A small community model for the transmission of infectious diseases: comparison of school closure as an intervention in individual-based models of an influenza pandemic.

Background: In the absence of other evidence, modelling has been used extensively to help policy makers plan for a potential future influenza pandemic.

Method: We have constructed an individual based model of a small community in the developed world with detail down to exact household structure obtained from census collection datasets and precise simulation of household demographics, movement within the community and individual contact patterns. We modelled the spread of pandemic influenza in this community and the effect on daily and final attack rates of four social distancing measures: school closure, increased case isolation, workplace non-attendance and community contact reduction.

Brain coordination dynamics: true and false faces of phase synchrony and metastability.

Understanding the coordination of multiple parts in a complex system such as the brain is a fundamental challenge. We present a theoretical model of cortical coordination dynamics that shows how brain areas may cooperate (integration) and at the same time retain their functional specificity (segregation). This model expresses a range of desirable properties that the brain is known to exhibit, including self-organization, multi-functionality, metastability and switching.

A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from approximately 0.3 g of bone.

Mode level cognitive subtraction (MLCS) quantifies spatiotemporal reorganization in large-scale brain topographies.

Contemporary brain theories of cognitive function posit spatial, temporal and spatiotemporal reorganization as mechanisms for neural information processing. Corresponding brain imaging results underwrite this perspective of large-scale reorganization. As we show here, a suitable choice of experimental control tasks allows the disambiguation of the spatial and temporal components of reorganization to a quantifiable degree of certainty.

Social coordination dynamics: measuring human bonding.

Spontaneous social coordination has been extensively described in natural settings but so far no controlled methodological approaches have been employed that systematically advance investigations into the possible self-organized nature of bond formation and dissolution between humans. We hypothesized that, under certain contexts, spontaneous synchrony-a well-described phenomenon in biological and physical settings-could emerge spontaneously between humans as a result of information exchange. Here, a new way to quantify interpersonal interactions in real time is proposed.

Population transcriptomics of life-history variation in the genus Salmo.

In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 transcript probes in 90 individuals originating from six brown trout (Salmo trutta) and one Atlantic salmon (Salmo salar) population, which follow either a migratory or a sedentary life history. We identified several candidate genes associated with preparatory adaptations to different life histories in salmonids, including genes encoding for transaldolase 1, constitutive heat-shock protein HSC70-1 and endozepine.

PatMaN: rapid alignment of short sequences to large databases.

Unlabelled: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched.

An Essay on Understanding the Mind.

Several conjectures by A. S. Iberall on life and mind are used as a backdrop to sketch a theory of mental activity that respects both the contents of thought and the dynamics of thinking.

Effectiveness of multifaceted narrative intervention on the stories told by a 12-year-old girl who uses AAC.

Children who use augmentative and alternative communication (AAC) have been found to experience difficulties in the elicited generation of both personal and fictional narratives. The purpose of this single case study was to evaluate the effects of a multifaceted intervention program designed to support the development of autonomous narrative skills in children who used AAC. The relationship between exposure to the intervention program and increases in the narrative skills of the focus child was investigated using a single case, multiple probe baseline design.

Identification and analysis of genomic regions with large between-population differentiation in humans.

The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations.

Accelerating Scientific Discovery Through Computation and Visualization III. Tight-Binding Wave Functions for Quantum Dots.

This is the third in a series of articles that describe, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing, visualization, and machine learning to accelerate scientific discovery. In this article we focus on the use of high performance computing and visualization for simulations of nanotechnology.

Activating basic category exemplars in sentence contexts: a dynamical account.

This paper examines the influence of context on the processing of category names embedded in sentences. The investigation focuses on the nature of information available immediately after such a word is heard as well as on the dynamics of adaptation to context. An on-line method (Cross Modal Lexical Priming) was used to trace how this process unfolds in time.

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies.

Background: Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability.

Patterns of damage in genomic DNA sequences from a Neandertal.

High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation.

The influence of instruction modality on brain activation in teenagers with nonverbal learning disabilities: two case histories.

Teenagers with nonverbal learning disabilities (NLD) have difficulty with fine-motor coordination, which may relate to the novelty of the task or the lack of "self-talk" to mediate action. In this study, we required two teenagers with NLD and two control group teenagers to touch the thumb of each hand firmly and accurately to the fingertips of the same hand, in an order specified by verbal or tactile instruction. Brain activity patterns (measured using functional magnetic resonance imaging) suggest that unlike control participants, the NLD participants used internalized speech to facilitate the novel task only when instructions were verbal.

The phi complex as a neuromarker of human social coordination.

Many social interactions rely upon mutual information exchange: one member of a pair changes in response to the other while at the same time producing actions that alter the behavior of the other. However, little is known about how such social processes are integrated in the brain. Here, we used a specially designed dual-electroencephalogram system and the conceptual framework of coordination dynamics to identify neural signatures of effective, real-time coordination between people and its breakdown or absence.

Assessing obesity and other related health problems of mentally ill Hispanic patients in an urban outpatient setting.

Objective: This paper describes the role of an agency Clinical Director in developing a project to assess and begin to address obesity-related health problems of patients treated in a community-based mental health clinic in New York City. After a five year review of outpatient deaths revealed a high rate of deaths from cardiovascular and diabetes-related issues, the Clinical Director assembled a group of clinicians, researchers, and administrative staff to design a pilot project to assess health and nutrition status of primarily Hispanic day treatment patients with severe and persistent mental illness.

Method: About 69 of the 105 patients at the clinic were assessed by chart review, interview about nutritional habits and medical care, and somatic measurements for blood pressure, weight, girth, body mass index (BMI), glucose and lipid levels.

Application of topical corticosteroids to sites of positive immediate-type allergy skin tests to relieve itching: results of a double-blind, placebo-controlled trial.

Background: In many allergy clinics topical corticosteroid cream is applied to sites of positive skin tests in an attempt to alleviate itching.

Objectives: To determine whether or not this practice is effective.

Methods: Patients with 5 or more positive skin test results were randomly assigned to 1 of 3 groups after skin test result reading: application of 2.

Comparison of protein and mRNA expression evolution in humans and chimpanzees.

Even though mRNA expression levels are commonly used as a proxy for estimating functional differences that occur at the protein level, the relation between mRNA and protein expression is not well established. Further, no study to date has tested whether the evolutionary differences in mRNA expression observed between species reflect those observed in protein expression. Since a large proportion of mRNA expression differences observed between mammalian species appears to have no functional consequences for the phenotype, it is conceivable that many or most mRNA expression differences are not reflected at the protein level.

A splice variant of the human CCA-adding enzyme with modified activity.

The human CCA-adding enzyme (tRNA nucleotidyltransferase) is an essential enzyme that catalyzes the addition of the CCA terminus to the 3' end of tRNA precursors, a reaction which is a fundamental prerequisite for mature tRNAs to become aminoacylated and to participate in protein biosynthesis. To date only one form of this enzyme has been identified in humans. Here, we describe the sequence and activity of a splice variant of the human CCA-adding enzyme identified in public cDNA databases.

Measurement Tools for the Immersive Visualization Environment: Steps Toward the Virtual Laboratory.

This paper describes a set of tools for performing measurements of objects in a virtual reality based immersive visualization environment. These tools enable the use of the immersive environment as an instrument for extracting quantitative information from data representations that hitherto had be used solely for qualitative examination. We provide, within the virtual environment, ways for the user to analyze and interact with the quantitative data generated.