Significance of Automatically Detected Word Recurrences in Dream Associations

Verbal data files including dream reports and associations with the report items were subjected to automatic analysis aiming at the recognition of word recurrences. The research was based on the following assumptions: the associations can provide information about the dream sources; the recognition of word recurrences in text files can be a useful tool for the study of dreaming; the identification of links between different dream sources can provide an interesting insight into the phenomenon of dreaming. The principal result obtained was that word recurrences often evidence possible significant links between dream sources. A number of the possible links evidenced by the automatic analysis not only escaped the subject's notice, but might also be unexpected for an analyzer not assisted by a computer.     

Haptoglobin polymorphism among fourteen populations of India

Haptoglobin (HP) is a serum protein that has the capability of binding the extracorpuscular haemoglobin released during haemolysis. It plays an important role in protection of haemolytic disease by reducing the oxidative and peroxidative potential at free haemoglobin. The present study was aimed to determine the prevalence of HP polymorphism among different Indian populations, anthropologically belonging to diverse ethnicity. The polymorphism was screened among 642 unrelated individuals belonging to 14 population groups of India including both tribal and non-tribal caste groups from different geographical regions of India with distinct linguistic affiliations. An attempt is also made to understand the distribution of HP polymorphism among the studied populations. The result reveals the HP gene to be polymorphic in all the studied populations. Except the two tribal populations (Thotis of Andhra Pradesh and Patelias of Rajasthan) and one caste population (Rajput of Himachal Pradesh), all the studied populations are found to obey the Hardy-Weinberg equilibrium. The significance of the present study is elucidated with the prevalence of high mutant HP*2 allele frequency in India. Selection could be one of the most plausible explanations for this high HP frequency because of its uniformly high occurrence among all the studied populations.     

Dream Intensity Inventory and Chinese people's dream experience frequencies.

The present study aimed to devise a parsimonious instrument for evaluating both the quantitative and qualitative aspects of dream experiences and to quantify Chinese people's dream experiences in ways that facilitated cross-cultural comparisons. The Dream Intensity Inventory was developed and administered to 348 Chinese university students. Individual differences in dream recall frequency were observed, with some participants recalling dreams almost every morning whereas others recalled dreams less than once a month. By contrast, the Chinese participants exhibited less diverse dream awareness frequencies. Multiple dreams in a single night and nightmares were found to be prevalent among the Chinese participants. On the other hand, fewer than half of the participants experienced regularly voluntary control over dream activities and consciousness. The factor analyses of the items in the Dream Intensity Inventory resulted in three readily interpreted factors, which were labeled as the "dream quantity," "altered dream episodes," and "dream vividness" subscales, respectively. When compared with men, women participants had higher frequencies of regular dream experiences including dream awareness, nightmares, and multiple dreams, as measured by the dream quantity subscale. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Recurrence of typical dreams and the instinctual and delusional predispositions of dreams.

The present study investigated the recurrence of typical dreams and refined Yu's measures for assessing the delusional inclination during dreaming. The Dream Themes Inventory, which consists of typical, delusional, appetitive-instinctual dream themes, was administered to 608 participants. The results indicate that some dream motifs are not only shared by a majority of people but also regularly recur within a person. Moreover, this study demonstrates that virtually all types of delusions and paranoid suspiciousness—including grandiose, persecutory, religious, somatic, jealous, and erotomanic delusions—can be observed in dreams. In addition to fine-tuning Yu's previous Ego Ideal, Grandiosity, and Persecution scales, Erotomania, Appetite-instinct, and Sensorimotor Excitement scales were developed to supplement the assessment of the intrinsic predispositions that modulate dream content. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Automated discovery of food webs from ecological data using logic-based machine learning

Networks of trophic links (food webs) are used to describe and understand mechanistic routes for translocation of energy (biomass) between species. However, a relatively low proportion of ecosystems have been studied using food web approaches due to difficulties in making observations on large numbers of species. In this paper we demonstrate that Machine Learning of food webs, using a logic-based approach called A/ILP, can generate plausible and testable food webs from field sample data. Our example data come from a national-scale Vortis suction sampling of invertebrates from arable fields in Great Britain. We found that 45 invertebrate species or taxa, representing approximately 25% of the sample and about 74% of the invertebrate individuals included in the learning, were hypothesized to be linked. As might be expected, detritivore Collembola were consistently the most important prey. Generalist and omnivorous carabid beetles were hypothesized to be the dominant predators of the system. We were, however, surprised by the importance of carabid larvae suggested by the machine learning as predators of a wide variety of prey. High probability links were hypothesized for widespread, potentially destabilizing, intra-guild predation; predictions that could be experimentally tested. Many of the high probability links in the model have already been observed or suggested for this system, supporting our contention that A/ILP learning can produce plausible food webs from sample data, independent of our preconceptions about "who eats whom." Well-characterised links in the literature correspond with links ascribed with high probability through A/ILP. We believe that this very general Machine Learning approach has great power and could be used to extend and test our current theories of agricultural ecosystem dynamics and function. In particular, we believe it could be used to support the development of a wider theory of ecosystem responses to environmental change.     

The probability of extinction in a bovine respiratory syncytial virus epidemic model

Backward bifurcation is a relatively recent yet well-studied phenomenon associated with deterministic epidemic models. It allows for the presence of multiple subcritical endemic equilibria, and is generally found only in models possessing a reasonable degree of complexity. One particular aspect of backward bifurcation that appears to have been virtually overlooked in the literature is the potential influence its presence might have on the behaviour of any analogous stochastic model. Indeed, the primary aim of this paper is to investigate this possibility. Our approach is to compare the theoretical probabilities of extinction, calculated via a particular stochastic formulation of a deterministic model exhibiting backward bifurcation, with those obtained from a series of stochastic simulations. We have found some interesting links in the behaviour between the deterministic and stochastic models, and are able to offer plausible explanations for our observations.     

Costly signaling and cooperation.

We propose an explanation of cooperation among unrelated members of a social group in which cooperation evolves because it constitutes an honest signal of the member's quality as a mate, coalition partner or competitor, and therefore results in advantageous alliances for those signaling in this manner. Our model is framed as a multi-player public goods game that involves no repeated or assortative interactions, so that non-cooperation would be a dominant strategy if there were no signaling benefits. We show that honest signaling of underlying quality by providing a public good to group members can be evolutionarily stable, and can proliferate in a population in which it is initially rare, provided that certain plausible conditions hold, including a link between group-beneficial signaling and underlying qualities of the signaler that would be of benefit to a potential mate or alliance partner. Our model applies to a range of cooperative interactions, including unconditionally sharing individually consumable resources, participating in group raiding or defense, and punishing free-riding or other violations of social norms.     

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

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.     

Condensation of amino acids to form peptides in aqueous solution induced by the oxidation of sulfur(iv): An oxidative model for prebiotic peptide formation

Condensation of amino acids to peptides is an important step during the origin of life. However, up to now, successful explanations for plausible prebiotic peptide formation pathways have been limited. Here we report that the oxidation of sulfur (IV) can induce the condensation reaction of carboxylic acids and amines to form amides, and the condensation reaction of amino acids to form peptides. This might be a general reaction contributing to prebiotic peptide formation.     

A Chado case study: an ontology-based modular schema for representing genome-associated biological information

MOTIVATION: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. RESULTS: Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. AVAILABILITY: GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).     

Facilitating dream recall in Chinese people.

The aim of this study was to examine the frequency of dream recall in Chinese people and to develop nonintrusive procedures to facilitate dream recall. Guidelines for remembering dreams (dream recall instructions) were established based on a review of the existing literature on dream recall and its associated factors. The efficacy of the dream recall experience was explored using this procedure in neurologically healthy individuals. One hundred seventy Chinese participants were included in the study: 100 received the dream recall instructions, and 70 did not. The recall instructions were shown to be effective in triggering dream recall in the participants. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources

Inferring regulatory networks from experimental data via probabilistic graphical models is a popular framework to gain insights into biological systems. However, the inherent noise in experimental data coupled with a limited sample size reduces the performance of network reverse engineering. Prior knowledge from existing sources of biological information can address this low signal to noise problem by biasing the network inference towards biologically plausible network structures. Although integrating various sources of information is desirable, their heterogeneous nature makes this task challenging. We propose two computational methods to incorporate various information sources into a probabilistic consensus structure prior to be used in graphical model inference. Our first model, called Latent Factor Model (LFM), assumes a high degree of correlation among external information sources and reconstructs a hidden variable as a common source in a Bayesian manner. The second model, a Noisy-OR, picks up the strongest support for an interaction among information sources in a probabilistic fashion. Our extensive computational studies on KEGG signaling pathways as well as on gene expression data from breast cancer and yeast heat shock response reveal that both approaches can significantly enhance the reconstruction accuracy of Bayesian Networks compared to other competing methods as well as to the situation without any prior. Our framework allows for using diverse information sources, like pathway databases, GO terms and protein domain data, etc. and is flexible enough to integrate new sources, if available.     

When can dispersal synchronize populations?

While spatial synchrony of oscillating populations has been observed in many ecological systems, the causes of this phenomenon are still not well understood. The most common explanations have been the Moran effect (synchronous external stochastic influences) and the effect of dispersal among populations. Since ecological systems are typically subject to large spatially varying perturbations which destroy synchrony, a plausible mechanism explaining synchrony must produce rapid convergence to synchrony. We analyze the dynamics through time of the synchronizing effects of dispersal and, consequently, determine whether dispersal can be the mechanism which produces synchrony. Specifically, using methods new to ecology, we analyze a two patch predator-prey model, with identical weak dispersal between the patches. We find that a difference in time scales (i.e. one population has dynamics occurring much faster than the other) between the predator and prey species is the most important requirement for fast convergence to synchrony.     

Understanding reporting bias in the dietary recall data of 11-year-old girls

Objective: This study describes patterns of bias in self‐reported dietary recall data of girls by examining differences among girls classified as under‐reporters, plausible reporters, and over‐reporters on weight, dietary patterns, and psychosocial characteristics. Research Methods and Procedures: Participants included 176 girls at age 11 and their parents. Girls’ weight and height were measured. Three 24‐hour dietary recalls and responses to psychosocial measures were collected. Plausibility cut‐offs for reported energy intake as a percentage of predicted energy requirements were used to divide the sample into under‐reporters, plausible reporters, and over‐reporters. Differences among these three groups on dietary and psychosocial variables were assessed to examine possible sources of bias in reporting. Results: Using a ±1 standard deviation cut‐off for energy intake plausibility, 50% of the sample was categorized as plausible reporters, 34% as under‐reporters, and 16% as over‐reporters. Weight status of under‐reporters was significantly higher than that of plausible reporters and over‐reporters. With respect to reported dietary intake, under‐reporters were no different from plausible reporters on intakes of foods with higher nutrient densities and lower energy densities and were significantly lower than plausible reporters on intakes of foods with lower nutrient densities and higher energy densities. Over‐reporters reported significantly higher intakes of all food groups and the majority of subgroups, relative to plausible reporters. Under‐reporters had significantly higher levels of weight concern and dietary restraint than both plausible reporters and over‐reporters. Discussion: Techniques to categorize plausible and implausible reporters can and should be used to provide an improved understanding of the nature of error in children's dietary intake data and account for this error in analysis and interpretation.