye movement (NREM) and rapid eye movement (REM) sleep should be associated with different brain oscillations. Here, we report that cortical brain oscillations of human sleep are predictive of successful dream recall. In particular, after morning awakening from REM sleep, a higher frontal 5-7 Hz (theta) activity was associated with successful dream recall. This finding mirrors the increase in frontal theta activity during successful encoding of episodic memories in wakefulness. Moreover, in keeping with the different EEG background, a different predictive relationship was found after awakening from stage 2 NREM sleep. Specifically, a lower 8-12 Hz (alpha) oscillatory activity of the right temporal area was associated with a successful dream recall. These findings provide the first evidence of univocal cortical electroencephalographic correlates of dream recall, suggesting that the neurophysiological mechanisms underlying the encoding and recall of episodic memories may remain the same across different states of consciousness.

Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences among Ontologies

Science.gov (United States)

Peng, Yefei

2010-01-01

An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'s ability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the…

Dreams as a source of supernatural agent concepts.

Science.gov (United States)

McNamara, Patrick; Bulkeley, Kelly

2015-01-01

We present a theory of the creativity of dreams as well as psychopathology of religious delusions with respect to production of fundamental forms of religious cognition-specifically supernatural agent (SA) cognitions. We suggest that dream cognitions are particularly efficient at producing highly memorable and impactful experiences with SAs because dreams involve three processes that are prerequisites for the generation of god concepts: (1) mental simulations of alternative realities, (2) theory of mind attributions to the extra-natural dream characters and divine beings, and (3) attribution of ultimate value (exemplified by 'good spirit beings'), and dis-value (exemplified by demonic monsters) to the supernatural dream characters. Because prefrontal cortex is deactivated during rapid eye movements (REM) sleep agentic impulses and internally generated ideas are not reliably attributed to Self or dreamer. Instead an exaggerated degree of agency is attributed to these supernatural dream characters who are then embedded in stories in dreams and in myths of waking life which explain their supernatural abilities. These dream-based SAs are salient characters that are processed in sleep-related memory systems according to rules of Lleweelyn's ancient art of memory model and therefore more easily remembered and reflected upon during waking life. When REM sleep intrudes into waking consciousness, as is the case with some forms of schizophrenia, religious delusions are more likely to emerge.

Dreams as a source of supernatural agent concepts

Science.gov (United States)

McNamara, Patrick; Bulkeley, Kelly

2015-01-01

We present a theory of the creativity of dreams as well as psychopathology of religious delusions with respect to production of fundamental forms of religious cognition—specifically supernatural agent (SA) cognitions. We suggest that dream cognitions are particularly efficient at producing highly memorable and impactful experiences with SAs because dreams involve three processes that are prerequisites for the generation of god concepts: (1) mental simulations of alternative realities, (2) theory of mind attributions to the extra-natural dream characters and divine beings, and (3) attribution of ultimate value (exemplified by ‘good spirit beings’), and dis-value (exemplified by demonic monsters) to the supernatural dream characters. Because prefrontal cortex is deactivated during rapid eye movements (REM) sleep agentic impulses and internally generated ideas are not reliably attributed to Self or dreamer. Instead an exaggerated degree of agency is attributed to these supernatural dream characters who are then embedded in stories in dreams and in myths of waking life which explain their supernatural abilities. These dream-based SAs are salient characters that are processed in sleep-related memory systems according to rules of Lleweelyn’s ancient art of memory model and therefore more easily remembered and reflected upon during waking life. When REM sleep intrudes into waking consciousness, as is the case with some forms of schizophrenia, religious delusions are more likely to emerge. PMID:25852602

Dreams as a source of supernatural agent concepts

Directory of Open Access Journals (Sweden)

Patrick eMcnamara

2015-03-01

Full Text Available We present a theory of the creativity of dreams as well as psychopathology of religious delusions with respect to production of fundamental forms of religious cognition—specifically supernatural agent cognitions. We suggest that dream cognitions are particularly efficient at producing highly memorable and impactful experiences with supernatural agents because dreams involve three processes that are prerequisites for the generation of god concepts: 1 mental simulations of alternative realities, 2 theory of mind attributions to the extra-natural dream characters and divine beings and 3 attribution of ultimate value (exemplified by ‘good spirit beings’ and dis-value (exemplified by demonic monsters to the supernatural dream characters. Because prefrontal cortex is deactivated during REM sleep agentic impulses and internally generated ideas are not reliably attributed to Self or dreamer. Instead an exaggerated degree of agency is attributed to these supernatural dream characters who are then embedded in stories in dreams and in myths of waking life which explain their supernatural abilities. These dream-based supernatural agents are salient characters that are processed in sleep-related memory systems according to rules of Lleweelyn’s AAOM model and therefore more easily remembered and reflected upon during waking life. When REM sleep intrudes into waking consciousness, as is the case with some forms of schizophrenia, religious delusions are more likely to emerge.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Science.gov (United States)

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

I had a dream

Institute of Scientific and Technical Information of China (English)

By William E. Wright

2012-01-01

I had a dream. Like Martin Luther King, Jr. said in a speech memorized by almost all Chinese students, I had a dream. My dream was that one day I would teach in a foreign country. Little did I know how fascinating and rich teaching in the Law School of Shandong University would be.

[Exploring dream contents by neuroimaging].

Science.gov (United States)

Horikawa, Tomoyasu; Kamitani, Yukiyasu

2014-04-01

Dreaming is a subjective experience during sleep that is often accompanied by vivid perceptual and emotional contents. Because of its fundamentally subjective nature, the objective study of dream contents has been challenging. However, since the discovery of rapid eye movements during sleep, scientific knowledge on the relationship between dreaming and physiological measures including brain activity has accumulated. Recent advances in neuroimaging analysis methods have made it possible to uncover direct links between specific dream contents and brain activity patterns. In this review, we first give a historical overview on dream researches with a focus on the neurophysiological and behavioral signatures of dreaming. We then discuss our recent study in which visual dream contents were predicted, or decoded, from brain activity during sleep onset periods using machine learning-based pattern recognition of functional MRI data. We suggest that advanced analytical tools combined with neural and behavioral databases will reveal the relevance of spontaneous brain activity during sleep to waking experiences.

Big Dreams

Science.gov (United States)

Benson, Michael T.

2015-01-01

The Keen Johnson Building is symbolic of Eastern Kentucky University's historic role as a School of Opportunity. It is a place that has inspired generations of students, many from disadvantaged backgrounds, to dream big dreams. The construction of the Keen Johnson Building was inspired by a desire to create a student union facility that would not…

Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana

KAUST Repository

Muraro, D.

2013-01-01

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in systems biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyze two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, and assess causality of their regulatory interactions by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation. © 2004-2012 IEEE.

Approximation Methods for Inference and Learning in Belief Networks: Progress and Future Directions

National Research Council Canada - National Science Library

Pazzan, Michael

1997-01-01

.... In this research project, we have investigated methods and implemented algorithms for efficiently making certain classes of inference in belief networks, and for automatically learning certain...

Information retrieval system with ability of analogical inference using semantic network and function of fuzzification

Energy Technology Data Exchange (ETDEWEB)

Nakamura, K; Iwai, S

1982-01-01

In information retrieval system, it is necessary to grasp user's subject of interest in order to present appropriate documents to the user. In this paper, the authors propose a model of human ability of analogical inference based on association between key words and, using it, construct an information retrieval system in which the computer with the ability learns its user's subject of interest through question-answering with the user. In this system, the association between key words is represented by a semantic network, and a function of fuzzification of input information is introduced in the semantic network to implement the ability of analogical inference based on the association. Finally, the effect of analogical inference on the learning efficiency of the system is investigated. 5 references.

[Dreams in normal and pathological aging].

Science.gov (United States)

Guénolé, Fabian; Marcaggi, Geoffrey; Baleyte, Jean-Marc; Garma, Lucile

2010-06-01

Although most of scientific knowledge in dream research is based on young adult studies, this article provides a review of the effects of normal and pathological aging on dream psychology. It starts with preliminary comments about epistemological and methodological principles of dream research, its singularities in aged persons, and the modifications of sleep physiology with age. The whole literature agrees that dream recall progressively decreases from the beginning of adulthood - not in old age - and that dream reports become less intense, perceptually and emotionally. This evolution occurs faster in men than women, with gender differences in the content of dreams. The chronological modifications could be explained partly by changes in lifestyle and attitude towards dreams in early adulthood, but mainly by modifications of sleep physiology, particularly the decrease and qualitative changes of rapid eye movement (REM) sleep. Dreams have usually little subjective importance in the mental life of aged persons. However, working with dreams can be a valuable tool for psychotherapy in the aged. According to the few existing data, patients suffering degenerative dementia dream much less than healthy aged persons. In Alzheimer's disease, this could be linked to the decrease of REM sleep, and atrophy of associative sensory areas of the cerebral cortex. Most studied aspects of dreaming in degenerative cognitive disorders are REM sleep behavior disorders, and nightmares induced by cholinesterase inhibitors. More studies are needed to better characterize the evolution of dreams with age, particularly studies performed in sleep laboratory.

Dreams and creative problem-solving.

Science.gov (United States)

Barrett, Deirdre

2017-10-01

Dreams have produced art, music, novels, films, mathematical proofs, designs for architecture, telescopes, and computers. Dreaming is essentially our brain thinking in another neurophysiologic state-and therefore it is likely to solve some problems on which our waking minds have become stuck. This neurophysiologic state is characterized by high activity in brain areas associated with imagery, so problems requiring vivid visualization are also more likely to get help from dreaming. This article reviews great historical dreams and modern laboratory research to suggest how dreams can aid creativity and problem-solving. © 2017 New York Academy of Sciences.

SSRI treatment suppresses dream recall frequency but increases subjective dream intensity in normal subjects.

Science.gov (United States)

Pace-Schott, E F; Gersh, T; Silvestri, R; Stickgold, R; Salzman, C; Hobson, J A

2001-06-01

Clinical lore and a small number of published studies report that the selective serotonin reuptake inhibitors (SSRIs) intensify dreaming. This study examines the dream effects of paroxetine and fluvoxamine in order to both increase clinical knowledge of these agents and to test an important potential method for probing the relationship between REM sleep neurobiology and dreaming in humans. Fourteen normal, paid volunteers (4 males, 10 females; mean age 27.4 year, range 22--39) free of medical or neuropsychiatric symptoms as well as of psychotropic or sleep affecting drugs completed a 31-day home-based study consisting of: 7 days drug-free baseline; 19 days on either 100 mg fluvoxamine (7 Ss) or 20 mg paroxetine (7 Ss) in divided morning and evening doses; and 5 days acute discontinuation. Upon awakening, subjects wrote dream reports, self-scored specific emotions in their reports and rated seven general dream characteristics using 5-point Likert scales. Dream reports were independently scored for bizarreness, movement and number of visual nouns by three judges. REM sleep-related measures were obtained using the Nightcap ambulatory sleep monitor. Mean dream recall frequency decreased during treatment compared with baseline. Dream report length and judge-rated bizarreness were greater during acute discontinuation compared with both baseline and treatment and this effect was a result of the fluvoxamine-treated subjects. The subjective intensity of dreaming increased during both treatment and acute discontinuation compared with baseline. Propensity to enter REM sleep was decreased during treatment compared with baseline and acute discontinuation and the intensity of REM sleep increased during acute discontinuation compared with baseline and treatment. The decrease in dream frequency during SSRI treatment may reflect serotonergic REM suppression while the augmented report length and bizarreness during acute SSRI discontinuation may reflect cholinergic rebound from

Dreams, reality and memory: confabulations in lucid dreamers implicate reality-monitoring dysfunction in dream consciousness.

Science.gov (United States)

Corlett, P R; Canavan, S V; Nahum, L; Appah, F; Morgan, P T

2014-01-01

Dreams might represent a window on altered states of consciousness with relevance to psychotic experiences, where reality monitoring is impaired. We examined reality monitoring in healthy, non-psychotic individuals with varying degrees of dream awareness using a task designed to assess confabulatory memory errors - a confusion regarding reality whereby information from the past feels falsely familiar and does not constrain current perception appropriately. Confabulatory errors are common following damage to the ventromedial prefrontal cortex (vmPFC). Ventromedial function has previously been implicated in dreaming and dream awareness. In a hospital research setting, physically and mentally healthy individuals with high (n = 18) and low (n = 13) self-reported dream awareness completed a computerised cognitive task that involved reality monitoring based on familiarity across a series of task runs. Signal detection theory analysis revealed a more liberal acceptance bias in those with high dream awareness, consistent with the notion of overlap in the perception of dreams, imagination and reality. We discuss the implications of these results for models of reality monitoring and psychosis with a particular focus on the role of vmPFC in default-mode brain function, model-based reinforcement learning and the phenomenology of dreaming and waking consciousness.

Gene network inference and biochemical assessment delineates GPCR pathways and CREB targets in small intestinal neuroendocrine neoplasia.

Directory of Open Access Journals (Sweden)

Ignat Drozdov

Full Text Available Small intestinal (SI neuroendocrine tumors (NET are increasing in incidence, however little is known about their biology. High throughput techniques such as inference of gene regulatory networks from microarray experiments can objectively define signaling machinery in this disease. Genome-wide co-expression analysis was used to infer gene relevance network in SI-NETs. The network was confirmed to be non-random, scale-free, and highly modular. Functional analysis of gene co-expression modules revealed processes including 'Nervous system development', 'Immune response', and 'Cell-cycle'. Importantly, gene network topology and differential expression analysis identified over-expression of the GPCR signaling regulators, the cAMP synthetase, ADCY2, and the protein kinase A, PRKAR1A. Seven CREB response element (CRE transcripts associated with proliferation and secretion: BEX1, BICD1, CHGB, CPE, GABRB3, SCG2 and SCG3 as well as ADCY2 and PRKAR1A were measured in an independent SI dataset (n = 10 NETs; n = 8 normal preparations. All were up-regulated (p<0.035 with the exception of SCG3 which was not differently expressed. Forskolin (a direct cAMP activator, 10(-5 M significantly stimulated transcription of pCREB and 3/7 CREB targets, isoproterenol (a selective ß-adrenergic receptor agonist and cAMP activator, 10(-5 M stimulated pCREB and 4/7 targets while BIM-53061 (a dopamine D(2 and Serotonin [5-HT(2] receptor agonist, 10(-6 M stimulated 100% of targets as well as pCREB; CRE transcription correlated with the levels of cAMP accumulation and PKA activity; BIM-53061 stimulated the highest levels of cAMP and PKA (2.8-fold and 2.5-fold vs. 1.8-2-fold for isoproterenol and forskolin. Gene network inference and graph topology analysis in SI NETs suggests that SI NETs express neural GPCRs that activate different CRE targets associated with proliferation and secretion. In vitro studies, in a model NET cell system, confirmed that transcriptional

Dream Team - A pregraduate surgical talent development project

DEFF Research Database (Denmark)

Jensen, Rune Dall; Seyer-Hansen, Mikkel; Christensen, Mette Krogh

Dream Team is an extracurricular pregraduate surgical talent development project founded in 2009 at Aarhus University Hospital, Denmark. It aims to identify and develop laparoscopic surgical talents during medical school. Dream Team contains two parts: 1) a weeklong boot camp where app. 10 % of 8th...... the mentorship the students will be in operation room at least once a week and participate as much as their skills allow. Dream Team differs from similar pregraduate programs as it selects the most talented students, but does the boot camp select the best and does the mentorship program provide optimal learning......? A PhD project aims to critically analyze and develop Dream Team. The PhD project is based on theories about deliberate practice[1] and social learning[2]. In addition, we compare surgical talent development[3][4] with talent development in elite sport in order to inspire, refine and develop Dream Team...

[Are oppressive dreams indicators in bereavement?].

Science.gov (United States)

Purebl, György; Pilling, János; Konkolÿ, Thege Barna; Bódizs, Róbert; Kopp, Mária

2012-07-30

It is widely believed that oppressive dreams are frequent in bereavement--despite the lack of scientific investigations of the subject. The aims of our study were the analysis of dream quality as well as the correlates of oppressive dreams in bereavement. Participants with (N = 473) and without bereavement were compared upon the database of a national representative study (Hungarostudy Epidemiological Panel Survey 2006, N = 4329). Dream contents were assessed with the Dream Quality Questionnaire (DQQ). Depressive symptoms (BDI-S) and the presence anxiety were also investigated. Oppressive dreams occurred significantly higher frequency in the first year of bereavement (men: F = 17.525, p dreams were significantly associated with anxiety (F = 37.089, p dreams are significantly more frequent in the first year of bereavement, and may act as indicators of bereavement-linked mental health consequences like depression and anxiety. These are often masked by the symptoms of grief and therefore remain untreated. Our preliminary results could be a starting point for the development of further research aiming to clarify the relationship amongst dream contents, anxiety, and depression in bereavement.

The American Dream

OpenAIRE

Önnerth, Lars; Neubert, Mikkel; Omerbasic, Dejan; Heyman, Minch; Kimberly, Marie; Nielsen, Lyngbo; Mynte, Anne; Hørlyck Kaastrup, Markus

2015-01-01

This study examines the phenomenon that is the American Dream and its effect on the working and upper class citizens in American society. To give context to the American dream and its origin, we have made use of professor Jim Cullen’s book “The American Dream: A Short Story of an Idea that Shaped a Nation” from 2003. We have identified what we decided to call the “the traditional dream” and “the modern dream”, both representing different outlooks on lives and ethical standards. We have done t...

Digital dream analysis: a revised method.

Science.gov (United States)

Bulkeley, Kelly

2014-10-01

This article demonstrates the use of a digital word search method designed to provide greater accuracy, objectivity, and speed in the study of dreams. A revised template of 40 word search categories, built into the website of the Sleep and Dream Database (SDDb), is applied to four "classic" sets of dreams: The male and female "Norm" dreams of Hall and Van de Castle (1966), the "Engine Man" dreams discussed by Hobson (1988), and the "Barb Sanders Baseline 250" dreams examined by Domhoff (2003). A word search analysis of these original dream reports shows that a digital approach can accurately identify many of the same distinctive patterns of content found by previous investigators using much more laborious and time-consuming methods. The results of this study emphasize the compatibility of word search technologies with traditional approaches to dream content analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

Statistical inference approach to structural reconstruction of complex networks from binary time series

Science.gov (United States)

Ma, Chuang; Chen, Han-Shuang; Lai, Ying-Cheng; Zhang, Hai-Feng

2018-02-01

Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains challenging. We articulate a statistical inference based approach to this problem. In particular, exploiting the expectation-maximization (EM) algorithm, we develop a method to ascertain the neighbors of any node in the network based solely on binary data, thereby recovering the full topology of the network. A key ingredient of our method is the maximum-likelihood estimation of the probabilities associated with actual or nonexistent links, and we show that the EM algorithm can distinguish the two kinds of probability values without any ambiguity, insofar as the length of the available binary time series is reasonably long. Our method does not require any a priori knowledge of the detailed dynamical processes, is parameter-free, and is capable of accurate reconstruction even in the presence of noise. We demonstrate the method using combinations of distinct types of binary dynamical processes and network topologies, and provide a physical understanding of the underlying reconstruction mechanism. Our statistical inference based reconstruction method contributes an additional piece to the rapidly expanding "toolbox" of data based reverse engineering of complex networked systems.

Improvement of darts performance following lucid dream practice depends on the number of distractions while rehearsing within the dream - a sleep laboratory pilot study.

Science.gov (United States)

Schädlich, Melanie; Erlacher, Daniel; Schredl, Michael

2017-12-01

In a lucid dream, the dreamer is aware of the dream state and can deliberately practice motor skills. Two field studies indicated that lucid dream practice can improve waking performance in simple motor tasks. The present pilot study investigated the effect of lucid dream practice in a controlled sleep laboratory setting, using a pre-post design with dart throwing in the evening and morning. The experimental group practiced darts in lucid dreams. Because some participants were distracted during lucid dream practice, the group was divided into lucid dreamers with few (n = 4) and many distractions (n = 5). Change of performance was compared to a physical practice group (n = 9) and a control group (n = 9), showing a significant interaction (P = .013, η 2  = .368). Only the lucid dreamers with few distractions improved (18%) significantly over time (P = .005, d = 3.84). Even though these results have to be considered preliminary, the present study indicates that lucid dream practice can be an effective tool in sports practice if lucid dreamers find ways to minimise distractions during lucid dream practice. Moreover, the study emphasises the necessity to investigate lucid dream practice experiences on a qualitative level.

Dream content: Individual and generic aspects.

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Hobson, Allan; Kahn, David

2007-12-01

Dream reports were collected from normal subjects in an effort to determine the degree to which dream reports can be used to identify individual dreamers. Judges were asked to group the reports by their authors. The judges scored the reports correctly at chance levels. This finding indicated that dreams may be at least as much like each other as they are the signature of individual dreamers. Our results suggest that dream reports cannot be used to identify the individuals who produced them when identifiers like names and gender of friends and family members are removed from the dream report. In addition to using dreams to learn about an individual, we must look at dreams as telling us about important common or generic aspects of human consciousness.

Exploring the dreams of hospice workers.

Science.gov (United States)

Hess, Shirley A; Knox, Sarah; Hill, Clara E; Byers, Tara; Spangler, Patricia

2014-06-01

Nine adults who worked at least 1 year with patients at US hospice centers completed an in-person audiotaped dream session focusing on a dream about a patient. Data were analyzed using consensual qualitative research. Patients were generally manifestly present in participants' dreams, and dreams were typically realistic (i.e., not bizarre). In the dream, the dreamer typically interacted with the patient as a caretaker but was also typically frustrated by an inability to help as fully as desired. Dreams gave dreamers insight into the stress of hospice work, their own fears of death, and inter-/intrapersonal interactions beyond hospice work. Dreamers generally sought to take better care of themselves and find balance in their lives after the dream session. Implications for research and practice are discussed.

Transcending the caesura: reverie, dreaming and counter-dreaming.

Science.gov (United States)

Bergstein, Avner

2013-08-01

The author reflects about our capacity to get in touch with primitive, irrepresentable, seemingly unreachable parts of the Self and with the unrepressed unconscious. It is suggested that when the patient's dreaming comes to a halt, or encounters a caesura, the analyst dreams that which the patient cannot. Getting in touch with such primitive mental states and with the origin of the Self is aspired to, not so much for discovering historical truth or recovering unconscious content, as for generating motion between different parts of the psyche. The movement itself is what expands the mind and facilitates psychic growth. Bion's brave and daring notion of 'caesura', suggesting a link between mature emotions and thinking and intra-uterine life, serves as a model for bridging seemingly unbridgeable states of mind. Bion inspires us to 'dream' creatively, to let our minds roam freely, stressing the analyst's speculative imagination and intuition often bordering on hallucination. However, being on the seam between conscious and unconscious, dreaming subverts the psychic equilibrium and poses a threat of catastrophe as a result of the confusion it affords between the psychotic and the non-psychotic parts of the personality. Hence there is a tendency to try and evade it through a more saturated mode of thinking, often relying on external reality. The analyst's dreaming and intuition, perhaps a remnant of intra-uterine life, is elaborated as means of penetrating and transcending the caesura, thus facilitating patient and analyst to bear unbearable states of mind and the painful awareness of the unknowability of the emotional experience. This is illustrated clinically. Copyright © 2013 Institute of Psychoanalysis.

Free Energy and Virtual Reality in Neuroscience and Psychoanalysis: A Complexity Theory of Dreaming and Mental Disorder

Directory of Open Access Journals (Sweden)

Jim Hopkins

2016-07-01

Full Text Available The main concepts of the free energy (FE neuroscience developed by Karl Friston and colleagues parallel those of Freud’s Project for a Scientific Psychology. In Hobson, Hong and Friston (2014 these include an innate virtual reality generator that produces the fictive prior beliefs that Freud described as the primary process. This enables Friston’s account to encompass a unified treatment – a complexity theory – of the role of virtual reality in both dreaming and mental disorder.In both accounts the brain operates to minimize FE aroused by sensory impingements -- including interoceptive impingements that report compliance with biological imperatives -- and constructs a representation/model of the causes of impingement that enables this minimization. In Friston’s account (variational FE equals complexity minus accuracy, and is minimized by increasing accuracy and decreasing complexity. Roughly the brain (or model increases accuracy together with complexity in waking. This is mediated by consciousness-creating active inference – by which it explains sensory impingements in terms of perceptual experiences of their causes. In sleep it reduces complexity by processes that include both synaptic pruning and consciousness/virtual reality/dreaming in REM.The consciousness-creating active inference that effects complexity-reduction in REM dreaming must operate on FE-arousing data distinct from sensory impingement. The most relevant source is remembered arousals of emotion, both recent and remote, as processed in SWS and REM on ‘active systems’ accounts of memory consolidation/reconsolidation. Freud describes these remembered arousals as condensed in the dreamwork for use in the conscious contents of dreams, and similar condensation can be seen in symptoms.Complexity partly reflects emotional conflict and trauma. This indicates that dreams and symptoms are both produced to reduce complexity in the form of potentially adverse (traumatic or

Free Energy and Virtual Reality in Neuroscience and Psychoanalysis: A Complexity Theory of Dreaming and Mental Disorder.

Science.gov (United States)

Hopkins, Jim

2016-01-01

The main concepts of the free energy (FE) neuroscience developed by Karl Friston and colleagues parallel those of Freud's Project for a Scientific Psychology. In Hobson et al. (2014) these include an innate virtual reality generator that produces the fictive prior beliefs that Freud described as the primary process. This enables Friston's account to encompass a unified treatment-a complexity theory-of the role of virtual reality in both dreaming and mental disorder. In both accounts the brain operates to minimize FE aroused by sensory impingements-including interoceptive impingements that report compliance with biological imperatives-and constructs a representation/model of the causes of impingement that enables this minimization. In Friston's account (variational) FE equals complexity minus accuracy, and is minimized by increasing accuracy and decreasing complexity. Roughly the brain (or model) increases accuracy together with complexity in waking. This is mediated by consciousness-creating active inference-by which it explains sensory impingements in terms of perceptual experiences of their causes. In sleep it reduces complexity by processes that include both synaptic pruning and consciousness/virtual reality/dreaming in REM. The consciousness-creating active inference that effects complexity-reduction in REM dreaming must operate on FE-arousing data distinct from sensory impingement. The most relevant source is remembered arousals of emotion, both recent and remote, as processed in SWS and REM on "active systems" accounts of memory consolidation/reconsolidation. Freud describes these remembered arousals as condensed in the dreamwork for use in the conscious contents of dreams, and similar condensation can be seen in symptoms. Complexity partly reflects emotional conflict and trauma. This indicates that dreams and symptoms are both produced to reduce complexity in the form of potentially adverse (traumatic or conflicting) arousals of amygdala-related emotions

Model-free inference of direct network interactions from nonlinear collective dynamics.

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Casadiego, Jose; Nitzan, Mor; Hallerberg, Sarah; Timme, Marc

2017-12-19

The topology of interactions in network dynamical systems fundamentally underlies their function. Accelerating technological progress creates massively available data about collective nonlinear dynamics in physical, biological, and technological systems. Detecting direct interaction patterns from those dynamics still constitutes a major open problem. In particular, current nonlinear dynamics approaches mostly require to know a priori a model of the (often high dimensional) system dynamics. Here we develop a model-independent framework for inferring direct interactions solely from recording the nonlinear collective dynamics generated. Introducing an explicit dependency matrix in combination with a block-orthogonal regression algorithm, the approach works reliably across many dynamical regimes, including transient dynamics toward steady states, periodic and non-periodic dynamics, and chaos. Together with its capabilities to reveal network (two point) as well as hypernetwork (e.g., three point) interactions, this framework may thus open up nonlinear dynamics options of inferring direct interaction patterns across systems where no model is known.

Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana

KAUST Repository

Muraro, D.; Voss, U.; Wilson, M.; Bennett, M.; Byrne, H.; De Smet, I.; Hodgman, C.; King, J.

2013-01-01

thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based

Increased lucid dreaming frequency in narcolepsy

NARCIS (Netherlands)

Rak, M.; Beitinger, P.; Steiger, A.; Schredl, M.; Dresler, M.

2015-01-01

STUDY OBJECTIVE: Nightmares are a frequent symptom in narcolepsy. Lucid dreaming, i.e., the phenomenon of becoming aware of the dreaming state during dreaming, has been demonstrated to be of therapeutic value for recurrent nightmares. Data on lucid dreaming in narcolepsy patients, however, is

Dreaming Consciousness: A Contribution from Phenomenology

Directory of Open Access Journals (Sweden)

Nicola Zippel

2016-08-01

Full Text Available The central aim of this paper is to offer a historical reconstruction of phenomenological studies on dreaming and to put forward a draft for a phenomenological theory of the dream state. Prominent phenomenologists have offered an extremely valuable interpretation of the dream as an intentional process, stressing its relevance in understanding the complexity of the mental life of subject, the continuous interplay between reality and unreality, and the possibility of building parallel spheres of experience influencing the development of personal identity. Taking into consideration the main characteristics of dream experience emphasized by these scholars, in the final part of the paper I propose to elaborate a new phenomenology of dreaming, which should be able to offer a theoretical description of dream states. My sketched proposal is based on Eugen Fink’s notion of the dream as “presentification”. By combining the past and the present of phenomenological investigation, I aim at suggesting a philosophical framework to explain the intentional features of dreaming as Erlebnis.

An Algebraic Approach to Inference in Complex Networked Structures

Science.gov (United States)

2015-07-09

44], [45],[46] where the shift is the elementary non-trivial filter that generates, under an appropriate notion of shift invariance, all linear ... elementary filter, and its output is a graph signal with the value at vertex n of the graph given approximately by a weighted linear combination of...AFRL-AFOSR-VA-TR-2015-0265 An Algebraic Approach to Inference in Complex Networked Structures Jose Moura CARNEGIE MELLON UNIVERSITY Final Report 07

The Curious Connection Between Insects and Dreams.

Science.gov (United States)

Klein, Barrett A

2011-12-21

A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans' dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream's significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives.

A neuroscientific perspective on dreaming : collaboration between neuroscience and psychoanalysis is needed to progress in dream research

OpenAIRE

Perrine Marie RUBY

2011-01-01

Dreaming is still a mystery of human cognition though it has been studied at the experimental level since more than one century. Experimental psychology first investigated dream content and frequency. Then, the neuroscientific approach to dreaming arose at the end of the fifties and rapidly proposed a physiological substrate of dreaming : rapid eye movement sleep (REM). Fifty years later, this hypothesis was challenged because it could not explain all the characteristics of dream reports. Th...

Beyond DreamWeaving: Honoring Our Connections.

Science.gov (United States)

Russell, Martha M.

DreamWeavers listen for the dreams within themselves and within others. The process of career counseling, career management coaching and career/life planning invites practitioners to consistently listen for the dreams, understand that dreams are visions and that visions guide us to action. This paper highlights how career practitioners are called…

Innovation and Dream

Institute of Scientific and Technical Information of China (English)

杨玉娟

2009-01-01

The thesis is to attempt to discover the relationship between Carrie's American dream and American social innvoation by the end of 19th century. The purpose is to discuss Carrie's dream-searching while she stepped up to the peak of her life and career.

Variations in dream recall frequency and dream theme diversity by age and sex

Directory of Open Access Journals (Sweden)

Tore eNielsen

2012-07-01

Full Text Available We assessed dream recall frequency and dream theme diversity with an internet questionnaire among a cohort of 28,888 male and female participants aged 10 to 79 years in a cross-sectional design. Dream recall frequency increased from adolescence (ages 10-19 to early adulthood (20-29 and then decreased again for the next 20 years. The nature of this decrease differed for males and females. For males, it began earlier (30-39, proceeded more gradually, and reached a nadir earlier (40-49 than it did for females. For females, it began later (40-49, dropped more abruptly, and reached nadir later (50-59. Marked sex differences were observed for age strata 10-19 through 40-49 and year-by-year analyses estimated the window for these differences to be more precisely from 14-44 yrs. Dream theme diversity decreased linearly with age for both sexes up to 50-59 and then dropped even more sharply for 60-79. There was a sex difference favouring males on this measure but only for ages 10-19. Findings replicate, in a single sample, those from several previous studies showing an increase in dream recall frequency from adolescence to early adulthood, a subsequent decrease in dream recall frequency—primarily in early and middle adulthood, and different patterns of age-related decrease in the two sexes. Age-related changes in sleep structure, such as decreasing %REM sleep, parallel the observed dream recall changes but are much smaller and more gradual in nature. Changes in the phase and amplitude of circadian rhythms of REM propensity and generational differences in life experiences may also account for some part of the findings. However, that decreases in dream theme diversity parallel known age-related decreases in episodic and autobiographical memory may signify that the diversity measure indexes an aspect of autobiographical memory that is specific to dream recall.

Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks

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Stalin Muñoz

2018-03-01

Full Text Available Boolean networks are important models of biochemical systems, located at the high end of the abstraction spectrum. A number of Boolean gene networks have been inferred following essentially the same method. Such a method first considers experimental data for a typically underdetermined “regulation” graph. Next, Boolean networks are inferred by using biological constraints to narrow the search space, such as a desired set of (fixed-point or cyclic attractors. We describe Griffin, a computer tool enhancing this method. Griffin incorporates a number of well-established algorithms, such as Dubrova and Teslenko's algorithm for finding attractors in synchronous Boolean networks. In addition, a formal definition of regulation allows Griffin to employ “symbolic” techniques, able to represent both large sets of network states and Boolean constraints. We observe that when the set of attractors is required to be an exact set, prohibiting additional attractors, a naive Boolean coding of this constraint may be unfeasible. Such cases may be intractable even with symbolic methods, as the number of Boolean constraints may be astronomically large. To overcome this problem, we employ an Artificial Intelligence technique known as “clause learning” considerably increasing Griffin's scalability. Without clause learning only toy examples prohibiting additional attractors are solvable: only one out of seven queries reported here is answered. With clause learning, by contrast, all seven queries are answered. We illustrate Griffin with three case studies drawn from the Arabidopsis thaliana literature. Griffin is available at: http://turing.iimas.unam.mx/griffin.

An empirical Bayesian approach for model-based inference of cellular signaling networks

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Klinke David J

2009-11-01

Full Text Available Abstract Background A common challenge in systems biology is to infer mechanistic descriptions of biological process given limited observations of a biological system. Mathematical models are frequently used to represent a belief about the causal relationships among proteins within a signaling network. Bayesian methods provide an attractive framework for inferring the validity of those beliefs in the context of the available data. However, efficient sampling of high-dimensional parameter space and appropriate convergence criteria provide barriers for implementing an empirical Bayesian approach. The objective of this study was to apply an Adaptive Markov chain Monte Carlo technique to a typical study of cellular signaling pathways. Results As an illustrative example, a kinetic model for the early signaling events associated with the epidermal growth factor (EGF signaling network was calibrated against dynamic measurements observed in primary rat hepatocytes. A convergence criterion, based upon the Gelman-Rubin potential scale reduction factor, was applied to the model predictions. The posterior distributions of the parameters exhibited complicated structure, including significant covariance between specific parameters and a broad range of variance among the parameters. The model predictions, in contrast, were narrowly distributed and were used to identify areas of agreement among a collection of experimental studies. Conclusion In summary, an empirical Bayesian approach was developed for inferring the confidence that one can place in a particular model that describes signal transduction mechanisms and for inferring inconsistencies in experimental measurements.

The Social Life of Dreams

DEFF Research Database (Denmark)

Heijnen, Adriënne

The Social Life of Dreams: Thousand Years of Negotiated Meanings in Iceland is the first anthropological work that discusses how dreams, remembered upon awakening, motivate human action and influence social relations in contemporary Europe. Through detailed anthropological analyses of the ways...... in which many Icelanders see dreams as legitimate sources of knowledge, this book argues that sleeping and dreaming -- activities which are often considered to be psychological and “non-social”-- should be included in the analysis of social life....

Dreaming as mind wandering: evidence from functional neuroimaging and first-person content reports.

Science.gov (United States)

Fox, Kieran C R; Nijeboer, Savannah; Solomonova, Elizaveta; Domhoff, G William; Christoff, Kalina

2013-01-01

Isolated reports have long suggested a similarity in content and thought processes across mind wandering (MW) during waking, and dream mentation during sleep. This overlap has encouraged speculation that both "daydreaming" and dreaming may engage similar brain mechanisms. To explore this possibility, we systematically examined published first-person experiential reports of MW and dreaming and found many similarities: in both states, content is largely audiovisual and emotional, follows loose narratives tinged with fantasy, is strongly related to current concerns, draws on long-term memory, and simulates social interactions. Both states are also characterized by a relative lack of meta-awareness. To relate first-person reports to neural evidence, we compared meta-analytic data from numerous functional neuroimaging (PET, fMRI) studies of the default mode network (DMN, with high chances of MW) and rapid eye movement (REM) sleep (with high chances of dreaming). Our findings show large overlaps in activation patterns of cortical regions: similar to MW/DMN activity, dreaming and REM sleep activate regions implicated in self-referential thought and memory, including medial prefrontal cortex (PFC), medial temporal lobe structures, and posterior cingulate. Conversely, in REM sleep numerous PFC executive regions are deactivated, even beyond levels seen during waking MW. We argue that dreaming can be understood as an "intensified" version of waking MW: though the two share many similarities, dreams tend to be longer, more visual and immersive, and to more strongly recruit numerous key hubs of the DMN. Further, whereas MW recruits fewer PFC regions than goal-directed thought, dreaming appears to be characterized by an even deeper quiescence of PFC regions involved in cognitive control and metacognition, with a corresponding lack of insight and meta-awareness. We suggest, then, that dreaming amplifies the same features that distinguish MW from goal-directed waking thought.

Lucid dreaming in narcolepsy.

Science.gov (United States)

Dodet, Pauline; Chavez, Mario; Leu-Semenescu, Smaranda; Golmard, Jean-Louis; Arnulf, Isabelle

2015-03-01

To evaluate the frequency, determinants and sleep characteristics of lucid dreaming in narcolepsy. University hospital sleep disorder unit. Case-control study. Consecutive patients with narcolepsy and healthy controls. Participants were interviewed regarding the frequency and determinants of lucid dreaming. Twelve narcolepsy patients and 5 controls who self-identified as frequent lucid dreamers underwent nighttime and daytime sleep monitoring after being given instructions regarding how to give an eye signal when lucid. Compared to 53 healthy controls, the 53 narcolepsy patients reported more frequent dream recall, nightmares and recurrent dreams. Lucid dreaming was achieved by 77.4% of narcoleptic patients and 49.1% of controls (P dreamers achieved lucid REM sleep across a total of 33 naps, including 14 episodes with eye signal. The delta power in the electrode average, in delta, theta, and alpha powers in C4, and coherences between frontal electrodes were lower in lucid than non-lucid REM sleep in spectral EEG analysis. The duration of REM sleep was longer, the REM sleep onset latency tended to be shorter, and the percentage of atonia tended to be higher in lucid vs. non-lucid REM sleep; the arousal index and REM density and amplitude were unchanged. Narcolepsy is a novel, easy model for studying lucid dreaming. © 2015 Associated Professional Sleep Societies, LLC.

Maternal representations in the dreams of pregnant women: a prospective comparative study

Directory of Open Access Journals (Sweden)

Jessica eLara-Carrasco

2013-08-01

Full Text Available Dreams are thought to respond to self- and socially-relevant situations that evoke strong emotions and require rapid adaptation. First pregnancy is such a situation during which maternal mental representations (MMR of the unborn baby, the self and significant others undergo remodelling. Some studies suggest that dreams during pregnancy contain more MMR and are more dysphoric, but such studies contain important methodological flaws. We assessed whether dreamed MMR, like waking MMR, change from 7 months to birth, and whether pregnancy–related themes and non-pregnancy characteristics are also transformed. Sixty non-pregnant and 59 pregnant women (37 early and 22 late 3rd trimester completed demographic and psychological questionnaires and 14-day home dream logs. Dream reports were blindly rated and later analyzed following four dream categories: 1 Dreamed MMR, 2 Quality of baby/child representations, 3 Pregnancy-related themes, 4 Non-pregnancy characteristics. Controlling for age, relationship and employment status, education level and state anxiety, pregnant groups reported more dreams depicting themselves as a mother or with babies/children than did non-pregnant women (all p≤0.006. Baby/child representations were less specific in late 3rd than in early 3rd trimester (p=0.005 and than in non-pregnant women (p=0.01. Pregnant groups also had more pregnancy, childbirth and fetus themes (all p≤.01. Childbirth content was higher in late than in early 3rd trimester (p=0.01. Pregnant groups had more morbid elements than did the non-pregnant group (all p<.05. Dreaming during pregnancy appears to reflect daytime processes of remodelling MMR of the woman as a mother and of the unborn baby, and parallels a decline in the quality of baby/child representations in the last stage of pregnancy. More frequent morbid content in late pregnancy suggests that the psychological challenges of pregnancy are reflected in a generally more dysphoric emotional tone in

Maternal representations in the dreams of pregnant women: a prospective comparative study

Science.gov (United States)

Lara-Carrasco, Jessica; Simard, Valérie; Saint-Onge, Kadia; Lamoureux-Tremblay, Vickie; Nielsen, Tore

2013-01-01

Dreams are thought to respond to self- and socially-relevant situations that evoke strong emotions and require rapid adaptation. First pregnancy is such a situation during which maternal mental representations (MMR) of the unborn baby, the self and significant others undergo remodeling. Some studies suggest that dreams during pregnancy contain more MMR and are more dysphoric, but such studies contain important methodological flaws. We assessed whether dreamed MMR, like waking MMR, change from the 7th month of pregnancy to birth, and whether pregnancy–related themes and non-pregnancy characteristics are also transformed. Sixty non-pregnant and 59 pregnant women (37 early and 22 late 3rd trimester) completed demographic and psychological questionnaires and 14-day home dream logs. Dream reports were blindly rated according to four dream categories: (1) Dreamed MMR, (2) Quality of baby/child representations, (3) Pregnancy-related themes, (4) Non-pregnancy characteristics. Controlling for age, relationship and employment status, education level and state anxiety, women in both pregnant groups reported more dreams depicting themselves as a mother or with babies/children than did non-pregnant women (all p = 0.006). Baby/child representations were less specific in the late 3rd than in the early 3rd trimester (p = 0.005) and than in non-pregnant women (p = 0.01). Pregnant groups also had more pregnancy, childbirth and fetus themes (all p = 0.01). Childbirth content was higher in late than in early 3rd trimester (p = 0.01). Pregnant groups had more morbid elements than did the non-pregnant group (all p Dreaming during pregnancy appears to reflect daytime processes of remodeling MMR of the woman as a mother and of her unborn baby, and parallels a decline in the quality of baby/child representations in the last stage of pregnancy. More frequent morbid content in late pregnancy suggests that the psychological challenges of pregnancy are reflected in a generally more dysphoric

Dreaming scientists and scientific dreamers: Freud as a reader of French dream literature.

Science.gov (United States)

Carroy, Jacqueline

2006-03-01

The argument of this paper is to situate The Interpretation of Dreams within an historical context. It is, therefore, impossible to believe Freud entirely when he staged himself in his letters to Fliess as a mere discoverer. In reality Freud also felt he belonged to a learned community of dream specialists, whom I call "dreaming scientists" and "scientific dreamers." Instead of speaking, as Ellenberger does, in terms of influence, I will be offering as an example a portrait of Freud as a reader of two French authors, Maury, and indirectly, Hervey de Saint-Denys. I will analyze how Freud staged himself as replacing Maury and dreaming sometimes like Hervey de Saint-Denys. My premise in this work is that we must forget Freud, in order to adventure into a learned dream culture peculiar to the nineteenth century. Only afterwards can we come back to Freud and place him in this context as a creative heir.

Dream Recall Frequencies and Dream Content in Wilson's Disease with and without REM Sleep Behaviour Disorder: A Neurooneirologic Study.

Science.gov (United States)

Tribl, Gotthard G; Trindade, Mateus C; Schredl, Michael; Pires, Joana; Reinhard, Iris; Bittencourt, Thais; Lorenzi-Filho, Geraldo; Alves, Rosana Cardoso; de Andrade, Daniel Ciampi; Fonoff, Erich T; Bor-Seng-Shu, Edson; Machado, Alexandre A; Teixeira, Manoel J; Barbosa, Egberto R

2016-01-01

Objective. Violent dream content and its acting out during rapid eye movement sleep are considered distinctive for rapid eye movement sleep behaviour disorder (RBD). This study reports first quantitative data on dreaming in a cohort of patients with treated Wilson's disease (WD) and in patients with WD with RBD. Methods. Retrospective questionnaires on different dimensions of dreaming and a prospective two-week home dream diary with self-rating of emotions and blinded, categorical rating of content by an external judge. Results. WD patients showed a significantly lower dream word count and very few other differences in dream characteristics compared to age- and sex-matched healthy controls. Compared to WD patients without RBD, patients with WD and RBD reported significantly higher nightmare frequencies and more dreams with violent or aggressive content retrospectively; their prospectively collected dream reports contained significantly more negative emotions and aggression. Conclusions. The reduction in dream length might reflect specific cognitive deficits in WD. The lack of differences regarding dream content might be explained by the established successful WD treatment. RBD in WD had a strong impact on dreaming. In accordance with the current definition of RBD, violent, aggressive dream content seems to be a characteristic of RBD also in WD.

Comparison of evolutionary algorithms in gene regulatory network model inference.

LENUS (Irish Health Repository)

2010-01-01

ABSTRACT: BACKGROUND: The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. RESULTS: This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. CONCLUSIONS: Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established.

Consumption dreams: how night dreams reveal the colonization of subjectivity by the imaginary of consumerism

Directory of Open Access Journals (Sweden)

Marlon Xavier

2013-07-01

Full Text Available In this article I offer an overview of my doctoral dissertation, which studied the social imaginary of consumerism, and the psychological subjectivity it produces, through the dream - as both a leitmotif or thematic lens, and the empirical object of research. For such I employed an interdisciplinary exploratory outlook, whose theoretical framework first discusses the symbolic imaginaries (G. Durand and their relations with the unconscious psyche, dream, imagination, and subjectivity (C. G. Jung, and then explores their relationships with consumption (Baudrillard, Bauman and its semiotic imaginaries and ideology, focusing on the concepts of consumption dreams and dream-worlds of consumption. The main research aim was to explore how night dreams represent the colonization of subjectivity by the imaginary of consumerism. The method consisted in a multiple-case study in which each night dream was taken as a case and interpreted through Jungian hermeneutics. Findings stress that night dreams can offer a deep sociocultural critique; in them the imaginary of consumption appeared as a totalizing mass ideology engendering colonization of both symbolic imaginaries and the subject and her unconscious psyche. Conclusions emphasize such colonization as an anthropological mutation - the progressive commodification and dehumanization of the subject.

A neuroscientific perspective on dreaming : collaboration between neuroscience and psychoanalysis is needed to progress in dream research

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Perrine Marie RUBY

2011-11-01

Full Text Available Dreaming is still a mystery of human cognition though it has been studied at the experimental level since more than one century. Experimental psychology first investigated dream content and frequency. Then, the neuroscientific approach to dreaming arose at the end of the fifties and rapidly proposed a physiological substrate of dreaming : rapid eye movement sleep (REM. Fifty years later, this hypothesis was challenged because it could not explain all the characteristics of dream reports. The neurophysiological correlates of dreaming, as its functions, remain thus unclear and many questions are left unresolved. Do the representations constituting the dream emerge randomly from the brain or do they surface according to certain parameters? Is the organisation of the dream’s representations chaotic or is it determined by rules? Does dreaming have a meaning? Psychoanalysis provides hypotheses to answer these questions. Until now theses hypotheses have been barely considered in cognitive neuroscience, but the recent creation of neuropsychoanalysis brings new hopes of discussion between the two fields. Considering the psychoanalytical perspective in cognitive neuroscience would provide new directions/leads for dream research and would help to achieve a comprehensive understanding of dreaming. Notably, several subjective issues at the core of psychoanalytic approach, such as the concept of personal meaning, the concept of unconscious episodic memory and the subjects’ history are not addressed or considered in cognitive neuroscience. This paper argues that the expertise of psychoanalysis in singularity and personal meaning is needed to succeed in addressing these issues in cognitive neuroscience and to progress in the understanding of dreaming and psyche.

The phenomenology of lucid dreaming: an online survey.

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Stumbrys, Tadas; Erlacher, Daniel; Johnson, Miriam; Schredl, Michael

2014-01-01

In lucid dreams the dreamer is aware that he or she is dreaming. Although such dreams are not that uncommon, many aspects of lucid dream phenomenology are still unclear. An online survey was conducted to gather data about lucid dream origination, duration, active or passive participation in the dream, planned actions for lucid dreams, and other phenomenological aspects. Among the 684 respondents who filled out the questionnaire, there were 571 lucid dreamers (83.5%). According to their reports, lucid dreams most often originate spontaneously in adolescence. The average lucid dream duration is about 14 minutes. Lucid dreamers are likely to be active in their lucid dreams and plan to accomplish different actions (e.g., flying, talking with dream characters, or having sex), yet they are not always able to remember or successfully execute their intentions (most often because of awakening or hindrances in the dream environment). The frequency of lucid dream experience was the strongest predictor of lucid dream phenomenology, but some differences were also observed in relation to age, gender, or whether the person is a natural or self-trained lucid dreamer. The findings are discussed in light of lucid dream research, and suggestions for future studies are provided.

Dreams in ancient Greek Medicine.

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Laios, K; Moschos, M M; Koukaki, E; Vasilopoulos, E; Karamanou, M; Kontaxaki, M-I; Androutsos, G

2016-01-01

Dreams preoccupied the Greek and Roman world in antiquity, therefore they had a prominent role in social, philosophical, religious, historical and political life of those times. They were considered as omens and prophetic signs of future events in private and public life, and that was particularly accentuated when elements of actions which took place in the plot of dreams were associated directly or indirectly with real events. This is why it was important to use them in divination, and helped the growth of superstition and folklore believes. Medicine as a science and an anthropocentric art, could not ignore the importance of dreams, having in mind their popularity in antiquity. In ancient Greek medicine dreams can be divided into two basic categories. In the first one -which is related to religious medicine-dreams experienced by religionists are classified, when resorted to great religious sanctuaries such as those of Asclepius (Asclepieia) and Amphiaraos (Amfiaraeia). These dreams were the essential element for healing in this form of religious medicine, because after pilgrims underwent purifications they went to sleep in a special dwelling of the sanctuaries called "enkoimeterion" (Greek: the place to sleep) so that the healing god would come to their dreams either to cure them or to suggest treatment. In ancient Greek literature there are many reports of these experiences, but if there may be phenomena of self-suggestion, or they could be characterized as propaganda messages from the priesthood of each sanctuary for advertising purposes. The other category concerns the references about dreams found in ancient Greek medical literature, where one can find the attempts of ancient Greek physicians to interpret these dreams in a rational way as sings either of a corporal disease or of psychological distress. This second category will be the object of our study. Despite the different ways followed by each ancient Greek physician in order to explain dreams, their

Exploring the effects of galantamine paired with meditation and dream reliving on recalled dreams: Toward an integrated protocol for lucid dream induction and nightmare resolution.

Science.gov (United States)

Sparrow, Gregory; Hurd, Ryan; Carlson, Ralph; Molina, Ana

2018-06-27

An experimental home study examined the impact of a pre-sleep protocol for enhancing self-awareness, lucidity, and responsiveness in dreams. It included ingesting the cholinesterase inhibitor galantamine--which is widely reported to increase the frequency of lucid dreaming--prior to engaging in middle-of-the-night meditation and the imaginary reliving of a distressing dream while exercising new responses. Thirty-five participants completed an eight-night study, which included pre- and post-baseline nights and six conditions: waking for 40 min before returning to bed, called Wake-Back-to-Bed (WBTB); Wake-Back-to-Bed plus placebo (WBTB + P); Wake-Back-to-Bed plus galantamine (WBTB + G); meditation and dream reliving (MDR); meditation and dream reliving plus placebo (MDR + P); and meditation and dream reliving plus galantamine (MDR + G). The outcome measures included lucidity, reflectiveness, interactive behavior, role change, constructive action, and fear and threat, as measured by the participants' self-ratings. The results support the use of this protocol in further studies of lucid dream induction and nightmare/trauma resolution. Copyright © 2018 Elsevier Inc. All rights reserved.

DREAM Controls the On/Off Switch of Specific Activity-Dependent Transcription Pathways

Science.gov (United States)

Mellström, Britt; Sahún, Ignasi; Ruiz-Nuño, Ana; Murtra, Patricia; Gomez-Villafuertes, Rosa; Savignac, Magali; Oliveros, Juan C.; Gonzalez, Paz; Kastanauskaite, Asta; Knafo, Shira; Zhuo, Min; Higuera-Matas, Alejandro; Errington, Michael L.; Maldonado, Rafael; DeFelipe, Javier; Jefferys, John G. R.; Bliss, Tim V. P.; Dierssen, Mara

2014-01-01

Changes in nuclear Ca2+ homeostasis activate specific gene expression programs and are central to the acquisition and storage of information in the brain. DREAM (downstream regulatory element antagonist modulator), also known as calsenilin/KChIP-3 (K+ channel interacting protein 3), is a Ca2+-binding protein that binds DNA and represses transcription in a Ca2+-dependent manner. To study the function of DREAM in the brain, we used transgenic mice expressing a Ca2+-insensitive/CREB-independent dominant active mutant DREAM (daDREAM). Using genome-wide analysis, we show that DREAM regulates the expression of specific activity-dependent transcription factors in the hippocampus, including Npas4, Nr4a1, Mef2c, JunB, and c-Fos. Furthermore, DREAM regulates its own expression, establishing an autoinhibitory feedback loop to terminate activity-dependent transcription. Ablation of DREAM does not modify activity-dependent transcription because of gene compensation by the other KChIP family members. The expression of daDREAM in the forebrain resulted in a complex phenotype characterized by loss of recurrent inhibition and enhanced long-term potentiation (LTP) in the dentate gyrus and impaired learning and memory. Our results indicate that DREAM is a major master switch transcription factor that regulates the on/off status of specific activity-dependent gene expression programs that control synaptic plasticity, learning, and memory. PMID:24366545

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Science.gov (United States)

Miller, Martin L.; Gauthier, Nicholas P.; Jing, Xiaohong; Kaushik, Poorvi; He, Qin; Mills, Gordon; Solit, David B.; Pratilas, Christine A.; Weigt, Martin; Braunstein, Alfredo; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

2013-01-01

We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology. PMID:24367245

Supervised dictionary learning for inferring concurrent brain networks.

Science.gov (United States)

Zhao, Shijie; Han, Junwei; Lv, Jinglei; Jiang, Xi; Hu, Xintao; Zhao, Yu; Ge, Bao; Guo, Lei; Liu, Tianming

2015-10-01

Task-based fMRI (tfMRI) has been widely used to explore functional brain networks via predefined stimulus paradigm in the fMRI scan. Traditionally, the general linear model (GLM) has been a dominant approach to detect task-evoked networks. However, GLM focuses on task-evoked or event-evoked brain responses and possibly ignores the intrinsic brain functions. In comparison, dictionary learning and sparse coding methods have attracted much attention recently, and these methods have shown the promise of automatically and systematically decomposing fMRI signals into meaningful task-evoked and intrinsic concurrent networks. Nevertheless, two notable limitations of current data-driven dictionary learning method are that the prior knowledge of task paradigm is not sufficiently utilized and that the establishment of correspondences among dictionary atoms in different brains have been challenging. In this paper, we propose a novel supervised dictionary learning and sparse coding method for inferring functional networks from tfMRI data, which takes both of the advantages of model-driven method and data-driven method. The basic idea is to fix the task stimulus curves as predefined model-driven dictionary atoms and only optimize the other portion of data-driven dictionary atoms. Application of this novel methodology on the publicly available human connectome project (HCP) tfMRI datasets has achieved promising results.

REM dream activity of insomnia sufferers: a systematic comparison with good sleepers.

Science.gov (United States)

Pérusse, Alexandra D; De Koninck, Joseph; Pedneault-Drolet, Maude; Ellis, Jason G; Bastien, Célyne H

2016-04-01

The dream activity of patients with primary insomnia (PI) has rarely been studied, especially using in-laboratory dream collection, although dreams could be linked to their state of hyperarousal and their negative waking experiences. The objective of the study was to compare patients with PI and good sleeper controls (GSCs) in terms of dream recall frequency and dream content. Polysomnography was recorded in 12 patients with PI and 12 GSCs (aged between 30 and 45 years) for five consecutive nights. Rapid eye movement (REM) sleep awakenings were enforced on nights 3 and 5 for dream collections. The REM dream collections revealed that the groups were similar in terms of dream recall frequency (p ≤ 0.7). With respect to dream content variables, the dreams of GSCs tended to comprise more positive emotions (p = 0.06), whereas the dreams of patients with PI were characterized by more negative elements than positive ones (p = 0.001). Subjectively, GSCs characterized their dreams as being more pleasant and containing more joy, happiness, and vividness (p ≤ 0.03) than patients with PI. Finally, elevated negative dream content was associated with lower sleep efficiencies in insomnia (p = 0.004). These results suggest that less positive emotions and greater negative content characterize the dreams of patients with PI, which is in line with their waking experiences. One potential explanation could be hyperarousal exacerbating presleep negative mentation, thus contributing to poorer sleep quality. The lack of difference in dream recall frequency is most likely due to the forced awakening "dream collection" procedure. The study of dream activity seems a promising avenue for understanding the 24-h experience of insomnia better and exploring the potential benefits of dream management techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Religion and spirituality in contemporary dreams

Directory of Open Access Journals (Sweden)

Werner Nell

2012-02-01

Full Text Available This article examines the spiritual value and role of dreams in the lives of South African Christians, based on the findings of a qualitative research project in which semistructured interviews were used to examine the dream-related beliefs and practices of contemporary Christians. The findings indicated that dreams are still considered to be of distinct religious value and importance by a significant number of the Christian participants who took part in the study. Specifically, the participants reported that their dreams often serve as source of spiritual inspiration, insight and guidance, as well as feedback on decisions and ways of living. It was also indicated that dreams sometimes constituted an important natural resource in coming to terms with bereavement. In response to this, the article closes with a call for a re-evaluation of the position and value of dreams in contemporary Christianity, and offers several practical suggestions for working with dreams in a spiritual context.

Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.

Science.gov (United States)

Ellwanger, Daniel Christian; Leonhardt, Jörn Florian; Mewes, Hans-Werner

2014-12-01

Understanding how regulatory networks globally coordinate the response of a cell to changing conditions, such as perturbations by shifting environments, is an elementary challenge in systems biology which has yet to be met. Genome-wide gene expression measurements are high dimensional as these are reflecting the condition-specific interplay of thousands of cellular components. The integration of prior biological knowledge into the modeling process of systems-wide gene regulation enables the large-scale interpretation of gene expression signals in the context of known regulatory relations. We developed COGERE (http://mips.helmholtz-muenchen.de/cogere), a method for the inference of condition-specific gene regulatory networks in human and mouse. We integrated existing knowledge of regulatory interactions from multiple sources to a comprehensive model of prior information. COGERE infers condition-specific regulation by evaluating the mutual dependency between regulator (transcription factor or miRNA) and target gene expression using prior information. This dependency is scored by the non-parametric, nonlinear correlation coefficient η(2) (eta squared) that is derived by a two-way analysis of variance. We show that COGERE significantly outperforms alternative methods in predicting condition-specific gene regulatory networks on simulated data sets. Furthermore, by inferring the cancer-specific gene regulatory network from the NCI-60 expression study, we demonstrate the utility of COGERE to promote hypothesis-driven clinical research. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Curious Connection Between Insects and Dreams

Directory of Open Access Journals (Sweden)

Barrett A. Klein

2011-12-01

Full Text Available A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans’ dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream’s significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives.

The Curious Connection Between Insects and Dreams

Science.gov (United States)

Klein, Barrett A.

2011-01-01

A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans’ dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream’s significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives. PMID:26467945

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

Directory of Open Access Journals (Sweden)

Ingkasuwan Papapit

2012-08-01

Full Text Available Abstract Background Starch serves as a temporal storage of carbohydrates in plant leaves during day/night cycles. To study transcriptional regulatory modules of this dynamic metabolic process, we conducted gene regulation network analysis based on small-sample inference of graphical Gaussian model (GGM. Results Time-series significant analysis was applied for Arabidopsis leaf transcriptome data to obtain a set of genes that are highly regulated under a diurnal cycle. A total of 1,480 diurnally regulated genes included 21 starch metabolic enzymes, 6 clock-associated genes, and 106 transcription factors (TF. A starch-clock-TF gene regulation network comprising 117 nodes and 266 edges was constructed by GGM from these 133 significant genes that are potentially related to the diurnal control of starch metabolism. From this network, we found that β-amylase 3 (b-amy3: At4g17090, which participates in starch degradation in chloroplast, is the most frequently connected gene (a hub gene. The robustness of gene-to-gene regulatory network was further analyzed by TF binding site prediction and by evaluating global co-expression of TFs and target starch metabolic enzymes. As a result, two TFs, indeterminate domain 5 (AtIDD5: At2g02070 and constans-like (COL: At2g21320, were identified as positive regulators of starch synthase 4 (SS4: At4g18240. The inference model of AtIDD5-dependent positive regulation of SS4 gene expression was experimentally supported by decreased SS4 mRNA accumulation in Atidd5 mutant plants during the light period of both short and long day conditions. COL was also shown to positively control SS4 mRNA accumulation. Furthermore, the knockout of AtIDD5 and COL led to deformation of chloroplast and its contained starch granules. This deformity also affected the number of starch granules per chloroplast, which increased significantly in both knockout mutant lines. Conclusions In this study, we utilized a systematic approach of microarray

Dreaming and Interventional Cardiology： Case Report

Institute of Scientific and Technical Information of China (English)

Rafal Sztembis[1] Joanna Sztembis[2] Andrzej Przybylski[2] Janusz Romanek[2

2017-01-01

Sleep and dreaming play important physiological and psychological role in human life. And though dreams playedimportant role and sometimes even changed course of mankind history, very seldom both doctors and patientstalked about it. Article is case report of precongnitive dream of patient with heart attack and analysis of populationof consecutive 100 patients admitted to hospital with heart attack in relation to presence and meaning ofprecognitive dreams. Our study proves that we can talk about precognitive dreams in population of patients withheart attack however what may be their influence on patients＇ wellbeing is matter of open questions.

Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions.

Science.gov (United States)

Takemoto, Kazuhiro; Aie, Kazuki

2017-05-25

Host-pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. We re-evaluated the importance of the reverse ecology method for evaluating host-pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host-pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host-pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host-pathogen interactions.

Dreams Rewired

DEFF Research Database (Denmark)

Thomsen, Bodil Marie Stavning; Luksch, Manu

2016-01-01

Bidraget kommenterer filmen Dreams Rewired og skaber refleksive spor i det vidt forgrenede film-arkiviske materiale om mere end et århundredes tele- og real-time kommunikation, hvor kropslig bevægelse bl.a gøres til data.......Bidraget kommenterer filmen Dreams Rewired og skaber refleksive spor i det vidt forgrenede film-arkiviske materiale om mere end et århundredes tele- og real-time kommunikation, hvor kropslig bevægelse bl.a gøres til data....

Three Dreams

Institute of Scientific and Technical Information of China (English)

冯静

1996-01-01

Once three young men went hunting in the woods and took a-long another to be the cook.They hunted all day long withoutstopping to eat,and when evening came they had caught nothingbut one partridge(鹧鹕).One little bird was hardly enough for four hungry men,sothey hit upon(突然想起)a plan.They would save the partridgefor breakfast,and whoever dreamed the best dream in the nightshould have it.Then they went to sleep.

The genius of the dream.

Science.gov (United States)

Palombo, S R

1983-01-01

In Act V of A Midsummer Night's Dream, Theseus and Hippolyta exchange views on the dreamlike adventures reported by the young lovers. Theseus dismisses their stories as fantasies of wish fulfillment, but Hippolyta points out that despite their strangeness, the tales reflect an adaptive change in the psychic reality of the lovers. The dramatic action of the play supports Hippolyta's view. The release of Demetrius from his transferential infatuation with Hermia comes at the moment of awakening from a dream in which he has matched his current feelings for Hermia with a repressed libidinal fantasy of childhood. This example of a correction dream illustrates how condensation in dreams functions adaptively in matching a new experience with previously stored representations of related events in the past. It also illustrates the ability of the matching process to go beyond the narrow logical categories of waking thought to reach deeper levels of experience otherwise inaccessible to the dreamer. This ability accounts for the important role played by dreaming in the creative process generally and in the day-to-day working-through process of psychoanalytic therapy. The adaptive function of dreaming is subject at many points to interference from the censorship mechanisms discovered and emphasized by Freud. A theory of dreaming combining these antagonistic processes is more consistent with the data of the sleep laboratory than the traditional psychoanalytic theory alone. It also provides a better fit with the introspective date more familiar to the analyst as illustrated by Freud's well-documented analysis of his own dreams.

Dream Recall Frequencies and Dream Content in Wilson’s Disease with and without REM Sleep Behaviour Disorder: A Neurooneirologic Study

Directory of Open Access Journals (Sweden)

Gotthard G. Tribl

2016-01-01

Full Text Available Objective. Violent dream content and its acting out during rapid eye movement sleep are considered distinctive for rapid eye movement sleep behaviour disorder (RBD. This study reports first quantitative data on dreaming in a cohort of patients with treated Wilson’s disease (WD and in patients with WD with RBD. Methods. Retrospective questionnaires on different dimensions of dreaming and a prospective two-week home dream diary with self-rating of emotions and blinded, categorical rating of content by an external judge. Results. WD patients showed a significantly lower dream word count and very few other differences in dream characteristics compared to age- and sex-matched healthy controls. Compared to WD patients without RBD, patients with WD and RBD reported significantly higher nightmare frequencies and more dreams with violent or aggressive content retrospectively; their prospectively collected dream reports contained significantly more negative emotions and aggression. Conclusions. The reduction in dream length might reflect specific cognitive deficits in WD. The lack of differences regarding dream content might be explained by the established successful WD treatment. RBD in WD had a strong impact on dreaming. In accordance with the current definition of RBD, violent, aggressive dream content seems to be a characteristic of RBD also in WD.

Dreaming and recall during sedation for colonoscopy.

Science.gov (United States)

Stait, M L; Leslie, K; Bailey, R

2008-09-01

Dreaming is reported by one in five patients who are interviewed on emergence from general anaesthesia, but the incidence, predictors and consequences of dreaming during procedural sedation are not known. In this prospective observational study, 200 patients presenting for elective colonoscopy under intravenous sedation were interviewed on emergence to determine the incidences of dreaming and recall. Sedation technique was left to the discretion of the anaesthetist. The incidence of dreaming was 25.5%. Patients reporting dreaming were younger than those who did not report dreaming. Doses of midazolam and fentanyl were similar between dreamers and non-dreamers, however propofol doses were higher in patients who reported dreams than those who did not. Patients reported short, simple dreams about everyday life--no dream suggested near-miss recall of the procedure. Frank recall of the procedure was reported by 4% of the patients, which was consistent with propofol doses commensurate with light general anaesthesia. The only significant predictor of recall was lower propofol dose. Satisfaction with care was generally high, however dreamers were more satisfied with their care than non-dreamers.

The Chinese Dream-A New Dream Provided By China For The World

Institute of Scientific and Technical Information of China (English)

张保

2013-01-01

Along With promotion of comprehensive national strength, Chinese dream, as a new term ,begins to more and more popular. It is introduced, explained and spread by officials, scholars and medias. Would it be another dream for the world beside the American one?

Experienced Sensory Modalities in Dream Recall

OpenAIRE

岡田, 斉

2000-01-01

The purpose of the present study is to survey the frequency of visual, auditory, kinaesthetic, cutaneous, organic, gustatory, and olfactory experience in dream recall. A total of 1267 undergraduate students completed a dream recall frequency questionnaire, which contained a question about dream recall frequency and about recall frequency of seven sensory modalities. Results showed that seven sensory modalities were divided into two groups; normally perceived sensory modalities in dreaming, wh...

An Efficient Forward-Reverse EM Algorithm for Statistical Inference in Stochastic Reaction Networks

KAUST Repository

Bayer, Christian; Moraes, Alvaro; Tempone, Raul; Vilanova, Pedro

2016-01-01

In this work [1], we present an extension of the forward-reverse algorithm by Bayer and Schoenmakers [2] to the context of stochastic reaction networks (SRNs). We then apply this bridge-generation technique to the statistical inference problem

The Use of Dream Discussions in Counseling.

Science.gov (United States)

Miller, Mark J.; And Others

1982-01-01

Reviews the historical underpinnings of dream theories and suggests that discussions of dreams in counseling can aid in setting up and maintaining therapeutic contact with clients. A number of theoretical positions on the function of dreams are discussed. Specific dream counseling techniques are also delineated. (JAC)

Dream controller

Science.gov (United States)

Cheng, George Shu-Xing; Mulkey, Steven L; Wang, Qiang; Chow, Andrew J

2013-11-26

A method and apparatus for intelligently controlling continuous process variables. A Dream Controller comprises an Intelligent Engine mechanism and a number of Model-Free Adaptive (MFA) controllers, each of which is suitable to control a process with specific behaviors. The Intelligent Engine can automatically select the appropriate MFA controller and its parameters so that the Dream Controller can be easily used by people with limited control experience and those who do not have the time to commission, tune, and maintain automatic controllers.

Autobiographical memory sources of threats in dreams.

Science.gov (United States)

Lafrenière, Alexandre; Lortie-Lussier, Monique; Dale, Allyson; Robidoux, Raphaëlle; De Koninck, Joseph

2018-02-01

Temporal sources of dream threats were examined through the paradigm of the Threat Simulation Theory. Two groups of young adults (18-24 years old), who did not experience severe threatening events in the year preceding their dream and reported a dream either with or without threats, were included. Participants (N = 119) kept a log of daily activities and a dream diary, indicating whether dream components referred to past experiences. The occurrence of oneiric threats correlated with the reporting of threats in the daily logs, their average severity, and the stress level experienced the day preceding the dream. The group whose dreams contained threats had significantly more references to temporal categories beyond one year than the group with dreams without threats. Our findings suggest that in the absence of recent highly negative emotional experiences, the threat simulation system selects memory traces of threatening events experienced in the past. Copyright © 2017 Elsevier Inc. All rights reserved.

Reconstructing Causal Biological Networks through Active Learning.

Directory of Open Access Journals (Sweden)

Hyunghoon Cho

Full Text Available Reverse-engineering of biological networks is a central problem in systems biology. The use of intervention data, such as gene knockouts or knockdowns, is typically used for teasing apart causal relationships among genes. Under time or resource constraints, one needs to carefully choose which intervention experiments to carry out. Previous approaches for selecting most informative interventions have largely been focused on discrete Bayesian networks. However, continuous Bayesian networks are of great practical interest, especially in the study of complex biological systems and their quantitative properties. In this work, we present an efficient, information-theoretic active learning algorithm for Gaussian Bayesian networks (GBNs, which serve as important models for gene regulatory networks. In addition to providing linear-algebraic insights unique to GBNs, leading to significant runtime improvements, we demonstrate the effectiveness of our method on data simulated with GBNs and the DREAM4 network inference challenge data sets. Our method generally leads to faster recovery of underlying network structure and faster convergence to final distribution of confidence scores over candidate graph structures using the full data, in comparison to random selection of intervention experiments.

An alternative view of the neurobiology of dreaming.

Science.gov (United States)

Vogel, G W

1978-12-01

The author critiques the recently proposed activation-synthesis hypothesis about the origin and formation of dreams. Many findings do not support the new hypothesis that specific pontine physiological processes, rather than mental processes, instigate dreams and produce their distortion. First, dreaming often occurs in the absence of the pontine processes. Second, forebrain activity (which can have mental correlates) is crucial to the instigation and maintenance of dreaming sleep. Finally, activity of the proposed pontine dream generator, which is claimed to cause dream distortion, is not reliably accompanied by dream distortion.

Expression of DREAM A and DREAM B in primary cultured nerve cells of mice%DREAM A和B在原代培养的小鼠神经细胞中的表达

Institute of Scientific and Technical Information of China (English)

赵雪花; 孙峰波; 周艳玲

2013-01-01

目的:研究DREAM蛋白的2个主要亚型DREAM A和DREAM B在原代培养的小鼠大脑皮层星形胶质细胞、小鼠大脑皮层γ-氨基丁酸能神经元以及小鼠小脑谷氨酸能神经元中的表达水平的差异.方法:提取原代培养的小鼠大脑皮层星形胶质细胞、小鼠大脑皮层γ-氨基丁酸能神经元以及小鼠小脑谷氨酸能神经元的RNA,采用普通PCR及real time PCR的方法检测上述各种细胞中DREAM蛋白2个亚型A和B的mRNA的表达水平.结果:DREAM的两个亚型A和B在上述三种神经细胞都存在.在发育成熟的原代培养细胞中,DREAMA的mRNA水平要远高于DREAM B.在三种不同的细胞中,谷氨酸能神经元表达DREAM A的水平最高.结论:DREAM的两个亚型A和B在小鼠三种原代培养的神经细胞中的表达水平及其差异提示DREAM A是成年小鼠中DREAM的主要亚型,DREAM A和B在不同类型的神经细胞中发挥的作用及其机制有所不同.%Objective: To study the difference of the expression level between the two main isoforms of DREAM A and DREAM B in the primary cultured cerebral cortical astrocytes, GABAergic nerons and cerebellar glutamatergic neurons of the mice. Methods: RNA of the above three primary cultured cells from mice were extracted and then detected about the DREAM A and DREAM B's mRNA level by the polymerase chain reaction (PCR) and real time PCR. Results; Both DREAM A and DREAM B existed in the above three nerve cells. In the mature primary culture cells, the mRNA level of the DREAM A was higher than that of DREAM B, and the expression level of DREAM A of the glutamatergic neurons was the highest among the three cells. Conclusion: The expression levels and differences of the DREAM A and DREAM B show that DREAM A was the main type of DREAM in adult mice, DREAM A and DREAM B may play different roles throug diffenent action mechanisms in different types of nerve cells.

Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective.

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Chen, Chen; Tong, Hanghang; Xie, Lei; Ying, Lei; He, Qing

2017-08-01

The increasingly connected world has catalyzed the fusion of networks from different domains, which facilitates the emergence of a new network model-multi-layered networks. Examples of such kind of network systems include critical infrastructure networks, biological systems, organization-level collaborations, cross-platform e-commerce, and so forth. One crucial structure that distances multi-layered network from other network models is its cross-layer dependency, which describes the associations between the nodes from different layers. Needless to say, the cross-layer dependency in the network plays an essential role in many data mining applications like system robustness analysis and complex network control. However, it remains a daunting task to know the exact dependency relationships due to noise, limited accessibility, and so forth. In this article, we tackle the cross-layer dependency inference problem by modeling it as a collective collaborative filtering problem. Based on this idea, we propose an effective algorithm Fascinate that can reveal unobserved dependencies with linear complexity. Moreover, we derive Fascinate-ZERO, an online variant of Fascinate that can respond to a newly added node timely by checking its neighborhood dependencies. We perform extensive evaluations on real datasets to substantiate the superiority of our proposed approaches.

Dreams In Jungian Psychology: The use of Dreams as an Instrument For Research, Diagnosis and Treatment of Social Phobia.

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Khodarahimi, Siamak

2009-10-01

The significance of dreams has been explained in psychoanalysis, depth psychology and gestalt therapy. There are many guidelines in analytic psychology for dream interpretation and integration in clinical practice. The present study, based on the Jungian analytic model, incorporated dreams as an instrument for assessment of aetiology, the psychotherapy process and the outcome of treatment for social phobia within a clinical case study. This case study describes the use of dream analysis in treating a female youth with social phobia. The present findings supported the three stage paradigm efficiency in the Jungian model for dream working within a clinical setting, i.e. written details, reassembly with amplification and assimilation. It was indicated that childhood and infantile traumatic events, psychosexual development malfunctions, and inefficient coping skills for solving current life events were expressed in the patient's dreams. Dreams can reflect a patient's aetiology, needs, illness prognosis and psychotherapy outcome. Dreams are an instrument for the diagnosis, research and treatment of mental disturbances in a clinical setting.

Personality and Adult Perceptions of Childhood Dreams.

Science.gov (United States)

Jacka, Brian

This study used adult recall of childhood dreams to test Cann and Donderi's (1986) findings that Jungian intuitives recall more archetypal dreams than do sensate subjects, and that introverts recall more everyday dreams than extraverts. It was hypothesized that since dreams recalled from childhood are relatively high in archetypal content, there…

Unraveling reported dreams with text analytics

NARCIS (Netherlands)

Hendrickx, Iris; Onrust, Louis; Kunneman, Florian; Hürriyetoglu, Ali; Stoop, Wessel; van den Bosch, A.

2017-01-01

We investigate what distinguishes reported dreams from other personal narratives. The continuity hypothesis, stemming from psychological dream analysis work, states that most dreams refer to a person’s daily life and personal concerns, similar to other personal narratives such as diary entries.

The dream between neuroscience and psychoanalysis.

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Mancia, M

2004-07-01

The dream is tackled sometimes from the neurobiological viewpoint, sometimes from the neuropsychological angle, or from the positions of experimental and psychoanalytical psychology. Interest in dreams started with psychoanalysis in 1900, and 53 years later the discovery of REM sleep by Aserinski and Kleitman, and subsequent psychophysiological findings took the dream into the realm of biology. The dichotomous model of REM and non-REM sleep is described, as a basis for thought-like activity (non-REM sleep) and dreaming (REM sleep). This led to Hobson and McCarley's theory of activation-synthesis, suggesting that the mind while dreaming is simply the brain self-activated in REM sleep. Psychophysiological research has shown that people dream in all phases of sleep, from falling asleep to waking, but that the characteristics of the dreams may differ in the different phases. Bio-imaging studies indicate that during REM sleep there is activation of the pons, the amygdala bilaterally, and the anterior cingulate cortex, and disactivation of the posterior cingulate cortex and the prefrontal cortex. The images suggest there is a neuroanatomical frame within which dreams can be generated and then forgotten. Psychoanalysis studies the dream from a completely different angle. Freud believed it was the expression of hallucinatory satisfaction of repressed desires. Today it is interpreted as the expression of a representation of the transference in the hic et nunc of the session. At the same time it also has symbol-generating functions which provide an outlet by which affective experiences and fantasies and defences stored as parts of an unrepressed unconscious in the implicit memory can be represented in pictorial terms, then thought and rendered verbally. From the psychoanalytical point of view, the dream transcends neurobiological knowledge, and looks like a process of internal activation that is only apparently chaotic, but is actually rich in meanings, arising from the

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

Directory of Open Access Journals (Sweden)

Chandra Nagasuma R

2009-02-01

Full Text Available Abstract Background A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN from transcript profiling data. Results The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting problem and solved finally by formulating a Linear Program (LP. A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known

Lee Acculturation Dream Scale for Korean-American college students.

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Lee, Sang Bok

2005-04-01

This study examined acculturation as represented in dream narratives of 165 Korean immigrant college students living in the USA. A total of 165 dreams were collected and evaluated using the Lee Acculturation Dream Scale, for which locations of dream contents were coded. 39% of the dreams took place in South Korea, while 38% were in the USA. Also, 16% of the dreams included both locations, whereas 7% had no specific dream location. The dreams contained overlapping dream messages, images, scenes, and interactions in both South Korea and the USA. A two-sample t test on the mean scores of the Lee Acculturation Dream Scale indicated no significant difference between men and women.

Bizarreness effect in dream recall.

Science.gov (United States)

Cipolli, C; Bolzani, R; Cornoldi, C; De Beni, R; Fagioli, I

1993-02-01

This study aimed to ascertain a) whether morning reports of dream experience more frequently reproduce bizarre contents of night reports than nonbizarre ones and b) whether this effect depends on the rarity of bizarre contents in the dream or on their richer encoding in memory. Ten subjects were awakened in rapid eye movement (REM) sleep three times per night for 4 nonconsecutive nights and asked to report their previous dream experiences. In the morning they were asked to re-report those dreams. Two separate pairs of judges scored the reports: the former identified the parts in each report with bizarre events, characters or feelings and the latter parsed each report into content units using transformational grammar criteria. By combining the data of the two analyses, content units were classified as bizarre or nonbizarre and, according to whether present in both the night and corresponding morning reports, as semantically equivalent or nonequivalent. The proportion of bizarre contents common to night and morning reports was about twice that of nonbizarre contents and was positively correlated to the quantity of bizarre contents present in the night report. These findings support the view that bizarreness enhances recall of dream contents and that this memory advantage is determined by a richer encoding at the moment of dream generation. Such a view would seem to explain why dreams in everyday life, which are typically remembered after a rather long interval, appear more markedly bizarre than those recalled in the sleep laboratory.

Chasing the Chinese Dream

Institute of Scientific and Technical Information of China (English)

无

2011-01-01

People’s pursuit of better lives pushes the nation forward The belief that anyone can live a better life in the United States through hard workis called the American Dream. Many European settlers were drawn to the new continent by the American Dream.

Dreams, Daydreams and Discovery.

Science.gov (United States)

Brown, R. A.; Luckcock, R. G.

1978-01-01

It has been discovered that dreams and daydreams can be productive states in the process of scientific innovation. An attempt is made to provide some typical examples of insights which have come to scientists during dream-like states and in sleep. (Author/MA)

To search new technology of dream

International Nuclear Information System (INIS)

Heo, Chang Uk

1998-08-01

This book deals with new technology of dream like cold nuclear fusion is possible, alchemy of the 21 century, cold transmutation of element, cold nuclear fusion on the desk, fire of multiarc recalling earth environment, like miracle fire and multiarc device, field fulfilling of dream, pioneers of anti gravity research, dream of anti gravity which is realized by mobius, N-machine and space energy, challenge for infinite power unit like engine of dream, Kawai magnet motor and attaching magnet on the motorcycle.

The role of calsenilin/DREAM/KChIP3 in contextual fear conditioning.

Science.gov (United States)

Alexander, Jon C; McDermott, Carmel M; Tunur, Tumay; Rands, Vicky; Stelly, Claire; Karhson, Debra; Bowlby, Mark R; An, W Frank; Sweatt, J David; Schrader, Laura A

2009-03-01

Potassium channel interacting proteins (KChIPs) are members of a family of calcium binding proteins that interact with Kv4 potassium (K(+)) channel primary subunits and also act as transcription factors. The Kv4 subunit is a primary K(+) channel pore-forming subunit, which contributes to the somatic and dendritic A-type currents throughout the nervous system. These A-type currents play a key role in the regulation of neuronal excitability and dendritic processing of incoming synaptic information. KChIP3 is also known as calsenilin and as the transcription factor, downstream regulatory element antagonist modulator (DREAM), which regulates a number of genes including prodynorphin. KChIP3 and Kv4 primary channel subunits are highly expressed in hippocampus, an area of the brain important for learning and memory. Through its various functions, KChIP3 may play a role in the regulation of synaptic plasticity and learning and memory. We evaluated the role of KChIP3 in a hippocampus-dependent memory task, contextual fear conditioning. Male KChIP3 knockout (KO) mice showed significantly enhanced memory 24 hours after training as measured by percent freezing. In addition, we found that membrane association and interaction with Kv4.2 of KChIP3 protein was significantly decreased and nuclear KChIP3 expression was increased six hours after the fear conditioning training paradigm with no significant change in KChIP3 mRNA. In addition, prodynorphin mRNA expression was significantly decreased six hours after fear conditioning training in wild-type (WT) but not in KO animals. These data suggest a role for regulation of gene expression by KChIP3/DREAM/calsenilin in consolidation of contextual fear conditioning memories.

A new and accurate fault location algorithm for combined transmission lines using Adaptive Network-Based Fuzzy Inference System

Energy Technology Data Exchange (ETDEWEB)

Sadeh, Javad; Afradi, Hamid [Electrical Engineering Department, Faculty of Engineering, Ferdowsi University of Mashhad, P.O. Box: 91775-1111, Mashhad (Iran)

2009-11-15

This paper presents a new and accurate algorithm for locating faults in a combined overhead transmission line with underground power cable using Adaptive Network-Based Fuzzy Inference System (ANFIS). The proposed method uses 10 ANFIS networks and consists of 3 stages, including fault type classification, faulty section detection and exact fault location. In the first part, an ANFIS is used to determine the fault type, applying four inputs, i.e., fundamental component of three phase currents and zero sequence current. Another ANFIS network is used to detect the faulty section, whether the fault is on the overhead line or on the underground cable. Other eight ANFIS networks are utilized to pinpoint the faults (two for each fault type). Four inputs, i.e., the dc component of the current, fundamental frequency of the voltage and current and the angle between them, are used to train the neuro-fuzzy inference systems in order to accurately locate the faults on each part of the combined line. The proposed method is evaluated under different fault conditions such as different fault locations, different fault inception angles and different fault resistances. Simulation results confirm that the proposed method can be used as an efficient means for accurate fault location on the combined transmission lines. (author)

Dream Content in Complicated Grief: A Window into Loss-Related Cognitive Schemas Running Head: Dreams in Complicated Grief

Science.gov (United States)

Germain, Anne; Shear, Katherine M.; Walsh, Colleen; Buysse, Daniel J.; Monk, Timothy H.; Reynolds, Charles F.; Frank, Ellen; Silowash, Russell

2012-01-01

Bereavement and its accompanying psychological response (grief) constitute potent experiences that necessitate the reorganization of cognitive-affective representations of lost significant attachment figures during both wakefulness and dreaming. The goals of this preliminary study were to explore whether the dream content of 77 adults with complicated grief (CG) differed from that of a normative sample, and to explore whether CG patients who dream of the deceased differ from CG patients who do not dream of the deceased on measures of daytime emotional distress. CG dreams were characterized by more family and familiar characters including the deceased (in women), and fewer social interactions and emotions compared to norms. Increased representations of familiar characters in CG dreams may reflect attempts to reorganize relational cognitive schemas to compensate for the loss. PMID:24524436

Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks.

Science.gov (United States)

Ghanat Bari, Mehrab; Ung, Choong Yong; Zhang, Cheng; Zhu, Shizhen; Li, Hu

2017-08-01

Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 10 8 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.

Dream Content and Adaptation to a Stressful Situation

Science.gov (United States)

De Koninck, Joseph M.; Koulack, David

1975-01-01

The present study considered whether it is better to dream about a stressful presleep experience and have anxious dreams, or is it better to dream about something else and have pleasant dreams. (Author/RK)

Dreams, katharsis and anxiety.

Science.gov (United States)

Kilborne, Benjamin

2013-06-01

Over the centuries, the importance and the nature of the relationship of "inside" and "outside" in human experience have shifted, with consequences for notions of mind and body. This paper begins with dreams and healing in the Asklepian tradition. It continues with Aristotle's notions of psuche and how these influenced his conception of katharsis and tragedy. Jumping then to the 17th century, we will consider Descartes' focus on dreams in his theories of thinking. Finally, we will turn explicitly to Freud's use of dreams in relation to his theories of anxiety, of psychic processes and of the Oedipus Complex.

Dreaming furiously? A sleep laboratory study on the dream content of people with Parkinson's disease and with or without rapid eye movement sleep behavior disorder.

Science.gov (United States)

Valli, Katja; Frauscher, Birgit; Peltomaa, Taina; Gschliesser, Viola; Revonsuo, Antti; Högl, Birgit

2015-03-01

Rapid eye movement (REM) sleep behavior disorder (RBD) has been related to altered, action-filled, vivid, and aggressive dream content, but research comparing the possible differences in dreams of Parkinson's disease (PD) patients with and without RBD is scarce. The dream content of PD patients with and without RBD was analyzed with specific focus on action-filledness, vividness, emotional valence, and threats. A total of 69 REM and NREM dream reports were collected in the sleep laboratory, 37 from nine PD patients with RBD and 32 from six PD patients without RBD. A content analysis of (1) action-filledness (actions and environmental events); (2) vividness (emotions and cognitive activity); (3) intensity of actions, events and emotions; (4) emotional valence, and (5) threatening events was performed on the transcripts. Altogether 563 dream elements expressing action-filledness and vividness were found. There were no significant between-group differences in the number or distribution of elements reflecting action-filledness or vividness, emotional valence or threats. In within-group analyses, PD patients with RBD had significantly more negative compared to positive dreams (p = 0.012) and compared to PD patients without RBD, a tendency to have more intense actions in their dreams (p = 0.066). Based on the results of this study, there are no major between-group differences in the action-filledness, vividness, or threat content of dreams of PD patients with and without RBD. However, within-group analyses revealed that dreams were more often negatively than positively toned in PD patients with RBD. Copyright © 2014 Elsevier B.V. All rights reserved.

The dream: a psychodynamically informative instrument.

Science.gov (United States)

Glucksman, M L

2001-01-01

The dream is a unique psychodynamically informative instrument for evaluating the subjective correlates of brain activity during REM sleep. These include feelings, percepts, memories, wishes, fantasies, impulses, conflicts, and defenses, as well as images of self and others. Dream analysis can be used in a variety of clinical settings to assist in diagnostic assessment, psychodynamic formulation, evaluation of clinical change, and the management of medically ill patients. Dreams may serve as the initial indicators of transference, resistance, impending crisis, acting-out, conflict resolution, and decision-making. A clinically functional categorization of dreams can facilitate an understanding of psychopathology, psychodynamics, personality structure, and various components of the psychotherapeutic process. Examples of different types of dreams are provided to illustrate their relevance and use in various clinical situations.

The nature of delayed dream incorporation ('dream-lag effect'): Personally significant events persist, but not major daily activities or concerns.

Science.gov (United States)

Eichenlaub, Jean-Baptiste; van Rijn, Elaine; Phelan, Mairéad; Ryder, Larnia; Gaskell, M Gareth; Lewis, Penelope A; P Walker, Matthew; Blagrove, Mark

2018-04-22

Incorporation of details from waking life events into rapid eye movement (REM) sleep dreams has been found to be highest on the 2 nights after, and then 5-7 nights after, the event. These are termed, respectively, the day-residue and dream-lag effects. This study is the first to categorize types of waking life experiences and compare their incorporation into dreams across multiple successive nights. Thirty-eight participants completed a daily diary each evening and a dream diary each morning for 14 days. In the daily diary, three categories of experiences were reported: major daily activities (MDAs), personally significant events (PSEs) and major concerns (MCs). After the 14-day period each participant identified the correspondence between items in their daily diaries and subsequent dream reports. The day-residue and dream-lag effects were found for the incorporation of PSEs into dreams (effect sizes of .33 and .27, respectively), but only for participants (n = 19) who had a below-median total number of correspondences between daily diary items and dream reports (termed "low-incorporators" as opposed to "high-incorporators"). Neither the day-residue or dream-lag effects were found for MDAs or MCs. This U-shaped timescale of incorporation of events from daily life into dreams has been proposed to reflect REM sleep-dependent memory consolidation, possibly related to emotional memory processing. This study had a larger sample size of dreams than any dream-lag study hitherto with trained participants. Coupled with previous successful replications, there is thus substantial evidence supporting the dream-lag effect and further explorations of its mechanism, including its neural underpinnings, are warranted. © 2018 The Authors. Journal of Sleep Research published by John Wiley & Sons Ltd on behalf of European Sleep Research Society.

LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

Directory of Open Access Journals (Sweden)

Rasmus Magnusson

2017-06-01

Full Text Available Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM, which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE for gene regulatory networks (GRNs. LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models

A replication of the 5-7 day dream-lag effect with comparison of dreams to future events as control for baseline matching.

Science.gov (United States)

Blagrove, Mark; Henley-Einion, Josie; Barnett, Amanda; Edwards, Darren; Heidi Seage, C

2011-06-01

The dream-lag effect refers to there being, after the frequent incorporation of memory elements from the previous day into dreams (the day-residue), a lower incorporation of memory elements from 2 to 4 days before the dream, but then an increased incorporation of memory elements from 5 to 7 days before the dream. Participants (n=8, all female) kept a daily diary and a dream diary for 14 days and then rated the level of matching between every dream report and every daily diary record. Baseline matching was assessed by comparing all dream reports to all diary records for days that occurred after the dream. A significant dream-lag effect for the 5-7 day period, compared to baseline and compared to the 2-4 day period, was found. This may indicate a memory processing function for sleep, which the dream content may reflect. Participants' and three independent judges' mean ratings also confirmed a significant day-residue effect. Copyright © 2010 Elsevier Inc. All rights reserved.

Fast Inference of Deep Neural Networks in FPGAs for Particle Physics

Energy Technology Data Exchange (ETDEWEB)

Duarte, Javier [Fermilab; Han, Song [MIT; Harris, Philip [MIT; Jindariani, Sergo [Fermilab; Kreinar, Edward [EIS Intl., Herndon; Kreis, Benjamin [Fermilab; Ngadiuba, Jennifer [CERN; Pierini, Maurizio [CERN; Rivera, Ryan [Fermilab; Tran, Nhan [Fermilab; Wu, Zhenbin [Illinois U., Chicago

2018-04-16

Recent results at the Large Hadron Collider (LHC) have pointed to enhanced physics capabilities through the improvement of the real-time event processing techniques. Machine learning methods are ubiquitous and have proven to be very powerful in LHC physics, and particle physics as a whole. However, exploration of the use of such techniques in low-latency, low-power FPGA hardware has only just begun. FPGA-based trigger and data acquisition (DAQ) systems have extremely low, sub-microsecond latency requirements that are unique to particle physics. We present a case study for neural network inference in FPGAs focusing on a classifier for jet substructure which would enable, among many other physics scenarios, searches for new dark sector particles and novel measurements of the Higgs boson. While we focus on a specific example, the lessons are far-reaching. We develop a package based on High-Level Synthesis (HLS) called hls4ml to build machine learning models in FPGAs. The use of HLS increases accessibility across a broad user community and allows for a drastic decrease in firmware development time. We map out FPGA resource usage and latency versus neural network hyperparameters to identify the problems in particle physics that would benefit from performing neural network inference with FPGAs. For our example jet substructure model, we fit well within the available resources of modern FPGAs with a latency on the scale of 100 ns.

Descartes' dreams.

Science.gov (United States)

Withers, Robert

2008-11-01

René Descartes is often regarded as the 'father of modern philosophy'. He was a key figure in instigating the scientific revolution that has been so influential in shaping our modern world. He has been revered and reviled in almost equal measure for this role; on the one hand seen as liberating science from religion, on the other as splitting soul from body and man from nature. He dates the founding of his philosophical methods to the night of 10(th) November 1619 and in particular to three powerful dreams he had that night. This article utilizes Descartes' own interpretations of the dreams, supported by biographical material, as well as contemporary neuroscientific and psychoanalytic theory, to reach a new understanding of them. It is argued that the dreams can be understood as depicting Descartes' personal journey from a state of mind-body dissociation to one of mind-body deintegration. This personal journey may have implications for a parallel journey from Renaissance to modern culture and from modernity to post-modern culture.

A comparative study of covariance selection models for the inference of gene regulatory networks.

Science.gov (United States)

Stifanelli, Patrizia F; Creanza, Teresa M; Anglani, Roberto; Liuzzi, Vania C; Mukherjee, Sayan; Schena, Francesco P; Ancona, Nicola

2013-10-01

The inference, or 'reverse-engineering', of gene regulatory networks from expression data and the description of the complex dependency structures among genes are open issues in modern molecular biology. In this paper we compared three regularized methods of covariance selection for the inference of gene regulatory networks, developed to circumvent the problems raising when the number of observations n is smaller than the number of genes p. The examined approaches provided three alternative estimates of the inverse covariance matrix: (a) the 'PINV' method is based on the Moore-Penrose pseudoinverse, (b) the 'RCM' method performs correlation between regression residuals and (c) 'ℓ(2C)' method maximizes a properly regularized log-likelihood function. Our extensive simulation studies showed that ℓ(2C) outperformed the other two methods having the most predictive partial correlation estimates and the highest values of sensitivity to infer conditional dependencies between genes even when a few number of observations was available. The application of this method for inferring gene networks of the isoprenoid biosynthesis pathways in Arabidopsis thaliana allowed to enlighten a negative partial correlation coefficient between the two hubs in the two isoprenoid pathways and, more importantly, provided an evidence of cross-talk between genes in the plastidial and the cytosolic pathways. When applied to gene expression data relative to a signature of HRAS oncogene in human cell cultures, the method revealed 9 genes (p-value<0.0005) directly interacting with HRAS, sharing the same Ras-responsive binding site for the transcription factor RREB1. This result suggests that the transcriptional activation of these genes is mediated by a common transcription factor downstream of Ras signaling. Software implementing the methods in the form of Matlab scripts are available at: http://users.ba.cnr.it/issia/iesina18/CovSelModelsCodes.zip. Copyright © 2013 The Authors. Published by

I Had a Dream: AAAI Presidential Address

OpenAIRE

Bledsoe, Woody

1986-01-01

Twenty-five years ago I had a dream, a daydream, if you will. A dream shared with many of you. I dreamed of a special kind of computer, which had eyes and ears and arms and legs, in addition to its "brain." I did not dream that this new computer friend would be a means of making money for me or my employer or a help for my country - though I loved my country then and still do, and I have no objection to making money. I did not even dream of such a worthy cause as helping the poor and handicap...

Dream recall and the full moon.

Science.gov (United States)

Schredl, Michael; Fulda, Stephany; Reinhard, Iris

2006-02-01

There is ongoing debate on whether the full moon is associated with sleep and dreaming. The analysis of diaries kept by the participants (N = 196) over 28 to 111 nights showed no association of a full moon and dream recall. Psychological factors might explain why some persons associate a full moon with increased dream recall.

Forecasting building energy consumption with hybrid genetic algorithm-hierarchical adaptive network-based fuzzy inference system

Energy Technology Data Exchange (ETDEWEB)

Li, Kangji [Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027 (China); School of Electricity Information Engineering, Jiangsu University, Zhenjiang 212013 (China); Su, Hongye [Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027 (China)

2010-11-15

There are several ways to forecast building energy consumption, varying from simple regression to models based on physical principles. In this paper, a new method, namely, the hybrid genetic algorithm-hierarchical adaptive network-based fuzzy inference system (GA-HANFIS) model is developed. In this model, hierarchical structure decreases the rule base dimension. Both clustering and rule base parameters are optimized by GAs and neural networks (NNs). The model is applied to predict a hotel's daily air conditioning consumption for a period over 3 months. The results obtained by the proposed model are presented and compared with regular method of NNs, which indicates that GA-HANFIS model possesses better performance than NNs in terms of their forecasting accuracy. (author)

Dream and Creative Writing

Institute of Scientific and Technical Information of China (English)

杨公建

2015-01-01

Freud asserts that the unconscious will express its suppressed wishes and desires. The unconscious will then redirect andreshape these concealed wishes into acceptable social activities, presenting them in the form of images or symbols in our dreams and/or our writings. Dream is the unconscious which promotes the creative writing.

What are the memory sources of dreaming?

Science.gov (United States)

Nielsen, Tore A; Stenstrom, Philippe

2005-10-27

Investigators since Freud have appreciated that memories of the people, places, activities and emotions of daily life are reflected in dreams but are typically so fragmented that their predictability is nil. The mechanisms that translate such memories into dream images remain largely unknown. New research targeting relationships between dreaming, memory and the hippocampus is producing a new theory to explain how, why and when we dream of waking life events.

The dream of an ultimate theory

International Nuclear Information System (INIS)

Weinberg, S.

1997-10-01

Steven Weinberg describes how the dream of an ultimate theory began when one tried to unify the fundamental laws governing the stars constellations as elementary particles: electromagnetism, weak-electro theory then standard model which gives only one quantity out of its fields, the gravitation. He tries to explain to what an ultimate theory could look like. but the dream of an ultimate theory is not yet realized, there are some elementary particles to find before and then to build superconducting super colliders. The europe made it. the dream of an ultimate theory became an european dream. (N.C.)

Sex differences in dreaming during short propofol sedation for upper gastrointestinal endoscopy.

Science.gov (United States)

Xu, Guanghong; Liu, Xuesheng; Sheng, Qiying; Yu, Fengqiong; Wang, Kai

2013-10-02

Previous reports suggest that sex differences may exist in dreaming under anesthesia, but their results were inconclusive. The current study explored sex differences in the incidence and content of dreams during short propofol sedation for upper gastrointestinal endoscopy and investigated whether sex differences or dream content affect patient satisfaction with sedation. A total of 200 patients (100 men and 100 women) undergoing upper gastrointestinal endoscopy participated in this study. Patients were interviewed with the modified Brice questionnaire about the incidence and the content of dreams, and satisfaction with sedation was assessed. The results showed that the incidence of dreaming was significantly higher in men (31%) than in women (17%) (P=0.02), but recovery time was similar. In men, 45% (14/31) of dreamers reported positive emotional content and only 6% (2/31) reported negative emotional content. In contrast, in women, 18% (3/17) reported positive and 29% (5/17) reported negative content (P=0.04). Men reported dreams that were more vivid, meaningful, familiar, and memorable (PDreamer satisfaction with sedation was not influenced by sex or dream content.

The fate of the dream in contemporary psychoanalysis.

Science.gov (United States)

Loden, Susan

2003-01-01

Freud's metapsychology of dream formation has implicitly been discarded, as indicated in a brief review of trends in psychoanalytic thinking about dreams, with a focus on the relationship of the dream process to ego capacities. The current bias toward exclusive emphasis on the exploration of the analytic relationship and the transference has evolved at the expense of classical, in-depth dream interpretation, and, by extension, at the expense of strengthening the patient's capacity for self-inquiry. This trend is shown to be especially evident in the treatment of borderline patients, who today are believed by many analysts to misuse the dream in the analytic situation. An extended clinical example of a borderline patient with whom an unmodified Freudian associative technique of dream interpretation is used with good outcome illustrates the author's contrary conviction. In clinical practice, we should neglect neither the uniqueness of the dream as a central intrapsychic event nor the Freudian art of total dream analysis.

Methods for Inferring Health-Related Social Networks among Coworkers from Online Communication Patterns

Science.gov (United States)

Matthews, Luke J.; DeWan, Peter; Rula, Elizabeth Y.

2013-01-01

Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1) the absolute number of emails exchanged, (2) logistic regression probability of an offline relationship, and (3) the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI) across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a social network. PMID

Methods for inferring health-related social networks among coworkers from online communication patterns.

Directory of Open Access Journals (Sweden)

Luke J Matthews

Full Text Available Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1 the absolute number of emails exchanged, (2 logistic regression probability of an offline relationship, and (3 the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a

Methods for inferring health-related social networks among coworkers from online communication patterns.

Science.gov (United States)

Matthews, Luke J; DeWan, Peter; Rula, Elizabeth Y

2013-01-01

Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1) the absolute number of emails exchanged, (2) logistic regression probability of an offline relationship, and (3) the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI) across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a social network.

Costly Signaling Theory of REM Sleep and Dreams

Directory of Open Access Journals (Sweden)

Patrick McNamara

2007-01-01

Full Text Available The function of REM sleep dreaming is still unknown. We situate our approach to understanding dream phenomenology and dream function within that part of evolutionary theory known as Costly Signaling Theory (CST. We contend that many of the signals produced by the dreaming brain can be and should be construed as “costly signals”—emotions or mental simulations that produce daytime behavioral dispositions that are costly to the dreamer. For example, often the dreamer will appear in the dream as handicapped in some way (i.e., no clothes, no ID, no money, is under attack, being chased etc.. The dreamer, during waking life, is then influenced by the carry-over effect of the unpleasant dream content. The informational and affective content of the dream creates a mental set in the dreamer that operates during the daytime to facilitate the signaling of a “handicapped” Self. The subtle signaling effect might be via display of the intense emotions or physical demeanor that had first appeared in the dream. When the dreamer shares his dream with others the dream has a more direct impact on waking life and social interactions. In effect, the dreamer uses his or her dreams to adopt a self-handicapping strategy when dealing with significant others. The increased use of costly signals (the self-handicapping strategy during the daytime then facilitates some vital communicative goal of the dreamer.

[Tertullianus and Agostinus. Approaches to dreams in ancient Christianity].

Science.gov (United States)

Genovese, Armando

2009-01-01

The author analyzes the nature and typologies of dreams in Tertullianus' De anima and, briefly, in the work of Agostinus, two centuries later. What are made dreams of? Are they autonomous productions of psyché or phantasia, or rather messages sent by demons or God, according to dreams' bad or good intimate nature? Is there a relation between time of the night and nature of the dreams? Moreover, is there a relation between seasons and dreams? Does a specific relationship between food, regimen and dreams exist? Which is the soul's faculty able to generate dreams? Is phantasia moved by some other deep and mysterious principle? Which are the connections linking human physiology and dreams?

Red balloon: approaching dreams as self-narratives.

Science.gov (United States)

Androutsopoulou, Athena

2011-10-01

In this article, dreams are seen as stories within a self-narrative. Dream stories, like all other stories, are told in an effort to make sense of experiences. Here, dream content is linked to current concerns, some aspects of which are not given voice in waking. Dreams depict restricting themes but also openings in self-narratives. Several examples are provided of how dreams can be linked to early, middle, and late therapy phases associated with recognizing, challenging, revising, and maintaining a revising stance. It is further suggested that dream stories can be used to trace, facilitate, and evaluate the process of reconstructing self-narratives. Finally, a number of therapeutic interventions are briefly presented to facilitate the work of narrative-informed family therapists working with individuals, families, and groups. © 2011 American Association for Marriage and Family Therapy.

Qualitative reasoning for biological network inference from systematic perturbation experiments.

Science.gov (United States)

Badaloni, Silvana; Di Camillo, Barbara; Sambo, Francesco

2012-01-01

The systematic perturbation of the components of a biological system has been proven among the most informative experimental setups for the identification of causal relations between the components. In this paper, we present Systematic Perturbation-Qualitative Reasoning (SPQR), a novel Qualitative Reasoning approach to automate the interpretation of the results of systematic perturbation experiments. Our method is based on a qualitative abstraction of the experimental data: for each perturbation experiment, measured values of the observed variables are modeled as lower, equal or higher than the measurements in the wild type condition, when no perturbation is applied. The algorithm exploits a set of IF-THEN rules to infer causal relations between the variables, analyzing the patterns of propagation of the perturbation signals through the biological network, and is specifically designed to minimize the rate of false positives among the inferred relations. Tested on both simulated and real perturbation data, SPQR indeed exhibits a significantly higher precision than the state of the art.

Autogenic training and dream recall.

Science.gov (United States)

Schredl, M; Doll, E

1997-06-01

The present study has investigated the relationship between Autogenic Training and dream recall for 112 participants in 16 beginning courses of 10 wk. Analyses confirmed the hypothesis that learning and practicing this relaxation technique enhanced dream recall.

Dream recall and its relationship to sleep, perceived stress, and creativity among adolescents.

Science.gov (United States)

Brand, Serge; Beck, Johannes; Kalak, Nadeem; Gerber, Markus; Kirov, Roumen; Pühse, Uwe; Hatzinger, Martin; Holsboer-Trachsler, Edith

2011-11-01

To explore associations between dream recall, gender, sleep, perceived stress, and creativity in a large sample of adolescents. In adults, women report a higher frequency of dream recall than men. Moreover, increased awakenings seem to increase dream recall, whereas low sleep quality is associated with low dream recall. In addition, there is some evidence that dream recall is associated with personality traits such as creativity. For adolescents, comparable data from larger samples are missing to date. A total of 5,580 adolescents (mean age: 18.23 years; 3,711 females and 1,869 males) participated in the present study. Participants completed an Internet-administered questionnaire related to dreaming, sleep, perceived stress, and creativity. As compared with males, female adolescents reported a higher dream recall rate and felt a stronger impact of dreams on the subsequent day. Female adolescents also described themselves as more creative, and reported suffering more from sleep complaints and perceived stress. Multiple regression analyses further revealed that increased dream recall was independently predicted by factors such as female gender, sleep quality, and creativity, whereas perceived stress, awakenings during the night, and sleep duration had no predictive value. Similar to the findings of studies conducted on adults, dream recall was also associated with female gender in a large sample of adolescents. Additionally, it seemed that several different factors such as good mood, increased sleep quality, and creativity influenced dream recall. These results can provide a basis for better understanding the psychology of dreams in adolescence. In contrast to nightmares, recalling dreaming is associated with health and well-being. Copyright © 2011 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Ultradian and circadian modulation of dream recall: EEG correlates and age effects.

Science.gov (United States)

Chellappa, Sarah Laxhmi; Cajochen, Christian

2013-08-01

Dreaming occurs during non-rapid eye movement (NREM) and rapid eye movement (REM) sleep, which both are regulated by homeostatic, ultradian, and circadian processes. However, the magnitude of how ultradian REM and NREM sleep and its EEG correlates impact onto dream recall remains fairly unknown. In this review, we address three questions: 1. Is there an ultradian NREM-REM sleep modulation in successful dream recall, which is gated by the circadian clock? 2. What are the key electrophysiological correlates that account for dream recall during NREM and REM sleep and 3. Are there age-related changes in the ultradian and circadian regulation in dream recall and its electrophysiological correlates? Knowledge on the specific frequency and topography NREM and REM sleep differences prior to dream recall may pinpoint to the cerebral correlates that account for this cognitive process, and hint to their possible physiological meaning. Copyright © 2013 Elsevier B.V. All rights reserved.

Insomnia, dreams, and suicide: Connecting links

Directory of Open Access Journals (Sweden)

Sagar B Karia

2016-01-01

Full Text Available Introduction: A growing empirical literature has examined insomnia symptoms as a possible risk factor for a range of suicidal behavior. Not much literature is available in normal adolescent population. Aims: The aim is to find insomnia prevalence, studying various dream factors, and suicidality prevalence among students of various courses. To check if there is a relation between insomnia and suicidal behavior and dreams, particularly nightmares and suicide. Materials and Methods: A total of 400 students of various courses were assessed using Insomnia Severity Index and The Mannheim Dream Questionnaire and Suicide Behaviour Questionnaire. Results: Insomnia was present in 11%, 23%, 19%, and 19% and suicide behavior in 16%, 17%, 12%, and 22%, respectively, in medical, commerce, engineering, and arts students. Statistically significant correlation was found between suicide and insomnia severity and various dream factors. Conclusions: Insomnia and dreams had relation with suicidality in normal adolescent population.

Comparison of dream content of depressed vs nondepressed dreamers.

Science.gov (United States)

Barrett, D; Loeffler, M

1992-04-01

Dreams of 20 college women classified as depressed by scores on the Beck Depression Inventory were compared with those of 21 nondepressed college women. The depressed group recalled fewer dreams, had significantly shorter dream length, and displayed less anger in their dreams. They also had fewer characters in their dreams and especially fewer strangers.

Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration.

Directory of Open Access Journals (Sweden)

Daniel Lobo

2015-06-01

Full Text Available Transformative applications in biomedicine require the discovery of complex regulatory networks that explain the development and regeneration of anatomical structures, and reveal what external signals will trigger desired changes of large-scale pattern. Despite recent advances in bioinformatics, extracting mechanistic pathway models from experimental morphological data is a key open challenge that has resisted automation. The fundamental difficulty of manually predicting emergent behavior of even simple networks has limited the models invented by human scientists to pathway diagrams that show necessary subunit interactions but do not reveal the dynamics that are sufficient for complex, self-regulating pattern to emerge. To finally bridge the gap between high-resolution genetic data and the ability to understand and control patterning, it is critical to develop computational tools to efficiently extract regulatory pathways from the resultant experimental shape phenotypes. For example, planarian regeneration has been studied for over a century, but despite increasing insight into the pathways that control its stem cells, no constructive, mechanistic model has yet been found by human scientists that explains more than one or two key features of its remarkable ability to regenerate its correct anatomical pattern after drastic perturbations. We present a method to infer the molecular products, topology, and spatial and temporal non-linear dynamics of regulatory networks recapitulating in silico the rich dataset of morphological phenotypes resulting from genetic, surgical, and pharmacological experiments. We demonstrated our approach by inferring complete regulatory networks explaining the outcomes of the main functional regeneration experiments in the planarian literature; By analyzing all the datasets together, our system inferred the first systems-biology comprehensive dynamical model explaining patterning in planarian regeneration. This method

HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation.

Science.gov (United States)

Deng, Yue; Zenil, Hector; Tegnér, Jesper; Kiani, Narsis A

2017-12-15

The use of differential equations (ODE) is one of the most promising approaches to network inference. The success of ODE-based approaches has, however, been limited, due to the difficulty in estimating parameters and by their lack of scalability. Here, we introduce a novel method and pipeline to reverse engineer gene regulatory networks from gene expression of time series and perturbation data based upon an improvement on the calculation scheme of the derivatives and a pre-filtration step to reduce the number of possible links. The method introduces a linear differential equation model with adaptive numerical differentiation that is scalable to extremely large regulatory networks. We demonstrate the ability of this method to outperform current state-of-the-art methods applied to experimental and synthetic data using test data from the DREAM4 and DREAM5 challenges. Our method displays greater accuracy and scalability. We benchmark the performance of the pipeline with respect to dataset size and levels of noise. We show that the computation time is linear over various network sizes. The Matlab code of the HiDi implementation is available at: www.complexitycalculator.com/HiDiScript.zip. hzenilc@gmail.com or narsis.kiani@ki.se. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The Five Star Method: A Relational Dream Work Methodology

Science.gov (United States)

Sparrow, Gregory Scott; Thurston, Mark

2010-01-01

This article presents a systematic method of dream work called the Five Star Method. Based on cocreative dream theory, which views the dream as the product of the interaction between dreamer and dream, this creative intervention shifts the principal focus in dream analysis from the interpretation of static imagery to the analysis of the dreamer's…

Testing and ground calibration of DREAMS-H relative humidity device

Science.gov (United States)

Genzer, Maria; Hieta, Maria; Nikkanen, Timo; Schmidt, Walter; Kemppinen, Osku; Harri, Ari-Matti; Haukka, Harri

2015-04-01

DREAMS (Dust Characterization, Risk Assessment and Environmental Analyzer on the Martian Surface) instrument suite is to be launched as part of the ESA ExoMars 2016/Schiaparelli lander. DREAMS consists of an environmental package for monitoring temperature, pressure, relative humidity, winds and dust opacity, as well as atmospheric electricity of Martian atmosphere. The DREAMS instruments and scientific goals are described in [1]. Here we describe testing and ground calibration of the relative humidity device, DREAMS-H, provided to the DREAMS payload by the Finnish Meteorological Institute and based on proprietary technology of Vaisala, Inc. The same kind of device is part of the REMS instrument package onboard MSL Curiosity Rover [2][3]. DREAMS-H is based on Vaisala Humicap® technology adapted for use in Martian environment by the Finnish Meteorological Institute. The device is very small and lightweighed, with total mass less than 20 g and consuming only 15 mW of power. The Humicap® sensor heads contain an active polymer film that changes its capacitance as function of relative humidity, with 0% to 100% RH measurement range. The dynamic range of the device gets smaller with sensor temperature, being in -70°C approximately 30% of the dynamic range in 0°C [3]. Good-quality relative humidity measurements require knowing the temperature of the environment in which relative humidity is measured. An important part of DREAMS-H calibration was temperature calibration of Vaisala Thermocap® temperature sensors used for housekeeping temperature measurements of the DREAMS-H device. For this, several temperature points in the desired operational range were measured with 0.1°C accuracy traceable to national standards. The main part of humidity calibration of DREAMS-H flight models was done in subzero temperatures in a humidity generator of the Finnish Center of Metrology and Accreditation (MIKES). Several relative humidity points ranging from almost dry to almost wet

A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data.

Science.gov (United States)

Baur, Brittany; Bozdag, Serdar

2015-04-01

One of the challenging and important computational problems in systems biology is to infer gene regulatory networks (GRNs) of biological systems. Several methods that exploit gene expression data have been developed to tackle this problem. In this study, we propose the use of copy number and DNA methylation data to infer GRNs. We developed an algorithm that scores regulatory interactions between genes based on canonical correlation analysis. In this algorithm, copy number or DNA methylation variables are treated as potential regulator variables, and expression variables are treated as potential target variables. We first validated that the canonical correlation analysis method is able to infer true interactions in high accuracy. We showed that the use of DNA methylation or copy number datasets leads to improved inference over steady-state expression. Our results also showed that epigenetic and structural information could be used to infer directionality of regulatory interactions. Additional improvements in GRN inference can be gleaned from incorporating the result in an informative prior in a dynamic Bayesian algorithm. This is the first study that incorporates copy number and DNA methylation into an informative prior in dynamic Bayesian framework. By closely examining top-scoring interactions with different sources of epigenetic or structural information, we also identified potential novel regulatory interactions.

The function of dreaming.

Science.gov (United States)

Staunton, H

2001-01-01

Theories on the function of REM sleep and dreaming, with which it has a contingent relationship, remain diverse. They include facilitation of memory storage, reverse learning, anatomical and functional brain maturation, catecholamine restoration, psychoanalytical (wish fulfilment or otherwise). It is possible that one function is grafted onto another as the personality develops. Given a close relationship between REM sleep and dreaming, and given that the neonate spends 18 hours asleep per day, of which 12 hours are spent in REM sleep, it is logical to look in the neonate for a primary function of dreaming. The two constants in the dreaming process are: 1) the dreamer is always present as first person observer; 2) there is always a topographical setting. Based on the foregoing, it is proposed that a major function of REM sleep is the development and maintenance of a sense of personal identity, through creating a 'being there' environment at regular intervals during prolonged periods of absence from a waking state in topographical surrounds. The infant cannot forget who he/she is. Thus, he/she develops a clear sense of his/her own identity, or the 'I'ness of me', and a sense of his/her separateness from the topographical world. At the same time, by largely forgetting the dreams, he/she is not burdened by the need for an elaborate method of storage of the vicarious and bizarre experiences.

TXRF-dreams in the past and future

International Nuclear Information System (INIS)

Gohshi, Y.

2000-01-01

Analysts thought that TXRF had excellent DL due to its inherent low background. Ultra trace analysis under very low background condition was the dream in the past. This initial dream ended when TXRF was applied to practical ultra or trace analysis. Continuum in an excitation beam was the cause of background. To solve this background problem, band pass or monochromatic excitation methods were introduced. Another dream they enjoyed. When TXRF was applied to Si wafer analysis, the dream, however, was terminated again. The next new trouble was the blank caused by the diffracted or scattered excitation beam. At present the excitation beam is well monochromatized. Appropriate geometry and careful choice of material are adopted in the design of TXRF instruments. So, we are again enjoying a new optimistic dream. Is there no nightmare? Dream and nightmare, these are repeated. Good analysts are always very cautious. Are the blank values obtained as low as the expected values? If not, it may be a starting point of another nightmare and dream. Several discussions will be made, though only quantitative. Various scattering processes (resonant, elastic, inelastic etc.) will be the cause of nightmare under horizon. In addition, chemical issues will emerge. (author)

Analysis of Dream in Firdawsi`s Shahname

OpenAIRE

h Mansoorian; b Torbatinezhad

2012-01-01

Dream has preoccupied humanâs mind since it is attached to him and is part of his spiritual and intellectual life. This subject has a significant position in Shahname. Dreams have significance for advancement of Shahname`s stories and Firdawsi`s lofty educationalâ religious and moral goals. This article classifies the dreams from the viewpoint of content and structure and pays attention to their role in the formation of stories. First, dreams are divided to direct and indirect on the ba...

Representation of the Self in REM and NREM Dreams

Science.gov (United States)

McNamara, Patrick; McLaren, Deirdre; Durso, Kate

2008-01-01

The authors hypothesized that representations of the Self (or the dreamer) in dreams would change systematically, from a prereflective form of Self to more complex forms, as a function of both age and sleep state (REM vs. non-REM). These hypotheses were partially confirmed. While the authors found that all the self-concept-related dream content indexes derived from the Hall/Van de Castle dream content scoring system did not differ significantly between the dreams of children and adults, adult Selves were more likely to engage in “successful” social interactions. The Self never acted as aggressor in NREM dream states and was almost always the befriender in friendly interactions in NREM dreams. Conversely, the REM-related dream Self preferred aggressive encounters. Our results suggests that while prereflective forms of Self are the norm in children’s dreams, two highly complex forms of Self emerge in REM and NREM dreams. PMID:19169371

Automatic gender detection of dream reports: A promising approach.

Science.gov (United States)

Wong, Christina; Amini, Reza; De Koninck, Joseph

2016-08-01

A computer program was developed in an attempt to differentiate the dreams of males from females. Hypothesized gender predictors were based on previous literature concerning both dream content and written language features. Dream reports from home-collected dream diaries of 100 male (144 dreams) and 100 female (144 dreams) adolescent Anglophones were matched for equal length. They were first scored with the Hall and Van de Castle (HVDC) scales and quantified using DreamSAT. Two male and two female undergraduate students were asked to read all dreams and predict the dreamer's gender. They averaged a pairwise percent correct gender prediction of 75.8% (κ=0.516), while the Automatic Analysis showed that the computer program's accuracy was 74.5% (κ=0.492), both of which were higher than chance of 50% (κ=0.00). The prediction levels were maintained when dreams containing obvious gender identifiers were eliminated and integration of HVDC scales did not improve prediction. Copyright © 2016 Elsevier Inc. All rights reserved.

How bizarre? A pluralist approach to dream content.

Science.gov (United States)

Rosen, Melanie G

2018-05-05

Are dreams bizarre, nonsensical experiences or real-world simulations? I introduce a pluralist approach to dream content that highlights the philosophical and empirical implications of treating dreaming as a highly varied experience that can be anywhere on a spectrum from truly bizarre and incoherent to wake-like and mundane. Here I discuss several explanations for why theorists disagree on whether dreams should be defined as primarily bizarre or convincing, real-world simulations. Rating scales can underestimate or overestimate bizarreness depending on the variables of the scale and interpretation of contextual factors. Although double blind analysis of dream reports is assumed to be the most accurate method of quantifying dream bizarreness, contextual factors can only be clarified by the dreamer themselves, since only they can judge whether an event would be bizarre in their own lives, however the dreamer might find elements bizarre after waking that they did not find unusual during the dream. Dreams can at times be so bizarre and incoherent that that they are difficult or impossible to report accurately, mundane and indistinguishable from waking life or anything in-between. Both bizarre and mundane dreams should be of great interest to philosophers of mind and cognitive scientists. Copyright © 2018 Elsevier Inc. All rights reserved.

The marginalisation of dreams in clinical psychological practice.

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Leonard, Linda; Dawson, Drew

2018-04-22

The longstanding human interest in dreams has led to a significant body of psychological and philosophical discourse, including research. Recently, however, dreams have been relegated to the periphery of clinical psychological practice. This is potentially problematic as clients continue to bring dreams to therapy and many psychologists lack the confidence or competence to respond effectively to dream material. Building on the structural, professional and research cultures surrounding psychology using a cultural-historical activity theory framework, we argue the marginalisation of dreams is due to cultural-historical factors. These factors include the political and economic context in which psychology developed; psychology's early attempts to differentiate from psychoanalysis by identifying with behaviourism and the natural sciences; and a discipline-specific definition of what constitutes evidence-based practice. These factors led to professional discourses within which dreams are seen as of little clinical or therapeutic value, or that dream work is only for long-term therapy and requires extensive therapist training. However, there are diverse models of dream work consistent with most theoretical orientations within contemporary psychological practice. We conclude with recommendations on how to rebuild clinical confidence and competence in the use of dream material within the current professional environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

The content of recurrent dreams in young adolescents.

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Gauchat, Aline; Séguin, Jean R; McSween-Cadieux, Esther; Zadra, Antonio

2015-12-01

Studies on children's recurrent dreams have been largely anecdotal and based on adults' recollections of dreams experienced during childhood. We collected 102 reports of recurrent dreams from a sample of young adolescents aged between 11 and 15years and scored the narratives using a range of content measures, including in relation to the threat simulation theory (TST) of dreaming. The most frequently reported themes involved confrontations with monsters or animals, followed by physical aggressions, falling and being chased. Recurrent dreams were more likely to include negative content elements than positive elements. Only half of the recurrent dreams contained threatening elements and their analysis provided mixed support for the TST. Differences between the content of recurrent dreams reported by young adolescent versus adults are discussed as are possible sex effects and key issues that remain to be addressed by future research. Copyright © 2015 Elsevier Inc. All rights reserved.

Great Gatsby-the Disillusionment of American Dream

Institute of Scientific and Technical Information of China (English)

赵玮

2005-01-01

American Dream is a mystery. It makes a lot of Americans prosperous, but also ruins some of them. In The Great Gatsby by F. Scott Fitzgerald, Gatsby is just such a character created to describe the disillusionment of the American Dream. Yet, his doom of failure results from his illusion actually. In this essay, we shall see how the American dream of Gatsby comes from illusion to disillusionment step by step. Besides, what kind of person Gatsby is and what kind of love Gatsby and his ideal love "Daisy" has are depicted in this essay to reveal the doom of Gatsby's dream. And a general understanding of the Jazz Age, the specific era Gatsby is set in, of the original sense of American Dream and also of the conflicts between two extreme classes in the face of the challenge of American Dream will make us clearer of how Gatsby - the tragic hero - met his fate.

Living the Behavioral Dream.

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Dixon, Mark R

2013-01-01

Most of us have had a workday where we left a bit frustrated about one thing or another and thought "if I was in charge, I know I could do it better." We dream of a better tomorrow where we tell our employer goodbye and become our own boss. Is that not the American Dream? We are told from early childhood that anything is possible and we can be anything we want to be if we just work hard. Somewhere between those naive childhood years and today we probably have come to realize these grand promises are more myths than truths and we become content with an approximation of this dream. To some individuals, however, approximations are not close enough.

Shattering a Cartesian Sceptical Dream

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Stephen Hetherington

2004-06-01

Full Text Available Scepticism about external world knowledge is frequently claimed to emerge from Descartes’s dreaming argument. That argument supposedly challenges one to have some further knowledge — the knowledge that one is not dreaming that p — if one is to have even one given piece of external world knowledge that p. The possession of that further knowledge can seem espe-cially important when the dreaming possibility is genuinely Cartesian (with one’s dreaming that p being incompatible with the truth of one’s accompany-ing belief that p. But this paper shows why that Cartesian use of that possi-bility is not at all challenging. It is because that putative sceptical challenge reduces to a triviality which is incompatible with the sceptic’s having de-scribed some further piece of knowledge which is needed, if one is to have the knowledge that p.

The Great Gatsby and the Collapse of American Dream

Institute of Scientific and Technical Information of China (English)

逄红

2014-01-01

Gatsby's dream is a typical American Dream. His failure signified the decay of the American post-war spirit. His death belled the alarm for the other disillusioned people from fantasy dreams and set them to reconsider the social reality.This thesis would discuss the collapse of the Gatsby's dream and that of American dream based on the book plot and the background of 1920s.

A bayesian inference-based detection mechanism to defend medical smartphone networks against insider attacks

DEFF Research Database (Denmark)

Meng, Weizhi; Li, Wenjuan; Xiang, Yang

2017-01-01

and experience for both patients and healthcare workers, and the underlying network architecture to support such devices is also referred to as medical smartphone networks (MSNs). MSNs, similar to other networks, are subject to a wide range of attacks (e.g. leakage of sensitive patient information by a malicious...... insider). In this work, we focus on MSNs and present a compact but efficient trust-based approach using Bayesian inference to identify malicious nodes in such an environment. We then demonstrate the effectiveness of our approach in detecting malicious nodes by evaluating the deployment of our proposed...

[Generation and functions of dreams].

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Medrano-Martínez, Pablo; Ramos-Platón, M José

2014-10-16

Over the last decade an ever-increasing number of articles have been published on dreams, which reflects the interest that several fields of neuroscience have in the topic. In this work we review the main scientific theories that have contributed to the body of knowledge on how they are produced and what function they serve. The article discusses the evolution of their scientific study, following a neurophysiological and neurocognitive approach. The first of these two methods seeks to determine the neurobiological mechanisms that generate them and the brain structures involved, while the second considers dreams to be a kind of cognition interacting with that of wake-fulness. Several different hypotheses about the function of dreams are examined, and more particularly those in which they are attributed with a role in the consolidation of memory and the regulation of emotional states. Although the exact mechanism underlying the generation of dreams has not been determined, neurobiological data highlight the importance of the pontine nuclei of the brainstem, several memory systems, the limbic system and the brain reward system and a number of neocortical areas. Neurocognitive data underline the relation between the cognitive and emotional processing that occurs during wakefulness and during sleep, as well as the influence of the surroundings on the content of dreams. With regard to their function, one point to be stressed is their adaptive value, since they contribute to the reprocessing of the information acquired in wakefulness and the control of the emotions. This suggests that dreams participate in the development of the cognitive capabilities.

Such stuff as dreams are made on? Elaborative encoding, the ancient art of memory, and the hippocampus.

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Llewellyn, Sue

2013-12-01

This article argues that rapid eye movement (REM) dreaming is elaborative encoding for episodic memories. Elaborative encoding in REM can, at least partially, be understood through ancient art of memory (AAOM) principles: visualization, bizarre association, organization, narration, embodiment, and location. These principles render recent memories more distinctive through novel and meaningful association with emotionally salient, remote memories. The AAOM optimizes memory performance, suggesting that its principles may predict aspects of how episodic memory is configured in the brain. Integration and segregation are fundamental organizing principles in the cerebral cortex. Episodic memory networks interconnect profusely within the cortex, creating omnidirectional "landmark" junctions. Memories may be integrated at junctions but segregated along connecting network paths that meet at junctions. Episodic junctions may be instantiated during non-rapid eye movement (NREM) sleep after hippocampal associational function during REM dreams. Hippocampal association involves relating, binding, and integrating episodic memories into a mnemonic compositional whole. This often bizarre, composite image has not been present to the senses; it is not "real" because it hyperassociates several memories. During REM sleep, on the phenomenological level, this composite image is experienced as a dream scene. A dream scene may be instantiated as omnidirectional neocortical junction and retained by the hippocampus as an index. On episodic memory retrieval, an external stimulus (or an internal representation) is matched by the hippocampus against its indices. One or more indices then reference the relevant neocortical junctions from which episodic memories can be retrieved. Episodic junctions reach a processing (rather than conscious) level during normal wake to enable retrieval. If this hypothesis is correct, the stuff of dreams is the stuff of memory.

Freud's private mini-monograph on his own dreams. A contribution to the celebration of the centenary of The interpretation of dreams.

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Blum, H P

2001-10-01

A virtually unknown brief commentary by Freud on the characteristics of his own dreams is described and discussed. Freud's mini-monograph, discovered after some 80 years, has autobiographical, theoretical and organisational significance in the enigmatic context of the early development of psychoanalysis. Found among papers of Alfred Adler, this extraordinary document adds to our knowledge of psychoanalytic history, including the significance of dreams in the evolution of psychoanalytic thought. Freud's commentary permitted the identification of a particular dream as his own. This dream had been presented in anonymity to the fledgling Vienna Psychoanalytic Society for interpretation. The dream was later inserted, again anonymously, into The Interpretation of Dreams with Freud's own remarkable pre-oedipal interpretation. Freud's conflicted relationships with Adler and Jung are considered in historical context.

Inferring a Drive-Response Network from Time Series of Topological Measures in Complex Networks with Transfer Entropy

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Xinbo Ai

2014-11-01

Full Text Available Topological measures are crucial to describe, classify and understand complex networks. Lots of measures are proposed to characterize specific features of specific networks, but the relationships among these measures remain unclear. Taking into account that pulling networks from different domains together for statistical analysis might provide incorrect conclusions, we conduct our investigation with data observed from the same network in the form of simultaneously measured time series. We synthesize a transfer entropy-based framework to quantify the relationships among topological measures, and then to provide a holistic scenario of these measures by inferring a drive-response network. Techniques from Symbolic Transfer Entropy, Effective Transfer Entropy, and Partial Transfer Entropy are synthesized to deal with challenges such as time series being non-stationary, finite sample effects and indirect effects. We resort to kernel density estimation to assess significance of the results based on surrogate data. The framework is applied to study 20 measures across 2779 records in the Technology Exchange Network, and the results are consistent with some existing knowledge. With the drive-response network, we evaluate the influence of each measure by calculating its strength, and cluster them into three classes, i.e., driving measures, responding measures and standalone measures, according to the network communities.

Psychoanalytic dream theory and recent neurobiological findings about REM sleep.

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Wasserman, M D

1984-01-01

I have reviewed Hobson and McCarley's activation-synthesis hypothesis of dreaming which attempts to show that the instigation and certain formal aspects of dreaming are physiologically determined by a brainstem neuronal mechanism, their reasons for suggesting major revisions in psychoanalytic dream theory, and neurophysiological data that are inconsistent with their hypothesis. I then discussed the concept of mind-body isomorphism pointing out that they use this concept inconsistently, that despite their denials they regularly view physiology as primary and psychological processes as secondary, and that they frequently make the error of mixing the languages of physiology and psychology in their explanatory statements. Finally, in order to evaluate Hobson and McCarley's claim that their findings require revision of psychoanalytic dream theory, I examined their discussions of chase dreams, flying dreams, sexual dreams, the formal characteristics of dreams, the forgetting of dreams, and the instigation of dreams. I concluded that although their fascinating physiological findings may be central to understanding the neurobiology of REM sleep, they do not alter the meaning and interpretation of dreams gleaned through psychoanalytic study.

[Is it still the "royal way"? The dream as a junction of neurobiology and psychoanalysis].

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Simon, Mária

2011-01-01

Some decades ago the dream seemed to be randomly generated by brain stem mechanisms in the cortical and subcortical neuronal networks. However, most recent empirical data, studies on brain lesions and functional neuroimaging results have refuted this theory. Several data support that motivation pathways, memory systems, especially implicit, emotional memory play an important role in dream formation. This essay reviews how the results of neurobiology and cognitive psychology can be fitted into the theoretical frameworks and clinical practice of the psychoanalysis. The main aim is to demonstrate that results of neurobiology and empirical observations of psychoanalysis are complementary rather than contradictory.